Biology: Assistant Professor of Biology - University of Richmond - Richmond, VA        
We seek a biologist who has expertise in analysis of big data, modeling, bioinformatics, genomics/transcriptomics, biostatistics, or other quantitative and/or...
From University of Richmond - Thu, 06 Jul 2017 23:17:18 GMT - View all Richmond, VA jobs
          Scientist - Product Science - Centrillion - Palo Alto, CA        
The R&D group at Centrillion is a multidisciplinary team of biologists, engineers, chemists, and computational biologists developing new genomics technologies,...
From Centrillion - Wed, 07 Jun 2017 02:24:59 GMT - View all Palo Alto, CA jobs
          Qué es la medicina Ayurvédica?        

¿Qué es la Medicina Ayurvédica o Ayurveda?


Ayurveda, la "ciencia de la vida", es la medicina tradicional de la India.


La palabra Ayurveda tiene su raíz en dos vocablos sánscritos, "Ayus" que significa longevidad y "Ved o Veda" que significa ciencia, definiendo el AyurVed como la "ciencia de la longevidad".


De acuerdo a la Medicina Ayurveda, el organismo humano esta compuesto de tres principios fundamentales mente-cuerpo conocidos como principios metabólicos o Doshas.


Estos tres elementos- Vata, Pitta y Kapha- gobiernan todas las funciones psicologicas,fisiologicas y fisiopatologicas de la mente, el cuerpo y la conciencia de cada uno.


La proporción especifica de estos principios metabólicos en un individuo determinado al momento de la concepción, hace que esta persona tenga un estilo particular de funcionamiento mental y físico.


Los principios metabólicos son responsables de la manutención y desarrollo de los tejidos biológicos, y todas las actividades metabólicas incluyendo el anabolismo (kapha), catabolismo (vata) y metabolismo (pitta). También gobiernan funciones psicológicas y son responsables de emociones tanto negativas como positivas.


Tipos constitucionales mente-cuerpo


Cada individuo hereda una particular proporción de los tres principios metabólicos, lo cual determina la característica constitucional de cada persona. Un único principio metabólico puede predominar, pero comúnmente son dos los mas representados. Toxinas físicas y mentales Luego de años de rutinas diarias y estacionales incorrectas, de hábitos desarmónicos, y de la acumulación de residuos tóxicos que no podemos digerir apropiadamente y presencia de "radicales libres" , surge la base para los desequilibrios agudos y crónicos. Estos residuos tóxicos obstruyen el flujo de nutrición e información, creando la posibilidad de enfermedad física o mental.


Cuando los "radicales libres" a nivel mental obstruyen el flujo de sentimientos positivos y de claridad, surge el distress emocional y psicológico, ya que la buena salud depende de la habilidad de la unidad mente-cuerpo para metabolizar plenamente la información nutricional, emocional y sensorial que "ingerimos" diariamente.


Los síntomas tempranos de acumulación de "radicales libres" incluyen: dolor articular, anorexia, depresión, debilidad, mal aliento, fatiga profunda, arrugas, irritabilidad e indigestión; además son la raíz de todas las enfermedades incluyendo resfrio, fiebre, alergias, asma, problemas coronarios, artritis, formación de tejidos anormales, envejecimiento prematuro, perdida de capacidades intelectuales, etc.


La Medicina Ayurveda dispone de las terapéuticas para eliminar "radicales libres" de los órganos internos, por medio del Sistema de Adyuvancia Natural AyurVed (S.A.N.A.) ó Panchakarma.


El Panchakarma es altamente aconsejado 3 veces al año, después de tratamientos farmacológicos extensos, post-quimioterapia, luego de intenso stress ó como método natural de rejuvenecimiento para una recuperación más rápida de las funciones corporales, disminuyendo los efectos del embate del stress o efectos secundarios de los agentes químicos.


El programa Panchakarma incluye diversos procedimientos, entre los que podemos enumerar: Abhyanga - Rejuvenecimiento de la piel. Garshana - Activación de la piel. Vishesh - Masaje profundo para eliminar impurezas. Udvartana - Procedimiento especial con pasta de hierbas para celulitis. Nasya - Programa de Descongestión Nasal. Pizzichilli - Sofisticado baño de aceites tibios herbalizados. Shirodhara - Programa para tranquilizar la mente. Marma-terapia - Técnicas manuales sobre puntos de enlaces mente-cuerpo. Netra - Baño especializado de ojos. Basti - Fórmulas especiales de limpieza colonica, diseñadas para eliminar toxinas y nutrir la fisiología. Parishek - Baños de leche y hierbas para la belleza.


Es probablemente la medicina natural más antigua del mundo originándose hace más de 5000 años. Por este motivo fue llamada la Madre de Todas las Curaciones.


La Medicina Ayurveda es reconocida mundialmente por la Organización Mundial de la Salud (OMS), por la Organización Europea de Medicinas Complementarias (EHPA), por el Centro de Medicinas Alternativas y Complementarias de EEUU (NCCAM) y por todos los gobiernos como la primera medicina alternativa del mundo por su importante valor terapéutico.


En Occidente, Ayurveda es un sistema de medicina naturista y abarca todos los campos que se enseñan en escuelas médicas de Naturismo.


La Medicina Ayurveda trata solidariamente el cuerpo, la mente y el espíritu, considerando a cada persona única de acuerdo a su constitución física, mental y espiritual. Sus objetivos son proveer una guía acerca de la alimentación y estilo de vida (actividad física, técnicas respiratorias) para que las personas sanas se mantengan sanas y las personas con problemas de salud puedan mejorarla.


Incluye técnicas de purificación y rejuvenecimiento y tratamiento con hierbas. La medicina ayurveda se complementa e integra al tratamiento de la medicina convencional occidental. Pero, a diferencia de esta última, el tratamiento ayurvédico no trata el síntoma sino que busca eliminar la causa que lo produce.


Fuentes: http://www.ayurvedaba.com.ar/

http://www.ayurveda.vaneduc.edu.ar/ayur-intro.htm



J Transl Med. 2008 Sep 9;6(1):48

Prasher B, Negi S et al

Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda

http://www.translational-medicine.com/content/6/1/48



J Transl Med. 2008; 6: 14.

Custer C Deocaris,1 Nashi Widodo et al

Merger of Ayurveda and Tissue Culture-Based Functional Genomics: Inspirations from Systems Biology

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18348714



           Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species         
Van de Putte, Anton P., Janko, Karel, Kasparova, Eva, Maes, Gregory E., Rock, Jennifer, Koubbi, Philippe, Volckaert, Filip A.M., Choleva, Lukas, Fraser, Keiron P.P., Smykla, Jerzy, Van Houdt, Jeroen K.J., and Marshall, Craig (2012) Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species. Marine Genomics, 8. pp. 23-34.
          Sudin Bhattacharya        
Biomedical Engineering
B.M.E., Mechanical Engineering, Jadavpur University, India,1997
M.S.M.E., Mechanical Engineering, University of Kentucky, 1999
Ph.D., Mechanical Engineering, University of Michigan, Ann Arbor, 2006

MSU Departments & Centers:

  • Biomedical Engineering
  • Pharmacology & Toxicology
  • Center for Research on Ingredient Safety (CRIS)

I am broadly interested in several areas of computational toxicology. A major focus of my work is the application of computational methods to study the signaling and transcriptional regulatory networks that underlie the determination of cell fate, and the perturbation of these networks by environmental pollutants like dioxin. Specifically, I am interested in integrating diverse genomic data sets to map and model transcriptional regulatory networks and their environmental perturbation in the immune system and the liver. I am also interested in the extraction of predictive features from genomic data sets to model the toxic potential of chemical agents and pharmaceuticals, and spatial multi-scale modeling of tissue-level phenomena like toxicant-induced liver injury. I rely primarily on mathematical and statistical modeling as a research tool, and work in close collaboration with experimental scientists.


          The Future of AI: Redefining How We Imagine        

FICO 25 years of AI and machine learning logo

To commemorate the silver jubilee of FICO’s use of artificial intelligence and machine learning, we asked FICO employees a question: What does the future of AI look like? The post below is one of the thought-provoking responses, from Sadat Nazrul, an analytic scientist at FICO, working in San Diego.

Looking at the next 20 years, I see us moving well beyond the productivity enhancements AI has brought about so far. With the advent of AI, we will be seeing a renaissance in our own personal lives as well as society as a whole.

Healthcare

Today, our gadgets have the ability to monitor the number of steps we take, the rate of our heart beat, as well as the contents of our sweat. All this rich information allows a team of doctors, engineers and analysts to monitor our well-being and to maintain our peak performance. Similarly, with innovations in genomic sequencing and neural mapping passing FDA trials, we will soon be seeing huge leaps in the field of personalized medicine. AI will help us understand individual physiological needs in order to come up with customized prescriptions and improve our overall health standards.

Cognitive Abilities

People are keen to improve cognition. Who wouldn’t want to remember names and faces better, to be able more quickly to grasp difficult abstract ideas, and to be able to “see connections” better? Who would seriously object to being able to appreciate music at a deeper level?

The value of optimal cognitive functioning is so obvious that to elaborate the point may be unnecessary. Today we express ourselves through art, movies, music, blogs, and a wide range of social media applications. In the field of image recognition, AI can already “see” better than we can by observing far more than the RGB. Virtual Reality allows us to feel as though we have teleported to another world. New idioms of data visualization and Dimensionality Reduction algorithms are always being produced for us to better experience the world around us.

We are constantly trying to enhance our 5 senses to go beyond our human limits. 10 years from now, these innovations, coupled with IoT gadgets, will act as extensions of who we are and help us experience our surroundings more profoundly.

Emotional Intelligence

Just as we enhance our 5 cognitive senses, so too do we enhance our ability to express ourselves and to understand those around us.

Many times, we don’t even know what we want. We strive to connect with those around us in a specific way or consume a particular product, just so we could feel a very unique emotion that we fail to describe. We feel much more than just happiness, sadness, anger, anxiety or fear. Our emotions are a complex combinations of all of the above.

With the innovations in neural mapping, we will better understand who we are as human beings and better understand the myriad emotional states that we can attain. Our complex emotional modes will be better understood as we perform unsupervised learning on brain waves and help find innovative ways to improve our emotional intelligence. This would include both understanding our own emotions and being more sensitive towards those around us.

Perhaps we can unlock new emotions that we have never experienced before. In the right hands, AI can act as our extensions to help us form meaningful bonds with the people we value in our lives.

Experience and Imagination

The effect of AI on our experience and imagination would result from an aggregate of better cognitive abilities and emotional intelligence. The latest innovations in AI may help us unlock new cognitive experiences and emotional states.

Let’s imagine that the modes of experience we have today is represented in space X. 10 years from now, let’s say that the modes of experience are represented in space Y. The space Y will be significantly bigger than space X. This futuristic space of Y may have access to new types of emotions other than our conventional happy, sad and mad. This new space of Y can even allow us to comprehend abstract thoughts that reflect what we wish to express more accurately.

This new space of Y can actually unlock a new world of possibilities that lies beyond our current imagination. The people of the future will think, feel and experience the world at a much richer degree than we can today.

Communication

10 years ago, most of our communication were restricted to phones and emails. Today, we have access to video conferences, Virtual Reality and a wide array of applications on social media. As we enhance our cognitive abilities and emotional intelligence, we can express ourselves through idioms of far greater resolution and lower levels of abstractions.

We already have students from the University of Florida achieving control of drones using nothing but the mind. We even have access to vibrating gaming consoles that take advantage of our sense of touch for making that Mario Kart game that much more realistic. 10 years from now, the way we communicate with each other will be much deeper and more expressive than today. If we are hopeful enough, we might even catch a glimpse of the holograms of Star Wars and telepathic communications of X-Men.

Virtual Realities of today only limit us to our vision and sense of hearing. In the future, Virtual Realities might actually allow us to smell, taste and touch our virtual environment. Along with access to our 5 senses, our emotional reaction to certain situations might be fine-tuned and optimized with the power of AI. This might mean sharing the fear of our main characters on Paranormal Activity, feeling the heartbreak of Emma or being excited about the adventures of Pokemon. All this can be possible as we explore the theatrical arts of smart Virtual Reality consoles.

Information Security

AI allow us to unearth more unstructured data at higher velocity to generate valuable insight. However, the risk of those very sensitive data falling into the wrong hands will also escalate.

Today, cybersecurity is a major concern on everyone’s mind. In fact, 2017 is the year the fingerprint got hacked. With the help of AI, information technology will get more sophisticated in order to protect the things we value in our lives.

It is human nature to want to go beyond our limits and become something much more. Everyone wants to live longer healthy lives, experience more vividly and feel more deeply. Technology is simply a means to achieve that end.

See other FICO posts on artificial intelligence.

The post The Future of AI: Redefining How We Imagine appeared first on FICO.


          åŸºå› æ•°æ®ï¼šä¸­ç¾Žè¾ƒé‡çš„新领域        

基因数据:中美较量的新领域

作者:戴维J林奇

美国执法者担心中国正在获取美国基因组数据,这场潜在争端将对两国商业关系和生物医学研究的未来产生影响。

在美国联邦调查局(FBI),没有很多特工像埃德尤(Ed You)那样。在这个鼓励工作人员让自己看上去平淡无奇的工作环境中,他那剃得锃亮的光头十分抢眼。尽管他的多数同事都是出了名的口风严密,但尤却是科技会议上健谈的明星,例如西南偏南大会(South-by-Southwest)和拉斯维加斯国际黑客大会(DEFCON)。


基因数据:中美较量的新领域

他还处在一场中美潜在争端的前沿,这场争端可能对这两个全球最大经济体的商业关系以及生物医学研究的未来产生影响。

尤的高调作风是FBI一项不同寻常的行动的一部分,该行动的目的是突出美国仓促寻求破解人类基因组秘密的风险。作为FBI生物对策部门一位负责监管的特工,尤警告称,美国没有保护用来制造有利可图的新药的基因组数据,而这些数据可能还被用来开发可怕的生化武器。

“我们不知道有多少生物数据流到了国外,”他表示,“我们对生物学安全的概念需要扩大。”
基因数据:中美较量的新领域
这让他关注中国,这位经验丰富的执法者表示,中国正获取美国基因组数据,即管理人体组织的生物软件。最近几年,中国投资者购入专门研究基因组的美国生物医学公司的股权或与它们合作。同时,据信为中国人的、由政府资助的黑客潜入了存放其他重要患者记录的实验室、健康保险公司和医院。尤认为,在哪些健康数据可以转移到海外(中国和其他国家)方面,可能需要加强控制。
在第一个人类基因组被解密近20年后,该领域成为生物医学研究最令人兴奋的领域之一,它依赖开放的国际合作网络。

但也正是在这一领域,国家安全问题(有关中国的目的以及中国企业与政府的关系)正使得一些人发出保护美国经济重要行业的呼声。

自2014年美国禁止华为(Huawei)进入美国电信基础设施市场部分领域以来,美国阻止了中国企业收购一家俄勒冈州风力涡轮公司、一家加州云计算公司以及一家德国半导体制造商在美国的分公司。美国国防部对中国在人工智能领域的投资感到担忧。

FBI的大规模杀伤性武器部门传统上主要关注防范埃博拉(Ebola)或炭疽病毒等病毒落入不法分子手中并导致新的细菌武器扩散。

如今FBI担心,事实可能证明,数字数据集也具有同样的杀伤力。对美国大量基因数据正被大肆收集的担忧,有助于解释为何一家执法机构要追踪美国竞争优势的潜在丧失。尤表示:“经济影响是主要的近期威胁:大规模数据集的变现。”

一些观察人士认为,美国政府就中国在基因组领域投资的影响提出疑问是正确之举。“我从未看到过FBI突然冒出来这么做,”美国国会批准创建的顾问组织——美中经济与安全评估委员会(US-China Economic and Security Review Commission)成员迈克尔韦赛尔(Michael Wessel)表示,“这个关键领域需要更多关注……这是真正的威胁。”

另有一些人担心,美国对中国生物医学投资设置过多障碍将是破坏性的。纽约荣鼎咨询(Rhodium Group)创始合伙人丹罗森(Dan Rosen)指出,过去5年,中国在美国生物技术和制药领域投资逾32亿美元,随之而来的往往是优秀的中国科学家。在一些领域,例如大规模低成本基因测序领域,中国领先于美国。他表示,如果中国公司在美国变得不那么受欢迎,他们会到别处去。

“我认为围绕生物技术划定界限并把整个行业称为关键行业不会达到目的,”罗森表示,“我们必须能够继续对投资具体情况具体分析。”
基因数据:中美较量的新领域
基因组研究有望带来精准靶向药物的新时代,这种药物使传统的通用药物看起来就像是二战时的傻瓜炸弹。但针对病人个人基因组的定制治疗方案仍然处于早期阶段。

美国(目前公认的全球领头羊)和中国都在积极研究癌症、囊性纤维化和阿尔茨海默症(Alzheimer’s)等疾病的个人化治疗。去年中国公布了一项90亿美元的15年研究计划,令奥巴马时代为美国国家卫生研究院(NIH)拨款2.15亿美元的计划相形见绌。

自从2000年首次对人类基因组测序后,DNA科学呈现飞跃式发展。曾经需要花费数年时间、数十亿美元的工作,如今用1000美元不到一周就能搞定。美国正在从逾100万名志愿者收集基因数据,以便自动化实验室系统可以研究个人基因如何相互作用。

“第一个问题是数据……你需要很多数据,”位于华盛顿的威尔逊中心(Wilson Center)的埃莱奥诺雷保韦尔斯(Eleonore Pauwels)表示。

北京方面在该领域的野心使得一些中国企业走上收购之路——特别是在美国。例如,1月深圳的碳云智能(iCarbonX,旨在把人工智能和大型基因数据库结合起来以打造个性化健康治疗方案)向PatientsLikeMe投资逾1亿美元。这家美国公司自称全球最大的个性化健康网,逾50万人在此分享了医疗细节。位于马萨诸塞州坎布里奇的PatientsLikeMe表示,其数据是匿名的,存放在美国境内的服务器。

这类数据——储存在100 GB到1TB的文件内——可以用于研发新药物。实验室收集海量此类数据,之后把它们与详细的人口统计、饮食习惯、健康和生活方式等记录数据相结合。超级计算机寻找规律,识别基因缺陷并提供新的治疗建议。
基因数据:中美较量的新领域
然而,同样的数据集也可以用于研发生物武器。FBI于2014年末首次提出对生物医学的担忧,目前尚未正式提出政策建议。拥有生物化学和分子生物学硕士学位的尤建议,收紧健康记录方面的法规,使之更难转移到海外。

尽管特朗普政府在科技领域的大多数高级职位目前仍处于空缺,但尤坚持认为FBI的顾虑已经开始在政府内“产生更大影响”。

政府之外,人们的看法不一。“我不认为他是杞人忧天。他提出了一些需要提出和回答的问题,”美国国家亚洲研究局(National Bureau of Asian Research)高级研究员本肖伯特(Ben Shobert)表示。

但麦肯研究院(Milken Institute) FasterCures中心的高级研究员伯纳德穆尼奥斯(Bernard Munos)称,FBI的担忧夸张了。“他们能从我们这里偷的是数据,”他这样说竞争对手,“数据是必要条件,但不是充分条件。你需要聪明人从数据中提取知识,再根据知识设想可能的新疗法。现在,中国人实现这一点的能力有限。”

FBI官员意识到,科学是一项全球努力,如果局限在国界线内,这项努力将会凋敝。

例如,如果没有英国、德国、法国、日本和中国的帮助,美国人类基因组计划(Human Genome Project)会耗费更长时间。穆尼奥斯表示,美国约40%的生物医学科学家来自中国或印度。

“如果没有这些人,美国生物医学研究今天很难运转,”他表示,“合作是必不可少的部分。”

这就是迄今为止跨境收购几乎没有遭到反对的原因。2013年,美国政府外国投资委员会(Cfius)批准了深圳华大基因(BGI-Shenzhen)收购位于加州的完整基因公司(Complete Genomics)。后者对超过2万个人类基因组进行了测序。
基因数据:中美较量的新领域
美中经济与安全评估委员会成员韦赛尔表示,如今这样的交易可能遭到否决。其中一个原因是缺少互惠性。肖伯特表示,尽管中国企业持股了美国生物医学公司,但中国法规不允许外国企业将基因数据带出中国。

美国外国投资委员会也不跟踪大部分的外国贷款、股份不足10%的非控股性投资——比如碳云智能的收购——或对初创企业的入股。

“最初期的有趣的东西,在车库里研究的东西,可能被中国的资金渗透,这可把FBI吓坏了,”罗森表示。

在国会,共和党领导层成员、参议员约翰康宁(John Cornyn)计划引入立法,将政府审核外国投资的范围扩大到合资企业和其他技术公司收购。“中国投资的现状是不可持续的,”康宁在美国外交关系委员会(Council on Foreign Relations) 6月一次活动中表示。
基因数据:中美较量的新领域
跨境收购不是美国基因数据面临的唯一风险。医疗行业出了名的容易受到网络攻击。尤表示,尽管迄今为止大多数公众关注都集中在身份盗用或信用卡信息被盗上,但病人医疗记录往往更易被窃取。他3月向美中经济与安全评估委员会表示,最近一些黑客事件涉及“真正渗透和获取临床数据”。

去年12月,黑客潜入探索诊断公司(Quest Diagnostics)得到了3.4万份病人记录,其中包括实验室成果。该公司自诩拥有全世界最大的临床实验室数据库。

尽管没有证据表明外国势力参与此次事件,但加州监管部门在1月宣布与保险商Anthem达成的和解方案时表示,美国官员认为代表中国政府的黑客于2014年攻入了Anthem的网络,并且花了一年的时间翻遍了7880万客户的记录。

“总体上,医疗保健行业远没有其他很多行业和部门安全。因此,如果下定决心的行动者有动力的话,他们的能力肯定足以获得此类信息,”网络安全公司曼迪昂特(Mandiant)的副总裁查尔斯卡玛卡尔(Charles Carmakal)表示,“我们只是还没遇到罢了。”

与此同时,国家安全风险若隐若现。美国政府长期投资于抵御会造成“严重”健康风险的约60种病原体和10种毒素的手段,包括埃博拉病毒、H1N1流感病毒和蓖麻毒素等。

但基因编辑和新一代DNA测序等技术进步使得科学家可以把新病毒变成武器,或许包括用定制病原体攻破现有免疫系统或抵抗现有药物的影响。一些专家对用来杀死特定人群、甚至个人的生物武器发出了警告。

去年,国家情报总监詹姆斯克拉珀(James Clapper)把旨在制造新生物武器的基因编辑列入国家最大安全威胁。“风险是实实在在的,”白宫一个科学顾问小组去年11月表示,“而且会随着未来几年生物技术日益复杂而越来越危险。”

内部威胁:科学家被控窃取行业机密

拥有生物化学博士学位和4项专利的薛瑜(Yu Xue)是“全世界最顶级的蛋白质生物化学家之一”,检察官在指控薛瑜从其供职公司窃取行业机密时表示。

薛瑜坐在她在葛兰素史克(GlaxoSmithKline)的办公室内——位于宾州上梅里恩(Upper Merion)一个高尔夫球场对面——把机密文件通过电子邮件发给了同谋嫌疑人,同时把其他文件下载在拇指驱动器内。

薛瑜当时正在帮助研发一款单克隆抗体——它就像一种自动寻的装置,搭载药剂直达癌细胞,以减缓癌细胞生长或杀死癌细胞。这是精准医学的早期例子,精准医学给治疗一些疑难杂症、并使西方制药公司保持全球领先带来很大希望。该案突显了美国官员所说的中国获取美国技术机密的全面行动。

根据费城美国地方法院(US District Court) 5月24日提交的最新起诉书,同谋嫌疑人在中国南京成立了一家名为南京任诺药业有限公司(Renopharma Inc.)的公司来销售盗取来的机密,其中包括进行试验的“分步说明”、葛兰素史克对注入患者体内的蛋白质进行纯化的过程、以及实验结果。

任诺药业共同所有者、同样面临指控的李涛表示,该公司得到了中国政府的资金、低息贷款、免税期和4000平方英尺的免租金实验室。

“不同层级的政府帮了我们很多,”检察官援引他在一封邮件中写道的内容称,“这向我们证明了我们选择的这条路是对的。”

另一份邮件表示,任诺药业预计通过生产“拥有中国知识产权的新型药物”,今年销售额将接近7500万美元。

李涛、薛瑜及其同样被指控的孪生姐妹薛天均提出无罪抗辩。同样曾就职于葛兰素史克的席露(Lucy Xi)尚未提出抗辩,法院文件中没有列出最后一名被告梅谚的律师。葛兰素史克的总部位于英国。

薛瑜曾经在邮件中发送了一篇关于礼来(Eli Lilly)一名科学家被控窃取机密的文章。“太可怕了,”她说。

End.

转载请注明来自36大数据(36dsj.com):36大数据 基因数据:中美较量的新领域


          The Nexus of Stem Cell-Derived Beta-Cells and Genome Engineering.        
Related Articles

The Nexus of Stem Cell-Derived Beta-Cells and Genome Engineering.

Rev Diabet Stud. 2017;14(1):39-50

Authors: Sackett SD, Rodriguez A, Odorico JS

Abstract
Diabetes, type 1 and type 2 (T1D and T2D), are diseases of epidemic proportions, which are complicated and defined by genetics, epigenetics, environment, and lifestyle choices. Current therapies consist of whole pancreas or islet transplantation. However, these approaches require life-time immunosuppression, and are compounded by the paucity of available donors. Pluripotent stem cells have advanced research in the fields of stem cell biology, drug development, disease modeling, and regenerative medicine, and importantly allows for the interrogation of therapeutic interventions. Recent developments in beta-cell differentiation and genomic modifications are now propelling investigations into the mechanisms behind beta-cell failure and autoimmunity, and offer new strategies for reducing the propensity for immunogenicity. This review discusses the derivation of endocrine lineage cells from human pluripotent stem cells for the treatment of diabetes, and how the editing or manipulation of their genomes can transcend many of the remaining challenges of stem cell technologies, leading to superior transplantation and diabetes drug discovery platforms.

PMID: 28632820 [PubMed - in process]


          The proteins that domesticated our genomes         

EPFL scientists have carried out a genomic and evolutionary study of a large and enigmatic family of human proteins, to demonstrate that it is responsible for harnessing the millions of transposable elements in the human genome. The work reveals the largely species-specific gene-regulatory networks that impact all of human biology, in both health and disease.

read more


          YOU ONLY LIVE ONCE: Artemis Simpoulos-author of THE OMEGA DIET-on the greatness of Greece        


Dr. Artemis Simopoulos is a Founding Member of the International Society for the Study of Fatty Acids and Lipids (ISSFAL) in 1991, Secretary/Treasurer of ISSFAL from 1991 to 1998, and a member of the Editorial Board of the ISSFAL Newsletter from 1994 to 2000. She is the Founder of the International Society of Nutrigenetics/Nutrigenomics (ISNN) and was Past President of ISNN from 2005-2009. She is the author of The Omega Diet (HarperCollins, 1999) and has edited over 50 books and journal supplements, in addition to publishing over 350 scientific papers. She was the editor of the Karger series World Review of Nutrition and Dietetics from 1989-2011.

          YOU ONLY LIVE ONCE: Artemis Simopoulos-author of THE OMEGA DIET-on Hipporates and the concept of positive health        


...Long time ago #Hippocrates, father of Medicine, in #Kos#Greece invented the concept of  #positive#health. How to use your food as medicine and stay healthy and active.
Artemis P. Simopoulos, MD- author of THE OMEGA DIET-on Hippocrates and positive health
https://www.youtube.com/watch?v=I8UYmUKZC_I
Artemis P. Simopoulos, M.D., author of the Omega Diet, introduces us in less than two minutes in the basic principles of the Hippocratic philosophy.
Artemis P. Simopoulos, M.D. is the Founder and President of the Center for Genetics, Nutrition and Health, a nonprofit educational organization in Washington, D.C. since 1990. A graduate of Barnard College, Columbia University, with a major in Chemistry, and a graduate of the Boston University School of Medicine, she is a pediatrician and endocrinologist whose research at the National Institutes of Health (NIH) was on the nutritional aspects of genetic and endocrine disorders; evolutionary aspects of diet and fatty acids; and the importance of a balanced ratio of omega-6/omega-3 fatty acids in health and disease and in growth and development.

Dr. Simopoulos was chair of the Nutrition Coordinating Committee at the National Institutes of Health (NIH) that coordinated all Nutrition Research of the Federal Government in the U.S. in the Office of Science and Technology Policy at the White House. She was consultant to the Office of Consumer Affairs at the White House. Prior to that she was the Executive Secretary of the Division of Medical Sciences at the National Academy of Sciences (NAS) during which time she directed the Asilomar Conference on Recombinant DNA technology. While at the NAS she directed the Committee that developed the report Genetic Screening: Programs, Principles, and Research.

Dr. Simopoulos is a Founding Member of the International Society for the Study of Fatty Acids and Lipids (ISSFAL) in 1991, Secretary/Treasurer of ISSFAL from 1991 to 1998, and a member of the Editorial Board of the ISSFAL Newsletter from 1994 to 2000. She is the Founder of the International Society of Nutrigenetics/Nutrigenomics (ISNN) and was Past President of ISNN from 2005-2009. She is the author of The Omega Diet (HarperCollins, 1999) and has edited over 50 books and journal supplements, in addition to publishing over 350 scientific papers. She was the editor of the Karger series World Review of Nutrition and Dietetics from 1989-2011. 

          Swiss neuroprostheses explorations        
Over at the BrainSciencePodcast forum, a listener, jezcentral, contributed this link:

Launching of EPFL Center for Neuroprostheses

Excerpt:
"What's a neuroprosthesis? It's a device made up of sensors, connections and electronic chips that are embedded in the body to repair certain neurological deficiencies. Recent progress in artificial retinas and man-machine interfaces that permit communication or action via thoughts alone gives us a glimpse of the possibilities the future might hold for improving the lives of the handicapped. The new Center will concentrate on six main themes: vision (retinal implants), hearing (cochlear implants), mobility (cortical and spinal implants), non-invasive man-machine interfaces (piloting at distance, robotics), the micro-and nano-fabrication of implants, and neuronal coding (signal processing, sensors).

The Center will be inaugurated on January 1, 2009, and will formally be part of EPFL's School of Engineering, in collaboration with the School of Life Sciences and the School of Computer and Communication Sciences. This project also opens the door to fruitful collaborations with other institutions in the Lake Geneva area, such as University of Lausanne and the Cantonal Hospital (CHUV)), University of Geneva and its hospital (HUG), and the regional biomedical industry."

Other posts on how prolific neuroresearch appears to be in Switzerland:
1. Virtual Body Experience
2. Something in Swiss water?
3. More from Lausanne: Mapping the structural core of the human cerebral cortex
4. Smelling someone else's alarm bells


On a related topic, related in terms of collaborative projects done by teams of people, in this case by a private backer, reader Kent sent me a link to Piece of Mind, from the Economist.

Excerpt:
"When we first put the mouse-brain atlas online free, it was met by the research world with suspicion. People wondered what the catch was. Scientific research has long been a solitary endeavour—one researcher, one microscope. Findings are protected so that discovery credit can be clearly defined and awarded. This is a successful model and will continue to be.

However, the Human Genome Project demonstrated a different path: multiple teams working collaboratively towards a common goal (...) We wanted the mouse atlas to be free and available for all to use as the basis for foundational research and discovery.

A new generation of implantable pacemakers for the brain will be widely used to treat everything from depression to addiction and Parkinson’s disease

If we thought it would be a hit right out of the gate, we were slightly wrong. It took a while for people to trust that it really was free to use. No one believed in a free lunch.

Now, things have changed. Today we have many scientists using the atlas for their research into Alzheimer’s, bipolar disorders, Down’s syndrome, Parkinson’s, fragile x mental retardation and epilepsy. The atlas is also giving scientists insight into alcoholism, obesity, sleep, hearing and memory.

The greatest testament to what we did was that researchers of spinal-cord diseases, trauma and disorders approached the institute and asked us to create a spinal-cord atlas, which is now close to completion. We will launch the first phase of a human-brain atlas, a four-year project, in 2010.

Like the Human Genome Project, the Allen Brain Atlases and Spinal-Cord Atlas have helped democratise the scientific landscape. When you can log on to a map of gene expression from anywhere in the world, more people can enter the scientific conversation. The result is a massive saving in time, since without the atlas each researcher could spend a lifetime trying to gather complete gene-expression data for his or her work."

Nothing but good will come out of this, I'm sure. Seth Grant, who recently decoded human synapse proteomics, used free genomic data bases to arrive at new perspectives on how evolution of the nervous system has proceeded. (Here is a blog post about that.) Listen to Ginger Campbell's BrainSciencePodcast #51 interview with Dr. Grant. (It was my pleasure to transcribe the interview - the transcription is linked to the podcast shownotes.)




          359: Google Plus Subtracts        
Sara France and Nate Burr, a.k.a. Blunty, join Frederick to talk about the big changes over at Google Plus. Also a discussion about Imagenomic who just updated its popular portraiture retouching plug-in to handle video.
          Sex Change, It’s Not Epigenetics or DES        
Don’t be a fool and fall for all that false and misleading information like epigenetics and DES as causing Gender Dysphoria. Epigenetics For starters, take a look at a paper about epigenetics sent to me by a reader: “The disparate maternal aunt-uncle ratio in male transsexuals: an explanation invoking genomic imprinting.” by Green R, Keverne […]
          The Pseudoscientists Episode 122: An Important Time in Cosmology        

Podcast Feature Image 2 scale

Liz, Joanna and Jack brave apocalyptically-bleak Melbourne weather to delve into news about the efficacy of homeopathy, why a recent Melbourne study into acupuncture might not be so great, and how scientists found water under the surface of one of Saturn's moons, while Jargonauts gets personally drugged-up with "pharmacogenomics".
          NIH Investigating Genomics in Rare Eye Diseases, Fast Tracking Treatments        
The National Ophthalmic Disease Genotyping and Phenotyping Network (eyeGENE®) is a genomic medicine initiative created by the National Eye Institute (NEI), part of the National... Read More →
          Wildlife Disease Journal Digest        
Browse complete Digest publication library here.


Wild bird surveillance for avian influenza virus
Methods Mol Biol. 2014;1161:69-81. doi: 10.1007/978-1-4939-0758-8_7
Brown JD, Poulson R, Stallknecht DE.

Perpetuation and reassortment of gull influenza A viruses in Atlantic North America
Virology. 2014 May;456-457:353-63. doi: 10.1016/j.virol.2014.04.009. Epub 2014 Apr 28.
Huang Y et al.

Viral metagenomic analysis of feces of wild small carnivores
Virol J. 2014 May 15;11(1):89. doi: 10.1186/1743-422X-11-89.
Bodewes R et al.

Association of a lukM-positive clone of Staphylococcus aureus with fatal exudative dermatitis in red squirrels (Sciurus vulgaris)
Vet Microbiol. 2013 Mar 23;162(2-4):987-91. doi: 10.1016/j.vetmic.2012.10.025. Epub 2012 Nov 2.
Simpson VR et al.

Temporal patterns in immunity, infection load and disease susceptibility: understanding the drivers of host responses in the amphibian-chytrid fungus system
Functional Ecology. 2014 Jun; 28(3): 569–578. doi: 10.1111/1365-2435.12194
Stephanie S. Gervasi et al.

The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses
Database. 2014; bau008 doi: 10.1093/database/bau008
Filip Claes et al.

Monitoring Wildlife-Vehicle Collisions in the Information Age: How Smartphones Can Improve Data Collection
PLoS ONE. 2014; 9(6): e98613. doi:10.1371/journal.pone.0098613
Olson DD, Bissonette JA, Cramer PC, Green AD, Davis ST, et al.

Batrachochytrium dendrobatidis prevalence and haplotypes in domestic and imported pet amphibians in Japan
Tamukai K, Une Y, Tominaga A, Suzuki K, Goka K (2014)
Dis Aquat Org 109:165-175

First evidence of hemoplasma infection in free-ranging Namibian cheetahs (Acinonyx jubatus)
Vet Microbiol. 2013 Mar 23;162(2-4):972-6. doi: 10.1016/j.vetmic.2012.10.009. Epub 2012 Oct 16.
Krengel A et al.

Fish pathogens near the Arctic Circle: molecular, morphological and ecological evidence for unexpected diversity of Diplostomum (Digenea: Diplostomidae) in Iceland
Int J Parasitol. 2014 Jun 11. pii: S0020-7519(14)00122-2. doi: 10.1016/j.ijpara.2014.04.009. [Epub ahead of print]
Blasco-Costa I et al.

Gross and microscopic pathology of hard and soft corals in New Caledonia
J Invertebr Pathol. 2014 Jun 10. pii: S0022-2011(14)00082-2. doi: 10.1016/j.jip.2014.05.007. [Epub ahead of print]
Work TM et al.

Extreme Heterogeneity in Parasitism Despite Low Population Genetic Structure among Monarch Butterflies Inhabiting the Hawaiian Islands
PLoS One. 2014 Jun 13;9(6):e100061. doi: 10.1371/journal.pone.0100061. eCollection 2014.
Pierce AA1, de Roode JC1, Altizer S2, Bartel RA3.

Demographic consequences of heavy metals and persistent organic pollutants in a vulnerable long-lived bird, the wandering albatross
Proc Biol Sci. 2014 Jul 22;281(1787). pii: 20133313. doi: 10.1098/rspb.2013.3313. Epub 2014 Jun 11.
Goutte A et al.

Trichomonas stableri n. sp., an agent of trichomonosis in Pacific Coast band-tailed pigeons (Patagioenas fasciata monilis)
Int J Parasitol Parasites Wildl. 2013 Dec 28;3(1):32-40. doi: 10.1016/j.ijppaw.2013.12.002. eCollection 2014.
Girard YA et al.

Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States
Infect Genet Evol. 2014 Jun 6. pii: S1567-1348(14)00198-1. doi: 10.1016/j.meegid.2014.05.029. [Epub ahead of print]
Scotch M et al.

Evidence That Bank Vole PrP Is a Universal Acceptor for Prions 
PLoS Pathog 10(4): e1003990. doi:10.1371/journal.ppat.1003990
Watts JC, Giles K, Patel S, Oehler A, DeArmond SJ, et al. (2014)

Disease of Aquatic Organisms - May 2014
Vol. 109, No. 2

International Journal for Parasitology: Parasites and Wildlife - August 2014
Volume 3, Issue 2
          Glow-in-the-dark tool lets scientists find diseased bats and other wildlife health news        
TOP STORIES

Glow-in-the-dark tool lets scientists find diseased bats

Scientists working to understand the devastating bat disease known as white-nose syndrome now have a new, non-lethal tool to identify bats with WNS lesions -- ultraviolet, or UV, light. Millions of bats have died from this rapidly spreading disease and this new method allows for accurate detection of the disease without killing any more bats.

Science Daily
29 May 2014

>>> FULL ARTICLE

Cited Journal Article
Gregory G. Turner, et al. Nonlethal Screening of Bat-Wing Skin With the Use of Ultraviolet Fluorescence to Detect Lesions Indicative of White-Nose Syndrome. Journal of Wildlife Diseases, 2014; 140522114529005 DOI: 10.7589/2014-03-058

Other White-Nose Syndrome News
>>> 'Listening' helps scientists track bats without exposing the animals to disease


To Michigan's animal pathologist, solving wildlife deaths is 'a fun job'

... But while most wildlife enthusiasts would prefer to handle living animals, Cooley has spent the past 35 years up to his elbows in the carcasses of dead deer, waterfowl or other creatures that have met their demise from unknown circumstances. As the Michigan Department of Natural Resources’ animal pathologist, Cooley’s job is to solve the mysteries of wildlife death.

... The animals that end up in Cooley’s necropsy lab at Michigan State University come from the U.S. Fish and Wildlife Service, USDA Wildlife Services and the public. Sometimes, the cause of death is obvious. For example, an animal found on the side of the road with broken bones and bruises would likely have been hit by a car.

Other times, the answer is not as straightforward.

“You never know what you’re getting into,” said Julie Melotti, Cooley’s lab technician of seven years. “But sometimes you assume something is roadkill and it turns out to be something completely different.”

Cooley and his staff of two veterinarians, two lab scientists and two technicians are responsible for investigating and reporting trends in animal health throughout the state. Their role is to predict the next epidemic and make suggestions for preventing it, if possible.

“Wildlife health and human health, you can’t separate them. They are intertwined,” Cooley said. “The way people can travel and animals can travel, you can have a disease on the other side of the world and all of a sudden you find it in Michigan.”

Detroit News
01 Jun 2014

>>> FULL ARTICLE


Genome Sequences Reveal How Lemurs Fight Infection

New technique could aid conservation, disease surveillance

The young lemur named Eugenius started to get sick. Very sick. He was lethargic, losing weight and suffering from diarrhea. Duke Lemur Center veterinarians soon pinpointed the cause of his illness: Eugenius tested positive for Cryptosporidium, a microscopic intestinal parasite known to affect people, pets, livestock and wildlife worldwide.

In humans, thousands of cases of Cryptosporidium are reported in the United States each year, spread primarily through contaminated water.

Since Eugenius was the first animal diagnosed in 1999, the parasite has caused periodic diarrhea outbreaks at the Duke Lemur Center. All of the infected animals are sifakas — the only lemur species out of 17 at the center known to fall prey to the parasite — and most of them were under age five when they got sick.

Despite various efforts to stop the infection, such as quarantining infected lemurs and decontaminating their enclosures, more than half of the sifakas living at the center have tested positive for crypto at some point. While most animals recover, the pattern has veterinarians puzzled over why the outbreaks persist.

Now, thanks to advances in next-generation sequencing technology, researchers are getting closer to understanding how these endangered animals fight the infection and detecting the illness early enough to minimize its spread.

Red Orbit
01 Jun 2014


>>> FULL ARTICLE

Cited Journal Article
P. A. Larsen et al. Next-generation approaches to advancing eco-immunogenomic research in critically endangered primates. Molecular Ecology Resources. Ahead of print 29 May 2014. doi: 10.1111/1755-0998.12274



OTHER WILDLIFE HEALTH RELATED NEWS


           Genetics and genomics of pulmonary arterial hypertension         
Soubrier, Florent and Chung, Wendy K. and Machado, Rajiv and Grunig, Ekkehard and Aldred, Michaela and Geraci, Mark and Loyd, James E. and Elliott, C. Gregory and Trembath, Richard C. and Newman, John H. and Humbert, Marc (2013) Genetics and genomics of pulmonary arterial hypertension. Journal of the American College of Cardiology, 62 (25 SUP). D13-D21. ISSN 0735-1097
          So you think you know Marine Metagenomics?        
Metagenomics is so easy to understand, right? Scientists just go out and get DNA sequences from…stuff…in the environment. And then they answer lots of questions, like….um… Yeah sometimes I’m lost too. In metagenomics, researchers collect ocean water or soil samples and sequence random bits of DNA from whatever blob of gunk they collect–they end up […]
          The Future of Medicine by LA Health News         

Some experts say the world is on the cusp of a “golden age” of genomics By Maggie Fox, Julie Steenhuysen and Ben Hirschler
LA health news
Francis Collins, who helped map the human genome, did not get around to having his own genes analyzed until last summer. And he was surprised by what he learned.
Collins has a predisposition for type 2 diabetes, something he had never suspected. The lanky, former director of the National Human Genome Research Institute (NHGRI) discovered this through tests offered by Navigenics, 23andMe and DecodeMe • companies that charge customers a few hundred dollars for a peek at their genetic makeup. “I signed up for all three because I wanted to see if they gave the same answer,” he said. “They all agreed my diabetes risk is higher.”

Read more here...

          Efficient Identification of Protein-Coding Variants in a Model Organism Through Exome Sequencing, New Webinar Hosted by Xtalks        

During a live webinar on September 17, 2014, Mick Watson, Head of Bioinformatics, Edinburgh Genomics, University of Edinburgh, will discuss how he developed probe sets to capture domestic pig (Sus scrofa) exonic sequences based upon the current Ensembl pig gene annotation supplemented with mapped expressed sequence tags (ESTs). The broadcast begins at 12pm EDT.

(PRWeb August 22, 2014)

Read the full story at http://www.prweb.com/releases/2014/08/prweb12113624.htm


          The Evolution of RNA-Sequencing, Upcoming Live Webinar August 22 hosted by Xtalks        

Part 5 in this Genomic Series will examine the types of biological questions and problems RNA-Sequencing can address fully or be a key aid in addressing, as well as those it cannot. The live broadcast will be taking place on Friday, August 22, 2014 at 1pm EDT.

(PRWeb July 31, 2014)

Read the full story at http://www.prweb.com/releases/2014/08/prweb12060727.htm


          Sources of Error and the Role of Replicates in Next Generation Sequencing (NGS), Webinar Hosted by Xtalks        

Part 4 in this Genomic Series will cover the sources of experimental errors in NGS and better understand how replicates can be used to abate such errors in reducing the noise in data processing and in downstream analysis. The live broadcast takes place on Friday, July 25, 2014 at 1pm EDT.

(PRWeb July 16, 2014)

Read the full story at http://www.prweb.com/releases/2014/07/prweb12012706.htm


          Xtalks Announces Its July 2014 Webinars        

Join Xtalks for this month’s calendar of free webinars, which features insightful discussions about risk-based monitoring (RBM), inflammatory bowel disease, sepsis, autoimmune diseases, biopharma, drug development, medical devices, supply chain, clinical data management, clinical trial, genomics, and oncology.

(PRWeb June 27, 2014)

Read the full story at http://www.prweb.com/releases/2014/06/prweb11966854.htm


          Exome Sequencing and Analysis: Considerations for Sample Input, Capture Techniques and Pipelines Related to Variant Detection, Webinar Hosted by Xtalks        

Part 3 in this Genomic Series will cover the requirements of the clinical use of Exomes and highlight levels of error and assumption of risk when multiple regions are reported. The live broadcast takes place on Wednesday, June 25, 2014 at 1pm EDT.

(PRWeb June 05, 2014)

Read the full story at http://www.prweb.com/releases/2014/06/prweb11915385.htm


          Xtalks Announces its June 2014 Webinars        

Join us for this month’s calendar of free webinars, which features insightful discussions about clinical trials, drug development, oncology, Alzheimers, biomarkers, genomics, emerging markets, pharmaceutical outsourcing, medical devices, data management, clinical and pharmaceutical labels, RBM and pharmacovigilance in cosmetics.

(PRWeb June 02, 2014)

Read the full story at http://www.prweb.com/releases/2014/05/prweb11891015.htm


          Dovetail Genomics to Discuss Disruptive Technologies for Improving Disease-Resistant Crops        

In this free webinar, which LabRoots will host May 31, participants will better understand the role of genomics in developing durable disease resistance in crops and improving global food security.

(PRWeb May 05, 2017)

Read the full story at http://www.prweb.com/releases/2017/05/prweb14293769.htm


          This is what phylodiversity looks like        

Following on from earlier posts exploring how to map DNA barcodes and putting barcodes into GBIF it's time to think about taking advantage of what makes barcodes different from typical occurrence data. At present GBIF displays data as dots on a map (as do I in http://iphylo.org/~rpage/bold-map/). But barcodes come with a lot more information than that. I'm interested in exploring how we might measure and visualise biodiversity using just sequences.

Based on a talk by Zachary Tong (Going Organic - Genomic sequencing in Elasticsearch) I've started to play with n-gram searches on DNA barcodes using Elasticsearch, an open source search engine. The idea is that we break the DNA sequence into every possible "word" of length n (also called a k-mer or k-tuple, where k = n).

For example, for n = 5, the sequence GTATCGGTAACGAACTT would look like this:


GTATCGGTAACGAACTT

GTATC
TATCG
ATCGG
TCGGT
CGGTA
GGTAA
GTAAC
TAACG
AACGAA
ACGAAC
CGAACT
GAACTT

The sequence GTATCGGTAACGAACTT comes from Hajibabaei and Singer (2009) who discussed "Googling" DNA sequences using search engines (see also Kuksa and Pavlovic, 2009). If we index sequences in this way then we can do BLAST-like searches very quickly using Elasticsearch. This means it's feasible to take a DNA barcode and ask "what sequences look like this?" and return an answer qucikly enoigh for a user not to get bored waiting.

Another nice feature of Elasticsearch is that it supports geospatial queries, so we can ask for, say, all the barcodes in a particular region. Having got such a list, what we really want is not a list of sequences but a phylogenetic tree. Traditionally this can be a time consuming operation, we have to take the sequences, align them, then input that alignment into a tree building algorithm. Or do we?

There's growing interest in "alignment-free" phylogenetics, a phrase I'd heard but not really followed up. Yang and Zhang (2008) described an approach where every sequences is encoded as a vector of all possible k-tuples. For DNA sequences k = 5 there are 45 = 1024 possible combinations of the bases A, C, G, and T, so a sequence is represented as a vector with 1024 elements, each one is the frequency of the corresponding 5-tuple. The "distance" between two sequences is the mathematical distance between these vectors for the two sequences. Hence we no longer need to align the sequences being comapred, we simply chunk them into all "words" of 5 bases in length, and compare the frequencies of the 1024 different possible "words".

In their study Yang and Zhang (2008) found that:

We compared tuples of different sizes and found that tuple size 5 combines both performance speed and accuracy; tuples of shorter lengths contain less information and include more randomness; tuples of longer lengths contain more information and less random- ness, but the vector size expands exponentially and gets too large and computationally inefficient.

So we can use the same word size for both Elasticsearch indexing and for computing the distance matrix. We still need to create a tree, for which we could use something quick like neighbour-joining (NJ). This method is sufficiently quick to be available in Javascript and hence can be computed by a web browser (e.g., biosustain/neighbor-joining).

Putting this all together, I've built a rough-and-ready demo that takes some DNA barcodes, puts them on a map, then enables you to draw a box on a map and the demo will retrieve the DNA barcodes in that area, compute a distance matrix using 5-tuples, then build a NJ tree, all on the fly in your web browser.

Phylodiversity on the fly from Roderic Page on Vimeo.

This is all very crude, and I need to explore scalability (at the moment I limit the results to the first 200 DNA sequences found), but it's encouraging. I like the idea that, in principle, we could go to any part of the globe, ask "what's there?" and get back a phylogenetic tree for the DNA barcodes in that area.

This also means that we could start exploring phylogenetic diversity using DNA barcodes, as Faith & Baker (2006) wanted a decade ago:

...PD has been advocated as a way to make the best-possible use of the wealth of new data expected from large-scale DNA “barcoding” programs. This prospect raises interesting bio-informatics issues (discussed below), including how to link multiple sources of evidence for phylogenetic inference, and how to create a web-based linking of PD assessments to the barcode–of-life database (BoLD).

The phylogenetic diversity of an area is essentially the length of the tree of DNA barcodes, so if we build a tree we have a measure of diversity. Note that this contrasts with other approaches, such as Miraldo et al.'s "An Anthropocene map of genetic diversity" which measured genetic diversity within species but not between (!).

Practical issues

There are a bunch of practical issues to work through, such as how scalable it is to compute phylogenies using Javascript on the fly. For example, could we do something like generate a one degree by one degree grid of the Earth, take all the barcodes in each cell and compute a phylogeny for each cell? Could we do this in CouchDB? What about sampling, should we be taking a finite, random sample of sequences so that we try and avoid sampling bias?

There are also data management issues. I'm exploring downloading DNA barcodes, creating a Darwin Core Archive file using the Global Genome Biodiversity Network (GGBN) data standard, then converting the Darwin Core Archive into JSON and sending that to Elasticsearch. The reason for the intermediate step of creating the archive is so that we can edit the data, add missing geospatial informations, etc. I envisage having a set of archives, hosted say on GitHub. These archives could also be directly imported into GBIF, ready for the time that GBIF can handle genomic data.

References

  • Faith, D. P., & Baker, A. M. (2006). Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online. 2006; 2: 121–128. PMC2674678
  • Hajibabaei, M., & Singer, G. A. (2009). Googling DNA sequences on the World Wide Web. BMC Bioinformatics. Springer Nature. https://doi.org/10.1186/1471-2105-10-s14-s4
  • Kuksa, P., & Pavlovic, V. (2009). Efficient alignment-free DNA barcode analytics. BMC Bioinformatics. Springer Nature. https://doi.org/10.1186/1471-2105-10-s14-s9
  • Miraldo, A., Li, S., Borregaard, M. K., Florez-Rodriguez, A., Gopalakrishnan, S., Rizvanovic, M., … Nogues-Bravo, D. (2016, September 29). An Anthropocene map of genetic diversity. Science. American Association for the Advancement of Science (AAAS). https://doi.org/10.1126/science.aaf4381
  • Yang, K., & Zhang, L. (2008, January 10). Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Research. Oxford University Press (OUP). https://doi.org/10.1093/nar/gkn075

          iBOL DNA barcodes in GBIF        

I've uploaded all the COI barcodes in the iBOL public data dumps into GBIF. This is an update of an earlier project that uploaded a small subset. Now that dataset doi:10.15468/inygc6 has been expanded to include some 2.7 million barcodes. In the new GBIF portal (work in progress) the map for these barcodes looks like this:

Screenshot 2016 12 07 22 58 43

Many of these records have images of the specimens that were sequenced, and the new GBIF "gallery" feature displays these nicely, e.g.:

Screenshot 2016 12 08 10 04 00

Having done this, I've a few thoughts.

Why did I do this?

Why did I do this, or, put another why didn't iBOL do this already? In an ideal world, iBOL would be an active contributor to GBIF and would be routinely uploading barcodes. Since this isn't happening, I've gone ahead and uploaded the barcodes myself. From my perspective, I want as much data to be as discoverable and as accessible as possible, hence if need be I'll grab data from wherever it lives and add it to GBIF (for an earlier example see The Zika virus, GBIF, and the missing mosquitoes). A downside of this is that, long term, the relationship between data provider and GBIF may be as valuable to GBIF as the data, and simply grabbing and reformatting data doesn't, by itself, form that relationship. But in the absence of a working relationship I still need the data.

Where are the taxonomic names

Lots of barcodes lack formal scientific names, even though in many cases BOLD has them. The data in the public dumps often lacks this information. A next logical step would be to harvest data from the BOLD API and add taxonomic names as "identifications".

Where are the sequences?

The sequences themselves aren't in GBIF, which on the one hand is not surprising as GBIF isn't a sequence databases. However, I think it should be, in the sense that for a lot of biodiversity sequences are going to be the only way forward. This includes the eukaryote barcodes, bacterial sequences, and metabarcodes. Fundamentally sequences are just strings of letters, and GBIF already handles those (e.g., taxonomic names, geographic places, etc.). Furthermore, the following paper by Bittner et al. makes a strong case that rather than knowing "what is there?" it's more important to know "what are they doing?"

Bittner, L., Halary, S., Payri, C., Cruaud, C., de Reviers, B., Lopez, P., & Bapteste, E. (2010). Some considerations for analyzing biodiversity using integrative metagenomics and gene networks. Biology Direct. Springer Nature. https://doi.org/10.1186/1745-6150-5-47

In other words, a functional approach may matter more than a purely taxonomic approach to diversity. For a big chunk of biology this is going to depend on analysing sequences. Even if we restrict ourselves to just taxonomic diversity, there is scope for expanding our notion of what we display once we have sequences and evolutionary trees, e.g. Notes on next steps for the million DNA barcodes map.


          EOL Traitbank JSON-LD is broken        

Follow eol on twitterOne of the most interesting aspects of EOL is "TraitBank", which has been described in a recent paper:

Cynthia S. Parr, Katja S. Schulz, Jennifer Hammock, Nathan Wilson, Patrick Leary, Jeremy Rice, & Robert J. Corrigan. (2016). TraitBank: Practical semantics for organism attribute data. Semantic Web, 7(6), 577–588. https://doi.org/10.3233/SW-150190

TraitBank is available in JSON-LD, and so is potentially part of the Semantic Web. Unfortunately, the JSON-LD provided by TraitBank is broken, to the point that it's hard to believe that anyone's actually consuming the JSON-LD. I know that Google is using EOL data for their knowledge panels, but anyone using TraitBank JSON-LD in a semantic web client is going to run into problems.

First off, let's look at the example provided in the above paper, http://eol.org/api/traits/328067 which returns data for Potos flavus.

{ "@context": { "@vocab": "http://schema.org/", "dwc:taxonID": { "@type": "@id" }, "dwc:resourceID": { "@type": "@id" }, "dwc:relatedResourceID": { "@type": "@id" }, "dwc:relationshipOfResource": { "@type": "@id" }, "dwc:vernacularName": { "@container": "@language" }, "eol:associationType": { "@type": "@id" }, "rdfs:label": { "@container": "@language" }, "dc": "http://purl.org/dc/terms/", "dwc": "http://rs.tdwg.org/dwc/terms/", "eolterms": "http://eol.org/schema/terms/", "eol": "http://eol.org/schema/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gbif": "http://rs.gbif.org/terms/1.0/", "foaf": "http://xmlns.com/foaf/0.1/" }, "@type": "DataFeedItem", "dateModified": "2016-09-30", "item": { "@id": 328067, "@type": "dwc:Taxon", "scientificName": "Potos flavus (Schreber, 1774)", "dwc:taxonRank": "species", "dwc:parentNameUsageID": "http://eol.org/pages/14191", "potentialAction": { "@type": "EntryPoint", "target": { "@type": "Related", "url": "http://eol.org/pages/328067", "actionPlatform": [ "http://schema.org/DesktopWebPlatform", "http://schema.org/IOSPlatform", "http://schema.org/AndroidPlatform" ] } }, "sameAs": [ "http://www.iucnredlist.org/details/41679", "http://genomics.senescence.info/species/entry.php?species=Potos_flavus", "http://commons.wikimedia.org/wiki/Potos_flavus", "http://www.biolib.cz/en/taxon/id1790/", "http://www.iucnredlist.org/apps/redlist/details/41679", "http://www.discoverlife.org/mp/20q?search=Potos+flavus", "http://www.eco-index.org/search/keyword_complete.cfm?keyword=Potos flavus", "http://calphotos.berkeley.edu/cgi/img_query?seq_num=31541&one=T", "http://www.conabio.gob.mx/conocimiento/ise/fichasnom/Potosflavus00.pdf", "http://darnis.inbio.ac.cr/ubis/FMPro?-DB=UBIPUB.fp3&-lay=WebAll&-error=norec.html&-Format=detail.html&-Op=eq&-Find=&id=1689", "http://lod.taxonconcept.org/ses/2mOvV.html", "http://neotropnathistory.lifedesks.org/pages/45271", "http://www.boldsystems.org/index.php/Taxbrowser_Taxonpage?taxid=73392", "http://www.catalogueoflife.org/annual-checklist/details/species/id/6902599", "http://www.catalogueoflife.org/annual-checklist/details/species/id/6902599", "http://genomics.senescence.info/species/entry.php?species=Potos_flavus", "http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=621964", "http://en.wikipedia.org/w/index.php?title=Kinkajou", "http://www.iucnredlist.org/apps/redlist/details/41679", "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=29067", "http://eol.org/pages/328067", "http://animaldiversity.ummz.umich.edu/accounts/Potos_flavus/" ], "vernacularNames": [ { "@language": "af", "@value": "rolbeer", "gbif:isPreferredName": true }, { "@language": "af", "@value": "rolstaartbeer" }, { "@language": "de", "@value": "wickelbär", "gbif:isPreferredName": true }, { "@language": "en", "@value": "Kinkajou", "gbif:isPreferredName": true }, { "@language": "en", "@value": "honey bear" }, { "@language": "es", "@value": "Ak' a' mash", "gbif:isPreferredName": true }, { "@language": "es", "@value": "Chosna" }, { "@language": "es", "@value": "Cusu" }, { "@language": "es", "@value": "Martilla" }, { "@language": "es", "@value": "Martucha" }, { "@language": "es", "@value": "Mico de noche" }, { "@language": "es", "@value": "Mico león" }, { "@language": "es", "@value": "Mono michi" }, { "@language": "es", "@value": "Perro de monte" }, { "@language": "fi", "@value": "Kinkaju", "gbif:isPreferredName": true }, { "@language": "fr", "@value": "Kinkajou, Singe de nuit", "gbif:isPreferredName": true }, { "@language": "nl", "@value": "rolstaartbeer", "gbif:isPreferredName": true }, { "@language": "nl", "@value": "nachtaap" }, { "@language": "pt-BR", "@value": "Jupará", "gbif:isPreferredName": true } ], "traits": [ { "@id": "http://eol.org/pages/328067/data#data_point_949469", "eol:traitUri": "http://eol.org/resources/704/measurements/basalmetrate113", "@type": "dwc:MeasurementOrFact", "predicate": "metabolic rate", "dwc:measurementType": "http://www.owl-ontologies.com/unnamed.owl#Metabolic_rate", "value": "731.33", "units": "mL/hr O2", "eol:dataPointId": 949469, "http://purl.obolibrary.org/obo/VT_0001259": "http://eol.org/resources/704/measurements/metratemass113", "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Basal metabolic rate was measured when individual(s) were experiencing neither heat nor cold stress (i.e. are in their thermoneutral zone); are resting and calm; and are post–absorptive (are not digesting or absorbing a meal) and data were only accepted where there was also a measure of body mass for the same individual(s). Based on information from primary and secondary literature sources. This value represents a single measure of central tendency for this species. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "731.33", "dwc:measurementUnit": "http://eol.org/schema/terms/mlO2perhour", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_46140963", "eol:traitUri": "http://eol.org/resources/737/measurements/e5775a49cc4bbe3f3ae5c391776a467a", "@type": "dwc:MeasurementOrFact", "predicate": "population trend", "dwc:measurementType": "http://iucn.org/population_trend", "value": "Decreasing", "eol:dataPointId": 46140963, "dc:source": "http://eol.org/resources/737", "dwc:measurementValue": "Decreasing", "dwc:scientificName": "Potos flavus (Schreber, 1774)", "eolterms:resource": "http://eol.org/resources/737" }, { "@id": "http://eol.org/pages/328067/data#data_point_46140962", "eol:traitUri": "http://eol.org/resources/737/measurements/25c8b74374d04260b047bd57570e094b", "@type": "dwc:MeasurementOrFact", "predicate": "habitat", "dwc:measurementType": "http://rs.tdwg.org/dwc/terms/habitat", "value": "terrestrial habitat", "eol:dataPointId": 46140962, "dc:source": "http://eol.org/resources/737", "dwc:measurementValue": "http://purl.obolibrary.org/obo/ENVO_00002009", "dwc:scientificName": "Potos flavus (Schreber, 1774)", "eolterms:resource": "http://eol.org/resources/737" }, { "@id": "http://eol.org/pages/328067/data#data_point_949459", "eol:traitUri": "http://eol.org/resources/704/measurements/maxlongevity138", "@type": "dwc:MeasurementOrFact", "predicate": "total life span", "dwc:measurementType": "http://purl.obolibrary.org/obo/VT_0001661", "value": "348", "units": "months", "eol:dataPointId": 949459, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Maximum adult age measured either through direct observation, capture-recapture estimates, projected from physical wear or unspecified, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; in all localities. See source for details.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001114", "dwc:measurementValue": "348", "dwc:measurementUnit": "http://purl.obolibrary.org/obo/UO_0000035", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949460", "eol:traitUri": "http://eol.org/resources/704/measurements/littersperyear728", "@type": "dwc:MeasurementOrFact", "predicate": "litters per year", "dwc:measurementType": "http://eol.org/schema/terms/LittersPerYear", "value": "1", "eol:dataPointId": 949460, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Number of litters per female per year using non-captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "1", "dwc:scientificName": "Potos flavus", "dwc:sex": "http://purl.obolibrary.org/obo/PATO_0000383" }, { "@id": "http://eol.org/pages/328067/data#data_point_949461", "eol:traitUri": "http://eol.org/resources/704/measurements/littersize1554", "@type": "dwc:MeasurementOrFact", "predicate": "clutch/brood/litter size", "dwc:measurementType": "http://purl.obolibrary.org/obo/VT_0001933", "value": "1.11", "eol:dataPointId": 949461, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Number of offspring born per litter per female, either counted before birth, at birth or after birth, using captive, wild, provisioned, or unspecified populations; male, female, or sex unspecified individuals; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "1.11", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949462", "eol:traitUri": "http://eol.org/resources/704/measurements/interbirthinterval291", "@type": "dwc:MeasurementOrFact", "predicate": "inter-birth interval", "dwc:measurementType": "http://eol.org/schema/terms/InterBirthInterval", "value": "365", "units": "days", "eol:dataPointId": 949462, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "The length of time between successive births of the same female(s) after a successful or unspecified litter using non-captive, wild, provisioned, or unspecified populations; primary, secondary, or extrapolated sources; all measures of central tendency; in all localities. See source for details.", "eolterms:statisticalMethod": "http://eol.org/schema/terms/average", "dwc:measurementValue": "365", "dwc:measurementUnit": "http://purl.obolibrary.org/obo/UO_0000033", "dwc:scientificName": "Potos flavus", "dwc:sex": "http://purl.obolibrary.org/obo/PATO_0000383" }, { "@id": "http://eol.org/pages/328067/data#data_point_949463", "eol:traitUri": "http://eol.org/resources/704/measurements/grmaxlat1392", "@type": "dwc:MeasurementOrFact", "predicate": "latitude", "dwc:measurementType": "http://semanticscience.org/resource/SIO_000319", "value": "23.72", "units": "decimal degrees", "eol:dataPointId": 949463, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) were converted to the Wilson and Reeder (2005) taxonomy. These ranges were used to generate measures of geographic range extent and occupancy. Spatial analyses were performed using ArcGIS (version 9.0) (ESRI 2005) for areas and R (R Development Core Team 2005) for geographic coordinates. Value calculated using a global geographic projection.", "eolterms:statisticalMethod": "http://semanticscience.org/resource/SIO_001114", "dwc:measurementValue": "23.72", "dwc:measurementUnit": "http://eol.org/schema/terms/decimaldegrees", "dwc:scientificName": "Potos flavus" }, { "@id": "http://eol.org/pages/328067/data#data_point_949464", "eol:traitUri": "http://eol.org/resources/704/measurements/midrangelong3692", "@type": "dwc:MeasurementOrFact", "predicate": "longitude", "dwc:measurementType": "http://semanticscience.org/resource/SIO_000318", "value": "-68.67", "units": "decimal degrees", "eol:dataPointId": 949464, "dc:source": "Data set supplied by Kate E. Jones. The data can also be accessed at Ecological Archives E090-184-D1, http://esapubs.org/archive/ecol/E090/184/, http://esapubs.org/archive/ecol/E090/184/PanTHERIA_1-0_WR05_Aug2008.txt", "dc:bibliographicCitation": "Kate E. Jones, Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O'Dell, C. David L. Orme, Kamran Safi, Wes Sechrest, Elizabeth H. Boakes, Chris Carbone, Christina Connolly, Michael J. Cutts, Janine K. Foster, Richard Grenyer, Michael Habib, Christopher A. Plaster, Samantha A. Price, Elizabeth A. Rigby, Janna Rist, Amber Teacher, Olaf R. P. Bininda-Emonds, John L. Gittleman, Georgina M. Mace, and Andy Purvis. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently extinct mammals. Ecology 90:2648.", "dwc:measurementMethod": "Digital geographic range maps of all extant, non-marine mammals from Sechrest (2003) were converted to the Wilson and Reeder (2005) taxonomy. 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          The total information world        

Happy Thanksgiving (if you are an American)! It’s been a busy few days in the world of personal genomics. By coincidence I have a coauthored comment in Genome Biology out, Rumors of the death of consumer genomics are greatly exaggerated (it was written and submitted a while back). If you haven’t, please read the FDA’s […]

The post The total information world appeared first on Gene Expression.


          In Brief from the Canadian Forest Service, Laurentian Forestry Centre. 2012. No. 29.         
Are mixed forest stands better carbon sinks than pure stands?

Does CO2 have a fertilization effect on Canada's boreal forests?

Improving prediction of conifer growth in plantations.

Effects of small-scale disturbances in the boreal mixedwood forest.

Birds and post-fire salvage harvesting.

Forest genomics challenge: accelerating genetic selection.

          Les Brèves du Service canadien des forêts, Centre de foresterie des Laurentides. No 29.         
Are mixed forest stands better carbon sinks than pure stands?

Does CO2 have a fertilization effect on Canada's boreal forests?

Improving prediction of conifer growth in plantations.

Effects of small-scale disturbances in the boreal mixedwood forest.

Birds and post-fire salvage harvesting.

Forest genomics challenge: accelerating genetic selection.

          Life Update and Research Update        



Life Update
A little over a month ago I made a very "grown up" decision. I stood up for myself, my future, and my happiness. I learned how hard those decisions can be.

To put it nicely, I severed an engagement and ended a relationship with the person I had become comfortable with the idea of accompanying for the rest of my life. I did this because of a long series of events that have spanned our entire relationship.

I would like to say to masqueradestar, bubblingbeebles, jboing, knightofstarz (and more) that I should have listened to you almost a year ago. I should have listened to you when you said not to forgive an ultimate betrayal of trust. What's done has been done, and I have learned so much about myself and my boundaries of tolerance.

On the bright side, I got to have one of those scenes in your life you don't think actually happen because they seem too much like cinema. I threw the temporary ring into the Ohio river, where if it is found by someone in all of its silver and glass glory, they can have the joy of saying "I HAVE THE RING" and I will never know about it, happily.





Research Update
Due to a series of unfortunate events, my thesis proposal has been post poned until the beginning of fall semester. These unfortunate events mainly surround the fact that my committee and PI were both extremely difficult when it came to scheduling an exact time. This is okay - I am allowed to begin data collection and proceed with my first aim during the summer.

After the completion of my metagenomic analysis research in Dr. Edenborn's lab, we discussed the current microbial research in her lab, what has currently been completed/discovered, and I was given a long list of topics for reading of current literature.

I will be conducting a geostatistical/geospatial analysis of microbial selection of propolis on three probiotic firmicute genera in their relation to honey bee disease/CCD events across the contiguous United States in order to determine variations due to flora, climate, age of hive, and the type of agriculture related to the hives in order to access the risk of pesticide use. This is fun data because I get to play the fun games that consist of "mwahahahahaha I will be applying graph theory!", "I have this pickaxe and I will mine the shit out of your data!" and "It's [not] growing!".

Aim 1 (ish) involves the collection of a minimum of 10 propolis samples from each northern and southern USDA region for the contiguous United States from stationary commercial apiaries (this is a total of 60-80 samples as a minimum). I will also be collecting voluntary survey data from these apiaries on the hives of origin. This aim will be started this summer, and continued through the fall. These surveys upon return will be analyzed and compiled with data mined from USDA and EPA databases. The propolis samples returned will be profiled and tested to determine the zone of inhibition on each firmicute when supplied at "equal" concentrations (crude extractions always get tricky). At this point, a few basic statistical tests will be used in order to filter variables. (Aim 1 was originally split into 2)

Aim 2 is the fun part where I get to use topology. This will mostly involve examining relationships between variables determined to possibly have influence on clustering and more. Both luckily and sadly I will be primarily using software already in existence for the majority of the analysis.

Sorry to be rushed - have spent too much time on this post.

Best to everyone and have an amazing summer!




          Dr. Cohen-Maman Laureen        
Cohen Maman Laureen

Specialty

  • Pediatric cardiology and cardiac echocardiography

Clinical Experience

  • August 2014 - Actually: Cardiologist in Macabi and Private Practice-Marom medical center Kfar Saba
  • Feb 2013 - Actually Internal medicine doctor and cardiologist in Medix Medical service
  • Feb 2010 - May 2010 cardiologist in ICU Ambulance in Shahal 
  • Nov 2008 - May 2009: Weekly shifts as a cardiologist in Intensive care unit and inpatient. Clinic La Casamance - Aubagne and Clinic Clairval - Marseille

Academic Experience

  • Cardiologist in catheterization room as Echocardiographist Prof Banai
  • Cardiologist in internal medicine Unit- Pr Rogowsky
  • Cardiologist in cardio thoracic surgery in outpatient clinic
  • Tel Aviv Medical Center - Ihilov Pr Rogowsky
  • Tel Aviv Medical Center – Ihilov - Prof Oretsky
  • Tel Aviv Medical Center – Ihilov - Prof Yeshurun

Education

  • Sept 1998 - Oct 2004 Education Medical studies:University of Mediterranean Aix-Marseille II, School of medicine
  • DES (diploma of specialty) Oral exam passed in Oct 2008 on Transcatheter balloon dilation versus surgical treatment in neonates with critical aortic stenosis
  • DIU (subspecialty diploma) of pediatric cardiology
  • DU (subspecialty diploma) of cardiac echocardiography
  • Master degree in Human pathology specialty genomic and health - Prof J.L Mege
  • Certificates for completion of master
  • Secondary studies: Sept 1995 - jun1998 Lycée Yavné Marseille Scientific High School: Graduate with honors ( Baccalauréat avec mention)

Presentation in congresses

  • Jun 2009: L.Cohen, A.Dragulescu, V.Fouilloux, B.Bonello, B.Kreitmann, D.Metras, A. Fraisse, Timone Children's Hospital, Marseille, France“Transcatheter balloon dilation versus surgical commisurotomy in neonates with critical aortic stenosis”. L.Cohen, A.Fraisse, A.Dragulescu, P.Amedro, D.Metras, B.Kreitmann, S.Camilleri Timone Children's Hospital, Marseille “Outcome of pulmonary artery angioplasty in children”
  • 5th World congress of pediatric cardiology and cardiac surgery Cairns-Australia
  • Jan 2006: L.Cohen, A.Fraisse, F.Rouault, G.Habib, P.Ambrosi. Timones’s Hospital, Marseille “Patent Ductus arteriosus in the elderly” - Journées européennes de cardiologie Paris-France

Board Memberships and Affiliations

  • Israel heart association as affiliate
  • French society of cardiology as affiliate
  • European society of cardiology as affiliate
  • SAFIR Association of French medical practitioner as Treasurer

          Endo Pills - 3        
Informação cientifica de ação rápida

Ano 1 N°3

Curso de Especialização em Endocrinologia - PUC

Instituto Estadual de Diabetes e Endocrinologia Luiz Capriglione


Prof.: Luiz Cesar Povoa (A45)

Ricardo Martins Rocha Meirelles (A35)

Editor: Rosa Rita Santos Martins (A31)

Editores Associados: Walmir Coutinho (A19)

Edna Pottes (A32)

Composição Gráfica: Wallace Margoniner


O Projeto Genoma foi criado em 1990 através de dois grupos: um público envolvendo cientistas dos Estados Unidos, Inglaterra, França, Alemanha, Canadá e Japão com a direção do Dr. Francis Collins e uma empresa particular, a CELERA Genomics, sob a direção do Dr. Graig Venter. O objetivo de ambos: desenhar o genoma humano. Ambos usaram DNA de voluntários anônimos baseados no fato de que os genes codificantes de proteínas são os mesmos nos humanos. Em 2001, em conjunto, apresentaram o primeiro rascunho do genoma humano e a descrição dos genes codificantes foi considerada concluída em 2004. Estes resultados, entretanto, não incluíram a maior parte dos polimorfismos nem os genes codificantes das moléculas funcionais do RNA.

No Endo Pills deste mês apresentamos exemplos da aplicação dos objetivos do Projeto Genoma na Prática Médica: desenvolvimento de métodos diagnósticos em doenças de etiologia genética, otimização das medidas terapêuticas para essas doenças e doenças infecciosas e prevenção de doenças multifatoriais, como diabetes e hipertensão arterial.

Rosa Rita Santos Martins


ARTIGOS PUBLICADOS


1. GENÔMICA E MEDICINA PERSONALIZADA

O genoma humano, com seus 35 mil genes pode se considerado o manual de instruções do organismo. A Genômica estuda a estrutura individual de cada gene, além de suas interações com outros genes e com o meio. Esta ciência seria revolucionária, segundo o autor, pois promoveria a prática da “medicina personalizada”, ajudando na prevenção, diagnóstico e tratamento de doenças.

A medicina personalizada tenta responder a perguntas como: porque algumas pessoas desenvolvem câncer e outras não; porque o câncer é mais agressivo em determinada pessoa; porque determinada droga, ou dose, funciona para alguns e não para outros? Seu alvo é conseguir os melhores resultados terapêuticos para o perfil genético específico de cada paciente, podendo auxiliar inclusive familiares, médicos e na evolução de outros testes diagnósticos não genômicos.

A combinação da Farmacologia com a Genômica originou a Farmacogenômica, que é uma ciência que permite aos cientistas predizer a probabilidade de uma droga responder baseado no perfil gênico de uma pessoa. Segundo o Dr. Larry Lenko, do FDA, há três maneiras principais de se aplicar a Farmacogenômica:

• A primeira é a de ajudar a predizer a dose apropriada de uma determinada droga. Os genes regulam o metabolismo dos medicamentos. Diferenças na seqüência de um gene podem causar diferenças na atividade enzimática, resultando em diferentes apresentações dessas enzimas em cada indivíduo.

• A segunda é a de criar terapias específicas para cada doença, por alguns chamada de Genômica Tumoral. Testes genômicos têm ajudado na identificação de tumores que respondem melhor a um tratamento específico. Lenko cita drogas Gleevec (Imatinib) para leucemia mielóide crônica, Tarceva (Erlotinib) para câncer de pulmão e Herceptina (Transtuzumab) para câncer de mama como exemplos. As duas primeiras interagem com enzimas inibitórias tirosinoquinases, que ao serem inibidas previnem o crescimento celular tumoral. A última age em tumores que produzem grandes quantidades da proteína HER2, produzida pelo gene HER2, que quando estimulado em excesso aumenta a taxa de crescimento celular.

• A terceira forma de uso é a de selecionar o tratamento de pacientes com HIV de acordo com a resistência viral para as medicações disponíveis. O kit TRUGENE HIV-1 de genotipagem é um exemplo de detecção de variações gênicas que causam resistência a alguns anti-retrovirais.

Esse tipo de pesquisa poderá tornar mais efetivo o tratamento para várias doenças, tais como para a doença cardíaca, diabetes, depressão, asma, etc... além da resposta a quimioterápicos e antibióticos. Informações sobre esse tema podem ser acessados pelo site: http://www.fda.gov/fdac/features/2005/605_genomics.html

Dra. Nadja Zennig (C2) e Dra. Thalita Bittar Carneiro de Oliveira (C2)


2. EQUIPAMENTOS MÉDICOS E A “GENÔMICA”: NOVOS PARADIGMAS NA ÁREA DE SAÚDE:

Neste artigo, publicado “on line” na página da organização americana FDA (Food and Drug Administration), são comentados novos equipamentos médicos que fazem a análise genética de certas doenças.

Após a conclusão do projeto genoma humano e o desenvolvimento de tecnologias de análise genética e molecular, como o “MICROARRAY”, laboratórios começaram a desenvolver equipamentos que possibilitariam em questão de poucos dias, a análise do DNA à partir de amostra de sangue total ou saliva e com isso.

O “MICROARRAY” (ou “gene chip”) consiste numa fina plataforma de vidro ou plástico contendo milhares de segmentos gênicos como um microchip. Estes genes na verdade são “probes” (sondas DNA), consistem em pequenas seqüências conhecidas de DNA capazes de se combinar com o DNA da amostra do paciente e causar uma reação. Esta reação pode ser mensurada e, desta forma, é possível analisar ao mesmo tempo milhares de genes (ou seqüências conhecidas), avaliando mutações, susceptibilidade a doenças e resposta a medicamentos.

Esta técnica possibilita também avaliar qual gene está ativo e qual está inativo. Este tipo de tecnologia é chamada GENÔMICA e possui variações de acordo com o objetivo, como por exemplo, a FARMACOGENÔMICA (quais fármacos funcionam melhor em quais pacientes), METABOLÔMICA (estudo dos fluidos corporais para determinação de alterações no metabolismo) e PROTEÔMICA (estudo de proteínas num organismo ou tecido).

Exemplos de tecnologias que já estão em desenvolvimento são o TAG-IT CYSTIC FIBROSIS KIT, que detecta as variações genéticas mais comuns nos EUA causadoras de Fibrose Cística, ajudando no diagnóstico das crianças acometidas e também identificando carreadores adultos do gene. Outros tipos de teste em estudo são o TRUGENE HIV-1 que determina se o paciente é portador de uma cepa de HIV resistente à certas drogas, guiando o tratamento. O AMPLI-CHIP CYTOCROME P450 GENOTYPING TEST detecta variações num gene que determina a taxa de metabolismo e excreção de certos fármacos, possibilitando o ajuste da dose individual, e o UGT1A1 MOLECULAR ASSAY, que é semelhante ao Ampli-chip, porém específico para uma droga utilizada no tratamento do Câncer de Cólon, com isso avalia a possibilidade de resposta do tumor e minimiza os riscos de efeito colateral.

Estes exemplos demonstram o potencial de uso destas novas tecnologias que, no entanto, não são livres de falha. Uma das principais limitações é a falta de padronização nos resultados (tanto na nomenclatura quanto na identificação dos genes utilizados nas diferentes plataformas de microarray), o que pode vir a causar erros em potencial. Especialistas dizem que ainda é necessário padronizar, criar ferramentas de controle de qualidade, formato e interpretação de resultados para que estas ferramentas possam ser usadas na prática clínica.

Outras informações podem ser obtidas nos sites www.fda.gov?cder/genomics; www.personalizedmedicinecoalition.org; www.cdc.gov/genomics.

Thalita Bittar Carneiro de Oliveira (C2) e Juliana Gabriel Ribeiro de Andrade (C2)


3. VARIANTE DE GENE PODE PREDIZER DIABETES

Pesquisadores da Universidade Southwestern Medical Center, no Texas, identificaram uma variante gênica que poderá servir como preditora de DM tipo II. Segundo o Dr. Scott Grundy, diretor da Unidade de Nutrição Humana dessa Universidade, a variante do gene ENPPI foi 13% mais freqüente em pessoas com DM2 e naqueles em grande risco de desenvolvê-la. O gene ENPPI codifica uma proteína que bloqueia a ação da insulina e sua variação aumenta ainda mais essa inibição, contribuindo para a resistência insulínica. Nas três populações estudadas, uma de nativos de Chennai, na Índia, outra de imigrantes indianos habitantes em Dallas e a ultima de norte-americanos caucasianos de Dallas, divididas em dois grupos formados por não-diabéticos com alto risco e diabéticos, a variante do gene esteve presente em 25% do grupo não-diabético e 34% dos diabéticos na primeira população, em 33 e 45% naqueles imigrantes da segunda população e 26 e 39%, nos caucasianos não-diabéticos e diabéticos americanos, respectivamente. O estudo demonstrou que a variante desse gene nas três populações foi capaz de predizer o diabetes. Diabetes News – American Diabetes Association. In Diabetes Today. Gene Variant May Predict Diabetes, 04-JUL-2006. Originally Published: (20060101).

Dra. Nadja Zennig (C2)


4. ANÁLISE DA EXPRESSÃO GÊNICA DE TUMORES ADRENOCORTICAIS HUMANOS PELA ANÁLISE CDNA POR MICROARRAYS.

A análise comparativa cDNA por microarrays para o estudo da expressão gênica dos tumores adrenocorticais benignos e malignos permitiu a identificação de novos genes supressores tumorais e proto-oncogenes que ajudaram a delinear a tumorigênese corticoadrenal, até o momento pouco conhecida. A análise do RNA de 10 amostras de tecido tumoral de adenocarcinoma adrenal (ACC) e 10 adenomas adrenocorticais benignos, pareados com 10 exemplares de tecido adrenocortical normal revelou vários genes com diferentes expressões entre: ACC e tecido normal (42 genes), adenoma cortical e tecido normal (11 genes) e ACC e adenoma cortical (21 genes), respectivamente. Como confirmado pela técnica “PCR em tempo real”, o gene IGF2 estava significantemente estimulado no adenocarcinoma adrenal enquanto outros dois genes (o da cromatogranina B e o responsável pela resposta precoce ao fator de crescimento 1) se encontraram bloqueados nesses tumores malignos. Até o momento, as pesquisas com cDNA ajudaram a elucidar alguns aspectos moleculares associados a tumorigênese adrenal. Para a identificação da expressão de cada gene, mais análises serão necessárias, os resultados obtidos até hoje ainda não permitem elucidar as diversas etapas associadas a tumorigênese destes neoplasias. (Slater, E.P et al. Analysis by cDNA microarrays of gene expression patterns of human adrenocortical tumors. European Journal of Endocrinology, 154(4): 587-598, 2006).

Dra. Nadja Zennig (C2)


5. CÉLULAS TRONCO: FALTA CONSENSO, SOBRA ESPERANÇA.

Segundo o Professor Antônio Carlos Paes de Carvalho, da UFRJ, a definição clássica de célula tronco é: “uma célula não especializada com grande potencial de auto-renovação, capaz de originar diferentes tipos celulares no organismo”, que podem ser obtidas do feto e do adulto. As células embrionárias são capazes de gerar qualquer um dos tipos celulares presentes nos tecidos do organismo, mas sua utilização do ponto de vista clínico ainda está bastante distante, porque precisarmos ter um controle sobre a sua proliferação e diferenciação.

O projeto Ghente - Estudos sociais, éticos e jurídicos sobre o acesso e uso de genomas na saúde, da FIOCRUZ promoveu recentemente um fórum para esclarecimento das possibilidades atuais de aplicação das células tronco, dos limites da técnica e do uso seguro das terapias gênicas.

As principais conclusões foram:

• Os procedimentos ainda estão em fase de pesquisa e levarão pelo menos dois anos para sua aplicação (apesar de já haver resultados positivos, como a injeção de células-tronco no coração – Hospital Pró-cardíaco, que reduziu a isquemia de 15 % para 4,5%.

• A Lei de Biossegurança vigente no país contém grandes falhas no que diz respeito à célula-tronco embrionária, necessitando que ainda haja regulamentação da Reprodução Assistida. Por outro lado, a ANVISA está criando um cadastro nacional para controle e rastreamento dos embriões criados em clínicas de fertilização in vitro. Existe, contudo, uma ação no Supremo Tribunal Federal contra o artigo desta Lei que regulamentaria o uso dos embriões inviáveis em pesquisas.

• Para que se possa regulamentar todos os aspectos através de leis, que realmente são categóricas, e não através de portarias, passíveis à relatividade, ainda há que se debater de forma muito difundida com toda a sociedade para que os termos da lei realmente sejam democráticos.

O Dr. Antônio Carlos divulgou o Brasil Cord – banco público de células de cordão umbilical, integrado a uma rede mundial coordenada pela OMS. As doações são de fundamental importância, pois já ajudaram mais de 4 mil pessoas. As doações podem ser feitas direto por um parente também pra este banco, o que evitaria que bancos particulares induzissem os pais do recém-nato a gastos desnecessários. Além do uso terapêutico, estas células também são uma alternativa ao uso dos embriões nas pesquisas. Mais informações: Projeto Ghente: www.ghente.org (Bruno Rodrigues e Claúdia Lopes). RADIS, jul 2006

Thalita Bittar Carneiro de Oliveira(C2)


6. GLOSSÁRIO “OMICS”: SELEÇÃO DE TERMOS E CONCEITOS IMPORTANTES

• Aminoácido: uma das 20 diferentes formas estruturais que se combinam para formar proteínas. A estrutura e a função da proteína são determinadas pela seqüência de aminoácidos presentes.

• Base: uma das moléculas – adenina, guanina, citosina, timina, ou uracila, que formam partes da estrutura molecular do DNA ou RNA. A seqüência de bases moleculares do DNA determina a estrutura de proteínas codificadas por aquele DNA.

• Célula: unidade básica de um ser vivo.

• Cromossomo: estrutura intracelular que contém material genético para formação do gene. Cada cromossomo pode apresentar dezenas ou centenas de genes próprios. Cada espécie tem seu número específico de pares cromossômicos, no homem são 23 pares no interior do núcleo e uma molécula de DNA nas mitocôndrias.

• DNA: É a abreviação de ácido desoxirribonucléico, estrutura molecular dentro do núcleo de uma célula que carrega informações genéticas para formação do ser vivo.

• Enzima: proteína que age como catalisador na iniciação ou aceleração de uma reação química dentro da célula.

• Espectrometria de massa: método que utiliza um instrumento sofisticado que identifica substâncias químicas através do peso molecular.

• Expressão gênica: processo pelos quais as proteínas são constituídas no organismo através de instruções codificadas pelo DNA.

• Farmacogenômica: associação do estudo das drogas (farmacologia) com o estudo de todos os genes (genômica) com o objetivo de determinar como variações do genoma humano afetam a resposta individual aos medicamentos.

• Fenótipo: características e traços físicos de uma pessoa ou um organismo, como por exemplo, cor dos cabelos, peso, ou a presença ou ausência de uma doença.

• Gene: unidade básica de hereditariedade passada dos pais para os filhos, seqüências de DNA, que instruções para formação de proteínas ou outros componentes do ser vivo.

• Genoma: grupo completo de DNA que contém toda informação genética do indivíduo ou organismo.

• Genômica: estudo de todos os genes de um organismo vivo assim como suas funções e atividades e a interação entre eles e entre eles e o ambiente.

• Genótipo: informação genética de um indivíduo ou organismo.

• Marcadores biológicos: indicadores de doença ou risco de uma doença, por exemplo: colesterol sérico é um marcador biológico de risco de doença cardíaca.

• Metabolismo: todo processo físico e químico do organismo necessário para vida.

• Metabólito: qualquer molécula ou substância produzida a partir do metabolismo.

• Metabólito de Baixo Peso Molecular: metabólito de peso leve que pode apresentar indícios importantes sobre a saúde de uma pessoa, incluem aminoácidos, açúcares, carboidratos, e lipídios

• Metabólito Primário: metabólito essencial para o crescimento normal e desenvolvimento em um ser vivo. Os cientistas acreditam que existem no corpo humano em torno de 3000 metabólitos primários.

• Metabólito Secundário: metabólito não essencial para o crescimento e desenvolvimento em um ser vivo, mas podem combater infecções ou outras formas de stress.

• Microarray: ferramenta que estuda como o genes, em geral, interagem entre si e sua expressão nos tecidos alvos.

• Molécula: É a combinação de dois ou mais semelhantes ou diferentes átomos.

• Mutação: mudança na seqüência do DNA que pode levar a síntese de uma proteína alterada ou inativa ou perda da capacidade do gene de produzir proteína.

• Nucleotídeo: estrutura de ácidos nucléicos; consiste uma das cinco bases nitrogenadas: adenina, guanina, citosina, timina ou uracila.

• Polimorfismos: variação de bases que não incorrem em manifestação clínica, são observados numa freqüência igual ou acima de 1% e transmitidos com herança autossômico dominante.

• Projeto Genoma Humano: pesquisa internacional extensiva empenhada em determinar a seqüência pelo qual o DNA humano é organizado.

• Proteína: uma molécula que consiste em uma cadeia formada pela união de vários aminoácidos.

• Proteômica: campo de estudo que avalia todas as proteínas em um ser vivo, determinando sua formação, função e como elas interagem entre si.

• Seqüenciamento de DNA: uma técnica laboratorial usada para determinar a ordem exata dos pares de bases em um segmento do DNA.

• SNPs (single nucleotide polyorphism): sítios na seqüência do DNA do genoma humano que diferem os indivíduos. Estas variações podem ser usadas para rastrear herança familiar.

• Sonda de DNA: segmento de uma molécula do DNA usado em experimentos laboratoriais para detectar a presença ou perda de um gen.

Aline Barbosa Moraes (C2)

ARTIGOS PUBLICADOS ENDOCRINOLOGIA

7. HIPOTIREOIDISMO: O DEBATE CONTINUA...

O artigo debate sobre o tratamento com hormônios tireoidianos para pacientes com clínica sugestiva e laboratório normal voltou à tona recentemente. No início de 2006 a Sociedade de Endocrinologia recebeu uma petição contendo mais de 2000 assinaturas de pacientes que encaminharam uma reclamação formal contra os clínicos que “super estimavam” os resultados de laboratório “sub tratando” ou não tratando os sintomas, apesar do sofrimento dos pacientes. Um editorial do presidente da associação britânica de tireóide (BTA), Tony Weetman, dizendo que os clínicos possuem ferramentas laboratoriais robustas para direcionar o tratamento do hipotireoidismo, foi a causa das manifestações.

O debate não foi sobre o hipotireoidismo sub clínico e sim sobre o tratamento de pacientes com sintomas inespecíficos cujos resultados laboratoriais encontram-se dentro dos limites considerados “normais”. A BTA não recomenda tratamento nestes casos. Mesmo assim, em 2000 a BBC News noticiou que alguns clínicos continuam prescrevendo hormônios tireoidianos para pacientes sintomáticos e com exames normais, a despeito desta recomendação.

O artigo termina lembrando também que o tratamento de sintomas inespecíficos com hormônios tireoidianos não só submete o paciente aos riscos de um excesso destes hormônios como também desvia a atenção do médico para o diagnóstico correto da afecção que atinge o paciente, que pode ser inclusive mais grave.

Juliana Gabriel Ribeiro de Andrade (C2)


8. TERAPIA COM TESTOSTERONA EM HOMENS ADULTOS COM SÍNDROMES DE DEFICIÊNCIA ANDROGÊNICA: UM GUIA CLÍNICO PRÁTICO DA ENDOCRINE SOCIETY

O Hipogonadismo em homens é uma síndrome clínica que resulta da deficiência do testículo em produzir níveis fisiológicos de testosterona e número normal de espermatozóides pela deficiência de um ou mais níveis do eixo hipotálamo-hipófise-gonadal. A Endocrine Society promoveu grupo para produzir as diretrizes de diagnóstico e tratamento da Deficiência androgênica (DA), que foi composto por membros do sub-comitê de guidelines clínicos, outros cinco especialistas, um metodologista e um escritor profissional. Foi utilizada revisão sistemática para uso das recomendações-chave.

Recomendou-se fazer o diagnósticos de DA somente em homens com sintomas e sinais consistentes e nível sérico baixo de testosterona inequívoco. Preferiu-se a dosagem matinal da testosterona total por um método seguro como teste de diagnóstico inicial, com confirmação através da repetição do mesmo e, em alguns pacientes, pela dosagem do nível de testosterona livre ou bioativa.

Foi recomendado terapia com testosterona para homem sintomáticos com DA, que tem níveis baixos de testosterona, para induzir e manter características sexuais secundárias e aumentar sua função sexual, sensação de bem estar, densidade mineral óssea, massa e força muscular. Recomendou-se não utilizar terapia com testosterona em pacientes com câncer de mama ou de próstata, nódulo ou endurecimento prostática palpável, PSA maior ou igual a 3ng/ml, eritrocitose (hematócrito > 50%), hiperviscosidade, apnéia obstrutiva do sono não tratada, sintomas graves do trato urinário com IPPS (Internacional Prostate Symptom Score) maior que 19, ou insuficiência cardíaca classe III ou IV. Quando a terapia com testosterona é constituída, sugere-se monitorar o nível de testosterona, mantendo-os no meio normal de variação do método, com uso de qualquer formulação aprovada baseado na preferência do paciente, consideração da farmacocinética do medicamento e ônus do tratamento.(A descrição completa dos sinais e sintomas, dos dados de história do paciente e métodos de dosagem de testosterona podem ser obtidos no artigo: Matsumoto, MD & Vigersky, R.V. (2006), J Clin Endocrinol Metab 91: 1995-2010).

Karyne Lima (C2)


CASE REPORTS

9. PREDITORES DE DIABETES NO PÓS-PARTO EM MULHERES COM DIABETES GESTACIONAL

O Diabetes Mellitus Gestacional (DMG) é definido como a intolerância à glicose diagnosticada durante a gestação e está presente em 4% das mulheres grávidas. O DMG aumenta substancialmente o risco de desenvolvimento de diabetes no pós-parto e identifica uma população de alto risco para desenvolvimento de Diabetes mellitus (DM) tipo 1 e 2.

O objetivo desse estudo foi o de estratificar o risco no pós-parto de diabetes em mulheres que apresentaram DMG. Foram recrutadas 302 mulheres com DMG, no período entre 1989 e 1999, que foram submetidas ao teste oral de tolerância à glicose no nono mês e no segundo, quinto, oitavo e décimo primeiro ano após a gestação.

No oitavo ano de acompanhamento já havia uma incidência de 52,7% de DM, ou seja, 130 casos. Os fatores de risco positivos e estatisticamente significativos para o desenvolvimento de DM foram: anti-GAD e anti-IA2 positivos (p< 0,0001), necessidade de insulina durante a gestação (p<0,0001), IMC >30kg/m2 (índice de massa corporal) (p = 0,04) e mais do que duas gestações com DMG. Número de gestações, proteína C reativa, história familiar de DM, idade da gestante, duração da gestação e o peso de nascimento da criança não afetaram o risco na análise multivariada.

Conclui-se, então, com esse trabalho que é necessário o acompanhamento e a intervenção em mulheres com história de DMG que apresentam anticorpos positivos ou que necessitaram de insulina durante a gestação ou que são obesas. (Löbner K et al. Predictors of Pospartum Diabetes in Women with Gestacional Diabetes Mellitus: Diabetes, vol 55, 792-797, March 2006)

Luciana Lopes de Souza (C2)


10. ESTUDO DE CASO: INDUÇÃO DE FERTILIDADE EM HOMEM

Caso Clínico: homem de 40 anos, encaminhado para avaliação de hipogonadismo e infertilidade. Nos últimos 2 anos notou diminuição progressiva da libido, do volume ejaculatório e do tamanho testicular. Costuma beber 3 a 4 taças de vinho por semana, não usa nenhum remédio e não tem história patológica pregressa digna de nota. Na história familiar, seu pai teve cirrose hepática, provavelmente induzida por álcool. Ao exame físico, apresentava sinais vitais normais e IMC de 24, nódulos de Bouchard bilateralmente e nenhuma evidência de bócio. Caracteres sexuais secundários eram normais e não havia ginecomastia. Fígado palpável a 2cm do RCD mas sem estigmas de disfunção hepatocelular. O volume testicular era de 10ml bilateralmente.

Avaliação laboratorial inicial mostrava uma Testosterona total de 36ng/dL (1.3nmol/L), LH de 1,5 IU/L e FSH de 1,0 IU/L. O espermograma demonstrava azoospermia e volume de 0,5mL. T4 total era de 6,6mcg/dL (VR: 4,5-10,9), prolactina de 4,2ng/mL (VR: 2-18). TGP 88 (VR: 7-30) e TGO 70 (VR: 9-25). Glicemia de jejum era 105mg/dL.

Questões: 1. Quais testes adicionais seriam necessários para elucidação diagnóstica?

2. Como tratar o paciente?

Respostas:

1. Paciente com hipogonadismo hipogonadotrófico apesar de ter outras funções hipofisárias e RNM normais. A chave para o diagnóstico neste paciente é a hepatomegalia, artropatia e aumento de transaminases que levantam a possibilidade de HEMOCROMATOSE HEREDITÁRIA. O consumo relativamente pequeno de álcool e uma relação TGO/TGP abaixo de 1 diminuem a chance de uma hepatite alcoólica.

A hemocromatose é uma doença autossômica recessiva caracterizada por depósito excessivo de ferro no organismo, incluindo a hipófise. O hipogonadismo hipogonadotrófico é a anormalidade mais freqüente nesta condição. O hipogonadismo primário por depósito testicular de ferro também ocorre mas é muito menos freqüente.

Os testes adicionais para a confirmação diagnóstica seriam uma saturação de transferrina e ferritina aumentadas. O tratamento deve ser primeiramente voltado para a condição de base, que é a flebotomia terapêutica. A reversão do hipogonadismo após depleção de ferro foi descrita em alguns casos, mas é exceção, principalmente pela idade do paciente, que também torna a indução de espermatogênese questionável. O tratamento escolhido no caso deste paciente foi apenas à reposição de testosterona para recuperação da libido e potência.

Juliana Gabriel Ribeiro de Andrade (C2)
          Dog split from wolves earlier than thought        
New research carried out on an 35,000 wolf bone has revealed that dogs split from wolves earlier than we thought. Dogs’ special relationship to humans may go back 27,000 to 40,000 years, according to genomic analysis of an ancient Taimyr wolf bone reported in the Cell Press journal Current Biology on May 21. Earlier genome-based [&hellip
          Personalised Medicine: Dose By Design        
Vivienne Parry asks if the NHS can deliver the benefits of genomic medicine for all
          Upsurge in multidrug-resistant typhoid strain urges action        

Originally posted by the Coalition Against Tyhphoid. 

The abuse and misuse of antibiotics has led to the creation of bacterial strains that are resistant to standard medication, requiring more expensive and risky treatments for some diseases. Typhoid, a bacterial infection transmitted through contaminated food and water, is one of those diseases.

Typhoid is caused by the bacteria Salmonella typhi and kills more than 200,000 people each year. The H58 strain of Salmonella typhi is a multidrug-resistant (MDR) bacteria that has emerged over the past 20 years. Originating in Southern Asia, H58 can now be found in areas in sub-Saharan Africa that were previously not typhoid endemic. Since the emergence of this strain, MDR typhoid has skyrocketed in sub-Saharan Africa. For example, a study conducted by the Wellcome Trust in Malawi found MDR typhoid cases increased from 6.8 percent in 2010 to 97 percent in 2014. Genomic sequencing revealed that 47 percent of the MDR strains were a direct result of the H58 strain of typhoidOriginally ou

A similar study in Kenya covering 20 years of blood culture isolates (isolates are pure parts of a bacteria that have been “isolated” through the blood culture process in order to be analyzed for sensitivity to antibiotics) showed that 73.3 percent of isolates were able to be treated by antibiotics prior to 1993. But within the last seven years, this has changed, with only 22.8 percent of isolates able to be treated by antibiotics. The influx of MDR typhoid in Kenya is also attributed to the spread of H58.

MDR bacteria is not new to the global health community. The most well-known examples of a disease becoming resistant to first-line antibiotics are MDR tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB). Despite the emergence of these dangerous strains, global investment in tuberculosis has primarily focused on treatment, rather than prevention, to control the disease. Treatment for MDR-TB is now 50 to 200 times more expensive and the disease takes three times longer to cure than normal tuberculosis.

The typhoid community must learn from the tuberculosis experience. Without preemptive action, MDR typhoid could be the next deadly threat to global health. The current trends of H58 typhoid transmission show that this strain is not only stable, but also being transmitted to new countries. Typhoid can and must be addressed in a preventative manner to restrict the spread of MDR strains. Vaccines are available to prevent typhoid, but are currently underutilized in endemic countries. These vaccines, along with a new conjugate vaccine currently in development, have the potential to stop the spread of MDR strains and reduce the cost, impact and human suffering brought about by the disease.

The growing problem of drug resistance is finally getting the attention it deserves at a global level. At last year’s World Health Assembly, a Global Action Plan for Antimicrobial Resistance was launched. In April at a United Nations assembly, leaders discussed the implications of drug resistance on attaining the Sustainable Development Goals. The upcoming United National General Assembly in September will feature discussion of the system-wide reform needed to address the increasing threat of antimicrobial resistance.

This global attention is essential; however, more is needed. Beyond international meetings and the creation of new action plans, the global community must invest in surveillance, prevention and education to track transmission patterns and target intervention to high-risk groups. These measures are essential to stop the advancement of MDR typhoid to additional communities and countries, and to ensure it does not become a worldwide threat.


          The Coalition against Typhoid Secretariat Convenes the 9th International Conference on Typhoid and Invasive NTS Disease        

From April 30 to May 3, the Coalition against Typhoid (CaT) Secretariat, with coordination and support from PT Bio Farma, convened nearly 250 participants from 36 countries for the 9th International Conference on Typhoid and Invasive Non-Typhoidal Salmonella (iNTS) Disease. This four-day event, held in Bali, Indonesia, was the largest conference in CaT’s history.

Throughout the conference, prominent clinicians, scientists, policy makers and public health practitioners shared new research and pathways forward for typhoid and iNTS control. The conference’s lively panel discussions and presentations shed light on the global progress towards alleviating the needless suffering caused by these diseases.

Typhoid, a severely under-prioritized public health problem, impacts an estimated 21 million people every year, causing more than 216,000 deaths annually — predominantly among children younger than 15 years of age. However, recent progress in vaccine development, technology transfer and disease surveillance is bringing the world several steps closer to typhoid control.

The conference began with a welcome reception, featuring opening remarks from Brian Davis, Chief Operating Officer of the Sabin Vaccine Institute;  Dr. Anita Zaidi, Director of the Enteric and Diarrheal Diseases program at the Bill & Melinda Gates Foundation; and Dr. Pretty Mulihartina, Director of the Center for Biomedical Technology of Health, NIHRD in Indonesia. Each speaker highlighted the tremendous burden that typhoid and iNTS disease place on communities and families, while providing insight into the promising new research and development being carried forward by many of the conference’s participants.

The welcome reception was followed by three days of discussions and presentations focused on topics such as global disease burden; risk factors for typhoid, paratyphoid, and iNTS disease; disease modelling; water, hygiene, and sanitation (WASH) interventions; antimicrobial resistance; genomics; vaccine implementation strategies; and vaccine development.

Since the Coalition against Typhoid’s last international conference, key milestones have been achieved towards developing typhoid conjugate vaccines. While Vi polysaccharide vaccines exist for typhoid, these vaccines are not effective in young children. However, new conjugate vaccines can be used in infants starting at six months of age – and they also offer a longer duration of protection. Throughout the conference, presenters from various vaccine manufacturing companies, Gavi, the World Health Organization (WHO) and more provided new information on progress towards developing conjugate vaccines, and highlighted what is required to eventually introduce these vaccines into a country’s national immunization schedule.

Key milestones have also been achieved towards understanding the typhoid and iNTS disease burden. A number of panelists and presenters shared data and research collected from novel surveillance projects in Southeast Asia and Africa.  This data is helping the typhoid community better understand who is most affected by typhoid, and where.

The conference also brought to light the emerging incidence of iNTS disease in Africa. For the first time in the conference’s history, a number of presentations were devoted to better understanding the burden of iNTS disease, and what needs to be done to address it. Panel members discussed the need for improved understanding of the epidemiology of iNTS disease in Africa, as there is little knowledge of disease transmission. Until modes of transmission are clearly understood, it will be challenging to design non-vaccine intervention strategies.

The conference closed with a call to action from Dr. Zulfiqar Bhutta from the Hospital for Sick Children. He noted that the Coalition against Typhoid has “come of age” and shown that there is power in collaboration across various areas of typhoid research.

Echoing the views of several other speakers, Dr. Bhutta emphasized the need for increased typhoid and iNTS advocacy activity by Coalition members. He also stressed the need for “champions” in endemic countries that can rally support for prevention and control measures. Additionally, it will be crucial to involve policymakers in future Coalition meetings and activities.

To view the conference program and presentations, click here.

To view new journal articles highlighting strategies on typhoid vaccine use, new diagnostic tools, invasive non-typhoidal salmonella, and more in the recently release Vaccine journal supplement coordinated by the CaT Secretariat, click here. 


          The Strange Loop 2013        

This was my second time at The Strange Loop. When I attended in 2011, I said that it was one of the best conferences I had ever attended, and I was disappointed that family plans meant I couldn't attend in 2012. That meant my expectations were high. The main hotel for the event was the beautiful DoubleTree Union Station, an historic castle-like building that was once an ornate train station. The conference itself was a short walk away at the Peabody Opera House. Alex Miller, organizer of The Strange Loop, Clojure/West, and Lambda Jam (new this year), likes to use interesting venues, to make the conferences extra special.

I'm providing a brief summary here of what sessions I attended, followed by some general commentary about the event. As I said last time, if you can only attend one conference a year, this should be the one.

  • Jenny Finkel - Machine Learning for Relevance and Serendipity. The conference kicked off with a keynote from one of Prismatic's engineering team talking about how they use machine learning to discover news and articles that you will want to read. She did a great job of explaining the concepts and outlining the machinery, along with some of the interesting problems they encountered and solved.
  • Maxime Chevalier-Boisvert - Fast and Dynamic. Maxime took us on a tour of dynamic programming languages through history and showed how many of the innovations from earlier languages are now staples of modern dynamic languages. One slide presented JavaScript's take on n + 1 for various interesting values of n, showing the stranger side of dynamic typing - a "WAT?" moment.
  • Matthias Broecheler - Graph Computing at Scale. Matthias opened his talk with an interesting exercise of asking the audience two fairly simple questions, as a way of illustrating the sort of problems we're good at solving (associative network based knowledge) and not so good at solving (a simple bit of math and history). He pointed out the hard question for us was a simple one for SQL, but the easy question for us would be a four-way join in SQL. Then he introduced graph databases and showed how associative network based questions can be easily answered and started to go deeper into how to achieve high performance at scale with such databases. His company produces Titan, a high scale, distributed graph database.
  • Over lunch, two students from Colombia told us about the Rails Girls initiative, designed to encourage more young women into the field of technology. This was the first conference they had presented at and English was not their native language so it must have been very nerve-wracking to stand up in front of 1,100 people - mostly straight white males - and get their message across. I'll have a bit more to say about this topic at the end.
  • Sarah Dutkiewicz - The History of Women in Technology. Sarah kicked off the afternoon with a keynote tour through some of the great innovations in technology, brought to us by women. She started with Ada Lovelace and her work with Charles Babbage on the difference engine, then looked at the team of women who worked on the ENIAC, several of whom went on to work on UNIVAC 1. Admiral Grace Hopper's work on Flow-Matic - part of the UNIVAC 1 project - and subsequent work on COBOL was highlighted next. Barbara Liskov (the L in SOLID) was also covered in depth, along with several others. These are good role models that we can use to encourage more diversity in our field - and to whom we all owe a debt of gratitude for going against the flow and marking their mark.
  • Evan Czaplicki - Functional Reactive Programming in Elm. This talk's description had caught my eye a while before the conference, enough so that I downloaded Elm and experimented with it, building it from source on both my Mac desktop and my Windows laptop, during the prerelease cycle of what became the 0.9 and 0.9.0.2 versions. Elm grew out of Evan's desire to express graphics and animation in a purely functional style and has become an interesting language for building highly interactive browser-based applications. Elm is strongly typed and heavily inspired by Haskell, with an excellent abstraction for values that change over time (such as mouse position, keyboard input, and time itself). After a very brief background to Elm, Evan live coded the physics and interaction for a Mario platform game with a lot of humor (in just 40 lines of Elm!). He also showed how code updates could be hot-swapped into the game while it was running. A great presentation and very entertaining!
  • Keith Adams - Taking PHP Seriously. Like CFML, PHP gets a lot of flak for being a hot mess of a language. Keith showed us that, whilst the criticisms are pretty much all true, PHP can make good programmers very productive and enable some of the world's most popular web software. Modern PHP has traits (borrowed from Scala), closures, generators / yield (inspired by Python and developed by Facebook). Facebook's high performance "HipHop VM" runs all of their PHP code and is open source and available to all. Facebook have also developed a gradual type checking system for PHP, called Hack, which is about to be made available as open source. It was very interesting to hear about the pros and cons of this old warhorse of a language from the people who are pushing it the furthest on the web.
  • Chiu-Ki Chan - Bust the Android Fragmentation Myth. Chiu-Ki was formerly a mobile app developer at Google and now runs her own company building mobile apps. She walked us through numerous best practices for creating a write-once, run-anywhere Android application, with a focus on various declarative techniques for dealing with the many screen sizes, layouts and resolutions that are out there. It was interesting to see a Java + XML approach that reminded me very much of Apache Flex (formerly Adobe Flex). At the end, someone asked her whether similar techniques could be applied to iOS app development and she observed that until very recently, all iOS devices had the same aspect ratio and same screen density so, with auto-layout functionality in iOS 6, it really wasn't much of an issue over in Apple-land.
  • Alissa Pajer - Category Theory: An Abstraction for Everything. In 2011, the joke was that we got category theory for breakfast in the opening keynote. This year I took it on by choice in the late afternoon of the first day! Alissa's talk was very interesting, using Scala's type system as one of the illustrations of categories, functors, and morphisms to show how we can use abstractions to apply knowledge of one type of problem to other problems that we might not recognize as being similar, without category theory. Like monads, this stuff is hard to internalize, and it can take many, many presentations, papers, and a lot of reading around the subject, but the abstractions are very powerful and, ultimately, useful.
  • Jen Myers - Making Software Development Make Sense For Everyone. Closing out day one was a keynote by Jen Myers, primarily known as a designer and front end developer, who strives to make the software process more approachable and more understandable for people. Her talk was a call for us all to help remove some of the mysticism around our work and encourage more people to get involved - as well as to encourage people in the software industry to grow and mature in how we interact. As she pointed out, we don't really want our industry to be viewed through the lens of movies like "The Social Network" which makes developers look like assholes!.
  • Martin Odersky - The Trouble with Types. The creator of Scala started day two by walking us through some of the commonly perceived pros and cons of both static typing and dynamic typing. He talked about what constitutes good design - discovered, rather than invented - and then presented his latest work on type systems: DOT and the Dotty programming language. This collapses some of the complexities of parameterized types (from functional programming) down onto a more object-oriented type system, with types as abstract members of classes. Compared to Scala (which has both functional and object-oriented types), this provides a substantial simplification without losing any of the expressiveness, and could be folded into "Scala.Next" if they can make it compatible enough. This would help remove one of the major complaints against Scala: the complexity of its type system!
  • Mridula Jayaraman - How Developers Treat Ovarian Cancer. I missed Ola Bini's talk on this topic at a previous conference so it was great to hear one of his teammates provide a case study on this fascinating project. ThoughtWorks worked with the Clearity Foundation and Annai Systems - a genomics startup - to help gather and analyze research data, and to automate the process of providing treatment recommendations for women with ovarian cancer. She went over the architecture of the system and (huge!) scale of the data, as well as many of the problems they faced with how "dirty" and unstructured the data was. They used JRuby for parsing the various input data and Clojure for their DSLs, interacting with graph databases, the recommendation engine and the back end of the web application they built.
  • Crista Lopes - Exercises in Style. Noting that art students are taught various styles of art, along with analysis of those styles, and the rules and guidelines (or constraints) of those styles, Crista observed that we have no similar framework for teaching programming styles. The Wikipedia article on programming style barely goes beyond code layout - despite referencing Kernighan's "Elements of Programming Style"! She is writing a book called "Exercises in Programming Style", due in Spring 2014 that should showcase 33 styles of programming. She then showed us a concordance program (word frequencies) in Python, written in nine different styles. The code walkthrough got a little rushed at the end but it was interesting to see the same problem solved in so many different ways. It should be a good book and it will be educational for many developers who've only been exposed to one "house" style in the company where they work.
  • Martha Girdler - The Javascript Interpreter, Interpreted. Martha walked us through the basics of variable lookups and execution contexts in JavaScript, explaining variable hoisting, scope lookup (in the absence of block scope) and the foibles of "this". It was a short and somewhat basic preso that many attendees had hoped would be much longer and more in depth. I think it was the only disappointing session I attended, and only because of the lack of more material.
  • David Pollak - Getting Pushy. David is the creator of the Lift web framework in Scala that takes a very thorough approach to security and network fallibility around browser/server communication. He covered that experience to set the scene for the work he is now doing in the Clojure community, developing a lightweight push-based web framework called Plugh that leverages several well-known Clojure libraries to provide a seamless, front-to-back solution in Clojure(Script), without callbacks (thanks to core.async). Key to his work is the way he has enabled serialization of core.async "channels" so that they can be sent over the wire between the client and the server. He also showed how he has enabled live evaluation of ClojureScript from the client - with a demo of a spreadsheet-like web app that you program in ClojureScript (which is round-tripped to the server to be compiled to JavaScript, which is then evaluated on the client!).
  • Leo Meyerovich - Thinking DSLs for Massive Visualization. I had actually planned to attend Samantha John's presentation on Hopscotch, a visual programming system used to teach children to program, but it was completely full! Leo's talk was in the main theater so there was still room in the balcony and it was an excellent talk, covering program synthesis and parallel execution of JavaScript (through a browser plugin that offloads execution of JavaScript to a specialized VM that runs on the GPU). The data visualization engine his team has built has a declarative DSL for layout, and uses program synthesis to generate parallel JS for layout, regex for data extraction, and SQL for data analysis. The performance of the system was three orders of magnitude faster than a traditional approach!
  • Chris Granger - Finding a Way Out. Some of you may have been following Chris's work on LightTable, an IDE that provides live code execution "in place" to give instant feedback as you develop software. If you're doing JavaScript, Python, or Clojure(Script), it's worth checking out. This talk was more inspirational that product-related (although he did show off a proof of concept of some of the ideas, toward the end). In thinking about "How do we make programming better?" he said there are three fundamental problems with programming today: it is unobservable, indirect, and incidentally complex. As an example, consider person.walk(), a fairly typical object-oriented construct, where it's impossible to see what is going on with data behind the scenes (what side effects does it have? which classes implement walk()?). We translate from the problem domain to symbols and add abstractions and indirections. We have to deal with infrastructure and manage the passage of time and the complexities of concurrency. He challenged us that programming is primarily about transforming data and posited a programming workflow where we can see our data and interactively transform it, capturing the process from end to end so we can replay it forwards and backwards, making it directly observable and only as complex as the transformation workflow itself. It's an interesting vision, and some people are starting to work on languages and tools that help move us in that direction - including Chris with LightTable and Evan with Elm's live code editor - but we have a long way to go to get out of the "tar pit".
  • Douglas Hofstadter, David Stutz, a brass quintet, actors, and aerialists - Strange Loops. The two-part finale to the conference began with the author of "Gödel, Escher, and Bach" and "I am a Strange Loop" talking about the concepts in his books, challenging our idea of perception and self and consciousness. After a thought-provoking dose of philosophy, David Stutz and his troope took to the stage to act out a circus-themed musical piece inspired by Hofstadter's works. In addition to the live quintet, Stutz used Emacs and Clojure to provide visual, musical, and programmatic accompaniment. It was a truly "Strange" performance but somehow very fitting for a conference that has a history of pushing the edges of our thinking!

Does anything unusual jump out at you from the above session listing? Think about the average technical conference you attend. Who are the speakers? Alex Miller and the team behind The Strange Loop made a special effort this year to reach out beyond the "straight white male" speaker community and solicit submissions from further afield. I had selected most of my schedule, based on topic descriptions, before it dawned on me just how many of the speakers were women: over half of the sessions I attended! Since I didn't recognize the vast majority of speaker names on the schedule - so many of them were from outside the specific technical community I inhabit - I wasn't really paying any attention to the names when I was reading the descriptions. The content was excellent, covering the broad spectrum I was expecting, based on my experience in 2011, with a lot of challenging and fascinating material, so the conference was a terrific success in that respect. That so many women in technology were represented on stage was an unexpected but very pleasant surprise and it should provide an inspiration to other technology conferences to reach beyond their normal pool of speakers too. I hope more conferences will follow suit and try to address the lack of diversity we seem to take for granted!

I already mentioned the great venues - both the hotel and the conference location - but I also want to call out the party organized at the St Louis City Museum for part of the overall "wonder" of the experience that was The Strange Loop 2013. The City Museum defies description. It is a work of industrial art, full of tunnels and climbing structures, with a surprise around every corner. Three local breweries provided good beer, and there was a delicious range of somewhat unusual hot snacks available (bacon-wrapped pineapple is genius - that and the mini pretzel bacon cheeseburgers were my two favorites). It was quiet enough on the upper floors to talk tech or chill out, while Moon Hooch entertained loudly downstairs, and the outdoor climbing structures provided physical entertainment for the adventurous with a head for heights (not me: my vertigo kept me on the first two stories!).

In summary then, the "must attend" conference of the year, as before! Kudos to Alex Miller and his team!


           Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics         
Article Weber, M. , Teeling, H. , Huang, S. , Waldmann, J. , Kassabgy, M. , Fuchs, B. M. , Klindworth, A. , Klockow, C. , Wichels, A. , Gerdts, G. , Amann, R. and Glöckner, F. O. (2011) Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics , ISME journal, 5 , pp. 918-928 . doi:10.1038/ismej.2010.180 , hdl:10013/epic.37852
           Modular Evolution and Ecogenomics of Marine Pseudoalteromonas Phage H105/1         
Article Duhaime, M. , Wichels, A. , Waldmann, J. , Telling, H. and Glöckner, F. O. (2011) Modular Evolution and Ecogenomics of Marine Pseudoalteromonas Phage H105/1 , ISME Journal, Vol 5, Number 1, pp, pp. 107-121 . doi:10.1038/ismej.2010.94 , hdl:10013/epic.35512
           Modular Evolution and Ecogenomics of Marine Pseudoalteromonas Phage H105/1         
Conference -Poster Duhaime, M. , Wichels, A. , Telling, H. , Waldmann, J. and Glöckner, F. O. (2009) Modular Evolution and Ecogenomics of Marine Pseudoalteromonas Phage H105/1 , Gordon Research Conference 2009 Applied & Environmental Microbiology From Single Cells To The Environment, 12-17th July 2009, South Hadley, USA. . hdl:10013/epic.33043
           Marine phage genomics         
Conference -Poster Duhaime, M. , Wichels, A. , Gerdts, G. and Glöckner, F. O. (2007) Marine phage genomics , VAAM Annual Meeting, 1-4 April, Osnabrück, Germany. . hdl:10013/epic.26178
          Who Is An Indian? Race, Place, and the Politics of Indigeneity in the Americas        
ZA_whoisanindian
“A significant addition to research, Who Is an Indian? provides an extended examination and a clear picture of Indigenous identity issues in the Americas. Among the book’s important contributions are its examination of the site of interface between the modern state and Indigenous peoples, as well as its analysis of how state discourses of identities are interpolated by Indigenous peoples and come to be important sites of tension.” --David Newhouse, Department of Indigenous Studies, Trent University
“Who Is an Indian? makes a strong and distinct contribution to the literature on Indigenous identities. The contributors examine imposed markers of distinctiveness, particularly those racial categories that have often been formulated by experts and imposed by dominant societies. This is a topic that is rife with controversy, but it is handled here with directness and historical acumen.”--Ronald Niezen, Department of Anthropology, McGill University
Who Is An Indian? Race, Place, and the Politics of Indigeneity in the Americas  is my newest edited collection, published by the University of Toronto Press. It completes a trilogy of edited volumes on indigeneity in the Americas that I began in 2006 with Indigenous Resurgence in the Contemporary Caribbean: Amerindian Survival and Revival, and in 2010 with the publication of Indigenous Cosmopolitans: Transnational and Transcultural Indigeneity in the Twenty-First Century.

About this Book

Who is an Indian? This is possibly the oldest question facing Indigenous Peoples across the Americas, and one with significant implications for decisions relating to resource distribution, conflicts over who gets to live where and for how long, and clashing principles of governance and law. For centuries, the dominant views on this issue have been strongly shaped by ideas of both race and place. But just as important, who is permitted to ask, and answer this question?
This collection examines the changing roles of race and place in the politics of defining Indigenous identities in the Americas. Drawing on case studies of Indigenous communities across North America, the Caribbean, Central America, and South America, it is a rare volume to compare Indigenous experience throughout the western hemisphere. The contributors question the vocabulary, legal mechanisms, and applications of science in constructing the identities of Indigenous populations, and consider ideas of nation, land, and tradition in moving indigeneity beyond race.

Genesis of the Project

This latest volume is probably the longest I have worked on any one publication project. It first began to take shape in 2006, as an effort exclusively focused on race, motivated by recognition of the fact that there were no volumes, treating the Americas as a whole, that compared and contrasted different ideas and applications of race in the definition of Indigenous identity. This was the basis for the first symposium in 2006, “Indigeneity and Race: ‘Blood Politics’ and the ‘Nature’ of Indigenous Identity,” organized under the auspices of the Canadian Anthropology Society’s annual conference, held at Concordia University on May 13, 2006. The same theme carried over into a following seminar, “Who Is an Indian? Race, Blood, DNA, and the Politics of Indigeneity in the Americas” involving 14 participants and hosted at the Clarion Hotel in Montreal, August 2-5, 2007, with the support of the Social Sciences and Humanities Research Council of Canada. However, as a result of the discussions held at the second symposium, we came to the realization that race alone could not be the exclusive subject of our concerns in addressing who people have historically answered the question, “who is an Indian.” The role of place, land, and territoriality, and resistance to neoliberalism, figured prominently in a number of the papers to the extent that we concluded that both race and place should be our dual, framing concepts.

The original impetus for this project came from a very particular context of concern. My research in the Caribbean alerted me to the extent to which notions of “purity,” “blood,” and lately even DNA analysis came to figure prominently not just as ways of ascribing Indigenous identities, but also as means of claiming them in light of widespread, categorical assertions by colonial rulers and scholars that these peoples had vanished. To my surprise, similar politics of identity were being instituted in North America—indeed, the interest in DNA studies had spread from the U.S. to the Caribbean, and in North America as well I found a concern with blood, purity, and the stigma faced by “Black Indians” who were being rejected as claimants to Cherokee citizenship. In Canada, First Nations residents carry cards indicating what degree of Indigenous “blood” they possess. Also in Canada, I repeatedly hear Euro-Canadians refer to this or that Aboriginal figure as “not a real Indian…he looks white”. (I had encountered similar purist prejudices during my years in Australia, directed at some of the most prominent Aboriginal activists who, phenotypically and superficially appeared to be “mixed” if not “almost white”.) If race, blood, and DNA were so prevalent, could we find similar concerns spread out across all of the Americas? If so, why? If not, why not? Are race, blood, and DNA essentially the same thing? These were the very first, seemingly very simple questions that led to the emergence of this project.

Taking together all stages of this project, it included a total of as many as 21 scholars from across the Americas and from across the disciplines, only some of whom appear in this volume. In particular I would like to thank and acknowledge the advice, support, varying degrees of participation and interest, and correspondence of individuals who were involved at different stages of the project, including: Kimberly Tallbear, José Barreiro, Phil Bellfy, Marisol de la Cadena, Alice and Dennis Bartels, and the late Melissa Meyer who sadly for us passed away mid-way through the development of this project. We also benefited from the participation of Indigenous scholars, who comprised half the number of participants in the overall project. With an immense amount of research and writing taking place in the U.S., there was often a tendency to have greater American representation, more than Canadian, Latin American, and least of all, from the Caribbean. The result of this struggle, the constant revision and reinterpretation, we hope will offer some critical insights into the processes of making “race” out of (or against) Indigenous identity and the role of “place” in debates about Indigenous identity. The final product strikes some geographic balance, with two chapters on Canadian cases, two dealing with American Indians, two focused on Central America and the Caribbean, and two pertaining to South America.

What about DNA Testing?

The previous concern with DNA, represented by as many as four participants early on in the project, largely diminished and then vanished altogether, especially when we no longer had the same participants as in earlier stages of the project. This is not to say that DNA debates are absent in the volume as a whole, but rather that they no longer structure the volume as a leading focus, which in any case would be more relevant to the North American situation than elsewhere. Yet even that is not entirely accurate, as the use of DNA testing to determine Indigenous ancestry has traveled to Puerto Rico, the Dominican Republic, and to my great surprise to the very community I studied for four years in Trinidad & Tobago, as the result of the work a team from the Molecular Anthropology lab at Pennsylvania State University and the National Geographic Genographic Project. In the past, similar studies have also been conducted among the Garifuna in Central America and recently in St. Vincent & the Grenadines, in the latter case again by the Penn State team.

Sidebar on U.S. "Science": DNA Testing for Indigeneity Comes to Trinidad
DNA testing comes in for severe questioning and criticism in the volume, and I would also add here to my public objections to the DNA research done in Trinidad. Aside from the more than just questionable merits of using genetics to prove cultural identities and political constructs such as tribal affiliations, I also pointed out that, "given the harvesting of biometric data by U.S. universities with research ties to the Pentagon, there is always the risk that this information could be put to uses of which the Caribs are unaware." Indeed, one of the researchers involved in the Trinidad DNA study, Jada Benn-Torres, from a military family, has conducted research in the field funded by the U.S. Department of Defense. I cannot see any reasonable purpose for conducting the study in Trinidad, as the local Carib community has been officially recognized for decades, and is not possessed by any self-doubts of their identity. Indeed, not all of the Caribs in Arima chose to participate in the study, which raises more questions about the extent to which those examined are representative of the community as a whole, and thus places in doubt even the basic scientific merits of the study. What has also not been made known is what is the ultimate purpose of the research, where the information is stored and for how long, and who has access to the database.

The Historical Importance of a Bad Question

The collaboration that produced this volume through much iteration has been focused on what is arguably one of the worst questions to be posed to or against Indigenous Peoples ("Who is an Indian?"), one that ultimately calls on them to give an account of themselves, for being who they are in the light of foreign invasions and occupations. It’s as if being who they are is a problem, and furthermore, it is a problem that they caused. Worse yet, they may not even be who they think they are.

As with all bad questions, one can expect to get a lot of bad answers. So why address such a question, going as far as making it the leading question of this project? The answer is simple: the question, however one may assess its epistemological qualities, is a politically important question (the most important perhaps), an institutionalized question, a governing question that structures people’s lives, their access to resources, and even their self-perceptions. It is also a key historical question, one that continues to be asked repeatedly, and one that will inevitably lose relevance. That this question has been raised across the Americas, in different forms (substituting, as the case may be, any number of cognate or tribal labels in the place of “Indian”), is due to a shared history of colonization and state-building and the dominance of European theories of citizenship, nationhood, race, and identity. Here we can start to look beyond the constraints and limitations of that question and in seeing past the constraints imposed today by states.

It was not the intention of the contributors of the volume to either advance academic expertise as the ultimate arbiter of Indigenous identities, to provide an easy-to-follow menu for “accurately determining” who is Indigenous, or to provide advice that caters to the functioning of government bureaucracies and their micro-management of Indigenous affairs. Our greater concern was with the politics that work to preserve the dominance of a “bad question,” a very “bad” and yet historically very important question: “Who is an Indian”? Our hope is that readers will come away from this effort with a determination to ask better questions—better in the sense of being more analytically productive and with implications that are more socially just and fair. Among the questions we would like to see posed are those that posit indigeneity as a historically specific type of relationality, that involve issues of power and affectivity, without searching for the elusive “one size fits all” solution. If, however, we overcame the stigmatization of being Indigenous only to then treat it as a category implying “privilege” and uniquely demanding “proof” of belonging, then we will not have gone far past the point of endorsing extinction.

Setting the Stage: Some Opening Quotes to Remember

“When they get off the boat, they didn’t recognize us. They said: ‘Who are you?’ And we said: ‘We’re the People, we’re the Human Beings,’ and they said: ‘Oh Indians,’ because they didn’t recognize what it meant to be a human being. ‘I’m a Human Being, this is the name of my tribe, this is the name of my people, but I’m a human being.’ But the predatory mentality shows up and starts calling us ‘Indians’ and committing genocide against us as a vehicle of erasing the memory of being a human being….Even in our own communities, how many of us are fighting to protect our identity of being an Indian, and 600 years ago that word, ‘Indian,’ that sound was never made in this hemisphere—that sound [‘Indian’], that noise, was never ever made! Ever. We’re trying to protect that as an identity, see, so it affects all of us”. —John Trudell, Lakota poet and activist. 
“It is one of the many ironies of the American experience that the invaders created the category of Indians, imposed it on the inhabitants of the New World, and have been trying to abolish it ever since”. —David Maybury-Lewis, co-founder of Cultural Survival. 
“There’s tremendous racism in Peru. In Lima, brown people, the descendants of Indigenous people, try to live as white as possible. That’s because of the influence of the media and government. If you embrace your Indian-ness, you’re shunned. You’re less than a third-class person. It’s an insult to call someone an Indian. It’s the equivalent of calling someone stupid”. —Benjamin Bratt, actor. 
“The question of my identity often comes up. I think I must be a mixed blood. I claim to be male, although only one of my parents is male”. 
—Jimmie Durham, Cherokee artist. “What does part Indian mean? (Which part?)….you don’t get 50% or 25% or 16% treatment when you experience racism—it is always l00%”. —Joane Cardinal-Schubert.

Contents

Preface, pages vii-ix

Introduction: “Who Is an Indian?” The Cultural Politics of a Bad Question, pages 3-51 Maximilian C. Forte (Concordia University, Sociology and Anthropology)


In this chapter I discuss the genesis, multiple meaning and historical applications of this "bad question," across the Americas. In the process I also defend the thesis that the Americas as a whole serve as the appropriate unit for analysis in understanding the colonial, "scientific," ideological, and (geo)political efforts to define Indigenous identities. While I outline how the racialization of indigeneity spread across imperial domains in the Americas, I also examine the centrality of place, of territoriality, and how place also intersects race. I discuss the emergence of "Indian" as a racial construct, and from there I proceed to build the larger theoretical and analytical narrative which the various chapters help to form. Who is the "real Indian" and issues of "race mixture" and the impact of slavery and the plantation system in North and South America and the Caribbean forms one level of analysis. Another has to do with kinship and science, with blood, DNA, and how these relate to ideas of "race purity." Going beyond "blood quantum" and race, I provide some context and the wider debate around the critically important contribution by Julia Coates in this volume, on the always timely issue of the Freedmen and the Cherokee Nation. Debates around self-identification, and tribal politics, progress toward a discussion of the many cases of "Indian non-Indians" and "Non-Indian Indians". Finally I end with an overview of the problems involved with "recognition", with some discussion of the geopolitics of recognition and then, pointing toward the Conclusion, looking beyond the politics of recognition.

Chapter One Inuitness and Territoriality in Canada, pages 53-70 Donna Patrick (Carleton University, Sociology and Anthropology and the School of Canadian Studies)


“The question of who counts as Aboriginal [in Canada],” explains Donna Patrick (this volume), “has long been linked to the question of who owns traditional Aboriginal lands”. Patrick’s chapter explores “the question of categorizing Indigeneity in Canada by examining the linguistic, political, and judicial processes associated with the notions of territory, ancestry, and belonging that shape Indigeneity today,” with a focus on the Inuit in Canada, situated within a broader analysis of Aboriginal identity in Canada. “Inuitness” in Canada, as Patrick tells us, followed a different trajectory from that of First Nations, in that the construction of Inuit identity has been guided not just by state policy but by Inuit attachments to both land and language. In Patrick’s chapter we learn that for the Inuit “the notion of ‘territoriality’ operates together with the notion of ancestry” in shaping the identities of Inuit living in urban centres of the Canadian South as much as those living in the Arctic. Donna Patrick observes that Indigenous ideas of identity in early colonial Canada “had little to do with race, biology, or ethnicity” and that Indigenous Peoples in fact demonstrated in practice that they were guided by a “notion of inclusivity” whose existence “has been supported by numerous accounts of Euro-American settlers and soldiers being accepted and adopted into First Nations groups”. While Patrick argues that we do not see in Canada a dominant discourse about the bio-politics of Indigenous identities to the same extent that we find in the U.S., she admits that a “‘covert’ or de facto blood quantum” has been part of policies governing Aboriginal, and in particular First Nations, peoples.

Chapter Two Federally-Unrecognized Indigenous Communities in Canadian Contexts, pages 71-91 Bonita Lawrence (York University, Equity Studies)


In her chapter Bonita Lawrence points out the cases of First Nations that span the Canada-U.S. border, where for example “the Passamaquoddy Nation of New Brunswick, or the Sinixt Nation, in British Columbia, have federal recognition in the United States but not in Canada,” which underscores the arbitrary, shifting, and inconsistent standards used by states to “appraise” indigeneity, as Lawrence argues. Bonita Lawrence explores identity issues among two federally-unrecognized groups—the Algonquins of Eastern Ontario and the Mi’kmaqs of Newfoundland—which have been the subject of her research for the last decade, providing a window into how the Canadian state produces unrecognized Aboriginals. As she explains, “most federally-unrecognized bands or nations are created by the nature of the treaty process itself,” while other bands are federally-unrecognized “because Canada has refused to honour historic relationships or has disregarded the traditional boundaries of Indigenous nations”. The primary means for such communities to gain federal recognition, to legally become Aboriginal again, is to assert Aboriginal title through the courts (if there is a treaty governing particular territory), or as Lawrence outlines in her chapter, “to take part in the comprehensive claims process if no treaty has been signed in the territory”. Otherwise, federally-unrecognized Indigenous peoples are “incorporated simply as ‘citizens’ within the wider nation-state dominated by settlers”.

Chapter Three The Canary in the Coalmine: What Sociology Can Learn from Ethnic Identity Debates among American Indians, pages 92-123 Eva Marie Garroutte (Boston College, Sociology) and C. Matthew Snipp (Stanford University, Sociology)


Eva Marie Garroutte and Matthew Snipp in their chapter in this volume titled, “The Canary in the Coalmine: What Sociology Can Learn from Ethnic Identity Debates among American Indians,” devote considerable attention to debating the racialization of indigeneity. As just one example of the kinds of interests vested in the non-recognition of “mixed” American Indians, Garroutte and Snipp point to Donald Trump: as a competitor against the newly recognized Pequots, and their plans to open a casino, he produced a definition of “who is an Indian” in phenotypical terms: “they don’t look like Indians to me. They don’t look like Indians to Indians,” injecting his racial bias by further calling them “Michael Jordan Indians”. This is useful in showing how ultimately one of the most common ways of assigning Indigenous identity in the Americas is focused on appearance, and where racial discourses prevail, a specific type of appearance: phenotype. Garroutte and Snipp  also discuss some of the additional, problematic conceptual issues raised by the quantification of identity, which can apply to both genetic testing and blood quantum. Quantification establishes distance as a prerequisite for measurement, “with the corollary that, at some point, individuals’ connection to American Indian forebears becomes exhausted”. Quantification of identity presupposes distance, and tends toward disappearance. It raises physical standards about ideational and subjective identities, even as it creates new subjectivities around the use of scientific resources. The right to measure involves a power to erase, just as the power to speak for Indigenous peoples, and to assign their identities, is the power to silence them, permanently. The two case studies at the focus of their chapter, the Mashantucket Pequots and Kennewick Man, make for highly engaging and illuminating reading.

Chapter Four “This Sovereignty Thing”: Nationality, Blood, and the Cherokee Resurgence, pages 124-150 Julia Coates (University of California Davis, Native American Studies)


Julia Coates strongly and productively challenges a number of prominent, published perspectives that have been critical of definitions of Cherokee identity by the Tribal Nation’s government. Coates argues that legal definitions are often overlooked in discussions of indigeneity, while race and culture gain greater attention. Yet, as she explains, many tribal governments in the U.S. regard legal definitions, not as artificially imposed from external colonizing institutions, but as internally achieved definitions of nationality and their sovereign statuses. While the Cherokee Nation’s lack of cultural requirements are frequently not understood by non-Indians and derided by other tribal nations, the Cherokee Nation has continued to assert that nationality derived from their specific history of tribal citizenship is a more inclusive category for contemporary times than race or cultural markers. This is almost a reversal of arguments criticizing the Tribal Nation’s exclusion of certain persons. Based on interviews with what Coates calls “a particularly challenging group of Cherokee nationals,” the 60 percent of the citizenry living outside the tribal core in northeastern Oklahoma, her chapter examines the potential of nationality as a basis for self-identification for those in the Cherokee diaspora, and the role the concept of citizen plays in the contemporary Cherokee resurgence. Coates points to problems with a debate that “focuses on identity construction as located in race, heritage, DNA, and cultural attributes and expressions” and that leave out law and sovereignty. She says that one reason why the cultural, racial, and ethnic aspects of identity may be the primary sites for investigation and discussion, for many Indigenous Peoples is the fact that many of them are not formally organized into nominally sovereign political entities with an internal jurisdiction. Speaking of academics, Coates suggest that one reason most academics seem to differ from tribal governments’ rigid determinations of citizenship, is that academics tend to be more inclusive in their view of who is an American Indian, not wanting to serve as identity police and imposing definitions of Indigenous identity on Natives. Her emphasis is on nationality as a potential for retention and resurgence (or what some call resilience), rather than simply acting as a colonialist mechanism of control and exclusion.

Chapter Five Locating Identity: The Role of Place in Costa Rican Chorotega Identity, pages 151-171 Karen Stocker (California State University, Anthropology)


Designating a special place as the locus of persons with an Indigenous identity can be a way for an assimilationist state, one that historically rejected the Indigenous presence as in the case of Costa Rica, to create the illusion that indigeneity is minimal and marginal. As Karen Stocker explains in her chapter in this volume, in Chorotega some residents of what later became the reservation opposed reservation status given their “tremendous resentment at being the only community in the region officially designated as Indigenous when the whole area had Indigenous roots, and aversion to the stigma attached to Indigenous identity in a country that often projected an image of whiteness and European heritage”. The Costa Rican government’s imposition of an Indigenous identity on residents of Chorotega was a convenient way of removing that label from everyone else who resided outside of that particular place, using the assigned indigeneity of some to reassure others of their Europeanness. Karen Stocker’s chapter, based on ethnographic research carried out between 1993 and 2007, addresses how various residents of the Chorotega reservation, those who live just outside the reservation, scholars, legal discourse, historical discourse, those who have resided or studied in other Costa Rican reservations and, more recently, the tourism industry have “defined Indigenous identity in contradictory ways, and in manners that have had varying consequences for those labeled as Chorotega in Costa Rica”. She addresses the history and impact of these multiple competing definitions. Stocker traces the ways in which “one set of customs has gone from Indigenous to non-Indigenous, national custom, and back again, as a result of the shifting of discourses around it”. Stocker spotlights what she finds to be “a common thread through all of these definitions and interpretations of indigeneity,” and that is “the role of place, and how the same concept that mired inhabitants of the Chorotega reservation in discrimination now serves to authenticate its practices”.

Chapter Six Carib Identity, Racial Politics, and the Problem of Indigenous Recognition in Trinidad and Tobago, pages 172-193 Maximilian C. Forte (Concordia University, Anthropology)


My own chapter in this volume, based on four years of ethnographic research and ethnohistoric research dating to early colonial times, shares some features similar to both those by Donna Patrick and Karen Stocker. On the one hand, the state’s recognition of only one single, organized Indigenous community in just one of Trinidad’s 16 former mission towns—the Santa Rosa Carib Community in Arima, on the island of Trinidad—makes it seem, however implausibly, that indigeneity was somehow contained and delimited (which instead reflects the state’s bias in how indigeneity ought to be controlled and secluded). On the other hand, in articulating their own indigenous identity, members of the Carib Community point to a multitude of factors, beyond but including race, to include a history of residence in Arima. The structure of this chapter follows three basic lines of argument: first, that the political economy of the British colony dictated and cemented racializations of identity. Second, the process of ascribing Indigenous identities to individuals was governed by the economic rights attached to residents of missions, rights which were cut off from any miscegenated offspring. There were thus political and economic interests vested in the non-recognition of Caribs, and race provided the most convenient justification—a justification that took the form of a narrative of extinction. Third, over a century later, while racial notions of identity persist, current Carib self-identifications stress indigeneity as a cultural heritage, an attachment to place, a body of practices, and recognition of ancestral ties that often circumvent explicitly racial schemes of self-definition. State recognition of the Caribs occurs within this historical and cultural context, and therefore imposes limits and conditions that simultaneously create new forms of non-recognition.

Chapter Seven Encountering Indigeneity: The International Funding of Indigeneity in Peru, pages 194-217 José Antonio Lucero (University of Washington, The Henry M. Jackson School of International Studies)


As José Antonio Lucero explains in this volume, “blood” is already incorporated in national ideologies of race-mixture, and is not specific and particular enough to be used as part of the regimes of identifying the Indigenous. As Lucero adds, “in a region where ‘everyone’ has native blood, but not everyone is ‘Indian’ the social category and social fact of Indianness rely, necessarily, less on biology or blood than on the intersecting socio-cultural workings of politics, language, place, class, and gender”. More specifically, Lucero's chapter takes the work of Oxfam America as the focus of his case study, as it has been among “the earliest funders of Indigenous activism”. His chapter examines two different moments in the interactive process of legitimation between organizations such as Oxfam America and Indigenous political organizations in Peru, “as actors on both sides of the development encounter shape discourses over the meanings of development and indigeneity across local and global scales”. The “geopolitics of recognition” is what Lucero conceptualizes as regimes of indigeneity that span local, national and global scales. Lucero discusses how Indigenous people throughout the Americas (and beyond) have often found it inevitable, and sometimes useful, to engage a variety of legal, economic, and political systems. “Since the first contacts with missionaries,” he writes, “the state, and agents of global capital, Indigenous people have found that new systems of domination are not without points of entry within which they can contest the very terms of domination,” and in the present context, “the rising importance of non-state actors in the wake of aggressive neoliberal economic reforms (which shrank already weak states) provided an additional set of opportunities that Indigenous people have been able to use” (Lucero, this volume). However, one of the problems for Indigenous actors bound in relationships with external agencies is that the reconstruction of indigeneity that results is often Janus-faced, where “some discourses are for external consumption and have little to do with the lived ‘social fact’ of indigeneity at the local level”.

Chapter Eight The Color of Race: Indians and Progress in a Center-Left Brazil, pages 218-223 Jonathan Warren (University of Washington, International Studies, Chair of Latin American Studies)


Jonathan Warren begins by telling us that "since the 1990s a large number of Brazilian Indigenous communities have been federally recognized, successfully acquired land, established their own schools, and achieved a higher degree of autonomy and self-determination. Furthermore, anti-Indian violence is no longer condoned by the Brazilian government; racism has been officially acknowledged; race-cognizant government policies, such as affirmative action, have replaced race-neutral ones; and a number of antiracist commissions and initiatives have been established at federal, state and municipal levels. Finally, the first centre-left politicians in Brazilian history, Luiz Ignacio Lula da Silva (2003–2010) and Dilma Rousseff (2011–present), both of the Workers’ Party, have controlled the executive branch of government for almost a decade. Given these substantial changes, one could be forgiven for expecting a positive report on the state of Indigenous affairs in contemporary Brazil. Unfortunately, the outlook is rather dim. Perhaps most surprising is that many of the culprits are from the centre-left, namely the Workers’ Party, social scientists, and sectors of the movimento negro". Jonathan Warren’s chapter reveals to us that in Brazil, the racial question, and thus conceptions of antiracism—like much of “critical race studies,” he adds—simply removes the Indian from analysis, as if Indian subjectivities were entirely irrelevant. A key example of how this has occurred in critical race studies comes from Howard Winant’s very own analysis of racism in Brazil, which singles out Africans. This is odd, as Warren finds, given that as many as a third of Brazilians have some Indian ancestry. As Warren explains in this volume, Brazilian Indians are removed from the racial question in Brazil: “race is reduced to a question of blackness”. Indeed, throughout Latin America, Warren sees that Indigenous peoples are “not considered germane to race matters,” and quoting Peter Wade he adds: “the virtually unquestioned assumptions [prevails] that the study of blacks is one of racism and race relations, while the study of Indians is that of ethnicity and ethnic groups”. Warren also shows that phenotype is present in Brazilian estimations of “authentic” and “real” Indigenous identities, with those who have African and European features routinely dismissed as “racial charlatans,” in ways that echo experiences both in the U.S. and the Caribbean. Warren’s chapter is critical to this volume’s contention that race is a problem that needs to be studied in connection with indigeneity, not apart from it. His argument is critical not only for developing critical race studies, but also for political practice: the antiracist movement in Brazil cannot be just a Black movement.

ConclusionSeeing Beyond the State and Thinking beyond the State of Sight, pages 234-241 Maximilian C. Forte (Concordia University, Sociology and Anthropology)


Rather than restating or summarizing the contents of this volume, the Conclusion helps to sketch some of the ways in which critical Indigenous perspectives have sought to develop alternative ideas and practices of indigeneity and indigenization. In a hemisphere which sees, in most cases, Indigenous Peoples moving to cities, and an increased decoupling of indigeneity and territoriality, along with the incursion of the industrialization of ethnic ascription--the commerce in genetic identities--these issues become especially important. The volume closes with a sharp reminder of why "Who is an Indian?" is a bad question that produces even worse answers, and what our task as intellectuals ought to be when confronted with such questions.

Contributors, pages 243-246
Index, pages 247-254

A Little About the Contributors

Julia M. Coates (Cherokee Nation, Tahlequah, Oklahoma) is presently at the University of California, Los Angeles. Her title is Senior Writer/ Oral Interviewer in American Indian History for the Center for Oral History Research of the Charles Young Research Library. At the time of writing she was an assistant professor in the Department of Native American Studies at the University of California, Davis. Her research interests cover Native American diasporas, history, identity, women, and politics. She has conducted participant-observation fieldwork with hundreds of Cherokee citizens in California, Texas, and New Mexico. Coates also helped to form numerous Cherokee community organizations throughout California and in other states. For over six years, she was the project director and lead instructor for the award-winning Cherokee Nation history course, which brought her into personal contact with most of the employees of the Cherokee Nation, along with thousands of Cherokees in northeastern Oklahoma communities and throughout the country. She also serves on the Tribal Council of the Cherokee Nation as its “At Large” representative. At UC Davis she teaches the Introduction to Native American Studies as well as classes on race, women, development and history within Native America.

Eva Marie Garroutte (Cherokee Nation) is an associate professor in the Department of Sociology at Boston College. She has a background of research and publication related to the study of Native American issues, health and aging, racial/ethnic identity, and religion. She is the author of the influential book Real Indians: Identity and the Survival of Native America (University of California Press) and various articles in sociological and health-related journals. In collaboration with Cherokee Nation Health Services, she has conducted a series of research projects funded by the National Institute on Aging to examine medical communication needs among American Indian elders using tribal clinics. Her current service on editorial advisory boards includes the Journal of Native Aging and Health, American Indian Quarterly, and the University of Arizona Press series Critical Issues in Indigenous Studies. She is a past Area Commissioner of Indian Affairs in Tulsa, Oklahoma.

Bonita Lawrence (Mi’kmaw) is an associate professor at the School of Social Sciences of the Atkinson Faculty of Liberal and Professional Studies at York University in Toronto, Canada, where she teaches Indigenous Studies and anti-racism. Her research and publications have focused primarily on urban, non-status, and Métis identities, federally unrecognized Aboriginal communities, and Indigenous justice. She is the author of “Real” Indians and Others: Mixed-Blood Urban Native People and Indigenous Nationhood (UBC Press), and co-editor of Strong Women’s Stories: Native Vision and Community Survival, a collection of Native women’s scholarly and activist writing (Sumach Press). She is a traditional singer who sings with groups in Kingston and Toronto at Native social and political gatherings.

José Antonio Lucero is an assistant professor in the Henry M. Jackson School of International Studies, at the University of Washington in Seattle. He is the author of Struggles of Voice: The Politics of Indigenous Representation in the Andes (University of Pittsburgh Press) and the editor of Beyond the Lost Decade: Indigenous Movements, Democracy, and Development in Latin America (Princeton University Program in Latin American Studies). He teaches courses on government, politics, and social movements in Latin America, among others. His research interests focus on comparative politics, Latin American politics, democratization, social movements, and the politics of race and ethnicity.

Donna Patrick is professor in the Department of Sociology and Anthropology and the School of Canadian Studies at Carleton University in Ottawa, Canada. Her current SSHRC-funded research focuses on multiliteracies, identity, and community-building among urban Inuit in Ottawa. Her other interests lie in the broader area of Indigeneity and urban Aboriginality in Canada, as well as in the political, social, and cultural aspects of language use, with a focus on language endangerment discourse and Aboriginal languages in Canada. Her 2003 book, Language Politics and Social Interaction in an Inuit Community (Mouton de Gruyter), examines these issues in Arctic Quebec. She teaches courses in language, culture, and power and in Aboriginal and northern issues, with a focus on the Arctic. In teaching and research, Donna approaches the study of Aboriginal issues, language, and discourse through an interdisciplinary lens, focusing on historical, geographical, and social processes.

C. Matthew Snipp is a professor in the Department of Sociology at Stanford University where, among other positions, he has been the director of the Center for Comparative Studies of Race and Ethnicity. He teaches courses in contemporary and historical American Indian Studies as well as rural sociology. He is the author of American Indians: The First of the Land (The Russell Sage Foundation, New York), which was selected as an academic book of the year by CHOICE.

Karen Stocker is an assistant professor in the Department of Anthropology at California State University, Fullerton. She is a scholar of applied anthropology with interests in education, the social constructions of race and ethnicity, language, and Latin American ethnography. She is the author of “I Won’t Stay Indian, I’ll Keep Studying”: Race, Place and Discrimination in a Costa Rican High School (Colorado University Press).

Jonathan W. Warren is an associate professor in the Henry M. Jackson School of International Studies at the University of Washington in Seattle, where he is also the director of the Latin American and Caribbean Contributors Studies Program. Within the broad area of critical race studies he has focused on Whiteness, racism literacy, racial identity formations, and the links between everyday practices and racism in the U.S. and Brazil. He is the author of the highly regarded book Racial Revolutions: Antiracism and Indian Resurgence in Brazil (Duke University Press).

...and myself.

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What is your current professional position, title, affiliation, responsibilities? How long have you been in this position? I am currently a fourth year PhD student in the Crop and Soil Science Department at Washington State University. My research focuses on biotic/abiotic resistance breeding to effectively control current threats to wheat production worldwide in an attempt to reduce yield losses and ensure sufficient quantities of food available on a consistent

 basis. I am presently a member of the National Association of Plant Breeders (NAPB) and the Crop Science Society of America. Previously, I worked as a research assistant in the ICARDA Biodiversity and the Integrated Gene Management Program (BIGM).My MSc research focused on the identification of new sources of resistance to wheat stem rust from wild tetraploid species.

Who or what inspired you to work in wheat science and research and why? I have always had a passion for agriculture and a desire to be part of a system that would help feed the hungry. Wheat is a leading cereal crop in Syria and globally feeds 35% of the world population. Wheat production, however, is not reaching its full potential; there is an urgent need to increase food production at the same or at an increased rate in order to cope with an increasing population. Therefore, I want to contribute to improving wheat productivity and to ensuring access to safe and healthy food worldwide.

My passion has amplified during my time with ICARDA (International Center for Agricultural Research in the Dry Areas). It was exciting to link the knowledge I acquired from years of study at college with practical experience I learned in the field. I also had the opportunity to interact extensively with farmers, to understand their needs, and to assist them in using efficient agricultural strategies. I worked closely with female farmers (the participatory plant breeding project), and gained appreciation for their significant contributions to agriculture. However, I noticed that women were significantly underrepresented in leadership roles compared to their male counterparts. This has motivated me to advocate, support, and empower other young women and to highlight their vital role in the success of agriculture.

I was fortunate to begin my career with great mentors, like Dr. Francis Ogbonnaya, Dr. Rajaram Sanjaya, and Dr. Amor Yahyaoui, who have all inspired me in so many ways through their dedication, generosity, and passion for wheat research. I have also been inspired by the achievements of Dr. Norman Borlaug and his great role in saving so many from starvation and hunger.

What effect did the WIT Early Career Award have on your professional development? Winning the WIT Early Career Award was a unique opportunity and opened numerous avenues for myself and my career. The award has provided me the opportunity to meet and interact with agricultural scientists from different spectrums of society, share my work, and learn from others through workshops and training courses. Winning broadened my horizons and opened my eyes to major constraints currently facing agricultural productivity and to developing possible solutions. I was introduced to many inspirational and supportive women, such as Ms. Jeanie Borlaug-Laube and Ms. Sara Davidson Evanega, and others. Overall, this experience will help me tremendously as I prepare for my career. 

What are you currently working on, and how does it relate to wheat production and/or food security in your country? My PhD research focuses on the identification of new sources of resistance to Hessian fly and stripe rust in wheat, via linkage mapping, QTL mapping, association mapping, and identifying diagnostic DNA markers associated with multiple agronomic traits in wheat useful for genomic selection. The above threats continue to cause significant economic losses in spring wheat producing areas globally and in the United States. Genetic resistance is the most credible and sustainable remedy to controlling the recurring epidemics, and thus reducing yield losses. However, as a result of the fast evolutionary pace of the pathogen, most of the resistance genes have been failing, which emphasizes the need for collective efforts not only to identify new sources of resistance, but also to identify ‘breeder-friendly’ molecular markers tightly linked to the target gene(s) to accelerate incorporating these genes into regionally adapted wheat cultivars (This is where the significance of my research stems out).

Which recent scientific discoveries or new technologies do you think will affect wheat production in the next 10-15 years? The leverage of high-throughput genotyping approaches, such as the 9K and 90K iSelect SNP assays, the use of PstI-MspI restriction enzymes in genotyping by sequencing (GBS), and the availability of the entire wheat genome sequence,  will continue to advance wheat genetics research by enabling robust selection, precise gene mapping, gene transfer, gene pyramiding, and map-based cloning. I hope that genetic engineering becomes less controversial, so that we can exploit its effectiveness in advancing agricultural sustainability, and help crops adapt to climate change.

If you had access to unlimited funding toward wheat research as it relates to food security and improving life of small scale farmers, how would you invest it? I would invest in seed program, soil management in regards to conservation agriculture, find out the best rotation for the farming community, and of course, breed the best varieties in regards to yield, stability, and disease resistance. I would invest in quality research and conduct a large number of large plot varietal trials on farmer’s fields. I would also invest in educating and training farmers, farm management skills, marketing, and building community resources. I’d establish activities focused on mentoring and empowering women as leaders, youth involvement, networking and communication, and technology and social media.

What advice do you have for other women who are beginning their careers in agricultural science? Work closely with farmers and consumers and listen to their needs, share your knowledge with others who don’t have access to information, resources, and technologies. Use all your potential, work together to develop solutions to agricultural problems, choose your job/mentor/boss wisely, believe in yourself, turn adversity into opportunity.

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          Research Domain Criteria (RDoC)        


Research Domain Criteria (RDoC)

RDoC is a research framework for new ways of studying mental disorders. It integrates many levels of information (from genomics to self-report) to better understand…

Read it on Flipboard

Read it on nimh.nih.gov





          Reconstructing phylogenies of metastatic cancers        

Reconstructing phylogenies of metastatic cancers

Johannes G ReiterAlvin P Makohon-Moore, Jeffrey M Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine A Iacobuzio-Donahue, Bert Vogelstein, Martin A Nowak

Abstract

Reconstructing the evolutionary history of metastases is critical for understanding their basic biological principles and has profound clinical implications. Genome-wide sequencing data has enabled modern phylogenomic methods to accurately dissect subclones and their phylogenies from noisy and impure bulk tumor samples at unprecedented depth. However, existing methods are not designed to infer metastatic seeding patterns. We have developed a tool, called Treeomics, that utilizes Bayesian inference and Integer Linear Programming to reconstruct the phylogeny of metastases. Treeomics allowed us to infer comprehensive seeding patterns for pancreatic, ovarian, and prostate cancers. Moreover, Treeomics correctly disambiguated true seeding patterns from sequencing artifacts; 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Last, we performed in silico benchmarking on simulated tumor phylogenies across a wide range of sample purities (30-90%) and sequencing depths (50-800x) to demonstrate the high accuracy of Treeomics compared to existing methods.


          OpenHelix        

OpenHelix Search Portal provides a mechanism to search for and evaluate online bioinformatics and genomics resources by providing contextual displays of search results. In addition, OpenHelix empowers researchers by distributing extensive and effective tutorials and training materials on the most powerful and popular genomics resources, and by contracting with resource providers to provide comprehensive, long-term training and outreach programs.

Brief Description: 
OpenHelix Search Portal provides a mechanism to search for and evaluate online bioscience resources.
Access: 
Subscription
Campus: 
Ann Arbor
Mobile Version: 
No mobile friendly interface available.
Icons: 
Authorized UM users (+ guests in UM Libraries)
New Resource Indicator: 
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Mark as New Until: 
Wednesday, August 20, 2014
Type: 
Database
Vendor: 
OpenHelix
Internal Note: 
pricek 5/20/14
Creator: 
National Human Genome Research Institute (NHGRI) OpenHelix
High Level Browse: 
Keywords: 
genomics, bioinformatics
Database availability dates: 
Friday, April 3, 2015
Special Message Dates: 
Friday, April 3, 2015 to Saturday, October 3, 2015
Special Message: 

OpenHelix has been cancelled.   If you have questions or concerns, please email thlibrary@umich.edu.

 

Date to Unpublish Database: 
Saturday, October 3, 2015

          GenETHX        

Citations, some with abstracts or tables of contents, to literature on the ethical, legal, and social implications of genetic and genomic research and its applications from many disciplines and publication types including journals, newspapers, books, bills, laws, court decisions, reports, and audiovisuals.

Brief Description: 
Citations to literature on the ethical, legal, and social implications of genetic and genomic research and its applications.
Access: 
Free
Mobile Version: 
No mobile friendly interface available.
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Open access for all users
New Resource Indicator: 
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Language: 
ENGLISH
Type: 
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Vendor: 
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ST ID: 
UMI07209
Internal Note: 
sehanley - 8/25/2010
Raw ST Data: 
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High Level Browse: 
Keywords: 
bioethics, medical ethics, genetics

           Mapping and characterisation of genomic binding sites of the chromatin barrier protein VEZF1         
Strogantsev, Ruslan S. (2009) Mapping and characterisation of genomic binding sites of the chromatin barrier protein VEZF1. PhD thesis, University of Glasgow.
           Post-genomics studies and their application to non-invasive prenatal diagnosis         
Avent, N. D., Plummer, Z. E., Madgett, T. E., Maddocks, D. G. and Soothill, P. W. (2008) Post-genomics studies and their application to non-invasive prenatal diagnosis. Seminars in Fetal and Neonatal Medicine, 13 (2). pp. 91-98. ISSN 1744-165X Available from: http://eprints.uwe.ac.uk/7149
           Isolation of a Xenopus laevis genomic clone representing a novel N-cadherin related gene         
UNSPECIFIED. (1997) Isolation of a Xenopus laevis genomic clone representing a novel N-cadherin related gene. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1356 (3). pp. 253-257. ISSN 0167-4889
          25hydroxyvitamin Dsub3sub may Function via Genomic and NonGenomic actions        
Hirota Y, Suhara Y, Osakabe N, Sakaki T and Okano T
          MAGNETO: 300 years of Magnetism, Purity, Hygiene, Health & Electrical Shows (2007, CAA, Inventar, Public Space)        















This photos are from a former lecture at the CAA space of Lia Perjovschi's former atelier in 2007 during the INVENTAR (inventory) series organized by Lia at the Public Space project in Bucharest. The atelier itself becomes a mythical place. You can still see the familiar depot full of carton cases that you could sit on and peer into. An archive and ZACAMANT analysis place you could stumble upon very hard to find studies on the history and theory of art, as well as comic books by Art Spiegelman for example. While the CAA has grown and morphed into a Museum of Knowledge that has been moved to a new place in Sibiu, both Lia and Dan keep true to their brainstorming beginnings in Bucharest, as they both welcomed and introduced us to their brand new think- and wonder- tank place, a few weeks ago.

There is a certain urgency of publishing these lines here, as dietary supplements are being banned and severely restricted everywhere, both in the EU and the US. There is also the sense that we have entered an era of over-supplementing ourselves with Vitamins and Minerals. Government attitudes during and after WWII have run full spectrum, from enforced supplementation and rationalization of food and nutrition (both in the East and West) to the food scares, contaminants and biotech warnings of the present. Food hygiene tends to play a major role again, as the E-coli O104:H4 Outbreak of 2011 in Germany has shown us. Germany was the standard for ubercleanliness at least since 19th century, now this purity has gone awry. The Gram-negative favorite bacterium E. coli was also the darling of pharma and a truly wonderful lab model organism, being presently the most studied prokaryotic organism on Earth. Not studied enough maybe, since metagenomics (the study of genetic material extracted directly from the environment) is slow on identifying potentially harmful bacteria in their farmland or cropland environment. E. coli managed to instill fear and panic not seen since the 40s and 50s. Maybe after 50 years of European and Western over-cleanliness everybody concerned got sloppy.
Did people stop washing their hands? Did they stop washing veggies? Did they stop cooking food? Humans are always being painfully reminded about the possibility of inter-breeding E-coli strains transferring freely among themselves(with the help of bacteriophage partners) deadly virulence and antibiotic resistance. The natural capacity of bacteria and archea for Lateral Gene Transfer and Horizontal Gene Transfer has been a major advantage in their evolution and a headache for both taxonomists building the Tree of Life as well as their biomedical colleagues. And then the housefly - Musca domestica, the old incubator and transmitter of age-old diseases, is again to blame!

The introduction screen-shot is a woodcut of a poster used by Charles C Came for one of his electrical performances during the 1840s.
Came and other scientific wonder showmen like him were self-thought in the science and medicine of the day. He toured upstate New York with his horse and wagon selling patent medicines, and offering scientific lectures and electrical healing demonstrations. Accompanied by music from his self-played mechanical organs, he performed on a proscenium flanked by columns with two flaming urns on top.
Hijacking and re-using equipment developed by electrical demonstrators (Benjamin Franklin amongst them) they promoted a sense of magic and classical mystery plays in an age of mechanistic determinism. The mysteries of nature were bottled up, sucked out and teased from the scientific apparatus, a situation that got recharged constantly under the public view.
Exhibiting electrostatic generators, Leyden jars or Colt submarine batteries would produce bolts, sparks and shocks to the public. The Scientific and Industrial Revolution had to have a populist phase transition, and miracle-purveyors filled in immediately this role, providing the newest shocks, using and abusing the newest gimmicks and devices that would literally and physically electrify and shock the audience. They made science easy to touch and feel on a very personal bodily level.
We still have today this same mesmerizing tradition mainly incorporated and upgraded into different schools of alternative medicine, the wonder remedies of the new age with belts, corsets, headbands, shoe insoles, necklaces of magnetic therapy involving the use of magnetic static fields. This was a ZACAMANT area i have been introduced by the kinds efforts of my beloved aunt Mary since early childhood. She migrated to the States more than 30 years ago.

As a child of the 60s she had a strong interest in alternative medicine, Hypno-therapy, Iridology, Spiritualism, Enemas, Nutrition, Thought Field Therapy, Aromatherapy, Homeopathy, Reflexology and many many others ways to self-heal oneself in the age of Pharma domination and Sicko Health Care Apocalypse.
Her tremendous interest and curiosity in this area brought to me a plethora of books, oils, tapes, dvd's, magical pills, colloidal minerals, turquoise stones against computer radiation and magnets - that continuously immersed everybody around in a world of wonder steeped into natural and popular science. Even if i was deeply skeptical about the vaunted healing proprieties and the enthusiastic statements published on labels, packages, pamphlets, and books, i was totally hooked by its near-magical appeals and deeply mystifying techniques. I was introduced to a very bodily experience, a reconstruction of the familiar and invisible daily corpus as described and prescribed by a psychical and physical and more pure alternative; a fringe area that gathered and absorbed information from lots of apparently lost traditions, both popular, scientific and para-scientific. There was a state-sponsored herbal healing program of PLAFAR shops in Romania - it was even considered an important and obligatory task during the communist times to gather herbs and store them for medical purposes. Already then these plants were considered herbal ZACAMANT and powerful alternatives to the chemical revolution of the day.

After 1989 in Romania there was an apparent flood of alternative medicine information and associated therapies, grafted on top of the old core, evolving either into a cost-efficient alternative as ways to overcome prohibitive costs for the regular pharmaceuticals pushed on the pharmacy market. There was also another outcome as was felt pressure on local herbal medicine shops to transform into rated and more controlled and sometimes expensive bio-foods and naturist shops. We are still in the midst of the market transformation that transformed alternative folk medicine into dietary supplements and upper end green remedies. I am still very impressed by the old women in general, who in Romania, keep on gathering herbs and plants in cities all over the country to use them for private medicinal purposes. They are probably the only ones who managed to shortcut the system and preserve the old ways. Following the pressure of the Codex Alimentarius and EU Food Supplements ban, the transition from phytochemicals(anti-oxidants, anti-inflamatory but also many potentially toxic substances) to the labeled production and intake of dietary supplements is becoming a regulatory issue. 

I am still curious to find and research into the performative potential of health- and life- prolonging spectacular therapies, the way they keep a promise of renewal and protection for a fragile-looking post-industrial body, as possible and informed alternative against the aging processes and omnipresent pollution of modernity. Biomedical knowledge has also flourihannelsshed by giving a 'therapeutic' turn to the natural world. Natural elements or natural forces such as gravity, or objects such as magnets are there to orient and balance or unbalance us. The force of gravity and universal attraction is entering our consciousness after Einstein's General Relativity through multiple cultural channels. You could say that pre-Einstein, Newtonian mechanics is still very much acting on us. In our daily experience we see things falling down. We don't see space curbing around us or gravity playing tricks on beams of light. We notice things as they are being attracted by some huge magnetic force, found somewhere in the center of the earth.
Maybe the magical powers of magnets to still orient us in the age of GPS, or to wipe out and destroy nearly every high tech device in range (smartphone,laptop, etc), make them magnetically attractive and potent to us. The new educational floating earth Levitron's are also side-effects of this magnetic fascination. These new magnetic globes for a new age of electro-magnetic familiarity are made available by very cheap technology. Maybe we are witnessing a transition for the first time to a toy model of our planet as floating between magnetic fields, beyond the old geographic orrery of the fixed axis mundi so familiar in high school classes of the past.
(please notice a very lean Simion Cernica in these pictures. i miss him very much in Dr Taberei, and even if he is on Sunset Blvd right now, we miss his unswerving dedication to attend nearly every Bucharest presentation, lecture, concert, action, etc his missing from our lives will mark a huge gap in our miserable and severly limited audience)

A clear case of magnetic Z A C A M A N T!
          February 2017 Meeting        

Speaker: Nathan J. Edwards, Georgetown University

Topic: Beyond Peptide Identification Informatics: Multi-Search, Systems Proteomics, Proteogenomics, Phyloproteomics, and Glycoproteomics

Date: Monday, February 27, 2017

Time: 6:15 pm Dinner, 7:15 pm: Presentation

Location: Shimadzu Scientific Instrument, Inc. Training Center 7100 Riverwood Drive, Columbia, MD 21046 (Directions)

Dinner: Please RSVP to Katherine Fiedler (Katherine.L.Fiedler@fda.hhs.gov) before February 27 if you will be attending the dinner or are a presenting as a vendor.

Abstract: Bottom-up proteomics by LC-MS/MS is one of the most widely used analytical workflows for characterizing the expressed proteins of the cell. With continued improvements in mass spectrometer speed, accuracy, and versatility, we can increase the depth of coverage and detail of protein characterization, but only if our data analysis capabilities keep pace with the size, and complexity, of the collected spectral data. Tens of spectral datafiles with tens of thousands of spectra are now passé. Protein sequence databases provide multiple proteoforms and amino-acid variants per gene, and the number of species and strains with genome sequences continues to grow. Connecting identified proteins with their pathways, to provide a functional context for differentially abundant proteins remains a challenge, and the exploration of non-template driven post-translational modifications, such as glycosylation, requires novel analytical and mass-spectrometry techniques that demand new data-analysis techniques. Crucially, each of these analytical contexts requires a careful consideration of the potential for false conclusions, and strategies for estimating statistical significance.…


          M & I Seminar Series        
Default thumb Mon, Aug 28 04:00 PM until 05:00 PM Eastern Time (US & Canada)
PRESENTED BY: MALCOLM WHITEWAY, PH.D, Professor and Tier 1 Canada Research, Chair in Microbial Genomics, Concordia University, Montreal, QC, Canada
Location: Chilcott Auditorium

          Plants, Genes and Health: a Growing Connection - Juvenon Health Journal        
Medical research is getting closer to “fine-tuning” the body’s biochemical reactions. Nutrigenomic studies underscore the importance of including plants in our diet.
          Biology: Assistant Professor of Biology - University of Richmond - Richmond, VA        
We seek a biologist who has expertise in analysis of big data, modeling, bioinformatics, genomics/transcriptomics, biostatistics, or other quantitative and/or...
From University of Richmond - Thu, 06 Jul 2017 23:17:18 GMT - View all Richmond, VA jobs
          Scientist - Product Science - Centrillion - Palo Alto, CA        
The R&amp;D group at Centrillion is a multidisciplinary team of biologists, engineers, chemists, and computational biologists developing new genomics technologies,...
From Centrillion - Wed, 07 Jun 2017 02:24:59 GMT - View all Palo Alto, CA jobs
          June 2014 Highlights        

Editor-in-chief Shawn Kennedy and Clinical Managing Editor Karen Roush present the highlights of the June issue of the American Journal of Nursing. A newborn appears on our cover this month, relating to our first CE, “Genomic Breakthroughs in the Diagnosis and Treatment of Cystic Fibrosis.” Our second CE (with podcast) discusses the health care disparities faced by the LGBT population.

We have the fourth installment of our systematic reviews series focusing on study selection and critical appraisal. Our Mental Health Matters column provides an overview of clinical depression and a new treatment: transcranial direct current stimulation. And an Ethical Issues column addresses the implications of denying smokers employment in health care, and Shawn Kennedy speaks with the author in a podcast this month. In addition, there’s an AJN Reports column on whether nurses are ready for retirement, News, Reflections, Viewpoint, Drug Watch, Art of Nursing, and more.

           The stealth episome: Suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola         
Godfrey, S., Lovell, H., Mansfield, J. W., Corry, D., Jackson, R. W. and Arnold, D. L. (2011) The stealth episome: Suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola. PLoS Pathogens, 7 (3). ISSN 1553-7366 Available from: http://eprints.uwe.ac.uk/14583
           Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the Genomic Island PPHGI-1         
Godfrey, S., Mansfield, J. W., Corry, D., Lovell, H., Jackson, R. and Arnold, D. L. (2010) Confocal imaging of pseudomonas syringae pv. phaseolicola colony development in bean reveals reduced multiplication of strains containing the Genomic Island PPHGI-1. Molecular Plant-Microbe Interactions, 23 (10). pp. 1294-1302. ISSN 0894-0282 Available from: http://eprints.uwe.ac.uk/11465
           In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola         
Lovell, H., Jackson, R. W., Mansfield, J. W., Godfrey, S. A. C., Hancock, J. T., Desikan, R. and Arnold, D. L. (2011) In planta conditions induce genomic changes in Pseudomonas syringae pv. phaseolicola. Molecular Plant Pathology, 12 (2). pp. 167-176. ISSN 1464-6722 Available from: http://eprints.uwe.ac.uk/11468
           Bacterial evolution by genomic island transfer occurs via DNA transformation in planta         
Lovell, H. C., Mansfield, J. W., Godfrey, S. A., Jackson, R. W., Hancock, J. T. and Arnold, D. L. (2009) Bacterial evolution by genomic island transfer occurs via DNA transformation in planta. Current Biology , 19 (18). pp. 1586-1590. ISSN 0960-9822 Available from: http://eprints.uwe.ac.uk/8275
          Brain Network Eigenmodes in Health and Disease, Olfactory Learning Without Mushroom Bodies, and Assessing Overlap of Genomic Features: the PLOS Comp Biol June Issue        
Check out our highlights from the PLOS Computational Biology June issue:   Brain Network Eigenmodes Provide a Robust and Compact Representation of the Structural Connectome in Health and Disease While the structural connectome of the
           Unraveling the biological mechanisms in Alzheimer's disease--lessons from genomics         
Borovečki, Fran and Klepac, Nataša and Muck-Šeler, Dorotea and Hajnšek, Sanja and Mubrin, Zdenko and Pivac, Nela (2011) Unraveling the biological mechanisms in Alzheimer's disease--lessons from genomics. Progress in Neuro-Psychopharmacology & Biological Psychiatry, 35 (2). pp. 340-7. ISSN 0278-5846
          Iowa State swine geneticist hopes to improve reproductive efficiency        

Serão brings several years of research and teaching experience in animal breeding and genetics, as well as collaborative ventures in areas such as nutrition, meat quality and reproduction.

Source: Iowa Pork Industry Center
Using genetics to improve reproductive performance and response to disease is a vital component of the future of the pork industry, and new Iowa State University animal scientist Nick Serão hopes his research will help with both areas. Serão began his position as assistant professor in swine genetics in March and has been developing his research team and program.

“Iowa State University is well-known for Animal Science and Animal Breeding & Genetics education, Extension and research, and the state of Iowa is the most important place to do work in swine,” he says. “I wanted to take my research program to a place where I know that we (my research group) are positively impacting the swine industry. Thus, being able to be part of all of this is a unique opportunity.”

Serão brings several years of research and teaching experience in animal breeding and genetics, as well as collaborative ventures in areas such as nutrition, meat quality and reproduction. He’s originally from Brazil where he earned both his bachelor of science degree in animal science and masters of science in breeding and genetics from the Federal University of Vicosa and worked on several swine research projects. He obtained his Ph.D. in animal genomics from the University of Illinois at Urbana-Champaign, and came to Iowa State for the first time in 2013 as a postdoctoral researcher working on disease response and feed efficiency in pigs, under Jack Dekkers. In August 2015, he became a faculty member at North Carolina State University until returning to Iowa State this past March.

“Although I’m more of a quantitative geneticist, I’m also interested in incorporating biological aspects into my primary research focus, and my goal is to help the industry improve reproductive efficiency through genetics,” he says. “However, this is complicated because these traits are usually lowly heritable. So, I look for new traits that are more heritable with a biologic relationship, so we can increase sow performance much quicker.”

Serão hopes and expects to be able to introduce new traits that are heritable, easy to measure and economically important, into selection indices, with the objective of improving genetic response for reproductive performance in sows and boars.

“A good component of my past, current and future research is on response to diseases, especially on PRRS. Thus, I hope my work can impact the swine industry to show that selection for improved response to diseases can be a reality,” he says.

In addition to research, Serão will teach animal breeding and genetics courses at the undergraduate and graduate levels, and will continue to promote the field of research to his students. He looks forward to sharing his research program and results with academic colleagues, students, the swine industry and producers.

He can be contacted by email at serao@iastate.edu and phone at 515-294-3435.


          Pencegahan dan Penanggulangan Middle East Respiratory Syndrome Coronavirus (MERS-CoV)         
Pengenalan MERS-CoV

—  Novel Corona Virus (virus Corona baru) yang menyebabkan penyakit pernapasan pada manusia berjangkit di Saudi Arabia sejak bulan Maret 2012, sebelumnya virus ini tidak pernah ditemukan.
—  The Corona Virus Study Group of The International Committee on Taxonomy of viruses(Komite International Taxonomy Virus) 28 Mei 2013 sepakat Virus corona baru bernama Middle East Respiratory Syndrome-Corona Virus (MERS-CoV) baik dalam komunikasi publik maupun komunikasi ilmiah.
—  Virus SARS tahun 2003 juga merupakan kelompok virus Corona dan dapat menimbulkan pneumonia berat akan tetapi berbeda dari virus MERS-CoV.
—  MERS-CoV adalah penyakit sindrom pernapasan yang disebabkan oleh virus Corona yang menyerang saluran pernapasan mulai dari yg ringan sampai berat.
—  Gejalanya klinis pada umumnya demam, batuk, gangguan pernafasan akut, timbul gambaran pneumonia, kadang-kadang terdapat gejala saluran pencernaan misalnya diare.

Jumlah kasus di dunia dan Kondisi Indonesia saat ini

—  Berdasarkan laporan WHO, sejak September 2012 sampai September 2013, telah ditemukan 130 kasus konfirmasi MERS-CoV dengan 58 meninggal (CFR: 44,6%). Sejak September 2012 sampai dengan Juni 2016, terdapat 1.399 kasus MERS pada manusia dimana 594 meninggal (CFR: 42,5%).
—  Hingga saat ini belum ada laporan kasus MERS-CoV di Indonesia.
—  Kelompok risiko tinggi mencakup usia lanjut (lebih dari 60 tahun), anak anak, wanita hamil dan penderita penyakit kronis (diabetes mellitus, Hipertensi, Penyakit Jantung dan ginjal pernafasan, dan defisiensi immunitas. 
—  Belum terdapat pengobatan spesifik dan belum terdapat vaksin untuk manusia

Masa Inkubasi

Masa inkubasi untuk MERS (waktu antara ketika seseorang terkena MERS-CoV dan ketika mereka mulai memiliki gejala) biasanya sekitar 5 atau 6 hari, tetapi dapat berkisar antara 2 sampai 14 hari.

Cara penularan MERS-CoV

—  Virus ini dapat menular antar manusia secara terbatas, dan tidak terdapat penularan penularan antar manusia secara luas dan bekelanjutan. Mekanisme penularan belum diketahui.
—  Kemungkinan penularannya dapat melalui :  (a) Langsung : melalui percikan dahak (droplet) pada saat pasien batuk atau bersin. (b)Tidak Langsung: melalui kontak dengan benda yang terkontaminasi virus.

Klasifikasi Virus
Group               :
Group IV
((+) ssRNA)
Order                :
Nidovirales
Family              :
Coronaviridae
Subfamily         :
Coronavirinae
Genus               :
Betacoronavirus
Species              :
MERS-CoV

Coronavirus merupakan virus berbentuk bulat dengan diameter sekitar 100-120 nm.

Kelelawar diduga berpotensi sebagai sumber spillover MERS-CoV dari hewan ke manusia

Ekspresi dipeptidyl peptidase 4 (DPP4) / CD26 pada permukaan sel berfungsi sebagai reseptor pada sel kelelawar terhadap Infeksi MERS-CoV.
MERS-CoV dapat tumbuh di dalam sel kelelawar.
Analisis filogenetik gen replikase dari coronavirus bahwa Mers-CoV terkait erat dengan Bat coronavirus Tylonycteris HKU4 dan Bat coronavirus Pipistrellus HKU5, yang merupakan prototipe dua spesies dalam garis keturunan C dari genus Betacoronavirus.

Bukti Unta terinfeksi MERS-CoV

—  Agustus tahun 2013, unta dromedary pertama kalinya diduga sebagai sumber infeksi pada manusia karena telah  diketahui terdapat antibodi Mers-CoV pada dromedary dari Spanyol (Canary Islands) dan Oman.
—  Terbukti bahwa:
(a)  Genom MERS-CoV terdeteksi pada swab hidung dari dromedary di Mesir, Iran, Israel, Saudi Arabia, Kuwait, Oman, Pakistan dan Qatar;
(b)Virus MERS-CoV diisolasi dari dromedary di Mesir, Saudi Arabia dan Qatar.

Tiga spesies CoV terdeteksi pada unta dromedaris (unta berponok satu)

                   1.MERS-CoV (betacoronavirus, kelompok C);
                   2.Betacoronavirus 1 (betacoronavirus, kelompok A); 
                   3. Human CoV 229E (alphacoronavirus).
—  Meskipun CoV terdeteksi hampir sepanjang tahun pada hewan tersebut, prevalensi yang relatif lebih tinggi adalah MERS-CoV dan Camelid α-CoV (diamati dari Desember 2014 hingga April 2015 di Saudi Arabia).
—  Unta muda (berusia 0,5-1 tahun) menderita infeksi pernapasan tertinggi baik oleh MERS-CoV maupun Camelid α-CoV.
—  Unta muda tampaknya memainkan peran epidemiologi yang lebih penting dalam memelihara kedua virus tsb.

Penularan dari Hewan ke Manusia

—  Coronavirus (CoVs) mampu menginfeksi manusia muncul melalui penularan lintas-induk semang dari hewan.
—  Ada bukti substansial terdapat kejadian MERS-CoV pada manusia dimana penularanannya berasal dari unta dromedari (unta berponok satu).
—  Sebagian besar didasarkan pada fakta bahwa virus yang terkait erat dengan MERS-CoV telah diisolasi dari unta berponok satu. 
—  Unta berponok satu yang seropositif Mers-CoV distribusi geografisnya cukup luas, maka masih memungkinkan terjadi penularan lanjutan pada waktu mendatang. 
—  Pemahaman lebih lanjut tentang penularan MERS-CoV lintas induk semang diperlukan untuk menurunkan risiko penularan virus ini kepada manusia.
—  Jalur penularan dari hewan ke manusia belum sepenuhnya dipahami
—  Unta cenderung menjadi induk semang reservoir utama Mers-COV dan menjadi sumber infeksinya dari hewan ke manusia.
—  MERS-CoV telah diisolasi dari unta di Mesir, Oman, Qatar, dan Arab Saudi. Mers-CoV tersebut identik dengan strain manusia.
—  Banyak spesies dan strain Coronavirus yang memiliki karakteristik yang berbeda, yang menyebabkan berbagai tanda penyakit dari ringan sampai berat, baik pada manusia maupun hewan.

Penyebaran Mers-CoV di beberapa negara

Sampai saat ini wabah sporadis MERS-CoV yang terjadi pada kasus manusia telah dideteksi di 17 negara :
          Timur Tengah : Jordan, Kuwait, Oman, Qatar, Saudi Arabia, Uni Emirat Arab, dan Yaman
          Eropa : Perancis, Jerman, Yunani, Italia, dan Inggris
          Afrika : Tunisia dan Mesir
          Asia: Malaysia dan Philipina
          Amerika : Amerika Serikat

Penularan MERS-CoV
    
—  Modus utama dari virus shedding dari MERS- dan Camelid α-CoVs adalah dari saluran pernapasan unta dromedaris.
—  Lebih dari setengah dari swab hidung Mers-COV-positif (56,6%) juga positif untuk camelid α-CoVs, menunjukkan sering infeksi campuran dari virus ini.
—  Dalam survei dari swab hidung ditemukan dua hewan berisi semua tiga spesies CoVs.
—  Prevalensi tinggi virus ini menunjukkan bahwa mereka enzootic di unta dromedaris.
—  Untuk menguji keragaman genetik dan evolusi CoVs unta, sequencing metagenomic dilakukan dengan menggunakan bahan swab asli yang positif dalam screening RT-PCR awal.
—  Tiga puluh delapan sampel ini terdapat infeksi campuran dari MERS-CoV dengan satu atau kedua dari dua spesies lain CoV, tetapi hanya 14 sampel yang dihasilkan dua genom lengkap.
—  β1-HKU23-CoVs telah terdeteksi pada unta di Dubai, dan camelid α-CoVs berhubungan erat dengan virus yang diisolasi dari alpacas di California pada tahun 2007.
—  Camelid α-CoVs sekelompok dengan humam CoV 229E, agen penyebab pilek umum pada manusia.
—  Prevalensi tinggi infeksi tanpa gejala dengan camelid α-CoVs di unta Arab Saudi menekankan peran penting bahwa spesies ini berperan dalam ekologi CoV.

Vaksinasi MERS-CoV pada hewan

—  Vaksin MERS-CoV dapat mengurangi jumlah virus yang diproduksi di unta yang terinfeksi, hal ini berpotensi menurunkan risiko bagi manusia. Mengurangi jumlah virus pada ekskresi setelah vaksinasi pada unta sehingga berpotensi mengurangi penularan ke manusia.
—  Vaksin (strain lemah virus MERS) secara signifikan dapat menurunkan keberadaan virus MERS dalam ingus dan air liur unta (Bart Haagmans, Science, Januari 2016).
—  Penularan MERS ke manusia terjadi terutama melalui ekskresi hidung unta dromedaris.
—  MERS pertama kali diidentifikasi di Arab Saudi pada 2012 dan telah mempengaruhi sekitar 1.400 unta dromedaris, menurut sebuah tulisan ilmiah yang terpisah pada kehadiran virus dan menyebar di negara itu (Science, Januari 2016). Penelitian ini menegaskan ingus unta sebagai pembawa utama virus.
—  Wabah besar MERS manusia dimulai Mei 2014. Virus menyebabkan demam, batuk dan sesak napas, dan juga dapat menyebabkan gagal ginjal dan pembekuan darah. Menyebabkan kematian sekitar sepertiga dari kasus manusia yang dilaporkan (Vaccine / scientific paper).
—  Untuk menguji mutu vaksin, 8 ekor unta ditantang dengan MERS-CoV.  Empat ekor telah divaksinasi melalui tetes hidung dan suntikan. Empat unta lainnya tidak divaksinasi sebagai kelompok kontrol.
—  Unta yang divaksinasi mengembangkan antibodi terhadap MERS dan tidak menunjukkan gejala infeksi. Tapi hewan pada kelompok kontrol memperlihatkan gejala klinis termasuk keluar ingus.
—  Terdapat tiga strain (MERS-CoV, Betacoronavirus 1, Human CoV 229E) yang berbeda, sehingga satu vaksin tidak mungkin efektif digunakan untuk semua kasus.
—  Hal ini tidak mungkin untuk mengembangkan vaksin tunggal untuk mencegah tiga atau lebih spesies coronavirus (Huachen Zhu, Universitas Hong Kong, Cina).
—  Belum diketahui berapa lama kekebalan protektif yang diinduksi oleh vaksin akan bertahan (Haagmans, Erasmus MC, Belanda)

Uji Lab MERS-CoV

—  Spesimen untuk pemeriksaan virus MERS-CoV adalah spesimen yang berasal dari saluran nafas bawah seperti dahak, aspirat trakea dan bilasan bronkoalveolar. Spesimen saluran pernafasan atas (nasofaring dan orofaring) tetap diambil terutama bila spesimen saluran pernafasan bawah tidak memungkinkan dan pasien tidak memiliki tanda-tanda atau gejala infeksi pada saluran pernapasan bawah.
—  Virus MERS-CoV juga dapat ditemukan di dalam cairan tubuh lainnya  seperti darah, urin, dan feses tetapi kegunaan sampel tersebut di dalam mendiagnosa infeksi MERS-COV belum pasti. Pemeriksaan diagnosis laboratorium kasus infeksi MERS-CoV dilakukan dengan metoda RT-PCR dan dikonfirmasi dengan teknik sekuensing.

Diagnostic Kit untuk Hewan Diregistrasi OIE

§  Disease: Middle East Respiratory Syndrome
§  Name of the Diagnostic kit: BIONOTE® Rapid MERS-CoV Ag Test;
§  Name of the Manufacturer: BioNote, Inc
§  Contact: bionote@bionote.co.kr
§  Type of kit: Immuno Chromatographic Assay
§  Purpose(s) validated: Resolution No 15 adopted in May 2016 by the World Assembly of the OIE Delegates
§  Date and Number of registration: May 2016
§  Registration Number: 20160212
§  Validation studies Abstract Sheet: AS Rapid MERS-CoV Test
§  Kit insert: User's manual.

Pencegahan Penularan MERS-CoV

—  Masyarakat yang akan berpergian ke negara-negara yang terdapat MERS-CoV menderita demam dan gejala sakit saluran pernapasan bagian bawah (batuk, atau sesak napas ) dalam kurun waktu 14 hari sesudah perjalanan, segera periksakan ke dokter.
—  Belum ada vaksin khusus yang dapat mencegah terjadinya penyakit ini.
—  Pencegahan tetap dapat dilakukan dengan memperkuat imunitas tubuh.
—  Tutuplah hidung dan mulut dengan tisu ketika batuk ataupun bersin dan segera buang tisu tersebut ke tempat sampah.
—  Hindari menyentuh mata, hidung dan mulut dengan tangan yang belum dicuci.
—  Menghindari kontak erat dengan penderita, menggunakan masker, menjaga kebersihan tangan dengan sering mencuci tangan dengan sabun dan menerapkan etika batuk ketika sakit.
—  Gunakan masker dan jaga sanitasi tubuh dan lingkungan. Bila diperlukan bagi penderita penyakit kronik, di kerumunan orang, badan tidak fit dan lain lain gunakan masker.

          DNA repair and telomeres, announced a relationship        
To maintain genomic stability, mammalian cells require the action of five proteins encoded by paralogous genes to that of RAD51, a molecule involved in DNA repair, implying orquesrado operation of certain protective mechanisms. In previous work on RAD51 protein, essential in homologous recombination, has established its relationship to repair mechanisms. Their action, in response to […]
          Artificial Life and Generative Genomics        
by John Lobell Artificial life (AL) is a concept pioneered by Christopher Langton. Langton starts with the cellular automata (CA) that were originated by John von Neumann and Stanislaw Ulam, developed by John Conway in his Game of Life, and widely promoted by Stephen Wolfram in A New Kind of Science. Langton distinguishes between those […]
          The Junk DNA Myth Takes a Well-Deserved Hit: A Review of The Myth of Junk DNA        
A new MP3 sermon from Reformation Church is now available on SermonAudio.com with the following details:

Title: The Junk DNA Myth Takes a Well-Deserved Hit: A Review of The Myth of Junk DNA
Speaker: W. J. Mencarow
Broadcaster: Reformation Church
Event: Audio Book
Date: 8/23/2013
Bible: Genesis 1:27; Genesis 2:22
Length: 27 min. (64kbps)

Overview: A review of -The Myth of Junk DNA- by Jonathan Wells -Discovery Institute Press Seattle, WA, 2011-. Reviewed by Jeffrey Tomkins -http---creation.com-review-wells-junk-dna-.-----One of the greatest evolutionary frauds of recent times is the myth that eukaryotic genomes, particularly the human genome, are largely composed of meaningless -junk- DNA sequences that serve no biological purpose. While many of the actual researchers working in the vast field of genomics now realize that virtually the entire genome is functional,1 a handful of influential and popular bio-science authors still authoritatively proclaim the fraudulent myth of -junk DNA-. Thus, the errant junk DNA myth is still widely perpetuated even though several decades of hard-hitting research profoundly declares otherwise.-----The problem is that the general public doesn-t often read the journal-based scientific literature, but instead rely on popular science authors to distill the pertinent research data into a more easily understood form. In this process, the truth about non-coding DNA is withheld and distorted by the popular media technical outlets. Unfortunately, the scientific technocracy of our time uses the junk DNA myth as a key component to perpetuate the overall myth of Darwinian evolution. A new book by molecular biologist and author Dr Jonathan Wells utterly and thoroughly destroys the cherished junk DNA paradigm. It is appropriately titled 'The Myth of Junk DNA.'-
          Research Technician - Genomics Technology Developments, Heidelberg (Germany)        
The new position is in Science services support at Heidelberg (Germany)
          See You at “Healthcare Gets Personal” on Thursday in Kendall Square        
We are all set for another great event in Boston. “Healthcare Gets Personal” is about the convergence of genomics, analytics, and portable/wearable devices in driving healthcare, personal medicine, and behavior change. It’s all taking place at Google’s offices in Kendall Square (4th floor), from 4-6 pm on Thursday, Dec. 12, and it’s going to be […]
          Healthcare Gets Personal on Dec. 12 at Google: Here’s the Agenda        
I first met George Church in the Connecticut backyard of literary agent John Brockman. It was 2007, and Church, the genomics pioneer, was giving an informal talk on synthetic biology. Afterwards, he got stung by some sort of weird-looking bee. The event stuck in my mind. Here’s hoping next Thursday, Dec. 12, will be just […]
          Reliance Appoint Life Sciences Business Development Executive         

Reliance are delighted to announce the appointment of Dr Ruth Brown as Business Development Executive within their Life Sciences business. Ruth will be responsible for introducing Reliance's products to the Life Sciences industry.

Ruth comes to Reliance from Illumina, a global leader in genomics, which revolutionised the sequencing process for DNA analysis. Working as their Territory Account Manager for Northern England, she covered a complete portfolio from microarray consumables to high-throughput sequencing platforms with integrated bioinformatics solutions. Prior to Illumina she was an Account Manager for Fisher Scientific, the distribution arm of ThermoFisher Scientific Group. With access to their full portfolio of consumables, equipment, laboratory design and consulting services, Ruth was responsible for developing sales relationships with customers in pharmaceuticals, academia, forensics and general industry.

As the Life Sciences industry continues to grow, applications are becoming more and more diverse. With her extensive experience and scientific knowledge, Ruth will be working alongside Reliance's customers to identify tangible solutions to help improve efficiency in applications such as cell culture, optical positioning, automation workflows and sample processing. Ruth is keen to develop particular areas within the industry, to complement the well-established engineering services Reliance has traditionally provided for mass spectrometry workflows and…

          Data Sharing: Perspectives from across the Academic Spectrum        

What are the barriers and benefits of sharing data and the move towards more transparency in science?  Nature’s “Data Matters” blog presents interviews with scientists, funders, and librarians wherein they share their thoughts on these and related matters.  From paleontology to neuroscience, from ecology to genomics, and including representatives of funding agencies and organizations that curate and safeguard data, the interviewees address issues such as the state of, and problems with, data sharing in their field, the importance of data sharing, and what needs to be done to bring about necessary/desired changes.

For more information about data management at UNH, visit http://www.unh.edu/research/data-management

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          Modelling haplotypes with respect to reference cohort variation graphs        
Abstract
Motivation: Current statistical models of haplotypes are limited to panels of haplotypes whose genetic variation can be represented by arrays of values at linearly ordered bi- or multiallelic loci. These methods cannot model structural variants or variants that nest or overlap.Results: A variation graph is a mathematical structure that can encode arbitrarily complex genetic variation. We present the first haplotype model that operates on a variation graph-embedded population reference cohort. We describe an algorithm to calculate the likelihood that a haplotype arose from this cohort through recombinations and demonstrate time complexity linear in haplotype length and sublinear in population size. We furthermore demonstrate a method of rapidly calculating likelihoods for related haplotypes. We describe mathematical extensions to allow modelling of mutations. This work is an important incremental step for clinical genomics and genetic epidemiology since it is the first haplotype model which can represent all sorts of variation in the population.Availability and Implementation: Available on GitHub at https://github.com/yoheirosen/vg.Contact:benedict@soe.ucsc.eduSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Abundance estimation and differential testing on strain level in metagenomics data        
Abstract
Motivation: Current metagenomics approaches allow analyzing the composition of microbial communities at high resolution. Important changes to the composition are known to even occur on strain level and to go hand in hand with changes in disease or ecological state. However, specific challenges arise for strain level analysis due to highly similar genome sequences present. Only a limited number of tools approach taxa abundance estimation beyond species level and there is a strong need for dedicated tools for strain resolution and differential abundance testing.Methods: We present DiTASiC (Differential Taxa Abundance including Similarity Correction) as a novel approach for quantification and differential assessment of individual taxa in metagenomics samples. We introduce a generalized linear model for the resolution of shared read counts which cause a significant bias on strain level. Further, we capture abundance estimation uncertainties, which play a crucial role in differential abundance analysis. A novel statistical framework is built, which integrates the abundance variance and infers abundance distributions for differential testing sensitive to strain level.Results: As a result, we obtain highly accurate abundance estimates down to sub-strain level and enable fine-grained resolution of strain clusters. We demonstrate the relevance of read ambiguity resolution and integration of abundance uncertainties for differential analysis. Accurate detections of even small changes are achieved and false-positives are significantly reduced. Superior performance is shown on latest benchmark sets of various complexities and in comparison to existing methods.Availability and Implementation: DiTASiC code is freely available from https://rki_bioinformatics.gitlab.io/ditasic.Contact:renardB@rki.deSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Discovery and genotyping of novel sequence insertions in many sequenced individuals        
Abstract
Motivation: Despite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects.There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi-sample data to “collectively” obtain a very high coverage dataset to accurately find insertions common in a given population.Result: Here, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one-end-anchored sequences to small-scale de novo assemblies of unmapped reads, and conducting strand-aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects.Availability and implementation: Pamir is available at https://github.com/vpc-ccg/pamir.Contact:fhach@{sfu.ca, prostatecentre.com} or calkan@cs.bilkent.edu.trSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields        
Abstract
Motivation: Incorporating gene interaction data into the identification of ‘hit’ genes in genomic experiments is a well-established approach leveraging the ‘guilt by association’ assumption to obtain a network based hit list of functionally related genes. We aim to develop a method to allow for multivariate gene scores and multiple hit labels in order to extend the analysis of genomic screening data within such an approach.Results: We propose a Markov random field-based method to achieve our aim and show that the particular advantages of our method compared with those currently used lead to new insights in previously analysed data as well as for our own motivating data. Our method additionally achieves the best performance in an independent simulation experiment. The real data applications we consider comprise of a survival analysis and differential expression experiment and a cell-based RNA interference functional screen.Availability and implementation: We provide all of the data and code related to the results in the paper.Contact:sean.j.robinson@utu.fi or laurent.guyon@cea.frSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Denoising genome-wide histone ChIP-seq with convolutional neural networks        
Abstract
Motivation: Chromatin immune-precipitation sequencing (ChIP-seq) experiments are commonly used to obtain genome-wide profiles of histone modifications associated with different types of functional genomic elements. However, the quality of histone ChIP-seq data is affected by many experimental parameters such as the amount of input DNA, antibody specificity, ChIP enrichment and sequencing depth. Making accurate inferences from chromatin profiling experiments that involve diverse experimental parameters is challenging.Results: We introduce a convolutional denoising algorithm, Coda, that uses convolutional neural networks to learn a mapping from suboptimal to high-quality histone ChIP-seq data. This overcomes various sources of noise and variability, substantially enhancing and recovering signal when applied to low-quality chromatin profiling datasets across individuals, cell types and species. Our method has the potential to improve data quality at reduced costs. More broadly, this approach—using a high-dimensional discriminative model to encode a generative noise process—is generally applicable to other biological domains where it is easy to generate noisy data but difficult to analytically characterize the noise or underlying data distribution.Availability and implementation:https://github.com/kundajelab/coda.Contact:akundaje@stanford.edu

          Exploiting sequence-based features for predicting enhancer–promoter interactions        
Abstract
Motivation: A large number of distal enhancers and proximal promoters form enhancer–promoter interactions to regulate target genes in the human genome. Although recent high-throughput genome-wide mapping approaches have allowed us to more comprehensively recognize potential enhancer–promoter interactions, it is still largely unknown whether sequence-based features alone are sufficient to predict such interactions.Results: Here, we develop a new computational method (named PEP) to predict enhancer–promoter interactions based on sequence-based features only, when the locations of putative enhancers and promoters in a particular cell type are given. The two modules in PEP (PEP-Motif and PEP-Word) use different but complementary feature extraction strategies to exploit sequence-based information. The results across six different cell types demonstrate that our method is effective in predicting enhancer–promoter interactions as compared to the state-of-the-art methods that use functional genomic signals. Our work demonstrates that sequence-based features alone can reliably predict enhancer–promoter interactions genome-wide, which could potentially facilitate the discovery of important sequence determinants for long-range gene regulation.Availability and Implementation: The source code of PEP is available at: https://github.com/ma-compbio/PEP.Contact:jianma@cs.cmu.eduSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Integrative deep models for alternative splicing        
Abstract
Motivation: Advancements in sequencing technologies have highlighted the role of alternative splicing (AS) in increasing transcriptome complexity. This role of AS, combined with the relation of aberrant splicing to malignant states, motivated two streams of research, experimental and computational. The first involves a myriad of techniques such as RNA-Seq and CLIP-Seq to identify splicing regulators and their putative targets. The second involves probabilistic models, also known as splicing codes, which infer regulatory mechanisms and predict splicing outcome directly from genomic sequence. To date, these models have utilized only expression data. In this work, we address two related challenges: Can we improve on previous models for AS outcome prediction and can we integrate additional sources of data to improve predictions for AS regulatory factors.Results: We perform a detailed comparison of two previous modeling approaches, Bayesian and Deep Neural networks, dissecting the confounding effects of datasets and target functions. We then develop a new target function for AS prediction in exon skipping events and show it significantly improves model accuracy. Next, we develop a modeling framework that leverages transfer learning to incorporate CLIP-Seq, knockdown and over expression experiments, which are inherently noisy and suffer from missing values. Using several datasets involving key splice factors in mouse brain, muscle and heart we demonstrate both the prediction improvements and biological insights offered by our new models. Overall, the framework we propose offers a scalable integrative solution to improve splicing code modeling as vast amounts of relevant genomic data become available.Availability and implementation: Code and data available at: majiq.biociphers.org/jha_et_al_2017/Contact:yosephb@upenn.eduSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          popFBA: tackling intratumour heterogeneity with Flux Balance Analysis        
Abstract
Motivation: Intratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single-cell genomic analyses are nonetheless unable to characterize the interactions among cancer subpopulations. In this study, we propose popFBA, an extension to classic Flux Balance Analysis, to explore how metabolic heterogeneity and cooperation phenomena affect the overall growth of cancer cell populations.Results: We show how clones of a metabolic network of human central carbon metabolism, sharing the same stoichiometry and capacity constraints, may follow several different metabolic paths and cooperate to maximize the growth of the total population. We also introduce a method to explore the space of possible interactions, given some constraints on plasma supply of nutrients. We illustrate how alternative nutrients in plasma supply and/or a dishomogeneous distribution of oxygen provision may affect the landscape of heterogeneous phenotypes. We finally provide a technique to identify the most proliferative cells within the heterogeneous population. Availability and implementation: the popFBA MATLAB function and the SBML model are available at https://github.com/BIMIB-DISCo/popFBA.Contact:chiara.damiani@unimib.it

          Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression        
Abstract
Motivation: A prime challenge in precision cancer medicine is to identify genomic and molecular features that are predictive of drug treatment responses in cancer cells. Although there are several computational models for accurate drug response prediction, these often lack the ability to infer which feature combinations are the most predictive, particularly for high-dimensional molecular datasets. As increasing amounts of diverse genome-wide data sources are becoming available, there is a need to build new computational models that can effectively combine these data sources and identify maximally predictive feature combinations.Results: We present a novel approach that leverages on systematic integration of data sources to identify response predictive features of multiple drugs. To solve the modeling task we implement a Bayesian linear regression method. To further improve the usefulness of the proposed model, we exploit the known human cancer kinome for identifying biologically relevant feature combinations. In case studies with a synthetic dataset and two publicly available cancer cell line datasets, we demonstrate the improved accuracy of our method compared to the widely used approaches in drug response analysis. As key examples, our model identifies meaningful combinations of features for the well known EGFR, ALK, PLK and PDGFR inhibitors.Availability and Implementation: The source code of the method is available at https://github.com/suleimank/mvlr.Contact:muhammad.ammad-ud-din@helsinki.fi or suleiman.khan@helsinki.fiSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Chromatin accessibility prediction via convolutional long short-term memory networks with k -mer embedding        
Abstract
Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k-mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k-mer co-occurrence information with recent advances in deep learning.Results: We fill this gap by addressing the problem of chromatin accessibility prediction with a convolutional Long Short-Term Memory (LSTM) network with k-mer embedding. We first split DNA sequences into k-mers and pre-train k-mer embedding vectors based on the co-occurrence matrix of k-mers by using an unsupervised representation learning approach. We then construct a supervised deep learning architecture comprised of an embedding layer, three convolutional layers and a Bidirectional LSTM (BLSTM) layer for feature learning and classification. We demonstrate that our method gains high-quality fixed-length features from variable-length sequences and consistently outperforms baseline methods. We show that k-mer embedding can effectively enhance model performance by exploring different embedding strategies. We also prove the efficacy of both the convolution and the BLSTM layers by comparing two variations of the network architecture. We confirm the robustness of our model to hyper-parameters by performing sensitivity analysis. We hope our method can eventually reinforce our understanding of employing deep learning in genomic studies and shed light on research regarding mechanisms of chromatin accessibility.Availability and implementation: The source code can be downloaded from https://github.com/minxueric/ismb2017_lstm.Contact:tingchen@tsinghua.edu.cn or ruijiang@tsinghua.edu.cnSupplementary information:Supplementary materialsSupplementary materials are available at Bioinformatics online.

          Constructing linkage maps in the genomics era with MapDisto 2.0        
Abstract
Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM).Results: MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps. It includes several new major features: (i) handling of very large genotyping datasets like the ones generated by GBS; (ii) direct importation and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of linkage groups in case of segregation distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute. Features i to iv operate through inclusion of new Java modules that are used transparently by MapDisto; (v) QTL detection via a new R/qtl graphical interface.Availability and Implementation: The program is available free of charge at mapdisto.free.fr.Contact:mapdisto@gmail.comSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Aozan: an automated post-sequencing data-processing pipeline        
Abstract
Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports.Availability and Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www.outils.genomique.biologie.ens.fr/aozan/. Aozan source code is available on GitHub: https://github.com/GenomicParisCentre/aozan.Contact:aozan@biologie.ens.fr

          SynMap2 and SynMap3D: web-based whole-genome synteny browsers        
Abstract
Summary: Current synteny visualization tools either focus on small regions of sequence and do not illustrate genome-wide trends, or are complicated to use and create visualizations that are difficult to interpret. To address this challenge, The Comparative Genomics Platform (CoGe) has developed two web-based tools to visualize synteny across whole genomes. SynMap2 and SynMap3D allow researchers to explore whole genome synteny patterns (across two or three genomes, respectively) in responsive, web-based visualization and virtual reality environments. Both tools have access to the extensive CoGe genome database (containing over 30 000 genomes) as well as the option for users to upload their own data. By leveraging modern web technologies there is no installation required, making the tools widely accessible and easy to use.Availability and Implementation: Both tools are open source (MIT license) and freely available for use online through CoGe (https://genomevolution.org). SynMap2 and SynMap3D can be accessed at http://genomevolution.org/coge/SynMap.pl and http://genomevolution.org/coge/SynMap3D.pl, respectively. Source code is available: https://github.com/LyonsLab/coge.Contact:ericlyons@email.arizona.eduSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data        
Abstract
Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene.Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution.Availability and Implementation: The PathwayMapper tool is accessible at http://pathwaymapper.org and the code is available on Github (https://github.com/iVis-at-Bilkent/pathway-mapper).Contact:ivis@cs.bilkent.edu.trSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          DNA Compass: a secure, client-side site for navigating personal genetic information        
Abstract
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data—an impediment for the general public.Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data. Users can query the status of their genomic variants for over 1658 markers or tens of millions of documented single nucleotide polymorphisms (SNPs). DNA Compass presents the relevant genotypes of the user side-by-side with explanatory scientific resources. The genotype data never leaves the user’s computer, a feature that provides improved security and performance. More than 12 000 unique users, mainly from the general genetic genealogy community, have already used DNA Compass, demonstrating its utility.Availability and Implementation: DNA Compass is freely available on https://compass.dna.land.Contact:yaniv@cs.columbia.edu

          Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets        
Abstract
Motivation: Visualization of genomic data is fundamental for gaining insights into genome function. Yet, co-visualization of a large number of datasets remains a challenge in all popular genome browsers and the development of new visualization methods is needed to improve the usability and user experience of genome browsers.Results: We present Dynamix, a JBrowse plugin that enables the parallel inspection of hundreds of genomic datasets. Dynamix takes advantage of a priori knowledge to automatically display data tracks with signal within a genomic region of interest. As the user navigates through the genome, Dynamix automatically updates data tracks and limits all manual operations otherwise needed to adjust the data visible on screen. Dynamix also introduces a new carousel view that optimizes screen utilization by enabling users to independently scroll through groups of tracks.Availability and Implementation: Dynamix is hosted at http://furlonglab.embl.de/Dynamix.Contact:charles.girardot@embl.deSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          swga: a primer design toolkit for selective whole genome amplification        
Abstract
Motivation: Population genomic analyses are often hindered by difficulties in obtaining sufficient numbers of genomes for analysis by DNA sequencing. Selective whole-genome amplification (SWGA) provides an efficient approach to amplify microbial genomes from complex backgrounds for sequence acquisition. However, the process of designing sets of primers for this method has many degrees of freedom and would benefit from an automated process to evaluate the vast number of potential primer sets.Results: Here, we present swga, a program that identifies primer sets for SWGA and evaluates them for efficiency and selectivity. We used swga to design and test primer sets for the selective amplification of Wolbachia pipientis genomic DNA from infected Drosophila melanogaster and Mycobacterium tuberculosis from human blood. We identify primer sets that successfully amplify each against their backgrounds and describe a general method for using swga for arbitrary targets. In addition, we describe characteristics of primer sets that correlate with successful amplification, and present guidelines for implementation of SWGA to detect new targets.Availability and Implementation: Source code and documentation are freely available on https://www.github.com/eclarke/swga. The program is implemented in Python and C and licensed under the GNU Public License.Contact:ecl@mail.med.upenn.eduSupplementary information:Supplementary dataSupplementary data are available at Bioinformatics online.

          Pseudoalignment for metagenomic read assignment        
Abstract
Motivation: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains.Results: We find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics setting. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics projects.Availability and Implementation: Pipeline and analysis code can be downloaded from http://github.com/pachterlab/metakallistoContact:lpachter@math.berkeley.edu

          POSTHUMOUS SIGHTINGS OF PASSENGER PIGEONS?        

Passenger pigeons (juvenile, left; male, centre; female, right), from Birds of New York by Louis Agassiz Fuertes, 1910 – did this species survive beyond 1914? (public domain)

The most numerous species of wild bird ever known was the phenomenally plentiful passenger pigeon Ectopistes migratorius, a dainty, slender-bodied, long-tailed bird with blue-grey head, neck, back, and wings, and cinnamon-pink underparts. It has been estimated that during the 19thCentury’s early years, its total population contained between five and ten thousand million birds. Or to put it another way, this single species may have accounted for as much as 45 per cent of the entire bird population of America! One of the most evocative descriptions of its immense numbers during its heyday appeared in The Mirror of Literature, Amusement, and Instruction for 16 November 1822:
 
The accounts of the enormous flocks in which the passenger, or wild pigeons, fly about in North America, seem to an European like the tales of Baron Munchausen; but the travellers are ‘all in a story.’ In Upper Canada, says Mr. Howison, in his entertaining ‘Sketches,’ you may kill 20 or 30 at one shot, out of the masses which darken the air. And in the United States, according to Wilson, the ornithologist, they sometimes desolate and lay waste a tract of country 40 or 50 miles long, and 5 or 6 broad, by making it their breeding-place. While in the state of Ohio, Mr. Wilson saw a flock of these birds which extended, he judged, more than a mile in breadth, and continued to pass over his head at the rate of one mile in a minute, during four hours — thus making its whole length about 240 miles. According to his moderate estimate, this flock contained two thousand two hundred and thirty millions, two hundred and seventy-two pigeons.

A flock of passenger pigeons being hunted in Louisiana, The Illustrated Shooting and Dramatic News, 1875 (public domain)

It seems inconceivable that less than a century after the above report had been published the passenger pigeon had been completely exterminated, but this is precisely what happened.

As a result of an unutterably ruthless, relentless programme of persecution (on a scale unparalleled even in man’s nefarious history of wildlife destruction), perpetrated by trigger-happy gun-toters attracted by the awesome spectacle of the birds’ mass migrations, by 1 September 1914 only one solitary specimen remained alive. This was a 29-year-old hen bird named ‘Martha Washington’, exhibited at Cincinnati Zoo. And shortly after noonon that fateful September day, this last humble survivor of an ostensibly indomitable, indestructible species died. The unthinkable had happened - the passenger pigeon, whose vast migrating flocks had virtually eclipsed the sun in the time of the great American painter John James Audubon, was no more.

Martha Washington, the last known passenger pigeon, pictured alive on left, and as a taxiderm specimen at Washington DC's Smithsonian Institution on right (public domain)

Officially, that is. For at least another decade, alleged sightings of passenger pigeons were frequently reported, but scientists tended to dismiss these as mistaken observations of the smaller but superficially similar mourning dove Zenaida macroura, still a common species today. In September 1929, however, a remarkable report emerged that could not be discarded so readily. This was the month in which Michigan University bacteriologist Prof. Philip Hadley, in the company of a Mr Foard, an old friend familiar with the land, had been hunting in a virtually uninhabited wilderness nestling within Michigan’s northern peninsula.

They had been hunting there for some time when Foard drew Hadley’s attention to a bird perched close by, and declared that it was a passenger pigeon - which he had observed in enormous numbers when younger. Needless to say, Hadley turned at once to spy this exceedingly unexpected specimen, but just as he caught sight of it the bird took flight. Nevertheless, it did seem to him to be pigeon-like in form, with a pointed tail, and he clearly believed the incident to be of significance, because he sent details to the eminent US journal Science, which in turn judged it to be important enough to warrant publication in its issue of 14 February 1930.

Passenger pigeon, from Pigeons, Sir William Jardine, 1835 (public domain)

Within his letter, Hadley also referred to a couple of other recent sightings, documented a month earlier by Kendrick Kimball in the Detroit News (5 January). One of these sightings had been made on 10 June 1929, by Robert H. Wright of Munissing, Michigan. Wright was convinced that the pair of birds that he saw at close range on Highway M-28, about 16 miles from Munissing, were passenger pigeons. In the other sighting, made between Indianapolis and Kokomo while driving from Florida, Dr Samuel R. Landes spotted a flock of approximately 15 birds that he readily identified as passenger pigeons. Both Wright and Landes were familiar with this species’ appearance — like so many others, they had shot hundreds of them during the late 1870s.

Nonetheless, the last confirmed wild specimen was shot in 1899, at Babcock, Wisconsin, so is it really possible that the birds reported three decades later by the eyewitnesses above were truly passenger pigeons? It seems rather unlikely, at least at first, because after the last major flocks had been slaughtered (in 1878), stragglers did not survive long, and matings became ever fewer. It seemed as if the species could only persist and reproduce when present in huge flocks. At the same time, of course, the familiarity of the eyewitnesses with the species makes their testimony all that more difficult to discount.

A pair of taxiderm passenger pigeons at San Antonio, Texas (© Jonathan Downes/CFZ)

Perhaps certain fairly secluded localities did house a last few specimens, which existed undetected beyond the date of Martha’s death, and possibly even mated every now and then, and which were encountered only when their flights traversed areas frequented by humans, or when humans occasionally passed by their hideaways. Yet without the immense congregations necessary to provide the stimulus for normal, full-scale reproduction, they could surely do no more than extend their species’ survival by a few years. Long before the last individual had died, whether in 1914 or in the 1930s, the passenger pigeon’s descent into extinction had already begun, irrevocably and inevitably, with the disappearance of its vast flocks. After that, it could only be a matter of time.

Surely, then, the ‘passenger pigeon’ spied in March 1965 at Homer, Michigan, by Irene Llewellyn (Fate, September 1965) and another spied the same year by Stella Fenell at New Jersey’s Park Ridge (Fate, January 1966), not to mention an intriguing series of recently-claimed passenger pigeon sightings chronicled online in 2014, 2015, and 2016 by the website HoriconBirds.com, were only mourning doves ... weren’t they?

John James Audubon's famous painting of a pair of passenger pigeons, from his spectacular tome The Birds of America, 1827-1838 (public domain)

An Antipodean equivalent of sorts is the flock pigeon Phaps (=Histriophaps)histrionica, also known as the flock bronzewing. In the 1800s, huge flocks, containing millions of birds, lived on the grass plains of New South Wales and Queensland. Today, though, it is a relatively rare species (it was once thought to be extinct), categorised as Threatened by the IUCN.

This time, however, the cause is not man himself but his animals. The flock pigeon is a seed-eater, but generations of grazing cattle and sheep have prevented the plains’ grass from seeding adequately.

A flock pigeon (© Christopher Walker/Wikipedia – CC BY-SA 3.0 licence)

Of course, courtesy of the extraordinary technological advances taking place daily in the modern-day world that we all inhabit, perhaps we should never say never in relation to the prospect of one day seeing bona fide passenger pigeons alive and well again. On 8 February 2012, a meeting was convened at Harvard Medical School in Boston, Massachusetts, by a group of interested researchers from the non-profit genetic research organisation Revive & Restore, to explore the technical plausibility of resurrecting this iconic species via genomic engineering, as well as to examine the potential cultural, social, political, and ecological ramifications of restoring it to life and perhaps even reintroducing it into the wild. After presentations by a range of participants and discussions concerning their contributions, the group concluded that the genetic technique proposed should be tested to see how effective it may be, and how it could be improved, with this goal in mind.

So who knows? Maybe one day the passenger pigeon will indeed return, if no longer to darken the skies with vast flocks as in former times but at least to live again in the land where it rightfully belongs and where it would certainly have remained had its existence not been wilfully extinguished by our own species.

Passenger pigeons, frontispiece to The Passenger Pigeon, 1907 (public domain)

Finally: by an extraordinary quirk of fate, one of the last passenger pigeon individuals whose demise in the wild state was formally documented was actually shot not anywhere in the New World but, remarkably, in the English countryside instead. An escapee from captivity, it was shot in Yorkshire during 1876, as recorded in  T.A. Coward's book The Birds of the British Isles and Their Eggs - Second Series (1920). Moreover, this was just one of at least eight passenger pigeon specimens recorded from the wild in Great Britain.

Were all of them merely captive escapees, or might one or more have been genuine transatlantic vagrants? Sadly, it is highly unlikely that we shall ever know the answer to this intriguing question. My grateful thanks to correspondent Philip Jensen for kindly bringing this fascinating snippet of information to my attention.

Passenger pigeon, Plate 23 in Vol 1 of The Natural History of Carolina, Florida and Bahamas by Mark Catesby, George Edwards, 1754 (public domain)

For my tribute in verse to the passenger pigeon, please click here; and for its philatelic prominence, please click here.

This ShukerNature blog article is excerpted and expanded from my book Extraordinary Animals Revisited.







          Obama Names Science & Technology Advisers        
President-elect Obama named four top science and technology advisers over the weekend, while highlighting the importance of restoring science as one of America's top priorities. In his weekly radio broadcast, Obama said, “promoting science isn’t just about providing resources, it’s about protecting free and open inquiry. It’s about ensuring that facts and evidence are never twisted or obscured by politics or ideology. It’s about listening to what our scientists have to say, even when it’s inconvenient—-especially when it’s inconvenient--because the highest purpose of science is the search for knowledge, truth, and greater understanding of the world around us. That will be my goal as President of the United States, and I could not have a better team to guide me in this work.” These are encouraging words, and we sincerely hope that his team will act quickly to change policies governing important environmental and medical issues.

As part of Obama’s new advisory team, John Holdren, a physicist and environmental policy professor at Harvard, will direct the White House Office of Science and Technology. Jane Lubchenco, a marine biologist at Oregon State University, will lead the National Oceanic and Atmospheric Administration. Nobel Prize-winning cancer researcher Harold Varmus and genomic researcher Eric Lander will also join Obama's team of science advisers.
          RHR: Genomic Testing for Chronic Illness—with Dr. Ritchie Shoemaker        

revolution health radio

In this episode, we discuss: 6:30 What is genomic testing? 13:52 The problem with current testing methods 17:05 Why looking at one gene isn't enough 23:00 Should people be cautious of genomic testing? 29:39 The importance of microRNA 32:19 Will the Progene DX test be worth the cost? [smart_track_player url="http://traffic.libsyn.com/thehealthyskeptic/RHR_Genomic_Testing_for_Chronic_Illness_with_Dr._Ritchie_Shoemaker.mp3" title="RHR: Genomic Testing for Chronic Illness with Dr. Ritchie Shoemaker" artist="Chris Kresser" social="true" social_twitter="true" social_facebook="true" social_gplus="true" ] Chris Kresser: I’m Chris Kresser and this is Revolution Health Radio. Hey, everybody, it’s Chris Kresser. Welcome to another episode of Revolution Health Radio. I’m really excited to welcome Dr. Ritchie Shoemaker back on the show for the second time as my guest. Dr. Ritchie Shoemaker is a pioneer in understanding how low-dose biotoxin exposure, including toxic mold and algae, impacts our health and contributes to disease. He’s the author of eight books and multiple published academic papers. His latest book, Surviving Mold: Life in the Era of Dangerous Buildings, is a guide through diagnosis, treatment, remediation, and return to health. Dr. Shoemaker is currently retired, but continues to lecture throughout the US on chronic inflammatory illnesses that are caused by exposure to moldy buildings and other biotoxins. If you’ve been listening to my podcast for a while or following my email list, you’ll know that this is a topic of great interest to me both professionally as a clinician because we’re starting to treat a lot of patients with CIRS, or chronic inflammatory response syndrome, and also personally because I recently discovered a mold issue in our home, and my entire family, my wife and our daughter, were all affected by that. We’ve since, fortunately, gotten out of that house, and we’re in a new house now, and we’re well along the path of recovery from that. This is something that I’m really fascinated by, and it’s something we’re seeing a lot in our practice, so I wanted to ask Dr. Shoemaker to come back to particularly talk about some new genomic testing that is becoming available that quite dramatically improves our ability to diagnose this condition and get a lot more specific about how to treat it. So far, there have been some tantalizing developments in the world of genetic testing,
          RHR: What Influences Methylation? An Interview with Dr. Ben Lynch        

revolution health radio

What I really want to do today is dive in a little bit deeper on the topic of methylation and specifically discuss the role that genetics and epigenetics and diet and lifestyle play, talk about some of the primary environmental influences that may affect methylation, go beyond MTHFR to talk about some of the other methylation-related genes, and then perhaps more than anything else, talk about what Dr. Lynch has learned in the last few years of really taking a deep dive into this material, and working with thousands of people, and hosting his conference, and what he is excited about and working on, and looking forward to.

In this episode, we cover:

The relative roles that genetics, epigenetics, and diet/lifestyle play in influencing methylation The primary environmental influences on methylation beyond diet Beyond MTHFR: the role of other methylation-related genes What Dr. Lynch is interested in now

[smart_track_player url="http://traffic.libsyn.com/thehealthyskeptic/RHR_-_What_Influences_Methylation_An_Interview_with_Dr._Ben_Lynch.mp3" title="RHR: What Influences Methylation? An Interview with Dr. Ben Lynch" artist="Chris Kresser" social="true" social_twitter="true" social_facebook="true" social_gplus="true" ] Chris Kresser: Hey, everyone, it’s Chris Kresser. Welcome to another episode of Revolution Health Radio. Today I’m really happy and excited to welcome Dr. Ben Lynch as my guest. I became aware of Ben’s work in methylation several years ago and have been really impressed with his contribution there. I’m sure many of you are familiar with his work and maybe have done some of his trainings or attended his conference. He’s a naturopathic physician, and he received his cell and molecular biology bachelor’s degree from the University of Washington and his ND from Bastyr University. His passion for identifying the cause of disease directed him toward nutrigenomics and methylation dysfunction. Currently he researches, writes, and presents worldwide on the topic of MTHFR and methylation defects, and you can learn more about Dr. Lynch and his work at www.MTHFR.net. Dr. Lynch is also the president and CEO of Seeking Health, which is a company oriented towards disease prevention and health promotion. He makes some really great supplements that we use in our clinic and I have used personally as well. He lives in Bothell, Washington—sorry, I’m not familiar with that town; I’m probably slaughtering the pronunciation—with his wife Nadia and three boys, Tasman, Mathew, and Theodor.
          Looking Good on Paper        
One of the prerequisites for being an academic is you have to look and sound very academic. Which is why you’ll rarely spot Elvis Presley sideburns or a Frank Zappa style soul patch among research scholars. Forget the nerdy dress sense, even the language has to be unapologetically abstruse. May be that’s why research papers are cold, clinical, and as unreadable as an engineering manual.

The idea behind penning papers like ‘Metagenomic insights into the pathogenome of cellulosimicrobium cellulans’ is the equivalent of sporting a t-shirt that reads, ‘If you didn’t get my PhD dissertation title, then you’re not PhD enough’.

Given the peer pressure to portray oneself as ‘lab-coatish’, it takes a brave heart to strike a discordant note and make science, very unscientific. Thankfully for every boring scholar, there’s a Feynman somewhere trying to break the mould and simplifying things.

Recently, I stumbled upon a stash of dissertations with titles that made me want to read them. On top of the list is ‘Ramanujan’s association with radicals in India’. It almost feels like a historical thriller about mathematicians and Naxalites. On the contrary, it’s an in depth study of Ramanujan’s work in the field of radicals or square root numbers!

Another one that fascinated me was the ‘Alpher-Bethe-Gamow’ paper on the origin of chemical elements. Doesn’t that sound like Alpha, Beta, and Gamma to you? Apparently, Alpher is the author of the thesis. George Gamow, the famed cosmologist was his guide. And they added Hans Bethe, the nuclear physicist’s name, almost whimsically, just to add some punch to the title.

Juan Bicarregui’s ‘Do Not Read This’ is equally compelling. It taps into the child in you and urges you to take a sneak peek without explicitly asking you to do so. Bailey and Borwein were even more brilliant. They put their key finding as the header: 'The 40 billionth binary digit of Pi is 1'. Anyone who reads it will gasp, ‘How could they know that without a computer?’ and will definitely want to explore their algorithm.

Ryter, Morse & Choi got it spot-on when they put out their findings on the similarities between Carbon Monoxide and Nitrous Oxide. They chose to play on Star Trek and worded their work as 'Carbon Monoxide: To boldly go where NO has gone before'. That level of wit can lift the clouds of dullness from any vapid verbiage masquerading as research.
          MTS57 - Forest Rohwer - Curing the Corals        

It never occurred to me that the human body and a coral reef have a lot in common--until I spoke to Forest Rohwer for this podcast. Rohwer is a microbiologist at San Diego State University, and he studies how microbes make coral reefs both healthy and sick. Just as we are home to a vast number of microbes, coral reefs depend on their own invisible menagerie of algae and bacteria to get food, recycle waste, and fend off invaders. But as Rohwer writes in his new book, Coral Reefs in the Microbial Seas, we humans have thrown this delicate balance out of kilter, driving the spread of coral-killing microbes instead.

Additional Reading:

Viral communities associated with healthy and bleaching corals.
The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem.
Metagenomic analysis of stressed coral holobionts.


          MTS40 - John Wooley - Exploring the Protein Universe        

John Wooley is Associate Vice Chancellor of Research and Professor of Chemistry-Biochemistry and of Pharmacology at the University of California San Diego. Wooley is a leader in the young field of metagenomics: the science of gathering vast numbers of genes from the oceans, soils, air, and the human body.

A generation ago biologist knew the sequences of a few thousand genes. Since then that figure has jumped to several million genes and it's only going to continue to leap higher in years to come. This wealth of data is allowing scientists to get answers to fundamental questions they rarely even asked a generation ago.

They're starting to understand how thousands of species of microbes coexist in our bodies. They're investigating how hundreds of genes work together inside a single cell and they're starting to get a vision of the full diversity of the billions of proteins that life produces, what scientists sometimes call the protein universe.

John Wooley has been at the center of this revolution, investigating some of these new questions and leading pioneering projects such as CAMERA, the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, to organize the unprecedented amount of data that scientists have at their disposal so that they can master that data rather than drown in it.

In this episode I spoke to Wooley about how metagenomics has revolutionized research on everything from marine ecology to human health, and how he and his colleagues cope with an influx of data on millions of new genes.


          MTS27 - Melanie Cushion - Pneumocystis carinii        

Melanie Cushion holds down two jobs: she’s a research career scientist at the Veterans Administration Medical Center in Cincinnati, Ohio, and she’s also professor and associate chair for research in the department of internal medicine at the University of Cincinnati College of Medicine.  Dr. Cushion focuses her research on the fungus, Pneumocystis carinii, which is a harmless commensal for most people, but a deadly pathogen for others. 

Pneumocystis carinii was shrouded in obscurity for many years until its fifteen minutes in the spotlight came in the 80’s, when, unfortunately, an outbreak of Pneumocystis pneumonia prefigured the AIDS epidemic.  Large numbers of previously healthy homosexual men in California became deathly ill with Pneumocystis pneumonia, and doctors knew something unusual (later found to be HIV) was going on.  Dr. Cushion says Pneumocystis pneumonia is an opportunistic infection: it strikes individuals with immune systems too weak to fend it off.  This explains why it was – and still is – a well-known sign that the patient is stricken with an active HIV infection or some other immune-suppressing disorder. 

Dr. Cushion heads up the Pneumocystis genome project and she’s also looking into a new line of drugs called glucan synthase inhibitors, which have a profound effect on Pneumocystis’s life cycle and may offer new insights into managing the pathogen.

In this interview, I talked with Dr. Cushion about some of the more surprising results to come out of her genomics work, why Pneumocystis is a tough nut to crack in the laboratory, and about why she’s not giving her young investigator award back to the Society of Protozoologists any time soon.


          MTS16 - Paul Keim, Ph.D. - The Science Behind the 2001 Anthrax Letter Attacks        

Dr. Paul Keim is a professor of biological sciences at Northern Arizona University, in Flagstaff, where his research program focuses on microbial forensics and the genomic analysis of pathogenic bacteria.  As an expert in Bacillus anthracis, the bacterium responsible for anthrax, Dr. Keim participated in the FBI’s investigation into the anthrax letter attacks back in 2001.

Microbial forensics is a field that developed in response to the twin threats of biological warfare and biological terrorism.  (What’s the difference between biological warfare and biological terrorism?  Both have the potential to reach beyond the site of the attack and both are a menace to innocent, unarmed citizens.  To me, there’s a fine line here.  But I digress.)

Dr. Keim’s interest in microbial forensics arose out of his postdoctoral work at the University of Utah.  After this training in phage recombination and genomics, Dr. Keim applied what he had learned about bacterial genetics in a collaboration with scientists working on resolving and identifying the various strains of B. anthracis.  Fast forward to this past summer, when the F.B.I. revealed that Dr. Keim used his expertise on B. anthracis to help in the investigation that concluded a researcher at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) perpetrated the anthrax attacks.  Dr. Keim, along with several other scientists who helped in the F.B.I.’s

 

In this podcast, I talked with Dr. Keim about his work with the F.B.I., whether the payoffs of bioterrorism research are worth the costs, and about how the plague (yes, the Black Death) made its way to North American shores and continues to sicken about a dozen people every year.


          PFT Technician openings in IGIB CSIR Institute of Genomics and Integrative Biology        
Education: MBBS, M.Sc, Job Location: Delhi (NCR), Vacancies:, Last Date: 15-08-2017

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]
          NetSuite Supports BRCA Foundation with New Registry Program        
Press Release

NetSuite Supports BRCA Foundation with New Registry Program

Pro Bono Volunteers Build Out Sophisticated Enhancements to Meet Needs of Nonprofit Using the SuiteCloud Development Platform

San Mateo, Calif.—Jul 19, 2017


Oracle NetSuite Global Business Unit, one of the world’s leading providers of cloud-based financials / ERP, HR, Professional Services Automation (PSA) and omnichannel commerce software suites, today announced that it has teamed up with the BRCA Foundation, a nonprofit created to fund research for the prevention of “BRCA cancers,” or cancers believed to be caused by “broken” BRCA genes, to help launch a BRCA registry project and help the BRCA Foundation gather information relevant to its mission and organizational vision. A four-person team from NetSuite, together with the BRCA Foundation, created customizations in NetSuite to encourage participants to sign up for the program and ultimately pass voluntary contact and demographic data from a genomics testing partner to the BRCA Foundation, using the NetSuite SuiteCloud development platform. This data will be used to provide individuals with news and information about BRCA cancers, and allow them to connect with potential studies in which they may want to participate.

Established in 2016 by NetSuite Co-founder and NetSuite Global Business Unit Executive Vice President of Development, Evan Goldberg, the BRCA Foundation was created to accelerate research and foster collaboration to prevent and cure BRCA cancers. BRCA1 and BRCA2 are genes that produce proteins that help repair damaged DNA. For people who have a mutation in those genes, DNA damage may not repair properly and are more likely to develop additional alterations that can lead to cancer. A nonprofit and a NetSuite customer, BRCA applied for pro bono services from Oracle NetSuite Social Impact to help it establish a registry to gather and share data to provide researchers with potential participants they might use to conduct studies that will lead to better treatment and preventative options.

“NetSuite has been incredibly helpful and supportive of our mission every step of the way,” said Gail Fisher, Deputy Director of the BRCA. “It’s amazing what talented people can do with such a flexible platform. The registry is going to go a long way in the fight against cancer and have a huge impact on people with BRCA.”

As a result of the project, the BRCA Foundation now has a button on its website allowing volunteers to sign up for a genetic cancer screening test from its genomic testing partner. If volunteers choose, they can provide the BRCA Foundation with contact and demographic data to be maintained securely within NetSuite. That data can then be used in the fight against cancer, for example by enrolling participants in clinical trials if they wish.

“This project was so gratifying to be a part of,” said Jerome Wi, Solution Consulting Manager at NetSuite and Project Manager for Suite Pro Bono. “I got to lend my development skills to support a project that will ultimately help to fight against cancer, all while using the SuiteCloud development platform.”


Contact Info
Christine Allen
Public Relations, Oracle NetSuite Global Business Unit
603-743-4534
PR@netsuite.com
About SuiteCloud

NetSuite’s SuiteCloud is a comprehensive offering of cloud-based products, development tools and services designed to help customers and commercial software developers take advantage of the significant economic benefits of cloud computing. Based on NetSuite, the industry’s leading provider of cloud-based financials/ERP software suites, SuiteCloud enables customers to run their core business operations in the cloud, and software developers to target new markets quickly with newly-created mission-critical applications built on top of mature and proven business processes.

The SuiteCloud Developer Network (SDN) is a comprehensive developer program for independent software vendors (ISVs) who build apps for SuiteCloud. All available SuiteApps are listed on SuiteApp.com, a single-source online marketplace where NetSuite customers can find applications to meet specific business process or industry-specific needs. For more information on SuiteCloud and the SDN program, please visit www.netsuite.com/developers.

About Oracle NetSuite Global Business Unit

Oracle NetSuite Global Business Unit pioneered the Cloud Computing revolution in 1998, establishing the world’s first company dedicated to delivering business applications over the internet. Today, Oracle NetSuite Global Business Unit provides a suite of cloud-based financials/Enterprise Resource Planning (ERP), HR and omnichannel commerce software that runs the business of companies in more than 100 countries. For more information, please visit http://www.netsuite.com.

Follow Oracle NetSuite Global Business Unit’s Cloud blog, Facebook page and @NetSuite Twitter handle for real-time updates.

About Oracle

The Oracle Cloud offers complete SaaS application suites for ERP, HCM and CX, plus best-in-class database Platform as a Service (PaaS) and Infrastructure as a Service (IaaS) from data centers throughout the Americas, Europe and Asia. For more information about Oracle (NYSE:ORCL), please visit us at www.oracle.com.

Trademarks

Oracle and Java are registered trademarks of Oracle and/or its affiliates. Other names may be trademarks of their respective owners.


Talk to a Press Contact

Christine Allen

  • 603-743-4534

          Microbes can draw the line between species        
News

Wasps' gut inhabitants can kill or save crossbreeds

By
4:52pm, July 18, 2013
Citations

R.M. Brucker and S.R. Bordenstein. The hologenomic basis of speciation: Gut bacteria cause hybrid lethality in the genus Nasonia. Science. Posted online July 18, 2013. doi: 10.1126/science.1240659. [Go to]
Further Reading

S. Milius. Gut microbes may put barrier between species. Science News Online. Posted online July 2, 2013. [Go to]

J. Raloff. Nurturing our microbes. Science News. Vol. 173, March 1, 2008, p. 138. [Go to]

S. Milius. Why play dead? Science News. Vol. 170, Oct. 28, 2006, p. 280. [Go to]

Sometimes it takes guts, or rather microbes in the guts, to make a species.

Genes are, of course, important. But the live-in microorganisms of jewel wasps play such an important role in keeping species separate that changing gut microbes can also change whether cross-species offspring live or die, Vanderbilt University researchers report July 18 in Science.

The paper gives more details of Nasonia wasp experiments reported at the Evolution conference in Utah last month (SN Online: 7/2/13). In the study, authors Robert Brucker and Seth Bordenstein revisited the known problem of doomed male offspring from crosses between N. vitripennis and N. giraulti wasps. The scientists showed that gut microbes may play a crucial role in keeping the two species separate.

Biologists tracing how organisms separate into new species traditionally focus on genes, Brucker says. But an organism, be it a human or monkeyflower or wasp, actually lives as a community containing billions of microorganisms with their own genes and cells. The microbial community may be an overlooked force in shaping how an organism evolves, Brucker and Bordenstein propose.

Their experiments roused excitement at the meeting, but not everyone is willing to treat organism-plus-microorganism as a unit for evolution. Evolutionary biologist Jürgen Gadau of Arizona State University in Tempe also studies Nasonia species but considers the microbes as just an important part of the wasps’ environment.  


          The Crypto Show: Kevin McKernan Of Medicinal Genomics, David & Nuno Martin Of Power Ledger        

On tonight's episode of "The Crypto Show," we talk to Kevin McKernan of Medicinal Genomics about some of their upcoming product rollouts. We also discuss the upcoming Raise Awareness Cruise for MAPS, the MDMA Assisted Psychotherapy group that focuses primarily on helping those with PTSD using MDMA. We also discuss the psychotherapeutic benefits of cannabis and psylocibin.

In the second hour we talk to Nuno and Dave, Chief Technology Officer and Managing Director, respectively, of Power Ledger, at https://powerledger.io. Power Ledger is a company that allows peer-to-peer buying and selling of power using blockchain technology, eliminating the power-industry middlemen. There is so much more to it though, so check out the show!Use crypto20 as coupon code for http://100xinvestors.com for your discount to the Blockchain Investors Summit.

Sponsored by: Dash, CryptoCompare and Defense Distributed

Links

https://www.amazon.com/dp/1119365597/ref=cm_sw_r_sms_c_api_IQPczbQHWJKP8

TheCryptoShow

FreeRoss

Social Media

The Crypto Show on Facebook

@TheCryptoShow

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@the_crypto_show instagram

The Crypto Show YouTube

Tip with Crypto

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LTBC: 1CevFxMT6srBtTkWx2qrNaJmjtgxbo7pBA,ETH: 0x10cfd6916832566e82b3ab38cc6741dfd7e6164fo


          Top searches (31/Dec/2016) Part27        
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          Top searches (31/Dec/2016) Part28        
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          CRISPRcon, Aug 16        
CRISPRcon will be held in Stanley Hall on August 16–17. Hosted by the Innovative Genomics Institute and other partners, this special event will be open to the public, and non-scientists are encouraged to attend.

The goal of this event is to bring together a broad selection of expected and unexpected voices to discuss the future of genome editing technology across all applications. Through keynotes, panels, interactive discussions, and networking opportunities, CRISPRcon will create a unique forum in which everyone with a stake in CRISPR can share their ideas, ask and answer questions, and make sure that their voices are heard.

Full details are available on the event website.
          Re-writing Genomes: A New Era in Genome Engineering, Aug 18        
In this fifth annual event, leading experts in genomics and molecular biology will explore how genome editing technologies are transforming basic research and biomedical engineering. The event is free and open to the public, but space is limited.

Click here to add your email address to the event mailing list -- we'll send you a message when registration opens in July.

(NOTE: INCLUSION ON THIS LIST IS NOT THE SAME AS EVENT REGISTRATION. YOU MUST STILL REGISTER FOR THE SYMPOSIUM ONCE REGISTRATION OPENS.)

Organizers
Dirk Hockemeyer, UC Berkeley
Jennifer Doudna, UC Berkeley, HHMI

Confirmed speakers
Andrea Crisanti, Imperial College London
Jennifer Doudna, UC Berkeley, HHMI
David Fidock, Columbia University Medical Center
Dirk Hockemeyer, UC Berkeley
J. Keith Joung, Massachusetts General Hospital
Joshua Modell, The Rockefeller University
Eric Olson, University of Texas
Leslie Vosshall, The Rockefeller University
Mark Walters, UCSF/Oakland Children's Hospital
Blake Wiedenheft, Montana State University
          Dalton Conley on the Use of Genomic Biology in Sociology        
Office Hours is back for fall semester! We welcome new producer Matthew Aguilar-Champeau, whose soundscaping includes a musical refresh courtesy of The Custodian of Records. Hosts Sarah Catherine-Billups and Caty Taborda kick things off with Princeton professor Dalton Conley, author of Being Black, Living in the Red and the popular sociology textbook You May Ask Yourself. Their conversation pries into the sometimes controversial, but always […]
          Microsoft’s Accidental Abolish-IP Advert        
Microsoft's reaction to kinect hacking is an accidental advert for abolishing IP
Read more ›

          Thought-Bubbles about Abundance        
Thought bubbles about abundance.
Read more ›

          The Abundance-Machine That Eats Everything        
Forebodings about abundance.
Read more ›

          Genomic Data Commons heralds new era of data sharing for cancer research        
The Genomic Data Commons, a next-generation platform that enables unprecedented data access, analysis and sharing for cancer research, publicly launched at the University of Chicago on June 6, opening the door to discoveries for this complex set of diseases. The Genomic Data Commons went live with approximately 4.1 petabytes of data from National Cancer Institute-supported […]
          Barry Aprison named 2015 AAAS fellow –        
Barry Aprison, PhD, a senior lecturer in the Biological Sciences Collegiate Division and education and outreach director for the Institute for Genomics and Systems Biology has been named fellow of the American Association for the Advancement of Science (AAAS) for his scientifically or socially distinguished efforts to advance science or its applications.
          Bryce Van de Geijn Thesis Defense        
Bryce van de Geijin (Jonathan Pritchard Lab) successfully defended his thesis on November 20, 2015  – “Genomic tools for robust quantitative trait locus discovery and interpretation.”   Bryce has accepted a Postdoctoral position at Harvard University and will be working in the Alkes Price lab. Congratulations Bryce!
          Cichlids, species and trees        
Lake Malawi, in south-eastern Africa, is famous for its large diversity of cichlid fishes. Indeed, it sometimes seems to have more biologists studying these fish than there are actual fish in the lake, even though there are allegedly hundreds of cichlid fish species in that lake. In this sense, it is somewhat similar to Lake Baikal, in southern Siberia, home to the sole species of freshwater seals.

The cichlid biologists are interested in describing the extensive fish diversity, pondering its origin, and thus its contribution to the study of speciation. After all, we are talking about what is usually claimed to be "the most extensive recent vertebrate adaptive radiation". So, we are talking here as much about population genetics as we are about ichthyology.


Inevitably, the genome biologists have been spotted in the vicinity of the lake; and we now have a preliminary report from them:
Milan Malinsky, Hannes Svardal, Alexandra M. Tyers, Eric A. Miska, Martin J. Genner, George F. Turner, Richard Durbin (2017) Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. BioRxiv 143859.
These authors summarize the situation like this:
We characterize [the] genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times.
The last sentence seems to be somewhat disingenuous. How could a single tree be expected to describe this scale of biodiversity? Any rapid radiation of diversity is unlikely to be completely tree-like. The increase in diversity can be modeled as a tree, sure, but it is very unlikely that there will be instant separation of the taxa, and so the tree model will be ignoring a large part of the evolutionary action. There will, for example, be ongoing introgression between the diverging taxa, as well as hybridization due to incomplete breeding barriers. These avenues for gene flow can best be modeled as a network, not a tree.

The issue here is that the authors write the paper solely from the perspective of an expected phylogenetic tree, and then feel compelled to explain why they do  not produce such a tree. Indeed, the authors present their paper as a study of "violations of the species tree concept".

For data analysis, they proceed as follows:
To obtain a first estimate of between-species relationships we divided the genome into 2543 non-overlapping windows, each comprising 8000 SNPs (average size: 274kb), and constructed a Maximum Likelihood (ML) phylogeny separately for each window, obtaining trees with 2542 different topologies.
So, only two sequence blocks produced the same tree, presumably by random chance. An example "tree" for 12 OTUs is shown in the diagram. It superimposes a possible mitochondrial trees on a summary of the "genome tree".

Example phylogeny from Malinsky (2012)

The authors continue:
The fact that we are using over 25 million variable sites suggests these differences are not due to sampling noise, but reflect conflicting biological signals in the data. For example, gene flow after the initial separation of species can distort the overall phylogeny and lead to intermediate placement of admixed taxa in the tree topology.
Note that gene flow is seen to "distort" the phylogeny rather than being an integral part of it. In this case, "phylogeny" apparently refers solely to the diversification part evolutionary history, rather than to the whole history.

The ultimate questions from this paper are: "what is a species concept?", and "what is a species tree?". The authors write a lot about species and trees, and yet their data provide very clear evidence that both "species" and "tree" are very restrictive concepts for studying the cichlids of Lake Malawi.

Coincidentally, another recent paper tackles the same problems:
Britta S. Meyer, Michael Matschiner, Walter Salzburger (2017) Disentangling incomplete lineage sorting and introgression to refine species-tree estimates for Lake Tanganyika cichlid fishes. Systematic Biology 66: 531-550.
The authors describe their work, on the same fish group but in a lake further north-west, as follows:
Because of the rapid lineage formation in these groups, and occasional gene flow between the participating species, it is often difficult to reconstruct the phylogenetic history of species that underwent an adaptive radiation. In this study, we present a novel approach for species-tree estimation in rapidly diversifying lineages, where introgression is known to occur, and apply it to a multimarker data set containing up to 16 specimens per species for a set of 45 species of East African cichlid fishes (522 individuals in total), with a main focus on the cichlid species flock of Lake Tanganyika. We first identified, using age distributions of most recent common ancestors in individual gene trees, those lineages in our data set that show strong signatures of past introgression ... We then applied the multispecies coalescent model to estimate the species tree of Lake Tanganyika cichlids, but excluded the lineages involved in these introgression events, as the multispecies coalescent model does not incorporate introgression. This resulted in a robust species tree.
Once again, phylogeny = species tree.


          A test case for phylogenetic methods and stemmatics: the Divine Comedy        

In a previous post I gave an outline of stemmatics, and briefly touched on the adoption and advantages of phylogenetic methods for textual criticism (On stemmatics and phylogenetic methods). Here I present the results of an empirical investigation I have been conducting, in which such methods are used to study some philological dilemmas of a cornerstone work in textual criticism, Dante Alighieri's Divine Comedy. I am reproducing parts of the text and the results of a paper still under review; the NEXUS file for this research is available on GitHub.


Before describing the analysis, I discuss the work and its tradition, as well as some of the open questions concerning its textual criticism. This should not only allow the main audience of this blog to understand (and perhaps question) my work, but it is also a way to familiarize you with the kind of research conducted in stemmatics. After all, the first step is the recensio, a deep review of all information that can be gathered about a work.

The Divine Comedy

The Divine Comedy is an Italian medieval poem, and one of the most successful and influential medieval works. It is written in a rigid structure that, when compared to other works, guaranteed it a certain resistance to copy errors, as most changes would be immediately evident. Composed of three canticas (Inferno, Purgatory, and Paradise), the first of its 100 cantos were written in 1306-07, with the work completed not long before the death of the author in 1321. Written mostly during Dante's exile from his home city, Florence (Tuscany), like many works of the time it was published as the author wrote it, and not only upon completion. In fact, it is even possible, while not proven, that the author changed some cantos and published revisions, thus being himself the source of unresolvable differences.

No original manuscript has survived, but scholarship has traced the development of the tradition from copies and historical research. The poem is one of the most copied works of the Middle Ages, with more than 600 known complete copies, besides 200 partial and fragmentary witnesses. For of comparison, there are around 80 copies of Chaucer's Canterbury Tales,which is itself a successful work by medieval standards

Commercial enterprises soon developed to attend the market demand of its success. In terms of geographical diffusion, quantitative data suggests that, before the Black Death that ravaged the city of Florence in 1348, scribal activity was more intense in Tuscany than in Northern Italy, where the author had died. Among the hypotheses for its textual evolution, the results of my investigation support the widespread hypothesis that Dante published his work with Florentine orthography in Northern Italy. That is, the first copies adopted Northern orthographic standards, which would then revert to Tuscan customs, with occasional misinterpretations, when the work found its way back to Florence. These essentials of the transmission must be considered when curating a critical edition, as the less numerous Northern manuscripts, albeit with an adapted orthography, can in general be assumed to be closer to the archetype (if there ever was one to speak of) than Florentine ones.

The tradition is characterized by intentional contamination, as the work soon became a focus of politics and grammar prescriptivism. Errors and contamination have already been demonstrated in the earliest securely dated manuscript, the Landiano of 1336 (cf. Shaw, 2011), and can be already identified in the first commentaries dating from the 1320s (such as in the one by Jacopo Alighieri, the author's son).

Critical studies

Here are some details about previous studies. I have included considerable stemmatic information, but I include a biological analogy to help make sense for non-experts.

The first critical editions date from the 19th century, but a stemmatic approach would only be advanced at the end of that century, by Michele Barbi. Facing the problem of applying Lachmann's method to a long text with a massive tradition, in 1891 Barbi proposed his list of around 400 loci (samples of the text), inviting scholars to contribute the readings in the manuscripts they had access to. His project, which intended to establish a complete genealogy without the need for a full collatio, had disappointing results, with only a handful of responses. Mario Casella would later (1921) conduct the first formal stemmatic study on the poem, grouping some older manuscripts in two families, α and β, of unequal number of witnesses but equal value for the emendatio. His two families are not rooted at a higher level, but he observed that they share errors supporting the hypothesis of a common ancestor, likely copied by a Northern scribe.

Casella's stemma, reproduced from Shaw (2011).

Forty years later, Giorgio Petrocchi proposed to overcome the large stemma by employing only witnesses dating from before the editorial activity of Giovanni Boccaccio, as his alterations and influence were considered to be too pervasive. Petrocchi defended a cut-off date of 1355 as being necessary for a stemmatic approach that would otherwise have been impossible, given the level of contamination of later copies. The restriction in the number of witnesses was contrasted by his expansion of the collatio to the entire text, criticizing Barbi's loci as subjective selections for which there was no proof of sufficiency.

Making use of analogies with biology, we may say that Barbi proposed to establish a tree from a reduced number of "proteins" for all possible "taxa". Casella considered this to be impracticable and, selecting a few representative "fossils", built a tree from a large number of phenotypic characteristics. Finally, Petrocchi produced a network while considering the entire "genome" for all "fossils" dated from before an event that, while well-supported in theory (we could compare its effects to a profound climate change), was nonetheless arbitrary.

Petrocchi's stemma, reproduced from Shaw (2011).

Questions about Petrocchi's methodology and assumptions were soon raised, particularly regarding the proclaimed influence of Boccaccio, without quantitative proofs either that his editions were as influential as asserted or that all later witnesses were superfluous for stemmatics. Later research focused on questioning his stemma. For example, the absence of consensus about the relationship between the Ash and Ham manuscripts, the supposedly weak demonstration of the polytomy of Mad, Rb, and Urb (the "Northern manuscripts"), and the dating of Gv (likely copied fifty to a hundred years after Petrocchi's assumption). Evidence was presented that Co, a key manuscript in his stemma, could not be an ancestor of Lau (its copyist was still active in the 15th century), and that Ga contained disjunctive errors not found in its supposed decedents. Abusing once more of the biological analogy, the dating of his "fossils" was in some cases plainly wrong.

Federico Sanguineti presented an alternative stemma in 2001, arguing that a rigorous application of stemmatics would evidence errors in Petrocchi. To that end, he decided to resurrect Barbi's loci and trace the first complete genealogy, without arbitrary and a priori decisions about the usefulness of the textual witnesses. Sanguineti defended the suggestion that, after this proper recensio, a small number of manuscripts (which he eventually set to seven) would be sufficient for emendation. His stemma, described as "optimistic in its elegance and minimalism" (Shaw 2011), resulted in a critical edition that heavily relied in a single manuscript, Urb, the only witness of his β family (as Rb was displaced from the proximity it had in Petrocchi's stemma, and Mad was excluded from the analysis). Keeping with the biological analogy, he proposed building a tree from an extremely reduced number of "proteins", but for all "taxa". In the end, however, the reduced number of "proteins" was considered only for seven "taxa", selected mostly due to their age.

Sanguineti's stemma, reproduced from Shaw (2011).

The edition of Sanguineti was attacked by critics, who confronted the limited number of manuscripts used in the emendatio, the position of Rb, the high value attributed to LauSC, and the unparalleled importance of Urb, all resulting in an unexpected Northern coloring to the language of a Florentine writer. Regarding his methodology, reviewers pointed out that stemmatic principles had not been followed strictly, as the elimination was not restricted to descripti, but extendied to branches that were considered to be too contaminated

The digital edition of Prue Shaw (2011) was developed as a project for phylogenetic testing of Sanguineti's assumptions. Her edition includes complete manuscript transcriptions, and the transcriptions include all of the layers of revision of each manuscript (original readings and corrections by later hands), and are complemented by high-quality reproductions of the manuscripts. After testing the validity of Sanguineti's method and stemma, Shaw concluded that his claims do not "stand up to close scrutiny", and that the entire edition is compromised, because Rb "is shown unequivocally to be a collaterale of Urb, and not a member of α as [Sanguineti] maintains".

Applying phylogenetic methods

With the goal of following and, to a large part, replicating Shaw (2011), I have analyzed signals of phylogenetic proximity for validating stemmatic hypotheses, produced both a computer-generated and a computer-assisted phylogeny (equivalent to a stemma), and evaluated the performance of suchphylogenies with methods of ancestral state reconstruction.

I wanted to investigate the proximity of witnesses and the statistical support for the published stemmas. After experiments with rooted graphs, I made a decision to use NeighborNets, in which splits are indicative of observed divergences and edge lengths are proportional to the observed differences. These unrooted split networks were preferable because they facilitated visual investigation, and also provided results for the subsequent steps. These involved exploring the topology and evaluating potential contaminations, guiding the elimination of taxa whose data would be redundant for establishing prior hypotheses on genealogical relationships. Analyses were conducted using all manuscript layers and critical editions, both with and without bootstrapping, thus obtaining results supported in terms of inferred trees as well as of character data.

NeighborNet of the manuscripts and revisions from my data, generated with SplitsTree
(Huson & Bryant 2006)

The analysis confirmed most of the conclusions of Shaw (2011) — there are no doubts about the proximity and distinctiveness of Ash and Ham, with Sanguineti's hypothesis (in which they are collaterals) better supported than Petrocchi's hypothesis (in which the first is an ancestor of the second). The proximity of Mart and Triv was confirmed; but the position of the ancestors postulated by Petrocchi and Sanguineti should be questioned in face of the signals they share with LauSC, perhaps because of contamination. The most important finding, in line with Shaw and in contrast with the fundamental assumption of Sanguineti, is the clear demonstration of the relationship between Rb and Urb.

The relationship analyses allowed the generation of trees for further evaluation. Despite the goal of a full Bayesian tree-inference, I discarded that option because, without a careful and demanding selection of priors, it would yield flawed results. As such, I made the decision to build trees using both stochastic inference and user design (ie. manually). This postponed more complex topology analyses for future research, but generated the structures needed by the subsequent investigation steps; both trees are included in the datafile.

The second tree (shown below), allowing polytomies and manually constructed by myself, tries to combine the findings of Petrocchi and Sanguineti by resolving their differences with the support of the relationship analyses. Using Petrocchi's edition as a gold standard, and considering only single hypothesis reconstructions, parsimonious ancestral state reconstruction agree with 9,016 characters (79.9%). When considering multiple hypotheses, instead, reconstructions agree with 10,226 characters (90.7%). Cases of disagreement were manually analyzed and, as expected, most resulted from readings supported by the tradition but refuted by Petrocchi on exegetic grounds.

My proposed tree for the manuscripts selected by Sanguineti,
generated with PhyD3 (Kreft et al., 2017).

This tree suggests that, in general, Petrocchi's network is better supported than the tree by Sanguineti, as phylogenetic principles lead us to expect — the first was built considering statistical properties and using all of available data, while the second relied in many intuitions and hypothesis never really tested. In particular, it supports the findings of Shaw and, as such, allows us to indicate the critical edition of Petrocchi as the best one. Even more important, however, it is a further evidence of the usefulness of phylogenetic methods, when appropriately used, in stemmatics.

References

Alagherii, Dantis (2001) Comedìa. Edited by Federico Sanguineti. Firenze: Edizioni del Galluzzo.

Alighieri, Dante (1994) La Commedia Secondo L’antica Vulgata: Introduzione. Edited by Giorgio Petrocchi. Opere di Dante Alighieri v. 1. Firenze: Le Lettere.

Huson, Daniel H.; Bryant, David (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267.

Inglese, Giorgio (2007) Inferno, Revisione del testo e commento. Roma: Carocci.

Kreft, Lukasz; Botzki, Alexander; Coppens, Frederik; Vandepoele, Klaas; Van Bel, Michiel (2017) PhyD3: a Phylogenetic Tree Viewer with Extended PhyloXML Support for Functional Genomics Data Visualization. BioRxiv. Doi: 10.1101/107276.

Leonardi, Anna M.C. (1991) Introduzione. In: La Divina Commedia, by Dante Alighieri. Milano: Arnoldo Mondadori Editore.

Shaw, Prue (2011) Commedia: a Digital Edition. Birmingham: Scholarly Digital Editions.

Trovato, Paolo (2016) Metodologia editoriale per la Commedia di Dante Alighieri. Ferrara. https://www.youtube.com/watch?v=BfKUOAR9PXA. Date of access: March 19, 2017.


          QBio Special Seminar: Hunting the wild microbe: Decoding microbial interactions from metagenomics to ecophysiology        
Elizabeth Wilbanks, Caltech
          Cooperation, conflict and the evolution of Darwinian individuality        
Megan McClean, Lewis-Sigler Inst for Integrative Genomics, Princeton U.
          Electrothermally-actuated SU8 Microgripper for Single-cell Manipulation        
Electrothermally Activated SU-8 Microgripper for Single Cell Manipulation The development of miniaturized systems for manipulating biological samples in solution has become a great technological challenge for the future of the rapidly growing area of genomics and proteomics. The use of microgrippers in those systems as the mechanical end-effectors that securely grasp and transport the micro […]
          Comment on Mark Tester by Tougher Crops for a Warmer World        
[...] Professor Mark Tester is a ARC Federation Fellow (Research Professor), member of the Executive Management Group of the Australian Centre for Plant Functional Genomics and Chair of the Research Committee in the School of Agriculture, Food & Wine, University of Adelaide. Tougher Crops for a Warmer World [ 45:16 ] Play Now | Play in Popup | Download podPressShowHidePlayer('1', 'http://www.media.adelaide.edu.au/researchtuesday/audio/Episode2-tougher_crops_for_a_warmer_world.mp3', 290, 24, 'false', 'http://media.adelaide.edu.au/opendays/images/video-placeholder-400px.jpg', 'Tougher Crops for a Warmer World', 'Professor Mark Tester');     Related Links [...]
          TRAC and MedGenome Licensing Agreement Aids Development of Novel Cancer Drugs        
Toronto Recombinant Antibody Centre (TRAC) has recently agreed to license patented oncology immunotherapy solution OncoPept by MedGenome, a provider of clinical genomics solutions for personalized healthcare. TRAC is based at the University of Toronto, Canada. The company will use this solution to develop potential biomarkers for their drug candidates proving useful against immune modulators to aid the treatment of various cancer types. The licensing agreement bodes well for a more elaborate collaboration between the two organizations, which can facilitate the development of powerful and cost-effective antibody drugs for the India pharmaceutical market. Identifying Patients Who Benefits Most from Immunotherapy Drugs The licensing agreement was announced at a symposium held at the Hilton Mumbai International Airport, India on July 20, 2017. The Symposium inaugurated by the Canadian Consul General in India was attended by pharmaceutical companies that included the stalwarts such as Glenmark Pharmaceuticals, Biocon, and Sun Pharmaceutical Ltd. The OncoPept platform will be used by several pharma companies in India to boost the efficacy of cancer therapeutics by identifying patients who can benefit the most from oncology immunotherapy drugs. In addition, the development of the platform will help select the right patients for the clinical trials. More Collaborations to Develop Cost-Effective Cancer Treatments The escalated cost of the cancer treatment is a key constraining factor limiting the development of effective therapies in an emerging market such as India. With this licensing and more collaborations expected to come between the players in the not-so-distant future, pharmaceutical companies can leverage the potential of the advanced platform to develop cost-effective treatments. The platform developed by TRAC has numerous screening technologies helpful in producing novel biologics. Incorporating the MedGenome’s genomics-based research and diagnostics, TRAC can consolidate its drug pipeline meant leading to the development of biomarkers and personalized therapies for cancer in India and other emerging markets. 

Original Post TRAC and MedGenome Licensing Agreement Aids Development of Novel Cancer Drugs source Twease
          Synthetic Genomic and ExxonMobil Joint Efforts Pave Way to Achievable Algae-based Renewable Energy        
A recent press release has announced that the partnership between ExxonMobil and Synthetic Genomics has led to the development of a modified strain of algae that is expected to bring the concept of algae-based energy a step closer to being a commercially viable source of alternate energy. Researchers have long projected that the only way that algae-based energy has a commercial future is a high content algae strain that can quickly grow is developed or discovered. Strain with Massive Rise in Oil Content Synthetic Genomic’s efforts in the area of cell engineering have managed to enhance the oil content of a high-content algae from 20 percent to 40 percent. An official report related to this feat was published in the Nature Biotechnology journal. This discovery could help move the alternate energy source a step closer to mass market usage. Research to be Taken Ahead This milestone could also help researchers restore their hopes in synthetic biology and the immense potential that algae have as a source of renewable energy. Synthetic Genomics is looking forward to continue the work in this area with ExxonMobil to achieve the goal of finding a strain of algae that can be an effective source of alternative energy. James Flatt, CTO at Synthetic Genomics, had earlier dismissed the viewpoint that simple modification of the genome of an algae can help the field of biofuel reach the state of commercial viability. Despite this, the laboratory and ExxonMobil reworked their agreement for the phase II research in the area with a fresh outlook focusing on basic science instead of creating a commercially viable research result. 

Original Post Synthetic Genomic and ExxonMobil Joint Efforts Pave Way to Achievable Algae-based Renewable Energy source Twease
          Bioinformatics: a Big Boon to the Field of Biological Investigation        
Bioinformatics refers to an interdisciplinary approach to store, retrieve, organize, and analyze biological and genetic data. A major part of this field comprises developing software tools to generate and process useful biological data. Bioinformatics is not to be confused with biological computation. While bioinformatics simply makes use of computers for the better understanding of biology can its related concepts, biological computation refers to the subfield of computer engineering that seeks to build biological computers by using biology and bioengineering concepts.  Bioinformatics is, however, much similar to computational biology, only the scale of application and study differs - bioinformatics studies biological data on a molecular scale with keen attention to details while computational biology studies biological data by building large-scale theoretical models of biological systems and studying them with an abstract view to expand our knowledge about them. Bioinformatics makes use of various laws of computer science, engineering, applied math and statistics to conceptualize biology in terms of bio-molecules (RNAs, DNAs) and process the resulting data in various ways in attempt to decode the code of life. The use of computers has made the process of reading complex biological data much faster and efficient than before. Huge databases and information systems are used to store and retrieve data; analytical algorithms in soft computing, artificial intelligence, data mining, image processing, etc. are used to analyze data; algorithms in turn depend on theoretical principles of statistics, applied and discrete mathematics, system theory and control theory. As such, bioinformatics uses a good mix of many fundamental principles as well as many applied theories and sciences to manage biological data. This field, which was originally developed for the analysis of biological sequences, has now grown to encompass a wide range of areas such as genomics, gene expression, and structural biology, allowing greater depth and breadth to biological investigations. This has essentially provided the opportunity to study individual systems in details with the ones that are related to reveal the similar traits between some systems and underline some unusual features, if any, which are unique to some. 

Original Post Bioinformatics: a Big Boon to the Field of Biological Investigation source Twease
          Metabolomics Market Driven by Growing R&D in Pharmaceuticals Sector        
Metabolomics is the study of the set of metabolites present in a cell and tissue of an organism. It is used to identify and quantify the cellular metabolites by making use of refined analytical technologies, with the help of statistical and multi-variant methods. According to a report published by a market intelligent company called Transparency Market Research (TMR), the global metabolomics market is projected to expand at a CAGR of 17.1% between 2016 and 2024 and reach US$2,494.8 mn by 2024. Rising Demand for Personalized Medicines to Boost Metabolomics Market The global metabolomics market is expected to witness a significant growth due to the rising demand for personalized medicines across North America and Europe especially. The growing research and development activities across pharmaceuticals and biotechnology sectors are expected to push the global metabolomics market. Furthermore, the combination of various academic research institutes with the leading players operating in the market is expected to drive the metabolomics market. On the other hand, the market is expected to be restrained by the reluctance to adopt advanced technology by traditional professionals.  High Performance Liquid Chromatography (HPLC) Segment Accounts for Highest Share of Market The global metabolomics market is segmented on the basis of technique into separation technique, detection technique. The separation technique includes the study of capillary electrophoresis, ultra-performance liquid chromatography (UPLC), gas chromatography, and high performance liquid chromatography (HPLC). Of these, the high performance liquid chromatography (HPLC) segment accounted for the largest share of the metabolomics market by technique.  The metabolomics market is segmented on the basis of drug assessment, biomarker discoveries, nutrigenomics, clinical toxicology, and others. The market is dominated by the presence of leading players such as Thermo Fisher Scientific, Inc., Biocrates Life Sciences AG, Shimadzu Corporation, and Human Metabolome Technologies, Inc. among others.

Original Post Metabolomics Market Driven by Growing R&D in Pharmaceuticals Sector source Twease
          A Fungus Threatens Chocolate Industry        
Chocolate production might get hit soon if a fungus has its way. According to scientists, a fungus that is impacting the cacao pods could be cloning itself rather than sexually reproducing. The fungus leads to frosty pod rot that can decrease the cacao plantations. The fungus, known as Moniliophthora roreri, is suspected to clone itself. Earlier, researchers and cacao producers were of the opinion that the fungus was reproducing sexually as it belongs to the group of fungi that produces mushrooms.  Frosty Cacao Pod Rot Caused by a Fungus That Might be Cloning Cocoa is one of the major crops produced by small farms. Volatility in the prices of cocoa makes it risky for the farm owners to invest in fungicides. The cocoa producers usually monitor their crop for the symptoms of frosty pod rot. Once detected, they bury the pods that show white dusting or dark lesions. In the last 60 years, the fungal disease has spread due to the accidental transportation of infected pods. Across some of the areas, frosty pod rot has decimated the cocoa yields by 100%. This has led cocoa producers to abandon their plantations. Researchers are taking special interest in the growth of this fungus to find out a remedy for the fungal infection in cacao pods. In the recent study, researchers have studied the genomics and population genetics of the fungus. The fungus is unusual as it might be cloning itself. Further studies on this fungus are expected to be economically and biologically valuable to reduce the disease’s damage to cocoa production. According to Jorge Diaz-Valderrama, a doctoral student at the Purdue University, biochemical components are being identified to control frosty pod rot.

Original Post A Fungus Threatens Chocolate Industry source Twease
          Biochips Market to Grow Due to Extensive Use of Biochips in Medical Diagnostics         
Biochips are tiny integrated devices that are used to monitor, perform diagnostics or help in research and development for biological and biochemical reactions. Biochips are increasingly adopted in the medical field owing to its distinctive intelligence, efficiency in terms of speed and parallelism, as well as providing health information or diagnostics at a relatively lower price. Biochips are used to identify pollutants, gene sequence, biochemical constituents, and airborne toxins.  Growth in Biochips Market due to its Various Applications: The Biochips market is flourishing all over the world owing to its innumerable applications in the fields of drug screening, genomics and proteomics, research applications, and molecular diagnostics. Biochips are used for high speed diagnostics of multiple diseases such as cancer, TB, HIV and bird flu, thus driving the market for biochips. Additionally the increasing healthcare awareness among people and increase in the government funding is also set to boost the market for biochips in the coming years. Increasing R&D investment along with outsourcing of pharmaceuticals are likely to boost the market in the Asia region. North America Dominates the Global Biochips Market A growing number of geriatric population in the North America region along with the broad technical applications of biochips has led to the dominance of the region in the global market for biochips. Asia followed by Europe is anticipated to show a high growth in the coming five years in the global biochips market. Availability of Alternative Technologies Challenging the Biochips Market Biochips technology is relatively new and thus there is limited awareness and a lack of technical knowledge regarding biochips. This is one of the challenges that the biochips market is currently facing. Other restraining factors include, lower adoption due to high cost, and availability of alternative technologies in the market.

Original Post Biochips Market to Grow Due to Extensive Use of Biochips in Medical Diagnostics source Twease
          Beijing’s Biomarker Technologies Corp purchases Genomics System        
California based BioNano Genomics announced on Wednesday that Beijing based biochemical company Biomarker Technologies Corporation has purchased an Irys System. Biomarker picked the platform by BioNano in order to allow a more comprehensive exploration of the structural variation of genomics and to improve de novo genome assemblies meant for different animal and plant species. These include those species that bear no reference today. The Irys system relies on its high throughput IrysChip and is the perfect discovery tool for structural variation since it can detect different types of SVs in just one run. Moreover, it can also allow accurate and rapid de novo genome assembly. Chief executive officer of Biomarker Mr Hongkun Zheng said that the company plans to join hands with BioNano in order to explore the fields of clinical research, life science, and applications service in a more in depth manner. The company is greatly impressed by the novel capabilities of the Irys system that can efficiently detect complex structural variations and largely enhance the quality of diploid genome assembly. This was featured in the Nature Method and Nature Genetics papers published over the past few weeks.  Mr Hongkun Zheng further said that the one of the goals of Biomarker Technologies is to investigate the biology that lies behind genomics. The company has been in search of a path that will enable the discovery of large and complex SVs that are not detected as easily by traditional methods such as NGS, DNA Arrays, and other platforms. The introduction of the Irys system will now allow the company to be able to deliver on the capability to witness the complexities of genomes of the population at large. Chief scientific officer and founder of BioNano Genomics Han Cao, Ph.D., said that the Irys System allows researchers to detect structural information in a rapid and accurate manner. This can be done over long range distances with the least amount of alteration during the course of sample preparation. 

Original Post Beijing’s Biomarker Technologies Corp purchases Genomics System source Twease
          Inching Toward Health IT Interoperability – #HITsm Chat Topic        
We’re excited to share the topic and questions for this week’s #HITsm chat happening Friday, 8/4 at Noon ET (9 AM PT). This week’s chat will be hosted by Alan Portela (@AlanWPortela) from Airstrip on the topic of “Inching Toward Health IT Interoperability.”

To some it may seem as though ‘interoperability’ is a stale health IT buzzword, but nothing could be further from the truth. Why? Because interoperability still isn’t a reality.
Data is digital, but not readily available; data exists in EHRs, but isn’t aggregated and shared in a way that makes sense for clinicians. In addition, precision medicine relies upon the ability to collect real time data from medical devices at the moment of care – physiologic phenotypes, genomic data, and the like. Precision medicine fundamentally depends on data to make unique diagnosis/care plans for individuals or populations. That cannot happen easily or effectively without interoperability.
Health IT could play a significant role in addressing more serious health issues, but a lack of interoperability and access holds us back. If we want precision medicine, then we need to recognize that interoperability is a must.
Questions we will explore in this week’s #HITsm chat include:
T1: Where have you seen the most success in health IT interoperability? #HITsm
T2: What have been your largest barriers to health ...Read more
          A Hospital CIO Perspective on Precision Medicine        
#Paid content sponsored by Intel.
In this video interview, I talk with David Chou, Vice President, Chief Information and Digital Officer with Kansas City, Missouri-based Children’s Mercy Hospital. In addition to his work at Children’s Mercy, he helps healthcare organizations transform themselves into digital enterprises.
Chou previously served as a healthcare technology advisor with law firm Balch & Bingham and Chief Information Officer with the University of Mississippi Medical Center. He also worked with the Cleveland Clinic to build a flagship hospital in Abu Dhabi, as well as working in for-profit healthcare organizations in California.
Precision Medicine and Genomic Medicine are important topics for every hospital CIO to understand. In my interview with David Chou, he provides the hospital CIO perspective on these topics and offers insights into what a hospital organization should be doing to take part in and be prepared for precision medicine and genomic medicine.
Here are the questions I asked him, if you’d like to skip to a specific topic in the video or check out the full video interview embedded below:

What’s the CIO’s perspective on precision medicine and genomics?
What do you need to do to prepare your organization for the shift to precision medicine?
What are some examples of where precision medicine-based care is already a reality?
Who should lead precision ...Read more
          Tute Genomics raises $2.3M for genome analytics platform        

Tute Genomics says it has developed a comprehensive cloud-based genome analytics platform that lets clinicians and researchers identify disease genes and biomarkers in complex genome sequencing data.


          Omicia hopes to boil down genomic big data into more useful information, raises $6.8M        

As we collect more and more genetic data, somebody’s got to do something with all that information. Omicia has a system for analyzing human genome sequences, and that might be just what the doctor ordered. Apparently investors agree: Omicia has picked up a $6.8 million series A led by Artis Ventures. Other investors include Buchanan […]


          Yuri Milner is betting big on genetics, pouring millions into GenapSys        

"What we are developing at GenapSys will enable the genomic revolution not only for healthcare, but for a wide range of applications," said Dr. Hesaam Esfandyarpour, GenapSys founder and chief executive.


          The personalized medicine revolution is almost here        

Genomics data is about to change the way doctors discover and treat disease -- but there are some significant obstacles standing in the way.


          Genomics startup gets $3M to usher in new era of ‘personalized medicine’        

The cost of sequencing the human genome has plummeted. But how will this benefit doctors and patients?


          Trade barriers won’t slow China in the genomics race; we need to out-innovate        

Attempts to regulate or restrict the export of American biotechnology are likely to backfire and hurt American competitiveness.


          Genomics field gets a boost with rare-cancer breakthrough        

A new cancer discovery puts the emerging field of genomics on the map, may speed up the drug approval process, and de-risks groundbreaking research for venture-funded biotech companies.


          A VC’s take on the Genomic Age        

Mohr Davidow Ventures partner Bill Ericson, who helped fund high-speed genome-sequencer Pacific Biosciences, is a big believer in the emerging Age of Genomics and its potential to transform medicine, health insurance and our understanding of ourselves. Check out my recent Q&A with the venture capitalist over at VentureBeat Life Sciences for a conversation that also […]


          Q&A with MDV’s Bill Ericson: On PacBio’s origin, why Gattaca isn’t our future, and throwing out your statins        

Bill Ericson doesn’t see much cause for pessimism about the dawning Genomic Age. The Mohr Davidow Ventures partner, who’s helped resuscitate the firm’s life-science practice since he came aboard in 2000, believes the widespread dissemination of genetic information will be a virtually unalloyed good, opening up a wealth of opportunities for more effective medicine, lower […]


          Life sciences briefing: Wednesday, Sept. 12, 2007        

Featured companies: Mawell, OpGen, Vital Therapeutics Optical genome-mapper OpGen raises $23.6M in a restart — OpGen, a Madison, Wisc., biotech developing a genomic test for identifying disease-causing microbes, raised $23.6 million in what the company is billing as a first funding round. In fact, however, the funding is more of a restart for the company, […]


          Powstanie ośrodek sekwencjonowania genomu ludzkiego?        
Firma Central Europe Genomics Center (CEGC), w której Inno-Gene, giełdowy producent testów DNA, ma 26,5 proc. udziałów, podpisała umowę inwestycyjną z Rubicon Partners Corporate Finance. Celem jest dofinansowanie CEGC na 30 mln zł., które mają zostać przeznaczone na utworzenie ośrodka sekwencjonowania genomu ludzkiego.
          Inno-Gene zwiększa zaangażowanie w spółce CEGC        
Inno-Gene zwiększył do 26,5 proc. swoje zaangażowanie w spółce Central Europe Genomics Centre (CEGC) posiadającej wyłączność w Polsce na technologię sekwencjonowania całogenomowego DNA w oparciu o urządzenie X-Ten.
          Helping People On A Path to Better Health with CVS @Retail        

“Helping people on their path to better health” is the mission-mantra of CVS Health. Re-branded from its previous identity as CVS/pharmacy, the organization convened a Health Innovation Summit with its vendor partners whose products fill the front-of-store shelves to empower, inspire and support consumers to manage health and wellness for themselves and their families. I was grateful for the opportunity to provide the first talk for the day, setting the context for the evolving retail health/care landscape with the consumer at the center. The consumer is, at any point in a 24-hour day: a person wearing many hats (a worker, a parent, a social animal, a community volunteer, a spiritual being); a patient, sometimes; and, increasingly, a payor, bearing more costs for healthcare. Steve Laughlin who leads IBM’s global consumer distribution effort, talked about the growing role of data in retail, and how the company’s cognitive computing and analytics engines can work with retailers to anticipate emerging epidemics and health trends in communities. Key retail trends to watch for are direct-to-consumer, hyper-personalization, re-imagined store formats, and new business models. “Just doing efficiency” doesn’t work in retail anymore; the sector must re-build the sort of intimacy it once had with customers when we purchased meat from the butcher, hand-picked and pinched produce at the green grocer’s, and worked across the counter with the department store make-up consultant for best advice on skin care. “The last best experience anyone has anywhere becomes their expectation everywhere,” Steve cautioned, asserting the importance of customer experience in retail. This is highly relevant for health/care. Helena Foulkes, President CVS Pharmacy, shared some of the company’s latest innovation news to address consumers’ retail pain points. Many learnings are emerging from the CVS digital learning lab based in Boston. One new initiative is CVS Pay, which addresses the challenge for a consumer whose family may have several people filling prescriptions at the same time. The company developed technology to consolidate all of these separate patient transactions onto one bar code requiring a single swipe at the point of purchase. Another project, CVS curbside, is based on the scenario of Mom or Dad driving home from work, tired or stressed with kids in the back seat of the car. Mom/Dad needs to pick up a few items at the store without getting out of the car, so CVS will provide curbside delivery with underlying technology that knows when the consumer is driving up to the store. This concierge-style approach was discussed later in the day by Paula Winkel of Kimberly-Clark, making the case for Boomer healthcare that’s served up with a high degree of customer service. Google’s health leader, Ryan Olahan, covered the “10x Mindset:” how companies need to think and go beyond incremental goal-setting to truly innovate health and healthcare (THINK: the Big Hairy Audacious Goal). 40% of Google Ventures funding is going toward healthcare, so the company continues to have a strong focus in the sector. One in 20 Google searches is health-related, Olahan shared, and now that 86% of consumers do health information searches on Google, a growing cadre of people are looking for good (let’s call it evidence-based) health content on YouTube. There can be 2 million views of a teenager talking about her experience with acne treatments, but for scientific content, not nearly so many. Olahan, a father himself, shared interesting data showing curves of search frequencies for “baby crying” and “baby formula.” Interestingly, at 4 am, Ryan noted, moms aren’t looking for information about formula but for how to ease a baby’s cries. This is an opportunity for health ecosystem players in the “Mom and baby business” to provide helpful advice in that targeted, lonely early am time-frame when a parent can feel quite alone, frustrated and worried. Under Armour’s first product was a compression garment, launched over 20 years ago. Since then, the company has been morphing from an athletic garment manufacturer to an organization committed to supporting a consumer to be the best athlete they can be. The brand’s mission is, according to Chris MacAuley, VP of Connected Fitness, “To make all athletes better through passion, design, and the relentless pursuit of innovation.” Chris played a wonderful video featuring some of UA’s history, focusing first on its Baltimore Harbor HQ and incorporating a clip of Bill Clinton waxing lyrically, “Baltimore’s great shining jewel of a company is Under Armour.” The company has played an important and pivotal role in Baltimore’s economic development, bringing jobs back to the city. “We’re not going anywhere,” a company leader asserts on the video, stating the UA’s commitment to Baltimore. [I will note that financial wellness, jobs, and a strong local economy help foster positive determinants of health for people in a community]. The company’s mantra among consumers is “I Will” or more specifically, “I Will What I Want.” As we were convening at an “Innovation Summit,” Chris explained that UA’s definitely of “innovation” is simple and practical: it’s the process of going from invention to adoption. When it comes to wearables, sustained adoption is a major challenge. So it’s impressive that UA’s community of 210 million registered users of its apps, logging 2.5 million workouts a day and countless food choices and recipe shares, makes it among the largest databases of healthy people on the planet – arguably the largest connected health and fitness community in the world, which makes its database extremely powerful. The scale is huge: the community has lost 200 million pounds to-date, and realizes an 88% success rate for weight loss among people who log for 7 days straight. The money quote here is Chris’s statement that UA’s is “community of people who share with us their greatest fears and vulnerabilities.” What underpins this is trust, which is a sine qua non for health engagement. Another innovation of interest to me and my health-everywhere ecosystem paradigm is UA’s work with Marriott, the hotel chain. UA has worked with Marriott’s Residence Inn hospitality brand to develop local running routes outside of the hotels to help travelers maintain healthy lifestyles while working on the road. I covered the health-hospitality convergence (aka “sports-pitality”) last week in Health Populi, and this Marriott/Residence Inn program is part of that market trend. Two panels discussed health innovations from consumer pharma, technology, and direct-to-consumer genomics companies, all of which are operating or undergoing consumer testing in the market. It was encouraging to see that each of these efforts had done their homework on consumer demands and design considerations, whether focused on helping people age with independence (such as the wearable watch, UnaliWear) or manage pain for greater mobility (which is the goal of the inspiring pioneer of BraceUnder). Bayer talked about value beyond the pill (thus, their development of the Aleve-branded TENS unit for pain), and the aforementioned Kimberly-Clark, addressing how Boomers can live with gusto using well-designed personal care products. Consumer health companies have been allocating greater shares of marketing budgets to digital channels, and Facebook is a go-to place for health among engaged patients. Aaron Calloway, Senior Client Partner at Facebook, detailed many tactics used by healthcare organizations on the platform, along with Instagram (which I pointed out in my talk as a well-used social network among consumers for health and wellness). The day’s content generated many conversations about partnering, experimenting, and risk-taking for the benefit of expanding health beyond healthcare legacy players. For CVS Health, it provided scores of ideas for innovative product categories, strategies, and plans. Health Populi’s Hot Points:  The necessity and importance of collaboration and partnering cannot be over-stated for building a health/care system that bakes in the social determinants of health. The U.S. does trauma and intensive sick care pretty well compared with other developed countries. Dealing with the chronic burden of noncommunicable diseases (NCDs) such as cardiovascular (heart), metabolic (diabetes), respiratory conditions (like COPD) and some cancers borne through lifestyle choices (such as lung) requires a takes-a-village approach to prevent the onset of disease and then address, early, the onset of NCDs. At the Summit, I learned about innovative collaborations across the pharmacy channel, over-the-counter medicines, and digital technologies both in terms of wearable tech and platforms (e.g., Facebook, Google, and IBM’s work with various retail partners). I used the Optum ad shown here as the last slide in my talk about the health/care ecosystem. Breaking down internal corporate silos, and partnering among different health care stakeholders with the consumer ruthlessly focused at the core of the partnership is the required approach. The smartest retail health players will be open to going deep and doubling down on this strategy, particularly those companies who will share and mash-up patient/consumer data for the ultimate benefit of that (opted-in) patient.  

The post Helping People On A Path to Better Health with CVS @Retail appeared first on HealthPopuli.com.


          Somatic and non somatic evolution        
Many ecologists study evolution of the non somatic kind. That is, evolution that happens as a consequence of mutations in the germ line of multicellular organisms during reproduction. The evolution of cancer is of the somatic kind. This means that it affects cells of the soma, the ones that are not transmitted to the offspring.

Some time ago I got this paper from Crespi and Summers (nicely enough, publicly available). I will probably talk about this paper, entitled Evolutionary biology of cancer (and presented to a readership of ecologists) some other time but I liked a table in which they compare somatic and non somatic evolution.

Phenotypic variation. In most ecosystems of multicellular organisms variation is attained through genetic recombination (sexual reproduction) and mutation. In a tumour we also have to consider also genomic instability (a hypothesis by which some individuals have a higher probability of mutation) and epigenetic alteration (the environment also affects the behaviour of cells in ways that could make tumour progression to cancer more or less likely).
Selection. In most ecosystems it means dealing better with competitors, avoiding predators, parasites and producing many fit successors. In a tumour means being good at competing for resources with other cells (tumour or otherwise), avoiding the immune system and coping with environmental signals designed to maintain homeostasis.
Drift. That is similar in both types of evolution.
Inheritance. In many cases that involves the transmission of genes from parents to offspring through sexual recombination. In tumours there is no sexual reproduction.
Result. In most ecosystems the result is adaptation across generations. In a tumour the end results is in many cases the death of the individual and thus of all the cells in the body, including the cancer cells.

I think that this is a quite interesting and useful comparison of evolution although I am not sure I agree with all the differences suggested. In my view the evolution in a tumour does not differ much from other types of evolution. For instance, epigenetic changes do play a role in other ecosystems asides from cancer. Genetic instability is not a source of variation, genetic mutations are (genetic instability just makes genetic mutations more likely). Also the fact that tumour cells reproduce asexually is not a big difference with more conventional ecosystems. At the end of the day most of the biomass of the planet is made of bacteria that reproduces asexually. What it is true is that as far as we know, the end result of cancer evolution is either the end of the cancer itself or the end of the individual that hosts the cancer and thus the end of the cancer cells. Thus the only way tumour cells have to be successful is to evolve in such a way that the life of the host is not threatened (you can call that tumour sustainable growth).
          The film “Machine of Human Dreams” – some comments by the human dreamer        


In which the primary subject of a recent documentary film rambles on a bit about the events the documentary covers, and some things that it leaves out...

These are amazing times for those of us who are passionate about AI and robotics. Finally, at ever so long last, the ideas and visions we've been talking about and working toward for decades, are getting embraced by the mainstream! Concepts that would get you laughed out of university departments or corporate research labs just 10 or 15 years ago, are now being adopted as research priorities by governments and major corporations. Believing that AIs with general intelligence at the human level and beyond may well get created during our lifetimes, no longer makes you a certifiable member of the lunatic fringe!

One practical consequence of this shift in the zeitgeist is that funding for advanced AI R&D is now less difficult to come by. It's still not easy – funding is always competitive, and the dynamics of various funding sources remains complex. But things are much better than they were a decade or two ago, and this shows not only in big-time funding events like Google buying Deep Mind for a half billion dollars or Elon Musk and friends soft-committing $1B to OpenAI, but also in smaller ways like the OpenCogproject I lead getting more donations and corporate backing. After a number of years of slow progress throttled by resource limitations, we are starting to move faster.

Another consequence of the increasing enthusiasm for AI is growing media attention. The number of calls and emails I get from journalists these days is remarkable. And this summer the second documentary film about my AI and robotics work is coming out – “Machine of Human Dreams”, by Roy Cohen and Roast Beef Productions.

The first film made about my work was Raj Dye's avant-garde documentary “Singularity or Bust”, which covered my collaboration with Hugo de Garis in China in 2009 (and is available for free now on YouTube). Raj's film won Best Documentary at the LA Film Festival of Hollywood, and I like it very much. The style is a bit home-movie-ish at times, but it works; the editing and direction are very thoughtful, and a certain slice of my life and work is captured with artistry and accuracy.

Machine of Human Dreams covers bits and pieces of my AI and robotics work in Hong Kong and Addis Ababa during the period 2013-2015. It also covers portions of my earlier life and career.

Not too surprisingly, I definitely recommend you to watch the film. I particularly like the parts of the movie covering my team's recent work in Hong Kong and Addis – I think these are excitingly shot and directed, and they show aspects of our recent robotics tinkering that there's no other way to get a visual look at. 

The footage of RoboSapien robots (that Ruiting and I brought from Hong Kong in our suitcases) dancing in the rugged streets of Addis Ababa packs a sociopolitical wallop along with the techno-pizazz … and David Hanson's Sophia robot, showcased near the end of the film, is just so frickin' beautiful and evocative.... 

The various futuristic discourses and diatribes the film captures me giving are mostly well selected, and get across my broad high-level vision for AGI fairly nicely. There's not much footage of me explaining the meat of my AI work, but then there are numerous YouTube videos of me giving such explanations already available, so anyone who cares can find such material.

Trying to cover so much stuff in just an hour or so, it's inevitable that the film leaves a bunch of important things out … and I have to admit that some of the choices Roy made regarding what to include and what (and who) to omit, were pretty different than the choices I would have made given all the footage he gathered of myself, my team, and my friends and family.  With this in mind, I have written this probably over-long blog post in order to comment on the events the film covers, and also to highlight some of the things the film leaves out, which I think are nonetheless fairly critical to understanding the events and individuals that the film presents.

So – my hope is that, for someone who has seen the film, this post will fill in some of the “missing links” and make the whole story clearer.  

If you haven't seen the film, there is probably still some useful and entertaining info in this post; but the choice of specific topics to discuss here is heavily driven by the various scenes shown in Machine of Human Dreams, so it will definitely make more sense if you've seen the movie. 

Also, I suppose that alongside their potential interest to AGI geeks, my comments here may also be of interest to anyone curious about the general nature of the complex relationship between documentary films and actual reality....

The Film Originates...

I first met Roy Cohen at the Global Future 2045 conference in New York in 2013, where David Hanson was planning to demonstrate one of his robots. The robot demo at the conference wound up not coming together for various logistical reasons, but David was there at the conference, and was there afterwards as well holed up in a hotel room getting his Philip K. Dick robot ready for a TV interview. Roy was trying to track down David, but David was busy fixing up his robot. But I had a little more free time. 

Roy seemed like a smart guy – he had a neuroscience background and a broad understanding of technology, and he was getting into film-making. He wanted to do a documentary project. I suggested he should make a documentary on the collaboration David Hanson and I were starting, aimed at applying my open-source OpenCog AGI software to control David's amazing humanoid robots.

We talked more and the concept grew on Roy. He scrabbled together some funding from Israel to do some preliminary shooting. He came to Hong Kong and got some footage of our robot lab; and he came to Ethiopia to film the team at iCog Labs, the AI/robotics development firm I co-founded there, that collaborates with OpenCog and Hanson Robotics. The preliminary footage he shot enabled him to gather enough funds to complete the film.

I liked the idea of Roy being a sort of “embedded video-journalist” in our project, popping up every now and then to gather footage of what our team was doing. Though him not being based in Hong Kong or Addis Ababa wasn't ideal – he didn't visit that often, and predictably enough, it seemed that the most interesting stuff happened when he wasn't around.

Production Progresses, and the Concept Drifts

As Roy's film project progressed, I noticed in our intermittent conversations that his vision of the movie was drifting a bit from what we had originally discussed. I had wanted him to focus on the progress of the technology, and on the international team making the progress happen. But he was gravitating more toward focusing on ME as a person – on making it more of a biographical film. This didn't interest me nearly so much, mostly because I was more interested to tell the world about our AGI work than about myself. 

But in any case, I liked Roy and was happy to support his project even as his vision drifted from what we'd originally discussed. He started asking me for access to various people in my family and from earlier parts of my career, and I sent emails putting him in touch. He ended up interviewing a sort of quasi-random sample of people from my past and present, including my mom and dad and kids, and my first wife (but not my second), and a couple of my AI collaborators from the late 1990s. There were also quite a few people I told him it was important for him to interview – if he was going to do the “dig into Ben's past life and work” thing – but he didn't, probably mostly for cost reasons (e.g. he ended up interviewing a bunch of people who lived near New York, and omitting folks who lived in other areas).

As 2015 advanced Roy seemed very eager to finish the film and get it launched. I tried to convince him to take a slightly slower pace, and keep filming through 2016. It seemed to me that in 2016 we were likely to get OpenCog to control David Hanson's robots in a really interesting way, and that this would make a great ending for his film. But he didn't want to wait – I suppose understandably, because after all his funds were limited, and the timing of research is hard to predict. What if he waited through 2016 and then the OpenCog-controlled Hanson robot got deferred till 2017?

Choices, choices, choices...

I didn't see any rough cuts of the film while it was in progress (except one very crude, early trailer) and I had a lot of other things going on in my life, so I didn't think about it often. Then in early 2016 I saw that the film was to be shown at the Sheffield Documentary Festival; and Roy sent me a DVD.

I liked a lot of what I saw. On the other hand, out of all the footage he'd gathered, many of the choices he'd made were not what I had expected.

Overall, I felt upon first viewing, his film portrayed me as a charismatic, utopian, somewhat don-Quixote-ish character, tirelessly pursuing a wild-eyed dream of benevolent superhuman AI, persistently and enthusiastically ignoring the world's repeated pushbacks. 

The Ben in the film keeps moving to some new location, launching a new AI project and not quite getting to the finish line, then moving somewhere new and trying again: New York, Hong Kong, Ethiopia....  He makes a few personal and business messes due to caring more about his AI dream than anything else. But ever optimistic, enthusiastic and visionary, he keeps on pushing. And finally, by the end of the movie, he has found a powerful, equally starry-eyed and brilliant collaborator in roboticist David Hanson. Together, they will keep on pushing – and maybe they'll even get there eventually!

This Ben-character in Machine of Human Dreams certainly has a lot truth about him....  And it's certainly understandable that, to make an hour-long movie about a 49 year old person's life and work, a lot of simplifications and short-cuts will be needed. Nevertheless, given that the guy in the film is a bunch of samples of ME, I couldn't help, when I viewed the film, reflecting on everything that was left out, and the patterns of inclusions and omissions.

Overall, I can't really judge the quality of Machine of Human Dreams as a film in any objective way, I'm obviously too close to it. What I do feel impelled to do, though – and will do in the rest of this post – is step through the key episodes that the movie covers, and explain briefly what elements and aspects of the real-life versions of these episodes the film leaves out (for reasons of time limitation and choice of emphasis).

The film is not entirely chronological, but in my remarks here I'm going to proceed mostly in chronological order. The film starts with a sort of wild ride through my current work in Hong Kong and various interviews with people who are working with me here. This part is evocative, and shows some intriguing stuff. Then after that the film gets semi-chronological and quasi-autobiographical, beginning with my childhood.

AGI as a Crazy Hippie Dream

I gave Roy access to my mom for the movie, and he used a nice chunk of the interview footage he gathered with her. Watching this part was rather moving for me; my mom is a truly good-hearted, sincere and compassionate human being, as well as extremely competent and intelligent and hard-working. Hearing her recount bits and pieces about my early childhood on film was cool! Indeed it was my mom, in my first 4 years before I started school, who got me started on science and math and philosophy and creative imaginative thinking generally.

One key omission in the film pops up here: my other parent. While the interview footage Roy gathered from my father Ted Goertzel didn't make it into the film, Ted was also extremely important to me in my formative years. Ted was a sociology prof at U. of Oregon and then (for about 40 years, until he recently retired) at Rutgers University, and it was he who got me started on critical and analytical thinking. Ted has also followed my research career quite closely, including co-authoring and co-editing with me various books and papers on the future and social implications of AGI.

After my birth and infancy in Brazil, I lived from age 1.5 to ago 7 in Eugene Oregon. This was the late 1960s and early 1970s and the place was rather wild and full of hippies at the time. Ever since I have considered myself some sort of quasi-hippie – though obviously I'm too geeky, too hard-working and have too much of a hard-edged punk-rock/New-Yorker aesthetic to really be a hippie in the classic sense. The part of Machine of Human Dreams dealing with my childhood makes much of the roots of my AGI aspirations in the dreamy-eyed utopian idealism of the 60s/70s era. This is fair enough. Changing the world was what the adults around me were all about in Eugene back then; and I absorbed from my parents and their friends the idea that utterly changing the world was a reasonable thing to do and probably the most valuable way to spend one's life. Until my mid-teens I was fairly optimistic about radically improving the world via education and social reform; but at a certain point I shifted my views and became convinced that extreme technological advance was the best path toward tremendous positive transformation.

The film symbolizes the 60s/70s era culture by showing a bunch of freaks banging on drums in a field somewhere or other. I don't remember ever seeing anything quite like that. I do remember a near-constant stream of funky bearded guys in torn jeans and long-haired women in loose dresses and beads, singing folk music and strumming guitars and smoking weed … and lots and lots of political demonstrations, holding up signs and chanting and so forth. That was a time when folks in the counterculture believed anything was possible. I still feel that way.


Thinking About Thinking Machines

After my childhood, the movie briefly treats my undergraduate career, interviewing two people who knew me in college: my girlfriend (later first wife) Gwen, and my old friend Ken Silverman (who later worked with me at Webmind).

Ken recounts how, back when we were 15-17 years old and in our first couple years at Simon's Rock Early College, we used to sit around for hours and scheme about creating thinking machines. Well yes we did. Many of the theory-of-mind ideas I later published in “The Hidden Pattern” were already in my head back then. And Ken had lots of his own interesting ideas too, though he always tended to come back to hardware-focused solutions to AI problems, whereas I was focused more on the philosophical or mathematical aspects.

An understandable omission here is: The other good friends I also mused about AI with back then. For example: my college friend Mike Duncan who is still a close friend and who, unlike Ken, is still collaborating with me on AI at this moment, working on applications of OpenCog to analyzing genomics data, and on designing an OpenCog-friendly motivational and emotional system for David Hanson's robots. 

Ken's view is valid and interesting, but Mike's view would have been interesting to show too, especially because I haven't worked with Ken since 2001, whereas Mike has seen the details of my AI thinking and practical work all the way from 1984 through 2016. But Roy didn't happen to interview Mike just because the logistics didn't work out – while Ken lives in New York, Mike lives in Florida and Roy didn't have budget to haul a crew down there just to talk to him.

The movie skips everything I did between 1985 and 1997 – i.e. my grad school at NYU and Temple University, and then my whole academic career, in which I was a professor in departments of mathematics, computer science and psychology in the US, New Zealand and Australia. This was the time period in which I turned my vague college inklings about AI and cognitive science into more fleshed-out conceptual/mathematical theories (though still with many ambiguities and not nearly enough details to guide software implementation in detail). I also made some valuable collaborators in this period, e.g. Dr. Matt Ikle' whom I met in 1993 when we were colleagues in the math department at the University of Nevada Las Vegas, and who later became a co-creator of OpenCog's probabilistic logic and attention allocation subsystems.

The Webmind Experience – and my path toward practicality

The film gives a fair bit of airtime to Webmind Inc., a company I co-founded with 4 others in 1997 and that grew to around 130 total employees before it crashed and burned (alongside a lot of other cool dot-com era companies) in early 2001. It features a fair bit of Lisa Pazer, who was a Webmind co-founder and Webmind's first CEO. Her family also invested some seed money in Webmind in the very early stages; and as the film alludes, we were briefly romantically involved prior to co-founding Webmind (though that aspect of our relationship never went that far and ended before the company was started).

Right after Webmind tanked in 2001, I wrote an essay called “Waking Up from the Economy of Dreams” about the experience. While that piece of writing feels naïve and off-target to me now in some ways, it does effectively summarize my state of mind and attitude on the topic at the time. In hindsight, knowing what I do now about practical software projects and the tech business, all of us in the Webmind leadership – including me, Lisa, Ken Silverman, our second CEO Andy Siciliano, my long-time AI collaborator Cassio Pennachin (who first worked with me at Webmind, and is still working with me today) – were incredibly naïve. Ken and Cassio and I were naïve about how to manage and plan a project of the complexity of the Webmind AI engine; Lisa and Andy were naïve about how to run a technology R&D company of this complexity … we were all smart and ambitious and sincerely trying to do great things, but none of us really knew what we were doing in the context in which we were trying to operate.

Certainly, as Lisa alludes in her interview in the film, I was quite unrealistic at that stage of my life in terms of project planning – I was way overoptimistic in terms of how much work it takes to turn conceptual/mathematical designs into working large-scale software systems. And the business side of the company was not blessed with any particular skill at realism either. Nevertheless, at certain points the company did come pretty close to a successful exit via acquisition. There are some not-that-different parallel universes in which we sold that company at the right time, and made ourselves wealthy and came out of the experience looking like business wizards.

After Webmind shut its doors, I turned largely back to theory, and started thinking hard about how to incorporate everything I'd learned from the 3 years of science and engineering we'd done at Webmind, in a new AGI software design. My main goal was to encompass all the key ideas and structures in the Webmind design in an alternative design that would be much smaller and simpler. Webmind had been a wild grab-bag of different AI algorithms, all acting on the same “weighted labeled hypergraph” knowledge store. My new objective was to reduce the set of AI algorithms to a much smaller set, and to engineer these algorithms so that they would work very closely together. I still thought one needed an integrative, multi-algorithm approach to capture the richness and diversity of human intelligence, but I realized one had to be less willy-nilly about it, and carefully sculpt a set of algorithms intended to help each other out of their ruts. Eventually I came to call this principle “cognitive synergy” and I formulated it in a mathematical way.

Out of this phase of theory work came the AGI design I called the “Novamente Cognition Engine”, which eventually (in 2008) got open-sourced and morphed into OpenCog, and into the AGI design described in my 2014 books Engineering General Intelligence (co-authored with Cassio Pennachin and Nil Geisweiller).

One major part of my professional life that the film omits is my career in narrow-AI consulting and application development. In parallel with trying to work out a better thinking machine design, in the period 2001-2011 I also worked on a wide variety of practical AI consulting projects. I was based in Washington DC most of this time, and worked on bioinformatics for the NIH and CDC, and also (indirectly via various other entities) for INSCOM (Army intelligence), NSA and the Air Force. Some of the military/intelligence oriented work was interesting and potentially important, e.g. we used some tools from OpenCog to create software predicting which Army staff are most likely to commit suicide.

My bioinformatics consulting work over the years has largely been tied in with another, perhaps more critical aspect of my life that the film passes over -- my work on the application of AI to biology, and in particular to understanding the genomics of longevity. Alongside questing to build thinking machine, I have also spent a fair number of mind-cycles thinking about how to use AI technology to help cure aging and radically prolong human life. Some of my investigations in this area have been fairly successful, including new discoveries into the genetic roots of Chronic Fatigue Syndrome, Alzheimers and Parkinsons. I also helped Genescient Inc. understand why their super-long-lived flies live so long, and design some valuable nutraceuticals based on my AI analytics results.

This applied-AI aspect of my career is not that sexy or exciting for the most part (though, OK, the use of AI-driven bioinformatics to push toward a cure of aging and a path to superlongevity is arguably not all THAT boring!). On the other hand, the film generally gives the impression that I keep struggling and failing at everything in spite of my big ambitions and vision and immense knowledge, etc. It is certainly true that I have failed to create human-level AGI so far. But in my consulting work I have succeeded at some simpler (but not that simple) things, which have in some cases been highly rewarding and useful in themselves.

At the start of Webmind I was writing a lot of software code, but gradually as my career progressed I drifted into a pattern of coding only occasionally, and doing more theoretical and management work. The core of OpenCog, back when it was the Novamente Cognition Engine, was originally written by Andre' Senna and Thiago Maia in Brazil, working closely with Cassio Pennachin. Since the creation of OpenCog in 2008, the two most important contributors have been Dr. Linas Vepstas (based in Austin) and Dr. Nil Geisweiller (based in France and Bulgaria). Those guys have worked wonders. Nil is probably the only guy on the planet to fully understand my AGI design on the philosophical and mathematical level, and ALSO know the OpenCog codebase very well on a software level. Linas brings tremendous practical experience and software chops as well as deep mathematical and AI insight. Roy interviewed both of them for the film but ended up not using the footage – understandable perhaps given the time constraints of the movie, but still a bit distressing to me since these two extraordinarily brilliant and dedicated guys are really the ones most responsible for making the actual OpenCog system work.


My Hong Kong AI Adventures

In 2011 I relocated from DC to Hong Kong. I had been sick of DC on the personal level for a long time, but had been “stuck” there due to having a (roughly) 50-50 custody sharing arrangement with my ex-wife, Gwen, for our 3 kids. But by 2011 our youngest, Scheherazade, was about to do a junior year of high school overseas, so it seemed the right time to shift somewhere more interesting.

Machine of Human Dreams interviews Gwen a fair bit, and even has her appearing to say (via splicing together of utterances she made in different contexts while being interviewed) that she filed for divorce from me because I was so obsessed with AGI and my work that I couldn't pay enough attention to other people. Well, OK, whatever – I mean, the actual story of our divorce was definitely a lot more complex and nasty than that and didn't have much to do with AGI, but whatever. In this particular case the simplifications of the movie are probably in everybody's best interest….

In terms of omissions, it felt a bit odd to me on a personal level that he included Gwen in the movie but barely mentioned our 3 kids, e.g. our oldest son Zarathustra who is now getting his MS in computer science and moving toward a career in AI himself. But even more so, it felt odd that my long-ago first wife Gwen was included but he omitted my second wife Izabela Lyon Freire and – yeesh! – my actual wife Ruiting, to whom I've been happily married for 6 years now.  Both Ruiting and Izabela are excellent AI researchers with significant contributions to OpenCog. Izabela helped design OpenCog's PLN probabilistic reasoning engine.  Ruiting helped create OpenCog's natural language processing and dialogue subsystems.

Overall, through the years, my AGI obsession has drawn me to brilliant, active-minded women who are fascinated by AGI and other scientific and intellectual topics -- though it's true that Gwen's interest in these topics diminished as our marriage went on, and she got more focused on religion and nutrition, which interest me less.  And whatever difficulties I've had with love relationships have had little directly to do with my AGI obsession and more to do with other personality factors.

Roy skipped interviewing Izabela for the film because he didn't want to travel to Brazil; Gwen, being in the DC area, was more convenient. He did interview Ruiting fairly extensively, but in the final film she just shows up for a few seconds, jokingly noting that she doesn't want to move to Ethiopia (though the truth is, while she prefers living the developed world, she is willing to relocate with me to Ethiopia for a while if that turns out to be the best thing for our AGI work).

As an aside, Raj Dye's film Singularity or Bust has some sweet footage of Ruiting and me interacting with a Nao robot, back before we got romantically involved --you can clearly see the early sparks of our relationship there, which is pretty cool from my point of view...

The budding love relationship with Ruiting – who lived in Xiamen at the time – was part of the reason I relocated to Hong Kong. Another part was that Cassio and I secured funding to start a machine learning based investment management company, Aidyia Limited – which finally started trading a small fund in early 2016. And finally, Gino Yu and I got some Hong Kong government research funding for an OpenCog project at Hong Kong Poly U, where Gino is a professor.

The film omits mention of Aidyia, but a long middle segment of the film focuses on some robotics prototyping work we were doing at the Poly U OpenCog Lab in 2014-2015. This part of the film captures some cool robot-lab work and social dynamics, yet also feels to me like one of the more oddly focused segments. While Roy was at Poly U filming, the OpenCog team there was preparing to show some small robots to some officials from the grant funding agency that was funding the project, and there was some nervousness about putting on a good show. Roy liked this energy and nervousness, and for a while he was considering to focus his whole film mainly on our push to make a good demonstration for the funding agency officials.

I argued with Roy long and hard about this, at the time – making the points that: a) this demonstration had no particularly profound meaning, as it pertained to a robotics prototyping project that was valuable but not really core to the OpenCog AGI initiative; b) the people involved in the robotics prototyping work at Poly U were not really the key players in the OpenCog project anyway. Eventually I did convince him that focusing on this funding agency demo would result in a very boring film – I dragged him (metaphorically) kicking and screaming to Hanson Robotics and convinced him to end the film with David's gorgeous robots.

Still, though, I seem not to have fully convinced him – because that funding agency demo still absorbs a chunk of the film that is quite disproportionate to its actual importance. Also, the film omits the outcome of the demo, probably because it was boring … in the end, the demo we gave to the officials was underwhelming but adequate, and after a bureacratic delay of a couple months we were given a passing grade and the research (and research funding) continued.

The film then shows a few staff leaving the project after the underwhelming demo, hinting not too subtly at a potential causal connection between that demo and any staff departures; but in fact no such causal connection existed. Staff turnover was very high on our Hong Kong Poly U OpenCog project, mostly because the grant funding we had didn't allow us to pay market salaries. And the researcher who the film shows quitting OpenCog and leaving Hong Kong, Aaron Nitzkin, is a great guy and a deep cognitive theorist, but actually contributed fairly little to OpenCog due to his lack of professional programming skills.

This brings us to a big omission in this section of the film -- its failure to note the deepest OpenCog work was being done all through that time period by Linas and Nil in the US and Europe, far away from and almost completely ignorant of the Hong Kong team's robot prototype demos.

Also, as a minor point, the film shows OpenCog software and robotics developer Mandeep Bhatia musing about potentially moving back to India; but while Mandeep likes to think about this periodically, in fact he's still here in Hong Kong, now working with me and the rest of the team on making OpenCog control Hanson robots.

One thing the film does depict very accurately is that I have had a fascinating and fantastic time doing AI and robotics development here in Hong Kong. With David Hanson's amazing robot heads, Mark Tilden's walking robot bodies (briefly discussed at the start of the film) and OpenCog intelligence, we have the potential to make the smart, emotional, physically able humanoid robots everyone expects from science fiction. Ultimately AGI will transcend the human form and the human mind. But as we walk along that path, robots with humanoid form will have an important role to play in shaping the emergence of AGI cognition, emotion and values, and in helping human society come to grips with the onset of ever more advanced AGI. Despite some peculiarities of focus, I think the Hong Kong footage in Machine of Human Dreams does get across some of these themes in a striking and visual way.


iCog Labs and the Ethiopian Singularity

The film briefly shows me in Ethiopia discussing AI at a university there, and demo-ing robots out in the street with a team of young Ethiopian programmers. The robots in the streets of Addis look splendidly incongruous; and Ethiopian writer and tech project manager Hruy Tsegaye gives a beautiful speech about the power of advanced tech to advance Africa.

The vague impression given in the movie is that, after things got tough in Hong Kong, I started roaming far and wide in search of somewhere new to go and push forward with AGI – and I was so adventurous and maybe desperate that I looked as far as wildest Africa! This is indeed poetically true, in that I am very interested in the notion of building a large AGI team in Ethiopia where the costs are low, the people are lovely and the food is delicions. On the other hand, the dynamics of my involvement with Ethiopia has been a bit different than the film suggests.

I co-founded iCog Labs – Ethiopia's first AI/robotics firm -- in 2013 together with Ethiopian roboticist Getnet Aseffa Gezaw and American investor Sander Olsen. The idea for iCog originated when I visited Getnet in Addis Ababa in 2012, after getting to know him via the Internet in 2011. OpenCog and Hanson Robotics have been outsourcing work to iCog since 2013, and iCog has also been helping me with various AI consulting projects. I have consistently been impressed with the intelligence and ambition of the young computer scientists and programmers of Ethiopia. I have a few times considered relocating to Addis to work full-time on growing iCog into the world's greatest AGI, robotics and bioinformatics research center -- but at the moment I have a lot of interesting stuff going on here in Hong Kong, so I'm just visiting iCog as often as I can find room for.

Dr. Hanson's Robo-Dreams

One of my bigger successes here in Hong Kong has been to facilitate my good friend Dr. David Hanson moving his company here! David was coming to Hong Kong periodically before I moved here, because he was getting some robots made across the border in Shenzhen. On one of his visits, I introduced him to some of my tech-scene contacts here, and these contacts ended up garnering him investment money for his company Hanson Robotics – which ultimately ended up in him and his family moving out here to start a new branch of the firm, Hanson Robotics Hong Kong.

Working with David has been an intriguing, exhilarating, and sometimes exhausting experience. While his focus is mainly on emotional and social robotics, he fully gets my AGI vision and my intended route toward it with OpenCog. He has been both a good friend and an able collaborator … the end bit of Machine of Human Dreams quite accurately depicts what I'm doing with Hanson Robotics these days (well, as of 2015 anyway). The footage Roy got of the first version of David's “Sophia” robot is strikingly beautiful. The new version of Sophia is even better.

Since the time Roy wrapped up shooting Machine of Human Dreams we already have made great progress connecting OpenCog to the Hanson robots, and at time of writing, it seems it should be a small integer number of months before we have the first fully OpenCog-controlled Hanson robot head. Over the next few years, I think the Hanson robots can be both an outstanding showcase for OpenCog AGI, and a practically valuable medium for supplying OpenCog systems with the perception, action and social/emotional interaction they need to learn and grow.


Intelligent Networks Spawning Intelligent Networks ...

One thing that my work with David Hanson and his team – with their background in art and theater – has given me a stronger sense for, is the powerful urge the human mind has to perceive and create narrative structures. At some deep level, our hearts, minds and brains really want to view things in “Hero's Journey” type terms – in terms of stories with a beginning, middle and end … in terms of individual protagonists meeting obstacles and overcoming them and growing in the process, and so forth. We often get ourselves into trouble by unconsciously imposing this structure in cases where it doesn't really exist, or plays at most a minor role.

The great biologist Michael Rose, whom I worked with at Genescient Corp. for a few years (mostly at a distance, but occasionally face to face), often railed against this tendency as it manifested itself in biologists. Biological systems, as he understands them, are highly complex networks with subtle nonlinear self-organizing dynamics. Most meaningful biological effects emerge from rich networks of causation spanning numerous biological systems on multiple levels – many genes and proteins, many kinds of molecules, many kinds of cells, many organs.... Many biologists want to explain a disease or some other phenomenon via finding a single gene or a single biological process that is The Answer, or a single dynamic with a beginning, middle and end. But in reality, Michael emphasizes, biology doesn't work that way. There is no narrative. There are just mind-numbingly complex networks, out of whose distributed multilevel dynamics complex effects emerge.

I think Rose's complaint is also at the root of my complex, perplexed feelings toward the many simplifications made in Machine of Human Dreams. I have some difficulties with the tendency to simplify things into a templated, stereotyped narrative structure, even when this structure captures only a small part of the actual dynamics one cares about.

In its quest for clearly comprehensible drama and narrative simplification, one important thing the film de-emphasizes is that I've been supported in my passionate transcontinental quest for AGI by a rich and diverse network of friends, family and collaborators. The film sidesteps this aspect by focusing mostly on people from various stages of my life with whom I worked temporarily and stopped, and bypassing the other people from the same stages of my life with whom I've had strong, ongoing relationships. In this way, the film makes it look like I've been far more of a wandering loner than has been the case, and plays down the self-organizing social graph that has helped hugely in propelling my work forward. This makes ME seem like a more of a lone wolf and less of a human-network-aggregator than I actually am; and it makes the quest for building AGI seem like much less of a team effort than it really is.

What I'm doing with my life is not pushing to build a thinking machine all on my own – what I'm doing is serving as the seed about which a network of other brilliant people can crystallize, and providing a core of ideas to guide their work. This may seem like a fine distinction, but it's actually a very important one.

I remember one moment in my apartment in Hong Kong, when Roy was there filming along with a colleague from Roast Beef (whose name I've forgotten). His colleague said to me, while interviewing me, something like “You've moved around a lot. When you run into a dead end somewhere, you just cut your ties and move on, huh?” --- I looked at him bemused. What I said is something like, “No, not at all. When I get frustrated and want more opportunities, I do tend to move on to new places – but I never cut my ties. I've kept so many of the friends and colleagues I've had over the years all over the world. I'm actually really good at keeping touch with old friends and colleagues via the wonders of the Internet. And if you look at my colleagues now, there are people I've been working with since the 80s and 90s from all over the globe, flying in here to Hong Kong to collaborate. A bunch have even gone to Ethiopia with me to work with the guys there. The network of people collaborating on this stuff is not tied to any one physical location. However, I've often found that funding sources are obsessed with you being in a certain physical location....” – And then Roy's colleague quickly changed the subject, and the interview ended shortly after. My answer wasn't what he wanted to hear. He had already put me in the box of “Mr. Cuts His Ties and Moves On” because he was thinking of the narrative of the film that way. I got the feeling that -- unlike Roy -- this colleague wasn't really concerned about the actual human being or the actual science and engineering project that the film was supposed to be reporting on – he was more interested in coaxing me to say stuff that would fit into the narrative structure in his own head.

Similarly, as Ruiting recalls, when she was being interviewed for the film, they probed her with questions oriented toward finding controversy ...  like “Does Ben care more about his AGI work than he does about you? Does he prioritize his work over your relationship?” She answered that one something like “Sometimes, maybe” – which was both honest and sufficiently boring that it didn't make it into the film. But if they'd chosen to poke in different directions, they would have found Ruiting had a lot of interesting things to say on other relevant topics. 

For instance, when she started working on OpenCog-based natural language dialogue, she thought it would be a relatively easy problem, because OpenCog had a semi-magic logical inference engine that would just solve everything. Indeed, if your inference engine is good enough, then you can just pose every aspect of natural language dialogue as an inference problem, and you're done! But over years of thinking about it and working on it, she came to grips more thoroughly with the nature of the problem – which is that, in order to perform usefully fast on linguistic problems, the inference engine needs to be guided by linguistic knowledge … but the linguistic knowledge can only be gathered by inference … so you actually have a “chicken or egg” problem … you have a complex cognitive system in which each part requires the others in order to function. 

How Ruiting's thinking about AGI and language processing has matured over the 6 years we've worked together would be a challenge to portray in a film – however, even a slight hint in this direction would have been interesting to show I think. As it is, the film doesn't even hint that this sort of aspect exists in my life – the fact that I'm joyfully married to a lovely young woman who is working and thinking together with me about AGI is utterly bypassed.

This hits on a larger point: It occurs to me that, if one looks at Machine of Human Dreams as a portrayal of my own personal journey through AGI development from a classic-narrative “Hero's Quest” type perspective, one major thing missing is any substantial depiction of the growth and transformation the “hero” goes through as a result of his trials and tribulations. The film gets across that I'm a dude who holds AGI as a Grand Goal and keeps on trying, and whose frustrations never last too long – when I hit an obstacle or setback I do sometimes get pissed off or even temporarily depressed, but ultimately I just ram into it again or look for some other way around, because I can see so damn clearly in my mind what's on the other side! But the film just shows me keeping on going, and doesn't really show how I've grown and adapted as result of keeping on going for 49 years. Compared to the real Ben Goertzel, the Ben G character in Machine of Human Dreams is a lot more Energizer Bunny like – he keeps on going and going admirably, but he never really changes.

In fact I've changed a lot in my life, in various phases, in multiple ways that are relevant to my AGI work. In the Webmind era I was fantastically unrealistic in my project planning and time estimates. I'm still a bit on the optimistic side, to be sure; but I'm now more within the scope of ordinary optimistic project leaders – there's a world of difference. I have undertaken great efforts to rid my mind of delusions insofar as possible, to really see what is feasible versus what I'd like to be feasible, to clearly distinguish intuition from solid knowledge and research projects from engineering projects. Again I have not become a hard-nosed pragmatist but I've become way way better at distinguishing how the world is from how I'd like it to be – while still pushing to make it become more the way I'd like it to be! Much of this learning has occurred as a result of doing various practical, applied narrow-AI consulting projects, a side of my life that is far more boring than the quest for superhuman AGI ... but yet if I do succeed at building superhuman AGI, this will partly be due to the modicum of discipline I learned from spending a bunch of time delivering real stuff for customers, sometimes successfully and sometimes not.

On a more personal side, I've gradually had to learn to stress out less about the frustration of my grand cosmic goals being so slow to achieve; and of spending so much of my time on stuff that I enjoy only moderately and that works only indirectly toward my grand goals (e.g. managing people, doing consulting projects, going around seeking funding,...). At times this has really made me feel like shit; but eventually, through various sorts of efforts and relaxations, I've untied a lot of knots in my mind and become OK with everything. These days I feel a deep inner contentment, even while working like hell toward difficult goals in chaotic situations – a feeling that visited me only much more intermittently in previous parts of my life. Most likely some of the crappy decisions I made in earlier phases of my life were rooted in a deep inner discontent, which plays a much lesser role in my psyche these days.

The film's portrayal of me as an obsessed AGI zealot is certainly accurate; but my own individual growth and transformations, which have impacted the flow of my AGI work in huge ways, have been driven as much by my various non-AGI passions and occupations – for instance, my explorations with psychedelics, and my research into psi phenomena, both of which are left out of Machine of Human Dreams for understandable reasons (all that is fascinating and important stuff, but would be distracting and hard to capture usefully in a brief way). As it happens, the three people who could have infused the film with some insight into the diverse factors driving my evolution as a human being and scientist – my wife Ruiting, my oldest son Zar, and my ex-wife Izabela – were omitted from the film, although Roy did interview Ruiting and Zar fairly extensively.

I can't especially fault Roy Cohen for not coming to grips with the depths of Ben Goertzel's psyche … I'm a complex, unique sort of weirdo, and Roy and I never had the kinds of conversations that would have enabled him to really understand me well. Roy and his colleagues always stayed pretty close to the surface in their interview questions; and I never tried to push them into grokking my individual character more thoroughly, mostly because I wanted their film to focus on OpenCog and the quest for superhuman AGI rather than me as a person. But of course, if you really want to dig deep deep deep into things, the motivations and networks inside my human mind and the motivations and networks in the AGI and OpenCog communities and the motivations and networks inside the still-incipient OpenCog AGI minds are all dynamically interpenetrating and growing in a coupled way. This shit is bloody complicated!

Conveying the complex social-dynamical phenomena via which networks of intelligent people are coming together to create networks of intelligent processing inside AGI systems … together with the inner growth and transformations of the people trying to crystallize such networks around breakthrough ideas – sure, this would be a big challenge from a film-making perspective, and I can see why Roy and his colleagues found it convenient to fall back on more of a standard narrative structure....

Net net, while it omits various relevant aspects of the underlying reality, still, the story Roy tells is pretty good. I do feel there's an even more fascinating kind of story lurking beneath. But I suppose that's usually the case...

Meanwhile, a film by nature is frozen in time, whereas reality moves on. Just in the last week -- i.e. 8 months or so after Roy finished shooting Machine of Human Dreams -- we've gotten OpenCog fully hooked up to the gorgeous Hanson robots, controlling their verbal and nonverbal behavior. Now it's down to making the robot smarter and smarter.

We're doing a low-cost-robot soccer contest in Ethiopia later this year and my hope is to have one of the Hanson robots give the speech at the opening ceremony, maybe with a funky African-style braided wig. Lots of high Ethiopian government folks will be there, I'm sure their jaws will drop. And we're still jamming with Mark Tilden, moving forward on plans for a humanoid walking body to go along with the Hanson heads and OpenCog mind.

And behind the scenes the AI keeps progressing. Nil (French, living in Bulgaria) and Eddie (from Vermont, but was just here in Hong Kong for a couple weeks) and Misgana (moved from the Ethiopia office to Hong Kong some time ago) have gotten OpenCog's probabilistic inference engine (first described in a 2006 book by me, my old Las Vegas + New York collaborator Matt Ikle', my ex-wife Izabela and my Finnish transhumanist friend Ari Heljakka) to do some cool inferences about the biology of longevity, as well as about what people say to the robot. The non-linear-dynamical attention allocation math that Matt and I worked out over a decade ago is actually finally working now, thanks to some work by Misgana and with some help from Roman, a German intern who also wrote a Lojban interface to OpenCog (Lojban is a speakable form of predicate logic, around for more than half a century spoken by a small community of awesome geeks on the Internet).

Overall – the international network of human minds is gradually bringing to life a plausible approximation of the cognitive network that Nil, Cassio and I described in Engineering General Intelligence in 2014. This emerging mind network is starting to display itself via the emoting faces of David Hanson's beautiful robots but also in other ways, such as finding patterns in complex networks of genomic data.

A new form of life is unfolding, little by little. Very fast on the historical scale, sometimes painstakingly slowly on the time-scale of daily endeavor. Machine of Human Dreams depicts a few interesting fragments of the process, captured during a brief slice of time. The AI work will progress a bunch further inbetween me writing these words and you reading them. 

Us personalities involved in building AGI and our individual narratives and stories are often colorful and interesting, but from a bigger view, we're kinda like the funky flashes of fire coming out of the bottom of a rocket as it blasts into space. Yes, the dancing yellow flames from the rocket are fascinating, and you can stare at them a while and get lost. But the flames on a campfire are fascinating also. The unique thing about the rocket is that it's going into space. The unique thing about the story Roy Cohen captured is that this is a group of people building a mind beyond the human. Even though I'm working toward this goal every day, and the step by step work can be difficult and tedious, it still blows my mind to think about what we're doing and its ultimate implications.





          Genomic Study Shows Maize Adapted to Highlands 4,000 Years Ago        
An international team led by researchers from Cornell University in New York and the Max Planck Institute for Developmental Biology in Tuebingen, Germany reveals that indigenous people in the American ... - Source: www.isaaa.org
          à¸šà¸£à¸£à¸žà¸šà¸¸à¸£à¸¸à¸©à¸ªà¸±à¸•à¸§à¹Œà¸¡à¸µà¸£à¸à¸­à¸²à¸ˆà¸¡à¸µà¸«à¸™à¹‰à¸²à¸•à¸²à¸„ล้ายหนูผี และไม่เคยอยู่ร่วมกับไดโนเสาร์        

บรรพบุรุษสัตว์มีรกอาจมีหน้าตาคล้ายหนูผี และไม่เคยอยู่ร่วมกับไดโนเสาร์


เป็นเวลานานกว่าสองทศวรรษที่นักชีววิทยาหาทางลงไม่ได้ว่าบรรพบุรุษของสัตว์เลี้ยงลูกด้วยนมกลุ่ม Placentalia (สัตว์เลี้ยงลูกด้วยนมที่เลี้ยงตัวอ่อนในครรภ์ด้วยรกที่สมบูรณ์ สัตว์เลี้ยงลูกด้วยนมปัจจุบันเกือบทุกชนิดรวมทั้งมนุษย์จัดอยู่ในกลุ่มนี้) เริ่มต้นสายวิวัฒนาการขึ้นมาเมื่อไรกันแน่ เพราะหลักฐานทางชีวโมเลกุลที่เรียกว่า molecular clock ระบุว่า Placentalia เริ่มโผล่ขึ้นมาบนโลกเมื่อประมาณ 100 ล้านปีที่แล้ว นั่นแปลว่าบรรพบุรุษ Placentalia จะต้องเคยมีชีวิตช่วงหนึ่งกับไดโนเสาร์ที่สูญพันธุ์ไปในรอยต่อยุค Cretaceous-Paleogene (K-Pg boundary) เมื่อประมาณ 65 ล้านปีที่แล้ว แต่นักวิทยาศาสตร์กลับไม่เคยเจอหลักฐานฟอสซิลของ Placentalia ที่มีอายุเกิน K-Pg boundary เลย อีกทั้งนักชีววิทยาหลายคนก็ยังเชื่อว่าสัตว์เลี้ยงลูกด้วยนมตัวเล็กๆ ไม่น่าจะแก่งแย่งแข่งขันกับไดโนเสาร์เจ้าโลกในขณะนั้นได้ การแตกกระจายของสายวิวัฒนาการ (radiation) ของสัตว์เลี้ยงลูกด้วยนมจึงควรเกิดหลังจากที่ไดโนเสาร์สูญพันธุ์ไปแล้วจนหมดสิ้น

หลักฐาน molecular clock นั้นมาจากการประมาณหาอายุของบรรพบุรุษร่วม (common ancestor) ของยีนหนึ่งๆ โดยมีสมมติฐานว่าอัตราการกลายพันธุ์คงที่สม่ำเสมอ นักวิทยาศาสตร์จะดูว่ายีนตัวเดียวกันในสิ่งมีชีวิตสองชนิด (หรือมากกว่า) แตกต่างกันขนาดไหน และคำนวณกลับว่าต้องใช้เวลานานเท่าไรจึงจะเกิดความแตกต่างเท่านั้นได้จากการกลายพันธุ์ จุดอ่อนของ molecular clock คือ ยีนหนึ่งๆ ไม่จำเป็นต้องมีการกลายพันธุ์คงที่สม่ำเสมอตลอดเวลา และ ยีนแตกต่างกันก็มีอัตราการกลายพันธุ์ต่างกันด้วย นักชีววิทยาที่เชื่อว่าวิวัฒนาการสัตว์เลี้ยงลูกด้วยนมเพิ่งจะแตกกระจายหลังการสูญพันธุ์ของไดโนเสาร์ก็เอาจุดอ่อนข้อนี้ขึ้นมาเถียง ส่วนนักชีววิทยาที่ฝักใฝ่หลักฐานชีวโมเลกุลก็โต้กลับว่าการที่พวกชอบขุดยังไม่เจอฟอสซิลก็ไม่ได้แปลว่าไม่มีฟอสซิลอยู่จริงๆ

ทีมวิจัยของนักวิทยาศาสตร์ 23 คนที่นำโดย Maureen O'Leary แห่ง Stony Brook University เห็นว่าไหนๆ ทั้งสองทางก็มีจุดอ่อนของตัวมันเองทั้งคู่ ทำไมไม่ลองเอาสองทางมาผสมผสานรวมกันหละ พวกเขาเริ่มต้นด้วยการเอาข้อมูลทางสัณฐานวิทยาและพันธุกรรมของสัตว์เลี้ยงลูกด้วยนมที่ยังมีชีวิตอยู่ในปัจจุบัน 46 สปีชีส์ ครอบคลุมทั้งกลุ่ม Monotremata (สัตว์เลี้ยงลูกด้วยนมที่ออกลูกเป็นไข่ เช่น ตุ่นปากเป็ด ตัวกินมดหนาม เป็นต้น), กลุ่ม Marsupial (พวกที่เลี้ยงดูตัวอ่อนด้วยรกเป็นระยะสั้นๆ แล้วก็คลอดมาเลี้ยงต่อในกระเป๋าหน้าท้อง เช่น จิงโจ้ เป็นต้น), และกลุ่ม Placentalia รายการข้อมูลทางสัณฐานวิทยาที่ใช้ในงานวิจัยนี้ยาวเหยียดถึง 4,541 รายการ มากกว่างานวิจัยก่อนๆ หน้าเกือบสิบเท่า แค่ระบุรายการที่ต้องใช้ก็กินเวลาปาเข้าไป 2 ปีแล้ว (เพราะนักวิทยาศาสตร์ที่ศึกษาสัตว์แต่ละกลุ่มใช้คำศัพท์แตกต่างกนออกไป à¸•à¸²à¸¡à¸›à¸£à¸°à¹€à¸žà¸“ีที่สืบๆ กันมา) ส่วนข้อมูลทางพันธุกรรมนั้นเปรียบเทียบความแตกต่างของยีนจำนวน 27 ยีน

ขั้นต่อไป นักวิจัยก็นำข้อมูลทางสัณฐานวิทยาที่พบในฟอสซิลของสัตว์เลี้ยงลูกด้วยนมที่สูญพันธุ์ไปแล้วอีก 40 สปีชีส์เข้ามารวม ขั้นตอนการรวบรวมข้อมูลทั้งหมดกินเวลา 3 ปี จากนั้นก็นำข้อมูลเปรียบเทียบทั้งหมดขึ้นไปอยู่บนซอฟท์แวร์ฐานข้อมูลกลุ่มเมฆที่ชื่อว่า"Morphobank" http://mammaltree.informatics.sunysb.edu/ à¸ªà¸±à¸•à¸§à¹Œà¹€à¸¥à¸µà¹‰à¸¢à¸‡à¸¥à¸¹à¸à¸”้วยนมแต่ละตัวจะถูกจัดตำแหน่งลงบนกิ่งก้านของวิวัฒนาการตามลักษณะของสัณฐานวิทยาประกอบกับข้อมูลทางพันธุกรรม และจากลำดับของสายกิ่งก้านเหล่านั้น นักวิจัยก็สามารถที่จะประเมินระยะห่างทางวิวัฒนาการของสัตว์เลี้ยงลูกด้วยนมแต่ละสาย ซึ่งเอามาคำนวณย้อนหาตำแหน่งจุดเวลาที่บรรพบุรุษของสัตว์เลี้ยงลูกด้วยนมกลุ่ม Placentalia กำเนิดขึ้นมาได้ นักวิจัยเรียกวิธีการนี้ว่า "Phylophenomics" เพื่อให้สอดคล้องกับศาสตร์ "Phylogenomics" ที่ใช้ข้อมูลทางพันธุกรรมในการลำดับสายวิวัฒนาการสิ่งมีชีวิต

ผลได้ออกมาว่า บรรพบุรุษของ Placentalia เกิดขึ้นประมาณ 200,000 - 400,000 ปีหลังจาก K-Pg boundary และภายในเวลาเพียงสองแสนปี สาย Placentalia ก็แยกออกเป็น 10 สายหลักแพร่เผ่าพันธุ์มาถึงยุคปัจจุบัน ดังนั้นจึงสนับสนุนทฤษฎีที่ว่าวิวัฒนาการของสัตว์เลี้ยงลูกด้วยนมแตกกระจายสายหลังจากการสูญพันธุ์ของไดโนเสาร์

ภาพจาก PhysOrg; Credit: Stony Brook University/ Luci Betti Nash

ในเมื่อการวิเคราะห์ครั้งนี้ใช้ข้อมูลทางสัณฐานวิทยาเป็นหลัก นักวิจัยจึงสามารถที่จะสร้างภาพจำลองของบรรพบุรุษต้นตระกูล Placentalia ขึ้นมาได้ด้วยการอนุมานจากลักษณะทางสัณฐานวิทยาที่มีอยู่ บรรพบุรุษในจินตนาการนี้มีหน้าตาคล้ายสัตว์ฟันแทะพวกหนูผี จมูกยื่นนาว หางยาวเป็นพวง ปีนต้นไม้เก่ง กินแมลงเป็นอาหาร หนักประมาณ 6-245 กรัม ตัวใหญ่ประมาณหนูหรือลูกแมวตัวเขื่องๆ สมองส่วนรับสัมผัสกลิ่นและ corpus callosum (มัดเส้นประสาทที่เชื่อมสมองซีกซ้ายและขวา) เจริญดี

ภาพจาก PhysOrg; Credit: Carl Buell

นอกจากนี้นักวิจัยยังพบเรื่องน่าประหลาดใจที่ขัดกับความเชื่อเดิมๆ อีกหลายอย่าง เช่น ค้นพบว่าสัตว์เลี้ยงลูกด้วยนมกลุ่ม Afrotherian (ได้แก่ ตัว aardvark, ช้าง, หมูน้ำ เป็นต้น) ไม่ได้ถือกำเนิดขึ้นในดินแดนแอฟริกาอย่างที่เคยเชื่อกัน มันเริ่มวิวัฒนาการในดินแดนทวีปอเมริกาใต้ ซึ่งตอนนั้นทั้งสองทวีปแยกห่างกันเป็นพันๆ กิโลเมตร ต้นตระกูลของ Afrotheria ส่วนหนึ่งน่าจะพลัดหลงมาไม่ทางใดก็ทางหนึ่ง แล้วมาแพร่พันธุ์ในแอฟริกา ขณะที่เพื่อนร่วมรุ่นของมันในอเมริกาใต้สูญพันธุ์ไปจนหมด

โครงการวิจัยนี้เป็นส่วนหนึ่งของโครงการ Assembling the Tree of Life (ATOL) ซึ่งได้รับเงินทุนสนับสนุนจาก National Science Foundation

อย่างไรก็ตาม นักวิทยาศาสตร์ที่ยังไม่อยากรีบฟันธงสรุปอะไร เช่น Mark Springer แห่ง University of California, Riverside ก็ติงว่างานวิจัยนี้ไม่ได้คำนึงถึงปรากฏการณ์ที่สัตว์ต่างกลุ่มจะเกิดวิวัฒนาการแบบ Convergent evolution (หมายถึงสิ่งมีชีวิตที่อยู่คนละสายมีวิวัฒนาการสร้างลักษณะที่คล้ายๆ กันขึ้นมาเพราะมีวิถีชีวิตคล้ายกัน) ข้อสรุปและผลที่ได้จึงอาจจะคลาดเคลื่อนผิดไปจากความเป็นจริง นอกจากนี้นักวิทยาศาสตร์บางคน เช่น Olaf Bininda-Emonds แห่ง Oldenburg University ก็ไม่เห็นว่า Phylophenomics จะมาช่วยหาทางลงอะไรได้ให้กับข้อถกเถียงเกี่ยวกับจุดกำเนิดของ Placentalia

งานวิจัยตีพิมพ์ใน Science DOI: 10.1126/science.1229237


          â€œCracking Cancer” on CBC’s The Nature of Things tonight        
Tonight’s episode of CBC documentary series The Nature of Things with David Suzuki features an in-depth look at the BC Cancer Agency’s Personalized Onco-Genomics (POG) project, which is exploring the feasibility of sequencing DNA and RNA from cancer cells to … Continue reading
          AURA's OPUS Software Licensed to Celera Genomics        

The Association of Universities for Research in Astronomy, Inc. (AURA) has reached an agreement with Celera Genomics Group, an Applera Corporation business in Rockville, MD, on the use of AURA's Operational Pipeline Unified Systems (OPUS) software package. Originally designed for use in the Hubble Space Telescope program, OPUS is being used by Celera to process bioinformatics data. OPUS was developed by the Space Telescope Science Institute, which is managed by AURA under contract with NASA's Goddard Space Flight Center. It is used to process astronomical data generated by the Hubble Space Telescope for use by researchers studying the universe, and it has been widely employed in other space observatories and NASA projects. Facing similar needs for the use of their large databases, Celera is licensing OPUS from AURA to assist in the processing of data from their proteomics and genomics projects.


          (USA-CT-RIDGEFIELD) Principal Scientist/Senior Principal Scientist, Molecular/Genomics Lab Lead, Cancer Immunology Biomarkers        
Boehringer Ingelheim is an equal opportunity global employer who takes pride in maintaining a diverse and inclusive culture. We embrace diversity of perspectives and strive for an inclusive environment which benefits our employees, patients and communities. **Principal Scientist/Senior PrincipalScientist,** **Moleucular/Genomics Lab Lead, Cancer Immunology Biomarkers** **Ridgefield, CT** **_The qualified candidate will be hired at the appropriate level commensurate with education/experience._** **Description:** **Molecular/Genomics Lab Lead-** In the Department of Cancer Immunology and Immune Modulation (CI&IM) we are currently looking for a highly motivated **Molecular/Genomics S** **enior Principal Scientist/Principal Scientist** to serve as a research laboratory lead within the **Cancer Immunology Biomarker Team** . The Biomarker group contributes to the discovery and identification of patient selection biomarkers as well as pharmacodynamic biomarkers in alignment with the respective project teams in research, preclinical and clinical development. Moreover the group is heavily involved in the characterization of the mode of action of novel immuno-oncology therapies. The Senior Principal Scientist/Principal Scientist will initiate, present and defend proposals and activities related to the mission of the Cancer Immunology Biomarker Team and the broader Cancer Immunology and Immune Modulation program. He/she will supervise a team of laboratory scientists and technicians, manage external collaborations and support the evaluation of novel technologies. As an employee of Boehringer Ingelheim, you will actively contribute to the discovery, development and delivery of our products to our patients and customers. Our global presence provides opportunity for all employees to collaborate internationally, offering visibility and opportunity to directly contribute to the companies' success. We realize that our strength and competitive advantage lie with our people. We support our employees in a number of ways to foster a healthy working environment, meaningful work, diversity and inclusion, mobility, networking and work-life balance. Our competitive compensation and benefit programs reflect Boehringer Ingelheim's high regard for our employees **Duties &Responsibilities - Senior Principal Scientist:** + Lead a molecular/genomics lab that provides genomic/molecularcharacterization of in vivo disease models (in collaboration with in vivopharmacology) and human cancer, tissue and blood samples to understand thetarget-disease link. + Profile drug candidates to identify predictiveand pharmacodynamic biomarkers. Coordinate effectively with other researchteams and disciplines across the global Discovery Research Organization. + Contribute to the profiling, validation andinitial application of biomarkers in clinical studies. + Establish and manage external collaborationswith academic partners and CROs, including evaluation of new technologies **Requirements -** **Senior Principal Scientist** **:** + Ph.D., MD, MD/Ph.D from anaccredited institution with relevant post-doctoural experience + With seven-plus (7+)years of experience in one or more of the field listed below. + Industry experience is desirable + Expertise in genomics and tumor biology and astrong desire to be actively involved at the bench + Experience in experimental pathology, cancerimmunotherapy and biomarker research is desirable. + Demonstrated ability to work inmultidisciplinary teams + Ability to plan, organize, troubleshoot, andpresent work independently and to show team leadership + Excellent communication and collaborativeskills, and a track record of publications in the field + Appropriate levelof understanding of applicable regulations + Ability tocommunicate effectively both orally and in writing in an inter-disciplinaryenvironment + Leadership experience **Duties & Responsibilities - Principal Scientist:** + Independently designs and performs scientific experiments with a predefined goal including developing new methodologies, protocols and or test procedures that contribute to core group/research goals and reflect expert knowledge; Direct and oversee experimental design and results of technicians and junior level scientists + Contributes to defining R&D team goals and collaborates with scientists within and outside functional area in achieving them; Assumes departmental responsibility for projects OR has ability to participate as representative on multiple project teams and contribute to defining expertise-related aspects of overall program goals + Prepares clear technical reports, publications and oral presentations. Independently communicate results in the form of reports and/ or presentations; Deliver updates to senior level management in context of overall project goals + Demonstrates an expertise in a specific project-relevant area OR technology; Provide guidance and expertise to advance specific projects OR evaluate and propose new technologies and concepts in support of multiple projects + Develops broad knowledge in field of expertise, including the ability to interpret current literature relevant to R&D projects, and visibility outside of functional area + Assumes responsibility for direct reports as needed including recruiting, managing, mentoring and developing scientific staff + Complies with all applicable regulations; Ensures that work performed in area of responsibility is conducted in a safe and compliant manner; Maintains proper records in accordance with SOPs and policies + Contributes to departmental administration; Demonstrates fiscal responsibility with respect to cost of experiments, technology, external collaborations, and travel **Additional Specifics Regarding Duties & Responsibilities – Principal Scientist** + Lead a molecular/genomics lab that provides genomic/molecularcharacterization of in vivo disease models (in collaboration with in vivopharmacology) and human cancer, tissue, and blood samples to understand thetarget-disease link. + Profile drug candidates to identify predictiveand pharmacodynamic biomarkers. Coordinate effectively with other researchteams and disciplines across the global Discovery Research Organization. + Contribute to the profiling, validation andinitial application of biomarkers in clinical studies. + Establish and manage external collaborationswith academic partners and CROs, including evaluation of new technologies. **Requirements - Principal Scientist:** + Ph.D., MD, MD/Ph.D from an accredited institution with relevant post-doctoral experience + With five-plus (5+) years’ experience in one of the fields listed below: + Expertise in genomics and tumor biology and astrong desire to be actively involved at the bench. + Experience in experimental pathology, cancerimmunotherapy and biomarker research is desirable. + Demonstrated ability to work inmultidisciplinary teams. + Ability to plan, organize, troubleshoot, andpresent work independently and to show team leadership. + Excellent communication and collaborativeskills, and a track record of publications in the field. + Appropriate level of understanding of applicable regulations + Ability to communicate effectively both orally and in writing in an interdisciplinary environment + Leadership experience **EligibilityRequirements:** + Must be legallyauthorized to work in the United States without restriction. + Must be willing totake a drug test and post-offer physical (if required) + Must be 18 years ofage or older **Our Culture:** Boehringer Ingelheim is a different kind of pharmaceutical company, a privately held company with the ability to have an innovative and long term view. Our focus is on scientific discoveries that improve patients' lives and we equate success as a pharmaceutical company with the steady introduction of truly innovative medicines. Boehringer Ingelheim is the largest privately held pharmaceutical corporation in the world and ranks among the world's 20 leading pharmaceutical corporations. At Boehringer Ingelheim, we are committed to delivering value through innovation. Employees are challenged to take initiative and achieve outstanding results. Ultimately, our culture and drive allows us to maintain one of the highest levels of excellence in our industry. Boehringer Ingelheim, including Boehringer Ingelheim Pharmaceuticals, Inc., Boehringer Ingelheim USA, Boehringer Ingelheim Animal Health USA, Inc., Merial Barceloneta, LLC and Boehringer Ingelheim Fremont, Inc. is an equal opportunity and affirmative action employer committed to a culturally diverse workforce - Minority/Female/Protected Veteran/Person with a Disability. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender, gender identity or expression; affectional or sexual orientation; disability; veteran or military status or liability for military status; domestic violence victim status; atypical cellular or blood trait; genetic information (including the refusal to submit to genetic testing) or any other characteristic protected by law. Boehringer Ingelheim is firmly committed to ensuring a safe, healthy, productive and efficient work environment for our employees, partners and customers. As part of that commitment, Boehringer Ingelheim conducts pre-employment verifications and drug screenings. *LI-DS1 *I-DS1 **Organization:** _US-BI Pharma/BI USA_ **Title:** _Principal Scientist/Senior Principal Scientist, Molecular/Genomics Lab Lead, Cancer Immunology Biomarkers_ **Location:** _Americas-United States-CT-Ridgefield_ **Requisition ID:** _177659_
          (USA-CT-RIDGEFIELD) Scientist III / IV - Molecular/Genomics Lab, Cancer Immunology Biomarkers        
Boehringer Ingelheim is an equal opportunity global employer who takes pride in maintaining a diverse and inclusive culture. We embrace diversity of perspectives and strive for an inclusive environment which benefits our employees, patients and communities. **_Scientist III-IV_** **_Molecular/Genomics Lab, Cancer Immunology Biomarkers_** **_Ridgefield, CT_** **_Thequalified candidate will be hired at the appropriate level commensurate with education/experience._** **Description:** In the Department of Cancer Immunology and Immune Modulation (CI&IM) we are currently looking for a highly motivated and result oriented **S** **cientist III/IV** to join the **Molecular/Genomics** laboratory within the Cancer Immunology Biomarker Team. The Molecular/Genomics lab will be focused on developing genomic based assays in addition to exploring new technologies centered on biomarker discovery during early development of therapeutic programs. The Biomarker group contributes to the identification and validation of patient selection biomarkers as well as pharmacodynamic biomarkers in alignment with the respective project teams in research, preclinical and clinical development. Moreover the group is also heavily involved in the characterization of the mode of action of novel immuno-oncology medicines. As an employee of Boehringer Ingelheim, you will actively contribute to the discovery, development and delivery of our products to our patients and customers. Our global presence provides opportunity for all employees to collaborate internationally, offering visibility and opportunity to directly contribute to the companies' success. We realize that our strength and competitive advantage lie with our people. We support our employees in a number of ways to foster a healthy working environment, meaningful work, diversity and inclusion, mobility, networking and work-life balance. Our competitive compensation and benefit programs reflect Boehringer Ingelheim's high regard for our employees **Duties &Responsibilities - Scientist IV:** + Design and execute non-routine experiments on the basis of literature analyses generally without supervision. + Train technicians and junior scientist in all areas of laboratory operations. + Assume departmental responsibility for discovery or development projects, if needed. + Perform all work in conformance with applicable regulation. Perform all work in a safe manner. + The primary scope of responsibility is within the immediate discipline and secondarily within a multi-disciplinary environment. + Initiates, designs, interprets accurately, troubleshoots and completes routine proceduresindependently and efficiently; initiates, designs, interprets accurately,troubleshoots and completes non-routineand difficult procedures generally without supervision; Conducts exploratoryexperiments + Proposes, gains support for and implements ideas from individual’sknowledge of science and technology and understanding of drug discovery process + Proposes, evaluates and implements new technologies; independently appliesbasic scientific principles, performs literature searches, attends scientificmeetings, and keeps abreast of literature in own field + Effectively communicates and defends own work, orally and in writing, inthe context of the team goals at meetings + Demonstrates a solid level of technical proficiency in field; trainstechnicians and junior level scientists in this field + Reports and treats data with a high level of integrity and ethics + Complies with applicable regulations, performing all work in a safe manner;Maintains proper records in accordance with SOPs and policies + Participate incross departmental project teams when assigned **Additional Specifics Regarding Duties & Responsibilities – Scientist IV** + Develop and validate molecular/genomic assays in addition toexploration of new technologies for in vivo disease models and human cancer tissueand blood samples. + Profile drug candidates to identify predictiveand pharmacodynamic biomarkers. Coordinate effectively with other members ofthe laboratory and other scientists in the Biomarker Group. + Establish molecular/genomic assays to investigate mechanismsof immune-mediated effects of novel immunotherapeutic concepts during thepreclinical development program. + Contribute to successful drug development as a memberof a multidisciplinary team. + Contribute to the profiling, validation andinitial application of biomarkers in clinical studies. **Requirements - Scientist IV:** + Master’s Degree (MS) from an accredited institution + With six-plus (6+) years of experience in a related scientific field + OR Bachelor’s Degree from an accreditedinstitution + With ten (10+) years of experience in a related scientific field + Advanced training in molecular/genomic basedassays + Demonstrated knowledge of cancer biology andimmunology + Ability to pose new experimental designs + Ability to plan and conduct laboratoryexperiments and evaluate and interpret data. + Ability to provide training and guidance tolaboratory personnel. + Ability to conduct probing experiments. + Appropriate level ofunderstanding of applicable regulations. + Requires an understanding for the discovery anddevelopment of molecular/genomicbased biomarkers and an understanding of novel therapeutic concepts. + Requires critical thinking e.g. by proposing andimplementing novel experimental approaches and concepts contributing to the cancerimmunology and immune modulation (CI&IM) research goals. **Duties & Responsibilities - Scientist III:** + Performs routine lab duties without supervision. + Designs and executes non-routine experiments on a basis of literature analyses with minimal supervision. + Assists in supervising/training technicians and junior scientist. + Performs all work in conformance with applicable regulations. + Performs all work in a safe manner. + The primary scope of responsibility is within the immediate discipline and secondarily within a multi-disciplinary environment. + Initiates and completes routine procedures in an independent and efficient manner; Troubleshoots effectively and solves scientific problems independently; Operates lab equipment and is independently responsible for maintenance + Designs and executes non-routine experiments on a basis of literature analyses with minimal supervision + Independently applies basic scientific principles, performs literature searches, attends scientific meetings, and keeps abreast of literature in own field + Proposes new experiments/technologies based on science as well as overall understanding of drug discovery/development process; Demonstrates expertise in field and contributes to training technicians and junior level scientists + Effectively communicates and defends own work in the context of team and department goals both orally and in writing + Reports and treats data with a high level of integrity and ethics; Write protocols, procedures, and technical reports; Provide input for scientific reports + Complies with applicable regulations, performing all work in a safe manner; Maintains proper records in accordance with SOPs and policies **Additional Specifics Regarding Duties & Responsibilities – Scientist III:** + Develop and validate molecular/genomic assays in addition to exploration of new technologies for in vivo disease models and human cancer tissue and blood samples. + Profile drug candidates to identify predictive and pharmacodynamic biomarkers. Coordinate effectively with other members of the laboratory and other scientists in the Biomarker Group. + Establish molecular/genomic assays to investigate mechanisms of immune-mediated effects of novel immunotherapeutic concepts during the preclinical development program. + Contribute to successful drug development as a member of a multidisciplinary team. + Contribute to the profiling, validation and initial application of biomarkers in clinical studies. **Requirements - Scientist III:** + Master’s Degree (MS) from an accredited institution + With three-plus (3+) years of experience in a related scientific field + OR Bachelor’s Degree from an accredited institution + With seven (7+) years of experience in a related scientific field + Training in molecular/genomic based assays. + Supplemental technical courses in cancerimmunology + Ability to operate laboratory equipment withindependence + Ability to draft technical reports + Demonstrate written and verbal communicationskills + Concise and accurate reporting of technicaldata and interpretation thereof + Proven problem solving ability + Able to act for supervisor in his/her absence + Appropriate level of understanding ofapplicable regulations + Requires an understanding for the discovery anddevelopment of molecular/genomicbased biomarkers and an understanding of novel therapeutic concepts. + Requires critical thinking e.g. by proposing andimplementing novel experimental approaches and concepts contributing to the cancerimmunology and immune modulation (CI&IM) research goals. **EligibilityRequirements:** + Must be legallyauthorized to work in the United States without restriction. + Must be willing totake a drug test and post-offer physical (if required) + Must be 18 years ofage or older **Our Culture:** Boehringer Ingelheim is a different kind of pharmaceutical company, a privately held company with the ability to have an innovative and long term view. Our focus is on scientific discoveries that improve patients' lives and we equate success as a pharmaceutical company with the steady introduction of truly innovative medicines. Boehringer Ingelheim is the largest privately held pharmaceutical corporation in the world and ranks among the world's 20 leading pharmaceutical corporations. At Boehringer Ingelheim, we are committed to delivering value through innovation. Employees are challenged to take initiative and achieve outstanding results. Ultimately, our culture and drive allows us to maintain one of the highest levels of excellence in our industry. Boehringer Ingelheim, including Boehringer Ingelheim Pharmaceuticals, Inc., Boehringer Ingelheim USA, Boehringer Ingelheim Animal Health USA, Inc., Merial Barceloneta, LLC and Boehringer Ingelheim Fremont, Inc. is an equal opportunity and affirmative action employer committed to a culturally diverse workforce - Minority/Female/Protected Veteran/Person with a Disability. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender, gender identity or expression; affectional or sexual orientation; disability; veteran or military status or liability for military status; domestic violence victim status; atypical cellular or blood trait; genetic information (including the refusal to submit to genetic testing) or any other characteristic protected by law. Boehringer Ingelheim is firmly committed to ensuring a safe, healthy, productive and efficient work environment for our employees, partners and customers. As part of that commitment, Boehringer Ingelheim conducts pre-employment verifications and drug screenings. *LI-DS1 *I-DS1 **Organization:** _US-BI Pharma/BI USA_ **Title:** _Scientist III / IV - Molecular/Genomics Lab, Cancer Immunology Biomarkers_ **Location:** _Americas-United States-CT-Ridgefield_ **Requisition ID:** _177651_
          (USA-CT-RIDGEFIELD) Executive Director, Principal Translational Medicine & Biomarker Expert        
Boehringer Ingelheim is an equal opportunity global employer who takes pride in maintaining a diverse and inclusive culture. We embrace diversity of perspectives and strive for an inclusive environment which benefits our employees, patients and communities. **Description:** As a Translational Medicine and Biomarker Expert you directly support Immuno-Oncology drug development projects in the transition from research to early clinical development and up to clinical phases by providing senior leadership in establishing strategies for pharmacodynamic, safety and patient selection selection biomarkers and assessing novel biomarker methods and assays. You will have responsibility for the following aspects: + Medical translational aspects of early clinical development strategy up to and including Proof of Clinical Principle, provide high quality, innovative, medical translational support to research for assigned projects and beyond + Collaborate with assigned project teams on the identification of relevant Immuno-Oncology biomarkers and ensure bringing such biomarkers into clinical development, includingclinical fit for purpose qualification/validation of biomarkers + Ensure optimal use of biomarkers for clinical development programs of assigned projects in close collaboration with other team members, eg in clinical Proof of Clinical Principle and other clinical studies, for early decision making or for stratification of patients in clinical development programs (eg stratified/personalized medicine approaches)and development of companion diagnostics, if applicable. You will provide Medical input and expertise in the development of biomarker strategies in Immuno-Oncology. These biomarkers may be clinical endpoints or biomarkers using biochemistry, molecular or imaging or any other appropriate technologies. The implementation of these biomarkers will be carried out in close collaboration with other Translational Medicine Scientists, Early Clinical Research Teams as well as Research Teams. As an employee of Boehringer Ingelheim, you will actively contribute to the discovery, development and delivery of our products to our patients and customers. Our global presence provides opportunity for all employees to collaborate internationally, offering visibility and opportunity to directly contribute to the companies' success. We realize that our strength and competitive advantage lie with our people. We support our employees in a number of ways to foster a healthy working environment, meaningful work, diversity and inclusion, mobility, networking and work-life balance. Our competitive compensation and benefit programs reflect Boehringer Ingelheim's high regard for our employees. **Duties & Responsibilities:** + Responsible for enabling the discovery, translation, implementation, and clinical fit for purpose qualification/validation of biomarkers in BI sponsored clinical trials - either in collaboration with inhouse experts or with CROs. Responsible for the selection of appropriate CROs considering its scientific and compliance skills as well as responsible for scientific monitoring of biomarker analyses/assay qualification/validation performed at a CRO. Complies with applicable regulations - either inhouse or in collaboration with CROs - and ensures that work performed in areas of responsibility is conducted in a compliant manner. + Responsibility for delivering medical translational aspects of early medical strategy for assigned projects up to and including Proof of Clinical Principle. + Ensure innovative and fast-to PoCP plans, including potential investigation of several indications per target. + Provide early medical translational support to assigned projects on the usefulness of specific targets in specific indications, contribute in identifying the right indication for the right target. Engage in team discussions and provide input on the identification of preclinical biomarkers and their usefulness during clinical development. + Identify and develop clinical surrogate markers revealing activity in the respective indication together with Biomarker Technology Experts, Pharmacogenomic Experts and Imaging scientists, seeking input from the respective Research and Clinical Teams. These markers may be used to investigate the therapeutic efficacy of a particular drug candidate, but also to explore potential side effects. + Ensure implementation of biomarkers in early clinical studies, Ensure clinical fit for purpose qualification/validation of biomarkers. This includes close collaboration with relevant internal teams and disciplines as well as external partners and CROs. Be accountable for the identification, acceptance and implementation of new potential surrogate endpoints also in Phase 2 and 3 studies. + Contribute in designing relevant exploratory clinical studies with the clear intent to establish early Proof of Clinical Principle in relevant indications. + Establish collaboration with leading academic experts in the assigned field. + Provide input into regulatory documents as needed and represent Translational Medicine at relevant internal and external meetings incl. agency meetings, as appropriate. + Provide expertise to the company on biomarkers related to the assigned indications. This will require close collaboration with other internal scientists as well as collaboration with world leading academic centers. + Represent Translational Medicine in relevant project teams. + Contribute to the implementation of Stratified Medicine for assigned projects. Contribute to the identification of the most promising assigned projects for a Stratified Medicine approach. + Contribute to critical evaluations to non-translational components of registrations and marketing strategy. + Act as an effective external representative to medically related experts and organizations and be externally recognized as an expert on Translational Medicine. Advance the interests of BI by knowledge, publications, style and personal skill, and enhance the position of the corporation with these individuals and groups. + As appropriate, lead multidisciplinary teams with the aim to elaborate an integrated Translational Medicine strategy as an integral part of the clinical development plan. + Act as an internal reference contact concerning translational approaches in a certain therapeutic disease area or with regard to special applications of certain biomarkers or methodologies (includes expert peer reviews of e.g. submission documents). **Requirements:** + PhD or MD plus specialization in assigned TA preferred. + If PhD scientist,deep familiarity withthe clinical and pathologic features of cancer as well as current therapeuticapproaches in oncology are expected and high scientific reputation in therespective field required as documented by excellent list of publications + If MD board certification as a specialist is preferred. + Distinguishedexpertise in Immuno-Oncology or related area required + Knowledge of overall drug development process. + Credible, in-depth knowledge and experience in clinical and exploratory medicine for assigned indications. + Credible, in-depth knowledge and experience of the implementation of biomarkers in drug development with understanding of the clinical application of such markers, their evaluation and analysis + Priordirect-line management experience is preferred + Ability to present a well reasoned business case, and influence other departmental leaders to support cross functional implementation of new initiatives and projects. + Ability to communicate effectively with internal and external opinion leaders including pharmaceutical regulatory agencies, e.g. FDA, EMEA. + Ability to work in a matrix type environment. **Eligibility Requirements:** + Must be legally authorized to work in the United States without restriction. + Must be willing to take a drug test and post-offer physical (if required) + Must be 18 years of age or older **Our Culture:** Boehringer Ingelheim is one of the world’s top 20 pharmaceutical companies and operates globally with approximately 50,000 employees. Since our founding in 1885, the company has remained family-owned and today we are committed to creating value through innovation in three business areas including human pharmaceuticals, animal health and biopharmaceutical contract manufacturing. Since we are privately held, we have the ability to take an innovative, long-term view. Our focus is on scientific discoveries and the introduction of truly novel medicines that improve lives and provide valuable services and support to patients and their families. Employees are challenged to take initiative and achieve outstanding results. Ultimately, our culture and drive allows us to maintain one of the highest levels of excellence in our industry. We are also deeply committed to our communities and our employees create and engage in programs that strengthen the neighborhoods where we live and work. Boehringer Ingelheim, including Boehringer Ingelheim Pharmaceuticals, Inc., Boehringer Ingelheim USA, Boehringer Ingelheim Animal Health USA, Inc., Merial Barceloneta, LLC and Boehringer Ingelheim Fremont, Inc. is an equal opportunity and affirmative action employer committed to a culturally diverse workforce. All qualified applicants will receive consideration for employment without regard to race; color; creed; religion; national origin; age; ancestry; nationality; marital, domestic partnership or civil union status; sex, gender identity or expression; affectional or sexual orientation; disability; veteran or military status, including protected veteran status; domestic violence victim status; atypical cellular or blood trait; genetic information (including the refusal to submit to genetic testing) or any other characteristic protected by law. Boehringer Ingelheim is firmly committed to ensuring a safe, healthy, productive and efficient work environment for our employees, partners and customers. As part of that commitment, Boehringer Ingelheim conducts pre-employment verifications and drug screenings. *LI-DS1 *I-DS1 **Organization:** _US-BI Pharma/BI USA_ **Title:** _Executive Director, Principal Translational Medicine & Biomarker Expert_ **Location:** _Americas-United States-CT-Ridgefield_ **Requisition ID:** _176142_
          Bowel cancer test research        

Australian researchers have developed gene expression biomarkers which can accurately discriminate pre-cancerous and cancerous colorectal growths from non-cancerous controls.

Being presented today at the Digestive Disease Week conference in Chicago, the preliminary findings are the result of a collaborative study involving CSIRO, Flinders University and Australian healthcare company, Clinical Genomics Pty Ltd designed to develop an improved screening/diagnostic test for detecting bowel cancer and significant pre-cancer lesions.

"If we can now show that the levels of these biomarkers in blood or stool also correlate strongly with disease state in a large group of patients with cancer or pre-cancer lesions (ie adenomatous polyps) we may have the basis for a very important new diagnostic weapon in the fight against bowel cancer," says CSIRO's Preventative Health National Research Flagship Theme Leader in Colorectal Cancer and Gut Health, Dr Trevor Lockett.

According to Professor Graeme Young from Flinders University's Centre for Cancer Prevention and Control, regular screening for bowel cancer in people aged 50 years and over is a powerful tool for reducing the impact of the disease in Australia.

"If we can develop a screening test that can point to the presence of clinically important pre-cancerous adenomas which are then removed during follow-up colonoscopy, we will actually be able to prevent the occurrence of bowel cancer in some cases," Professor Young says.

The CEO of Clinical Genomics Pty Ltd, Lawrence La Pointe, says if a more robust screening test for bowel cancer and especially pre-cancer lesions emerges, the research team will have achieved a major advance likely to further improve screening outcomes and more precisely identify those people most likely to benefit from colonoscopic investigation.
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          Genomic Health Study Shows Breast Cancers in Men Display Very Similar Gene Signatures to Those in Women        
ORLANDO, Fla., May 29, 2009 /PRNewswire-FirstCall via COMTEX/ ----Genomic Health, Inc. (Nasdaq: GHDX) today announced results from a study which summarized the gene signatures identified by the Oncotype DX(R) breast cancer test in a large number of male patients for whom the test was used to guide treatment with chemotherapy. The results, which will be presented in a poster presentation on Monday, June 1 (1:00 - 5:00 p.m. ET) at the American Society of Clinical Oncology (ASCO) annual meeting in Orlando, demonstrated that breast cancer in men displays similar gene signatures to female breast cancer.

"Breast cancer is not just a woman's disease, yet treatment for men is typically extrapolated from our experience in the female population since it is rare and there is little known about the biology of male breast cancer," said George Sledge, M.D., Ballve-Lantero Professor of Oncology at Indiana University in Indianapolis, and lead investigator of the study. "This is the largest genomic study to compare gene expression in female and male patients, and results support the clinical utility of Oncotype DX in providing quantitative information to help guide treatment decisions for men with breast cancer."

The study, "Molecular characterization of male breast cancer by standardized quantitative RT-PCR analysis: First large genomic study of 347 male breast cancers compared to 82,434 female breast cancers" (Abstract #549), analyzed quantitative gene expression by gender status in estrogen receptor (ER) positive tumor specimens. As with female breast cancer, a wide inter-patients variation was observed in gene expression in male breast cancer. The proportion of tumors with low risk of recurrence based on the Recurrence Score(R) was 53.6 percent in males versus 53.4 percent in females, intermediate risk of recurrence was 35.2 percent in males versus 36.3 percent in females, and high risk of recurrence was 11.2 percent in males versus 10.3 percent in females.

Despite the similarities between the two patient groups, there were also some differences. For example, male breast cancer patients had higher mean expression of the hormone receptor genes, likely due to the different hormonal context of men and women. In addition, male breast cancer patients were older, on average, and were less likely than women to have the lobular form of breast cancer.

"I was quite surprised when my doctor told me I had breast cancer and was not looking forward to the multiple rounds of chemotherapy that he originally recommended," said Mike Nelsen, a breast cancer patient from Baltimore. "After my Oncotype DX test results came back and I discussed them with my oncologist, I felt confident that I could avoid chemotherapy and its side effects without increasing the risk of my cancer returning."

Multiple Studies Highlight Application of Personalized Medicine in Oncology Setting

Additionally, Genomic Health, in partnership with investigators from several academic institutions, will present a separate study at ASCO evaluating the genotypic features of triple-negative breast cancer compared with hormone receptor-positive disease, as well as the genotypic features associated with recurrence. The study, "Genotypic characterization of phenotypically defined triple-negative breast cancer" (Abstract #500), demonstrated that there were significant differences in gene expression between the triple negative and hormone receptor positive groups, including genes for which targeted agents are currently being evaluated in the clinical environment. Full results will be discussed in an oral presentation on Sunday, May 31 (4:30 p.m. ET).

These presentations are in addition to Genomic Health's previously announced results regarding its Oncotype DX colon cancer test, from the landmark QUASAR validation study, demonstrating that the test can independently predict individual recurrence risk in stage II colon cancer patients following surgery. The study, "A quantitative multi-gene RT-PCR assay for prediction of recurrence in stage II colon cancer: Selection of the genes in 4 large studies and results of the independent, prospectively-designed QUASAR validation study" (Abstract #4000), which was highlighted on May 14 during ASCO's advance presscast, will be presented Saturday, May 30 (3:00 p.m. ET). Genomic Health plans to make its colon cancer test available to physicians and patients in early 2010.

"With these two breast cancer studies and the QUASAR colon cancer validation results, we continue to advance our understanding of the role of genomics in cancer," said Steve Shak, M.D., chief medical officer of Genomic Health. "As a leader in personalized medicine, we are committed to further increasing the clinical utility of our tests through additional studies, while expanding research and development efforts for other tumor types in an effort to individualize treatment for all cancer patients."

About Oncotype DX(R)

The widely adopted Oncotype DX breast cancer assay is the first and only multi-gene expression test commercially available that has clinical evidence validating its ability to predict the likelihood of chemotherapy benefit as well as recurrence in early-stage breast cancer. Additionally, the test report provides quantitative scores for certain individual genes. The Oncotype DX breast cancer assay has been extensively evaluated in thirteen clinical studies involving more than 4,000 breast cancer patients, including a large validation study published in The New England Journal of Medicine and a chemotherapy benefit study published in the Journal of Clinical Oncology. To date, more than 7,500 physicians have ordered more than 100,000 tests, and both Medicare and private health plans covering more than 90 percent of U.S. insured lives provided reimbursement for Oncotype DX through contracts, agreements or policy decisions. Both the American Society of Clinical Oncology and the National Comprehensive Cancer Network recommend the use of Oncotype DX for patients with node-negative breast cancer that is estrogen-receptor positive and/or progesterone-receptor positive. For more information about Oncotype DX, please visit http://www.oncotypedx.com.

About Genomic Health

Genomic Health, Inc. (Nasdaq: GHDX) is a life science company focused on the development and commercialization of genomic-based clinical laboratory services for cancer that allow physicians and patients to make individualized treatment decisions. In 2004, Genomic Health launched the Oncotype DX(R) breast cancer test, which has been shown to predict the likelihood of chemotherapy benefit as well as recurrence in early-stage breast cancer. The company was founded in 2000 and is located in Redwood City, California. For more information, please visit http://www.genomichealth.com.

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to the applicability of clinical study results to actual outcomes, the company's plans to commercialize a test for colon cancer and the proposed timing of such commercialization, and the company's expectation that it will increase the clinical utility of its tests and expand its research and development efforts. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially, and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: the risks and potential delays associated with commercialization of a new test; the risks and uncertainties associated with the regulation of the company's tests; the applicability of clinical study results to actual outcomes; and the other risks set forth in the company's filings with the Securities and Exchange Commission, including the risks set forth in the company's Quarterly Report on Form 10-Q for the quarter ended March 31, 2009. These forward-looking statements speak only as of the date hereof. Genomic Health disclaims any obligation to update these forward-looking statements.

NOTE: The Genomic Health logo, Oncotype, Oncotype DX and Recurrence Score are trademarks or registered trademarks of Genomic Health, Inc. All other trademarks and service marks are the property of their respective owners.

SOURCE Genomic Health

http://www.oncotypedx.com
          Breast health center gives TGen new research opportunities        

TGen partners with John C. Lincoln Health Network to prevent breast cancer



PHOENIX, Ariz. – May 4, 2009 – Today's opening of a new breast health center next to John C. Lincoln Deer Valley Hospital will provide significant research opportunities for the Translational Genomics Research Institute (TGen).


The 9,000-square-foot Breast Health and Research Center will include a tumor biorepository for TGen that will aid the non-profit research institute in discovering new ways to diagnose and treat breast cancer, which affects 1 in every 8 American women.


"What this partnership means is that breast cancer research at TGen will be significantly accelerated, specifically in development of more accurate diagnostic tests and smarter treatment options for newly-diagnosed breast cancer patients,'' said Dr. Heather Cunliffe, head of TGen's Breast & Ovarian Cancer Research Unit.



The new center is located in John C. Lincoln's Medical Offices 3, 19646 N. 27th Ave., just southwest of Interstate 17 and Loop 101, in northwest Phoenix.


"Our new state-of-the-art medical equipment allows the earliest possible detection of breast cancers when survival rates are highest and treatment is less invasive," said Sherry Gage, Clinical Director of John C. Lincoln's new center.


"But, our staff also knows the key component of the care they offer is their personalized and genuine concern for their patients. We're not just here to give the diagnosis, we're here to help patients at all stages," said Gage, a Registered Radiologic Technologist.


Breast cancer patients at the new center who agree to donate their tumor tissues will boost TGen's abilities to use genomic and proteomic research toward development of new ways to combat breast cancer.


TGen's role at the new center will be for research; not for TGen clinical trials.


"We are thrilled that JCL and TGen have developed a strong strategic partnership to benefit breast cancer patients,'' said Dr. Cunliffe, who also is an Investigator in TGen's Computational Biology Division.



The new center provides TGen with yet another avenue of assisting local hospital and research networks, including Arizona's three major universities, St. Joseph's Hospital and Medical Center, Banner Health and Scottsdale Healthcare.


"This is another example of how Arizona is forging new ground through fostering broadly the alignment of clinical centers of excellence, such as John C. Lincoln, with biomedical research organizations, such as TGen. The ultimate beneficiaries are of course our patients who have cancer and other debilitating diseases," said Dr. Jeffrey Trent, TGen's President and Research Director.


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About TGen

The Translational Genomics Research Institute (TGen) is a Phoenix-based non-profit organization dedicated to conducting groundbreaking research with life changing results. Research at TGen is focused on helping patients with diseases such as cancer, neurological disorders and diabetes. TGen is on the cutting edge of translational research where investigators are able to unravel the genetic components of common and complex diseases. Working with collaborators in the scientific and medical communities, TGen believes it can make a substantial contribution to the efficiency and effectiveness of the translational process. TGen is affiliated with the Van Andel Research Institute in Grand Rapids, Michigan. For more information, visit: www.tgen.org.


About John C. Lincoln

John C. Lincoln Health Network is an acclaimed not-for-profit system of hospitals, physician practices and community outreach programs. Honored for excellence by independent experts, John C. Lincoln doctors use advanced medical technology to deliver superior health care every day. Its focus on quality has earned John C. Lincoln Health Network the trust and respect of the patients and community members it serves. For more information visit JCL.com.


          Guilt-Free Procrastination: This Online Game Could Cure Genetic Diseases        

Have a brain for puzzles? What about ones that help advance science? A new online game called Phylo is harnessing the power of idle brains on the Internet–asking any and all to help align genomic sequences. Human brain power is used instead of computer power because, as the researchers explain in the press release, humans […]

The post Guilt-Free Procrastination: This Online Game Could Cure Genetic Diseases appeared first on Discoblog.


          Defining standards for genomes from uncultivated microorganisms        
As genomic data production has ramped up over the past two decades and is being generated on various platforms around the world, scientists have worked together to establish definitions for terms and data collection standards that apply across the board. Researchers have now developed standards for the minimum metadata to be supplied with single amplified genomes and metagenome-assembled genomes submitted to public databases.
          Being scared: academics getting death threats for having an opinion        
Kate Clancy is someone who I admire. She is someone who says stuff the needed saying. Like pointing out the high incidence of sexual harassment in field work.

For the second time today, I am compiling a Twitter thread about something important. Lightly edited.

My local paper, the News-Gazette, ran an editorial yesterday. That editorial, written by their staff, was half about me. I am the “ideologue” who got a James Watson talk cancelled. The thing is, date hadn’t been set yet, and Watson has a history of being implored to give science-focused talks then just saying racist shit. Perhaps I was the only one who publicly denounced the Woese Institute for Genomic Biology talk. But I wasn’t the only one who spoke against it.

Here’s what happened next: Julie Wurth of the News-Gazette called and asked to interview me about my tweets, and I said yes. So the News-Gazette was the first, and for a while only, story about the Watson cancellation. After that, the story got picked up by conservative websites and blogs. This is when I started getting hate mail. It turns out the smartest thing most conservative trolls can zing at me is that I’m a “fucking cunt.”

Unfortunately days went by and the story didn’t go away. For this reason, I eventually started getting more serious hate mail, threats. I involved campus police. One officer has been sympathetic. But the most I got was a form to fill out for a domestic violence safety plan.

So far, neither the University of Illinois nor Institute for Genomic Biology have corrected the record on my being the sole person against the Watson talk. Nor have they done anything to defend my academic freedom, nor support my personal safety. I’m 36 weeks pregnant by the way.

Today, the day after that editorial, I found a sticky note on the front door of my home asking me to check my email.

I want to say, very clearly, that I hold News-Gazette, the University of Illinois, and the Woese Institute for Genomic Biology responsible for this loss of my personal safety.

In response to another thread about science blogging and activism, Kate wrote:

Honestly, with the experience I’ve recently had and how the conservative trolls are getting worse, I’d advocate against speaking up.

This is how a lot of people lose. Kate loses, for obvious reasons. Academics lose, because they see someone who was a strong voice saying that it’s a mistake to be outspoken. News organizations and universities lose, because people lose trust in those institutions.

Intimidation is how fascism wins.

Update: Kate has asked for the following:

For those of you offering to help: first steps are to write News-Gazette and Institute for Genomic Biology for their lack of control/protection. Contact info for News-Gazette: http://www.news-gazette.com/contact. For head of Institute for Genomic Biology: generobi@illinois.edu.

           Genomics: applications to Antarctic ecosystems         
Peck, Lloyd S.; Clark, Melody S.; Clarke, Andrew; Cockell, Charles ; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Römisch, Karin and Rogers, Alex D. (2005). Genomics: applications to Antarctic ecosystems. Polar Biology, 28(5) pp. 351–365.
          Cancer Genomics Consortium (CGC) Annual Meeting        

          Nutrigenomic Functions of PPARs in Obesogenic Environments        
Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors that mediate the effects of several nutrients or drugs through transcriptional regulation of their target genes in obesogenic environments. This review consists of three parts. First, we summarize current knowledge regarding the role of PPARs in governing the development of white and brown/beige adipocytes from uncommitted progenitor cells. Next, we discuss the interactions of dietary bioactive molecules, such as fatty acids and phytochemicals, with PPARs for the modulation of PPAR-dependent transcriptional activities and metabolic consequences. Lastly, the effects of PPAR polymorphism on obesity and metabolic outcomes are discussed. In this review, we aim to highlight the critical role of PPARs in the modulation of adiposity and subsequent metabolic adaptation in response to dietary challenges and genetic modifications. Understanding the changes in obesogenic environments as a consequence of PPARs/nutrient interactions may help expand the field of individualized nutrition to prevent obesity and obesity-associated metabolic comorbidities.
          As Fears Subside in Mexico, Health Experts Urge Continued Caution        

One of the world’s largest cities has to get back to work, and still has to stay safe. The difficult pushes and pulls of democracy have given Mexican politicians a rough set of choices.

Not so long ago, the government would have acted unilaterally, without transparency, and without the consent of the governed. But here we are in 2009. If Mexican president Felipe Calderon had not acted quickly and thoroughly to contain the H1N1 flu virus, he would have been blamed for its spread and his failure to act. Since the combination of a weak virus and a tough and disciplined response meant the infection did not spread widely, the emergency measures look to some to be overreactions.

Until Wednesday night the mayor of Mexico City, Marcelo Ebrard, was under pressure from various business interests to lift the final restrictions on places like bars and sports stadiums. Then the mayor’s scientific committee decided the final bans were no longer needed.

People were urged to continue the personal hygiene habits and social distancing that appear to have worked so well, and Mexico City’s health secretary cited the burden on businesses the restrictions caused, and looked ahead to ringing cash registers this Mother’s Day weekend, which is as big a deal here in Mexico as it is in the U.S.

People are being urged to sit one-to-a-seat on the city’s vast fleet of public buses, though I can’t find any evidence there’s going to be twice as many buses plying the streets.

I spoke at length to Dr. Guillermo Ruiz Palacio, one of Mexico’s leading epidemiologists. He said all the information from the capital was that human transmission had slowed, nearly to a stop, so the more restrictive regime was no longer necessary. Here’s the other edge on that sword: Because people were so confident that human transmission had slowed to a stop, they were prepared to quickly drop many of the personal practices that had brought that terrific outcome.

Though political and scientific leaders have been clear about it from the very beginning, it’s one point that is difficult to hear over the din of the national hubbub. The people of this country have been told again and again that once the danger is past the H1N1 virus will not be eliminated. It will now be part of the natural world they live with, along with the chameleons clinging to the trees in their gardens, the jacarandas in the public parks, and the mules at work on the farms.

That message will have to be reinforced as the emergency recedes in the country’s rear view mirror, and as the annual flu season rises up in the distance.

Thursday morning results of a national poll were released that showed a quarter of Mexicans thought the epidemic was a myth. It’s a reminder of the residue of distrust, the well-earned cynicism that has marked the relationship between Mexicans and their governments.

In another animating reality revealed in another national poll, 94 percent of Mexicans told public opinion researchers they did not know anyone personally who had suffered from the flu. Turn on the TV, see a national crisis unfold. Walk out on the street, and everything’s the same. It’s not a long leap to conclude somebody’s not telling you everything.

When schools reopened Thursday after a top-to-bottom scrubbing, returning students found monitors at the front doors, ready to pull anyone aside who showed any flu systems. Not exactly scientific perhaps, but along with the cleaning up, a gesture clearly meant to reassure students and their families that the government took its responsibility to protect them seriously.

After the subdued street life of the emergency period it was remarkable how quickly necking returned. In the public parks, on street corners as crowds waited for the light to change, even in an ornate chapel in a breathtaking 17th century church, smooching came storming back onto the social scene. Handshaking still was not so much in evidence, and the social embrace upon meeting or parting may take a little while to come back too. People who neck apparently know each other on a different level from business associates. Or maybe the reward is more apparently worth the risk.

As life begins to get back to normal in the city, medical experts will be watching closely in the coming months and years for mutations in the H1N1 virus. Dr. Ruiz said this can happen on two different tracks.

One is an express lane called “shift,” in which changes in the genetic makeup of the bug can be observed over short periods of time as it is passed from person to person to person.

The other track is observed over months and years, and is called “drift.” Simply from living in various animal hosts, including humans, the virus is picking up and dropping off genetic material which, like a game of telephone, can reveal something very different after it’s passed through a long chain.

In the near term, it means a vaccine for the swine flu virus will continue to target an identified strain, but any formulation is going to have to be redone in coming years, just as the vaccines are for seasonal flu. Trying to hit that moving target means a vaccine is unlikely for the very near term, the coming weeks in which exposure will continue around the world.

Unfortunately, scientists will likely run out of time in the middle term. It would have been possible to add a swine flu component to the vaccine for the seasonal flu, which still kills thousands every year in Mexico. But the new vaccine would have to be ready by August in order to make its way to every part of the country for the start of the seasonal flu vaccine season in September.

Dr. Ruiz told me one thing working in their favor is that even with the establishment of the virus in more than a dozen countries, H1N1 2009 doesn’t appear to be a rapidly mutating strain. Advances in genomics makes it possible to rapidly compare the genetic material in virus samples from patients all over the world. They all have pretty much the same virus, so the medicine should continue to work for a while.

At the same time, this nationally-recognized epidemiologist worries about the widespread use of Tamiflu. Once it was observed that the drug was effective against this new virus strain, millions of doses were sent to every corner of the country, and nothing works to create a superbug like widespread use of a single drug.

There was one last hurdle to clear before getting out of the country. I was scanned along with my NewsHour colleagues, by a heat-sensitive camera to reveal the relative heat of exposed parts of the body. There I stood on the imaging screen, a big blue head, wearing a somewhat cooler beard and eyeglasses. No fever apparent. A declaration also had to be filled out with questions about body aches, fatigue, coughing and sneezing.

Now, certified by the government of the United States of Mexico to be no danger to my people, I am on my way back to the U.S.A.

The post As Fears Subside in Mexico, Health Experts Urge Continued Caution appeared first on PBS NewsHour.


          New FDA-approved method of lung cancer detection gives many hope        

(BPT) - Each year, more people die of lung cancer than any other form of cancer — more than colon, breast and prostate cancers combined. The American Cancer Society estimates of the 224,000 new cases of lung cancer diagnosed each year, 155,000 will succumb to the disease.

Many have heard the statistics about lung cancer, but for those who have lived through it, or who have a friend or loved one battling the disease, these numbers are even more personal and frightening. The low five-year survival rate (five to 14 percent) for late-stage lung cancer patients makes the search for a way to treat this deadly disease all the more urgent.

Genetic breakthroughs

To beat cancer, early detection is critical. Scientific research over the past several decades has revealed that cancer is a disease primarily caused by changes — or mutations — in the genes. This discovery has led to a major shift in how early cancer can be detected and treated. Now, researchers are able to identify mutations in the genetic code that are most likely to cause potentially deadly cancers. This has led to the development of new testing technology and drugs that target those specific mutations.

This approach is in stark contrast to traditional detection methods that are limited in their ability to test for a small number of specific mutations linked to only one possible treatment. This painstakingly long process can take several weeks to identify an effective treatment.

In a matter of days, modern techniques using next-generation sequencing technology can save valuable time by avoiding the need to run multiple tests by simultaneously screening tumor samples for multiple mutations and multiple potential therapies. The new technology also reduces the likelihood of subjecting patients to unnecessary and invasive secondary biopsy procedures.

New advancements in early detection and treatment

The U.S. Food and Drug Administration (FDA) recently approved the Oncomine(TM) Dx Target Test, a first-of-its-kind genetic screening solution that can detect multiple gene mutations associated with non-small cell lung cancer (NSCLC) from a single tissue sample. The test has also been approved to aid in selecting which specific FDA-approved NSCLC treatment the patient may be eligible for.

Take action and talk to your doctor

A recent survey by the Journal of Precision Medicine showed that only about a third of patients and caregivers had a good understanding of genomic tools for cancer detection. That’s why talking to a doctor, loved ones and others about new techniques like sequencing-based tests to help inform more effective treatment options is important. Doctors and healthcare networks have a responsibility to their patients to provide the most effective innovations so patients receive the best care possible.


          CellMax Life’s Precision, Non-Invasive Cancer Testing Now Available...        

CellMax Life and Asia Genomics enter broad partnership to serve Southeast Asia with CellMax non-invasive multi-biomarker oncology blood and saliva tests for personalized, precision cancer risk...

(PRWeb July 11, 2017)

Read the full story at http://www.prweb.com/releases/2017/07/prweb14489243.htm


          The revolution will not be revolutionary … soon        
In the Globe and Mail, Timothy Caulfield explains that we need to be careful not to drink the “healthcare revolution” Kool-Aid: It has been suggested that this technological advance will usher in a new health-care “revolution.” It will allow us, or so it’s promised, to individualize health-care treatments and preventive strategies — an approach often […]
          The genomic treasure trove of Quebec        
Thanks to relatively thorough genealogical records, the people of Quebec are of great and growing interest to genetic researchers: One of the great things about the mass personal genomic revolution is that it allows people to have direct access to their own information. This is important for the more than 90% of the human population […]
          Autism Speaks MSSNG program announces major genome release        
More than 5,000 whole genome sequences now available for research into autism subtypes and personalized treatments

More than 5,000 whole genome sequences now available for research into autism subtypes and personalized treatments

April 27, 2016

Today, the Autism Speaks MSSNG program announced its largest upload and release of whole genome sequences from people affected by autism and their family members. The release includes nearly 3,000 genome sequences from participants in the Autism Speaks Autism Genetic Resource Exchange (AGRE).

This brings the total number of whole genome sequences in MSSNG to 5,211 – making it the world’s largest genomic database on autism. The new upload also puts MSSNG over the halfway mark toward its goal of sequencing more than 10,000 genomes from families affected by autism.

A collaboration between Autism Speaks and Toronto’s Hospital for Sick Children, MSSNG uses a cloud-based portal built and managed by BioTeam to make this unprecedented resource available to qualified researchers and medical geneticists worldwide.

 “There’s never been a resource like this for the study of autism, with access to thousands of whole genome sequences and accompanying behavioral and medical information,” says MSSNG Project Director Stephen Scherer. “Already the research community is making use of MSSNG to define new genetic subtypes of autism that will lead to the next generation of diagnostics and treatment options.” Dr. Scherer directs the Centre for Applied Genomics at Toronto’s Hospital for Sick Children.

To date, more than 100 investigators from nine countries have been granted access to the privacy-protected database.

 “The MSSNG dataset has allowed us to discover new parts of the genome involved in autism,” says MSSNG user Michael Snyder, of the Stanford Center for Genomics and Personalized Medicine. “Without any doubt, this unique resource will improve our understanding of the condition.”

“MSSNG has successfully built not just a database but a community of researchers,” adds Autism Speaks Interim Chief Science Officer Mathew Pletcher. “They are truly realizing the goal of using open science and collaboration to answer key questions about autism.” 

As the program advances on its goal of sequencing 10,000 genomes, Autism Speaks seeks input from the research community on how to improve its research platform. Autism Speaks also sincerely thanks all the individuals and families who have contributed their privacy-protected information and DNA samples.

Learn more about MSSNG at www.mss.ng 
(info@mss.ng or call 646-385-8593)

Also see “Gene mapping is now unlocking the mysteries of autism” a special report on MSSNG, now online at CNBC.com. 


          Autism Speaks Names Stephen Scherer Director of AUT10K        
World-renowned geneticist will oversee world’s largest database of autism genomes–advancing understanding and treatment of ASD subtypes

World-renowned geneticist will oversee world’s largest database of autism genomes–advancing understanding and treatment of ASD subtypes

August 14, 2014

In addition to leading AUT10K, Dr. Scherer will continue as director of the Centre for Applied Genomics, at Toronto’s Hospital for Sick Children. Dr. Scherer also directs the University of Toronto’s McLaughlin Centre for genomic medicine.Autism Speaks has named world-renowned geneticist Stephen Scherer as director of its Ten Thousand Genomes Program (AUT10K). In this role, Dr. Scherer will provide leadership and oversee the development of the world’s largest database of genomic information on individuals with autism and their families.

Thomson-Reuters recently listed Dr. Scherer among its Most Highly Cited Scientists. He and his team have published more than 375 scientific papers advancing understanding of the role that genetic variation plays in disorders such as autism. A world pioneer in genetics and genomics, Dr. Scherer established the Database of Genomic Variants, the world’s first and most-used database of copy number variants (CNVs). Physicians and medical geneticists use this vital tool in making hundreds of thousands of medical diagnoses each year.

Recently, Dr. Scherer led a study, funded by Autism Speaks, that demonstrated how CNV testing can aid individualized diagnosis and treatment of autism subtypes. The study also added dozens of genes to the growing list of those known to contribute to the development of autism.

“We couldn’t be more excited to have Dr. Scherer and SickKids leading this game-changing program on behalf of Autism Speaks and our community,” says Autism Speaks Chief Science Officer Robert Ring. ““Dr. Scherer is a world-class geneticist and established leader in using genomic sequencing technology to improve our understanding of genetic risk underlying ASD and to demonstrate how genomic discovery can transform clinical practice.”

In June, Autism Speaks announced its collaboration with Google to store data from AUT10K on the Google Cloud Platform and establish an open-resource database to support autism research. Through it, scientists around the world will have access to the largest and most comprehensive collection of genomic information on autism.

Much of AUT10K’s sequencing efforts will focus on samples in the Autism Speaks Autism Genetic Resource Exchange (AGRE). With more than 12,000 registrants, AGRE is the largest private repository of publically available DNA samples paired with detailed, anonymous behavioral and medical information. For more than 15 years, AGRE has been a strategic resource for the autism research community.

"I am immensely excited because for the first time any scientist anywhere in the world will be able to bring their tools and analyses to the data in a ‘common cloud,’” Dr. Scherer says of the Autism Speaks-Google collaboration. “This paradigm shift in data access will bring uninhibited minds and both coherence and economy of scale that will surely fuel new discovery."

AUT10K focuses on genomic discoveries that will advance medical care and quality of life for individuals and families in the autism community. Its team has already completed the sequencing of 1,000 individuals and has close to 2,000 additional DNA samples in the process of being sequenced. With Dr. Scherer as the lead author, the results of the first 100 genomes appeared in the American Journal of Human Genetics last summer. These findings have already advanced understanding of ASD, and, in some cases, provided information useful in guiding diagnosis and treatment. As it moves toward completion, the AUT10K collaboration aims to identify various forms of autisms, with the potential to shape individualized treatments and therapies.

In 2014, targeted donor contributions to AUT10K have already totaled $5 million, including support from the Gordon & Llura Gund Foundation, Mel Karmazin Foundation and Allerton Foundation. Together with the AGRE collection, this represents most of the funding and resources needed to complete the full sequence of 10,000 genomes.

Dr. Scherer also oversees genome research funded by Steven Wise, chairman of the KRG Children’s Charitable Foundation as well as $5 million from Genome Canada and the province of Ontario and $2.5 million from the Canadian Institutes of Health Research. “Government support alongside the financial commitment of the public sector puts us within $25 million of our fundraising goal,” said Jill Farber, Executive Director of Autism Speaks Canada. “This is such promising research that will lead to more effective diagnosis and individualized treatment for individuals with ASD, and it’s happening right here in Canada.”  


          Autism Speaks To Sequence World’s Largest Collection of Autism Genomes        
Google Cloud Platform to be used for Unprecedented Ten Thousand Genomes Program, Accelerating Potential for Significant Breakthroughs in Autism Research

A collaboration with Google to develop the world’s largest database of genomic sequence information on individuals with autism

June 10, 2014

New York, N.Y. (June 10, 2014) – Autism Speaks, the world’s leading autism science and advocacy organization, today announced a collaboration with Google to develop the world’s largest database of genomic sequence information on individuals with autism spectrum disorder (ASD) and their family members. The collaboration represents a significant milestone in advancing genomic research of the disorder, and could lead to breakthroughs into the causes, subtypes and better diagnosis and treatment for ASD. The Autism Speaks Ten Thousand Genomes Program (AUT10K) is valued at $50 million dollars.

Autism Speaks will store data from AUT10K on Google Cloud Platform. Most significantly, this database will be an open resource to support autism research. Autism Speaks has accumulated the largest private collection of DNA samples, known as the Autism Genetic Resource Exchange (AGRE) from 12,000 autism cases with diagnoses and detailed phenotyping. AGRE has been a strategic resource for the autism research community for over 15 years and is valued at $25 million dollars. The amount of data collected by AUT10K creates unique challenges for storing, analyzing, and providing remote access to the research. Google Cloud Platform provides the engineering innovation needed to address those challenges. Connecting biological discoveries with the very best in large-scale cloud storage and computation will advance the field of genomics research.

“This announcement represents an unprecedented intersection of business, science and philanthropy that will drastically accelerate the pace of autism research,” said Bob Wright, co-founder of Autism Speaks. “The insight and expertise the Google team brings to the table is unmatched. Utilizing Google Cloud Platform further advances Autism Speaks' commitment to advancing cutting-edge science.”  

“Modern biology has become a data-limited science. Modern computing can remove those limits,” said David Glazer, engineering director for Google Genomics. “We are excited to be working with the Autism Speaks team on storage, processing, exploration, and sharing of the AUT10K data, and are even more excited about the opportunity for Google Cloud Platform to help unlock causes and treatments of autism.”

Building on AGRE, Autism Speaks launched AUT10K in collaboration with the Toronto based Hospital for Sick Children’s (SickKids) Centre for Applied Genomics. Dr. Steve Scherer, who directs the Center, and is a world pioneer in the study of genes, will be the director of AUT10K.

“The Autism Speaks AUT10K Program is a remarkable achievement,” Scherer said. “The collaboration between a pioneering tech company and the foremost autism science organization has the potential to transform the autism research landscape in exceptional ways. No other organization outside of major health institutions and academia has accomplished this much this quickly.”

Scherer oversees $10 million dollars in funding for genomic research, including contributions from Steven Wise, Chairman of the KRG Children Charitable Foundation as well as $7.5 million dollars from the Canadian federal government and the province of Ontario. In addition, in 2014, leadership contributions to AUT10K have totaled $5 million, including support from the Gordon & Llura Gund Foundation, Mel Karmazin Foundation and Allerton Foundation. With the AGRE collection valued at $25 million dollars, this represents most of the funding needed to complete the full sequence of 10,000 genomes.

“These collective assets put us within $10 million dollars of the finish line,” said Liz Feld, president of Autism Speaks. “This is the most promising autism research ever done and for those living with ASD, it will make a significant difference in the development of effective forms of diagnosis and treatment.”

AUT10K is enabling discoveries in ASD genomics research in ways that will have real-life impact on medical care and quality of life for individuals and families in the autism community. Aut10K has already completed the sequencing of 1,000 cases, and currently has close to 2,000 additional samples in the sequencing queue. The majority of cases being studied come from families in the AGRE program. Results from the first 100 genomes were published in the American Journal of Human Genetics last summer. These findings have already advanced understanding of ASD, and, in some cases, provided information useful in guiding diagnosis and treatment. Once completed, this historic collaboration could lead to the uncovering of various forms of autisms, like the various forms of cancers today, and this in turn could lead to individualized treatments and therapies for those with ASD.

"The AUT10K program holds the potential to radically transform our understanding of autism, and will undoubtedly have a role in shaping the future of medical care for those affected by the disorder,” said Rob Ring, Ph.D., chief science officer of Autism Speaks. “This is an incredibly important moment in autism genomic discovery, and we are poised to write a good part of the next chapter. Working with Google is a game-changer in that story.”

About Autism
Autism is a general term used to describe a group of complex developmental brain disorders – autism spectrum disorders – caused by a combination of genes and environmental influences. These disorders are characterized, in varying degrees, by communication difficulties, social and behavioral challenges, and repetitive behaviors. An estimated 1 in 68 children in the U.S. is on the autism spectrum.

About Autism Speaks
Autism Speaks is the world’s leading autism science and advocacy organization. It is dedicated to funding research into the causes, prevention, treatments and a cure for autism; increasing awareness of autism spectrum disorders; and advocating for the needs of individuals with autism and their families. Autism Speaks was founded in February 2005 by Suzanne and Bob Wright, the grandparents of a child with autism. Mr. Wright is the former vice chairman of General Electric and chief executive officer of NBC and NBC Universal. Since its inception, Autism Speaks has committed more than $500 million dollars to its mission, the majority in science and medical research. Each year Walk Now for Autism Speaks events are held in more than 100 cities across North America. On the global front, Autism Speaks has established partnerships in more than 40 countries on five continents to foster international research, services and awareness. To learn more about Autism Speaks, please visit AutismSpeaks.org.


          Autism Speaks Collaborative Releases First Full Genome Sequencing for Autism Spectrum Disorders        
Definitive Look at Inherited and De Novo Genetic Mutations and Risk Genes Found in Half of the Families Tested Holds Promise for Future Diagnosis, Prevention and Treatment

A collaborative formed by Autism Speaks has sequencing entire genome of individuals with autism and their family members.

July 11, 2013

NEW YORK, N.Y., (July 11, 2013) – A collaborative formed by Autism Speaks, the world’s leading autism science and advocacy organization, has found full genome sequencing examining the entire DNA code of individuals with autism spectrum disorder (ASD) and their family members to provide the definitive look at the wide ranging genetic variations associated with ASD. The study published online today in American Journal of Human Genetics, reports on full genome sequencing on 32 unrelated Canadian individuals with autism and their families, participants in the Autism Speaks Autism Genetic Resource Exchange (AGRE). The results include both inherited as well as spontaneous or de novo, genetic alterations found in one half of the affected families sequenced.

This dramatic finding of genetic risk variants associated with clinical manifestation of ASD or accompanying symptoms in 50 percent of the participants tested is promising, as current diagnostic technology has only been able to determine a genetic basis in about 20 percent of individuals with ASD tested. The large proportion of families identified with genetic alterations of concern is in part due to the comprehensive and uniform ability to examine regions of the genome possible with whole genome sequencing missed in other lower resolution genome scanning approaches.

"From diagnosis to treatment to prevention, whole genome sequencing efforts like these hold the potential to fundamentally transform the future of medical care for people with autism," stated Autism Speaks Chief Science Officer and study co-author Robert Ring, Ph.D.

The study identified genetic variations associated with risk for ASD including de novo, X-linked and other inherited DNA lesions in four genes not previously recognized for ASD; nine genes previously determined to be associated with ASD risk; and eight candidate ASD risk genes. Some families had a combination of genes involved. In addition, risk alterations were found in genes associated with fragile X or related syndromes (CAPRIN1 and AFF2), social-cognitive deficits (VIP), epilepsy (SCN2A and KCNQ2) as well as NRXN1 and CHD7, which causes ASD-associated CHARGE syndrome.

“Whole genome sequencing offers the ultimate tool to advance the understanding of the genetic architecture of autism,” added lead author Dr. Stephen Scherer, senior scientist and director of the Centre for Applied Genomics at The Hospital for Sick Children (SickKids) and director of the McLaughlin Centre at the University of Toronto. “In the future, results from whole genome sequencing could highlight potential molecular targets for pharmacological intervention, and pave the way for individualized therapy in autism. It will also allow for earlier diagnosis of some forms of autism, particularly among siblings of children with autism where recurrence is approximately 18 per cent.”  

This $1 million collaboration of Autism Speaks, SickKids, BGI and Duke University piloted Autism Speaks’ initiative to generate the world’s largest library of sequenced genomes of individuals with ASD announced in late 2011. “As we continue to test more individuals and their family members from the AGRE cohort, we expect to discover and study additional genetic variants associated with autism. This collaboration will accelerate basic and translational research in autism and related developmental disabilities,” concluded Autism Speaks Vice President for Scientific Affairs Andy Shih, Ph.D. who oversees the collaboration, “and this collection of sequenced genomes will facilitate new collaborations engaging researchers around the world, and enable public and private entities to pursue pivotal research.”

In this pilot effort, a total of 99 individuals were tested, including the 32 individuals with ASD (25 males and seven females) and their two parents, as well as three members of one control family not on the autism spectrum.  Using families in the Autism Speaks AGRE collection, this Autism Speaks initiative will ultimately perform whole genome sequencing on more than 2,000 participating families who have two or more children on the autism spectrum. The data from the 10,000 AGRE participants will enable new research in the genomics of ASD, and significantly enhance the science and technology networks of Autism Speaks and its collaborators.

This work was supported by Autism Speaks, Autism Speaks Canada, Autism Speaks Autism Genome Resource Exchange (AGRE), National Institutes of Health (NIH), National Science and Technology Ministry Project -973 program, National Science and Technology Ministry Project -863 program, National Natural Science Foundation of China-Major Program, the Shenzhen Municipal Government of China,  Enterprise Key Laboratory Supported by Guangdong Province, Shenzhen Key Laboratory of Gene Bank for National Life Science (National Gene Bank Project of China), NeuroDevNet, the Canadian Institutes for Advanced Research, the University of Toronto McLaughlin Centre, Genome Canada/ Ontario Genomics Institute, the government of Ontario, the Canadian Institutes of Health Research (CIHR) and SickKids Foundation.

AGRE is a research program based in the U.S. designed to accelerate the pace of science by providing a ready and available data base for researchers, thereby allowing them to focus their time and efforts on analyzing the data and looking for answers rather than collecting data on a study-by-study basis. AGRE provides DNA, clinical, and medical information to autism researchers worldwide. AGRE is the world’s largest private collection of multiplex autism families and is uniquely designed to allow continuing contact with the participating families to collect additional clinical data. For more information on AGRE visit the AGRE website for families and researchers.

About Autism
Autism is a general term used to describe a group of complex developmental brain disorders – autism spectrum disorders – caused by a combination of genes and environmental influences. These disorders are characterized, in varying degrees, by communication difficulties, social and behavioral challenges, as well as repetitive behaviors. An estimated one in 88 children in the U.S. is on the autism spectrum – a 78 percent increase in six years that is only partly explained by improved diagnosis.

About Autism Speaks
Autism Speaks is the world’s leading autism science and advocacy organization. It is dedicated to funding research into the causes, prevention, treatments and a cure for autism; increasing awareness of autism spectrum disorders; and advocating for the needs of individuals with autism and their families. Autism Speaks was founded in February 2005 by Suzanne and Bob Wright, the grandparents of a child with autism. Mr. Wright is the former vice chairman of General Electric and chief executive officer of NBC and NBC Universal. Since its inception, Autism Speaks has committed nearly $199 million to research and developing innovative resources for families. Each year Walk Now for Autism Speaks events are held in more than 95 cities across North America. On the global front, Autism Speaks has established partnerships and related activities in more than 40 countries on 5 continents to foster international research, services and awareness. To learn more about Autism Speaks, please visit www.AutismSpeaks.org.


          Tackling the Whole Autism Genome: Insights for Diagnosis & Care        
Early results from Autism Speaks “10K Autism Genome Project” show promise for improving diagnosis and personalizing treatments

Early results from Autism Speaks “10K Autism Genome Project” show promise for improving diagnosis and personalizing treatments

July 11, 2013

For the first time, researchers have analyzed the entire DNA sequence (whole genome) of individuals affected by autism and their families. In doing so, they were able to link autism symptoms to specific genetic changes in half the families studied. This more than doubles the success rate of standard genetic testing, which identifies autism-related gene changes just 20 percent of the time.

The researchers also went beyond merely identifying new autism genes to show how whole genome sequencing can guide diagnosis and treatment of autism and related medical conditions.

The study appears today in the American Journal of Human Genetics. It’s the first to come out of Autism Speaks “10K Autism Genome Project.” The project’s goal is the whole genome sequencing of 10,000 individuals in families affected by autism. As the project’s pilot study, today’s report included 32 Canadian families participating in Autism Speaks Autism Genetic Resource Exchange (AGRE).

“This pilot study has shown that whole genome sequencing can deliver clear and useful information for our families, while advancing our understanding of what causes autism,” says Autism Speaks Vice President for Scientific Affairs Andy Shih. Dr. Shih oversees the 10K Autism Genome Project, a collaboration with the Chinese genome-sequencing giant BGI.

"From diagnosis to treatment to prevention, whole genome sequencing efforts like these hold the potential to fundamentally transform the future of medical care for people with autism," adds Autism Speaks Chief Science Officer Rob Ring.

Drs. Ring and Shih are co-authors of the study, along with Autism Speaks Vice President of Clinical Programs Clara Lajonchere and Duke University’s Yong-hui Jiang. The study was led by Stephen Scherer, director of the Centre for Applied Genomics at the Hospital for Sick Children (SickKids), in Toronto. Dr. Scherer also directs the University of Toronto’s McLaughlin Centre for genomic medicine.

Moving beyond standard genetic sequencing
Standard genetic sequencing looks at the tiny portion of a person’s DNA that spells out instructions for making proteins. By contrast, whole genome sequencing analyzes genes in a more comprehensive manner by including the other 98 percent of a person’s DNA blueprint. Once considered “junk,” this portion of the genome is now recognized as vital for development and function.

In addition to finding and confirming known and suspected autism genes, the study identified four new autism genes and eight candidate autism genes. Several families had combinations of autism-related gene changes.

“The fact that we found notable genetic variants in 50 percent of the families reflects our new ability to apply genome sequencing to find spontaneous, or de novo, as well as inherited genetic variants often missed in other approaches,” Dr. Scherer notes. “It could also allow for earlier diagnosis of autism, particularly among siblings of children with autism.”

Providing vital information to families
Indeed, the study’s medical team is providing useful information to several of the families participating in the study. This includes:

* Alerting undiagnosed family members that they carry newly identified autism-risk genes and encouraging them to receive thorough evaluation and care.

* Alerting members of one family that they carry a newly identified gene change affecting the brain pathway involved in Fragile X syndrome. This family may benefit from medicines currently being evaluated for treating the social withdrawal associated with this syndrome.

* Alerting another family that several members carry an autism gene associated with CHARGE syndrome. A rare disorder, CHARGE involves developmental problems affecting the eyes, ears, heart and brain. In this instance, the newly identified gene has the potential to speed diagnosis and care of a difficult to identify syndrome.

* Reassuring news for a family carrying a newly identified gene associated with autism and infant seizures. Because these seizures are generally harmless, the information can reassure parents and physicians who might otherwise suspect a serious brain disorder.

“Whole genome sequencing offers the promise of being the ultimate tool to advance understanding of the genetic architecture of autism,” Dr. Scherer concludes. “In the future, results from whole genome sequencing could speed the diagnostic path and highlight molecular targets for pharmacological intervention, paving the way for individualized treatments in autism.”

Also see Guidance on Genetic Testing for Younger Sibling of Child with Autism in the "Got Questions?" blog.

 

You can explore all the research Autism Speaks is funding using this website’s grant searchSubscribe to Autism Speaks Science Digest for more autism research news, blogs and more, delivered biweekly to your inbox.

 

 

 

 

 

 


          Autism Speaks Awards 47 New Research Grants Funding $13.2 Million Over Next Three Years        
Global Autism Science and Advocacy Organization Advances Research in Epigenetic and Gene-Environment Influences, Neurobiology, and Studies Concerning Adolescents and Adults with Autism

Autism Speaks announced the awarding of 47 new research grants totaling $13,242,279 in funding over the next three years. Grants awarde

December 21, 2011

New York, N.Y. (December 21, 2011) – Autism Speaks, the world’s largest autism science and advocacy organization, today announced the awarding of 47 new research grants totaling $13,242,279 in funding over the next three years. Grants awarded this year not only respond to Autism Speaks funding priorities, but collectively move autism research forward toward improving diagnosis and treatment and quality of life for individuals with autism spectrum disorder (ASD). New this year is the Autism Speaks Translational Postdoctoral Fellowship Program, which encourages new investigators to enter into the field of ASD translational research – translating laboratory findings to clinical practice. These fellowships are critical in developing their careers so that their work can make a lasting impact on the field of autism research.

“Suzanne and I are extraordinarily proud that this is the largest set of grant awards in Autism Speaks history,” said Autism Speaks Co-founder Bob Wright. “These novel research projects have tremendous potential to open new avenues to understanding autism.”

“The Autism Speaks research portfolio is the core of our support for individuals impacted with ASD and their families,” added Autism Speaks President Mark Roithmayr. “We know that as families seek the best possible diagnosis, treatments and therapies for their loved ones, validated research is critical in giving families confidence and hope for improving the lives of individuals with ASD,” he continued. “Without the incredible generosity of our community and corporate partners, and the funds raised at hundreds of Walk Now for Autism Speaks events throughout the year, this research and this level of funding would not be possible.”

Studies will be funded to increase our understanding of environmental influences that may increase the risk of ASD among those who are genetically predisposed to the disorder; on biomarkers that may be useful for identifying infants at risk for developing ASD; and to improve early diagnosis in ways that can lead to earlier intervention and improved outcomes. The first U.S. autism prevalence study using total population sampling methods will be conducted, as current prevalence rates are based on reviews of records and may miss undiagnosed children and adults in the community. Funding this year will help create of the world’s largest whole-genome library of individuals with autism through a historic collaboration with the Beijing Genome Institute. Animal models designed to identify brain pathways involved in autism will be used to test five compounds that may help restore healthier functioning to these brain pathways. Autism Speaks is funding studies on adult development, including research into sleep disorders, quality of life assessments and predictors of positive long-term outcomes in adults with ASD, and will update the economic cost of autism, including assessment of how particular services and supports may reduce lifetime costs. New methods will be developed to increase access to diagnosis and early intervention services in underserved, low resource communities in North America and around the world.

“These projects will make a real impact on the lives of people with autism and their families,” states Autism Speaks Chief Science Officer Geraldine Dawson, Ph.D. “The wide range of outstanding projects we are funding will provide new and more accurate estimates of the prevalence and costs of autism, test new medicines that have the potential for alleviating core symptoms of autism, and innovative strategies for lowering the age of early detection and improving access to treatments in underserved communities.”

Basic & Clinical Grants

Cell-based models have increasingly become centerpieces in translational research aimed at understanding basic mechanisms impacted by the growing number of autism risk genes. An innovative project featuring a stem cell model of 15q duplication syndrome from Eric Levine, Ph.D., from the University of Connecticut will receive a two-year pilot grant to study the functional and structural properties of synapses in patient-derived neurons. Cortical interneurons derived from genetically modified animals will feature in another two-year pilot grant awarded to John Rubenstein, M.D., Ph.D., from the University of California San Francisco studying the impact of transplanting these cells on a variety of behavioral endpoints. Klaus Hahn, Ph.D., from the University of North Carolina will utilize a mouse model of Angeleman syndrome to study the involvement of signaling pathways in specific molecular, cellular, and circuit deficits that may lie at the heart of ASD pathogenesis in another two-year pilot grant.

The importance of animal models as platforms for evaluating the therapeutic potential of experimental drug candidates will be studied in several three-year “full” grants. Two examples of projects focused on mutant mouse models of Rett syndrome include David Katz, Ph.D., from Case Western Reserve, who will investigate the effects of a novel small molecule TrkB agonist (LM22A-4) on sensorimotor gating and behavioral endpoints. Mustafa Sahin, M.D., Ph.D., at Children’s Hospital Boston will use a different mouse model of Rett syndrome to examine neuronal connectivity in an effort to nail down the critical period for emergence of ASD-like phenotypes and sensitivity to treatment with rapamycin in a three-year grant. In an innovative project utilizing voles, Larry Young, Ph.D., of Emory University will study the mechanisms of action for oxytocin in social behaviors and seek to validate MC4R as a new drug target for social deficits in autism. Two-year pilot funding has been granted to Craig Powell, M.D., Ph.D.,  of the University of Texas Southwestern to collect preliminary data to establish the feasibility of reversing Shank3 mutant mice back to normal Shank3 after brain development is complete and identify which synaptic function differences and which behavioral differences are rescued.

Two projects will focus on epigenetic modification of gene function. The potential of epigenetics as a mechanism to explain gene and environment interactions in ASD will be addressed by Dani Fallin, Ph.D., of Johns Hopkins University, who received a full grant for three years to measure genome-wide DNA methylation in 600 individuals from the Study to Explore Early Development. The genome-wide distribution of a newly described type of epigenetic modification to DNA will be profiled in ASD in a project by Xuekun Li, Ph.D., from Emory University, in a two-year Pilot grant. Dr. Li has developed an innovative method for studying this potentially important form of epigenetic regulation.

Several studies focus on aspects of early behavioral risk for ASD.Judith Gardner, Ph.D., at the New York State Institute for Basic Research will receive a full grant with three years’ funding to prospectively follow high-medical-risk NICU infants from birth to two years to characterize early neurobehavioral markers as risk factors for ASD. Also focusing on high risk infants, Martha Kaiser, Ph.D., at the Yale Child Study Center will receive a full three-year grant to examine very early development of the social brain utilizing functional near-infrared spectroscopy (fNIRS) in a prospective, longitudinal study of infants at high risk for developing autism. Patrick Bolton, Ph.D., of Kings College London will be funded for three years with a full grant in which he aims to better describe a genetic disorder (tuberous sclerosis) and determine whether those affected also have an ASD, either in terms of the broader autism phenotype or significant autistic traits. In conjunction with the Baby Siblings Research Consortium and the Autism Genetic Resource Exchange, Lonnie Zwaigenbaum, Ph.D. from the University of Alberta will take a genetic approach to assess the relationship between ASD-related gene copy number variation and symptom trajectories of at-risk infants between ages 6 and 36 months in a full grant funded for three years. Finally, a treatment study by Rebecca Landa, Ph.D., CCC-SLP, from the Kennedy Krieger Institute will be funded by a three-year full grant to examine the efficacy of a social enhancement intervention on social processing in toddlers with ASD.

To identify risk factors on a population basis, Brian Lee, Ph.D., at DrexelUniversity will study a large, well characterized birth cohort in Sweden to examine whether early immune abnormalities may be associated with risk of ASD through a full, three-year grant. Paul Patterson, Ph.D., from California Institute of Technology will also receive a full, three-year grant to examine putative immune system involvement during fetal development in risk of developing autism by expanding his pioneering work in mouse models of maternal viral infection. A potential role for genetic defects in carnitine biosynthesis in risk for autism will be further explored in a two-year Pilot project awarded to Arthur Beaudet, M.D., at Baylor College of Medicine.

Four studies focus on the underserved population of adolescents and adults with ASD. Suzanne Goldman, Ph.D., FNP, BC, of Vanderbilt University is awarded a full three-year grant to investigate sleep behaviors in adolescents and young adults with autism and determine how sleep affects daytime behavior. Emily Simonoff, M.D., FRCPsych, of the Institute of Psychiatry, UK, and Marsha Seltzer, Ph.D., of the Waisman Center, University of Wisconsin, both receive full three-year grants to improve our understanding of the quality of life and outcomes for individuals of adults with ASD by tracking and characterizing different cohorts of adults who had previously been diagnosed during adolescence. A two-year pilot project is funded for J. Paul Leigh, Ph.D., CHPR, at the University of California Davis to focus on the economic burden created by ASD in current and future adult populations.

Basic & Clinical grants include both full grants which support researcher projects over three years based on the specific project scope and budget, and pilot grants which fund researchers for two years at a set funding rate of $60,000 per year. Grants were selected which focused on innovation, research strategy, and relevance of the topic to Autism Speaks research priority areas.

Postdoctoral Fellowships in Translational Autism Research

2011 is the inaugural year of the Autism Speaks Translational Postdoctoral Fellowship Program funding a total of $1,266,289 over two-years. The Translational Postdoctoral Fellowship seeks encourage new investigators to enter into the field of ASD translational research by providing funding for multidisciplinary training with at least two mentors. The fellows receive a stipend that varies according the years of experience of experience after their doctoral degree (based on the NIH scale) and a modest research expense allowance.

This first class of Translational Postdoctoral fellows will investigate a variety of innovative human neuroimaging approaches. Nicolaas Puts, Ph.D., at Johns Hopkins will focus on adapting magnetic resonance spectroscopy (MRS) to non-invasively characterize changes in brain neurochemistry associated with autism in pediatric populations. Isabelle Buard, Ph.D., from the University of Colorado Denver will also utilize MRS, but in combination with magnetoencephalography to define motor-specific features that are impaired in autism. In another integrative approach, Adam Naples, Ph.D., from Yale will concurrently measure eye movement and electrical brain activity (EEG) to study responses during simulated reciprocal social interactions. Using Diffusion Tensor Imaging, Rebecca Jones, M.Phil., from Weill Cornell Medical College seeks to examine behavioral and neural underpinnings of learning as predictors of response to intervention in young children. Daniel Campbell, Ph.D., from Yale addresses the critical need for solid statistical methods to ensure the success of imaging approaches. His project expands the development of novel techniques for predicting diagnostic outcome from a variety of different imaging and clinical data sources.

Translation works in both directions from the proverbial bench to beside and back to the laboratories. Additional grants fund the work of Post Doctoral Translational Fellows who will focus on characterizing animal models that were informed by human genetic risk factors identified for autism. Olga Penagarikano, Ph.D., from the University of California Los Angeles will expand the characterization of the CNTNAP2 knock-out mice, including evaluation of novel drug candidates. A novel electophysiological approach will be employed by Dr. Joao Peca from the Massachusetts Institute of Technology to study the neural circuitry underlying ASD phenotypes in the Shank3 mouse, a model of Phelan McDermid Syndrome. Portia McCoy, Ph.D., of the University of North Carolina Chapel Hill will examine the effects of a novel drug candidate, UNCilencer1, in reversing synaptic plasticity deficits in the UB3EA mouse model of Angelman syndrome. These projects have the potential to interpret the biological underpinnings of autism, which can be translated back to the bedside.

A variety of other fellowship projects were recommended for consideration. These include a project from Allison Knoll, Ph.D., of the University of Southern California, who has proposed studies in both mice and humans aimed at understanding the role oxytocin, vasopressin, and mu opioids in shaping early social learning and brain development. Haim Belinson, Ph.D., at University of California San Francisco will work to expand work identifying genomic factors that participate in the putative cortical abnormalities (“patches”) recently reported by Eric Courchesne’s lab. Melis Inan, Ph.D., at Weill Cornell Medical College will look at the role of candidate autism related genes on mitochondrial dynamics and functioning of PV+ cortical interneurons. Brandon Keehn, Ph.D., at Children’s Hospital Boston will be studying how measures of novelty processing, arousal, and joint attention correlate with the development of disengagement abilities to determine the impact of early attentional function on the development these processes.

About Autism
Autism is a general term used to describe a group of complex developmental brain disorders – autism spectrum disorders – caused by a combination of genes and environmental influences. These disorders are characterized, in varying degrees, by social and behavioral challenges, as well as repetitive behaviors. An estimated 1 in 110 children in the U.S. is on the autism spectrum – a 600 percent increase in the past two decades that is only partly explained by improved diagnosis.

About Autism Speaks
Autism Speaks is the world’s largest autism science and advocacy organization. Since its inception in 2005, Autism Speaks has made enormous strides, committing over $160 million to research and developing innovative resources for families. The organization is dedicated to funding research into the causes, prevention, treatments and a cure for autism; increasing awareness of autism spectrum disorders; and advocating for the needs of individuals with autism and their families. In addition to funding research, Autism Speaks has created resources and programs including the Autism Speaks Autism Treatment Network, Autism Speaks’ Autism Genetic Resource Exchange and several other scientific and clinical programs. Notable awareness initiatives include the establishment of the annual United Nations-sanctioned World Autism Awareness Day on April 2, which Autism Speaks celebrates through its Light it Up Blue initiative. Also, Autism Speaks award-winning “Learn the Signs” campaign with the Ad Council has received over $300 million in donated media. Autism Speaks’ family resources include the Autism Video Glossary, a 100 Day Kit for newly-diagnosed families, a School Community Tool Kit, a Grandparent’s Guide to Autism, and a community grant program. Autism Speaks has played a critical role in securing federal legislation to advance the government’s response to autism, and has successfully advocated for insurance reform to cover behavioral treatments in 29 states thus far, with bills pending in an additional 10 states. Each year Walk Now for Autism Speaks events are held in more than 80 cities across North America. To learn more about Autism Speaks, please visit www.autismspeaks.org.

About the Co-Founders
Autism Speaks was founded in February 2005 by Suzanne and Bob Wright, the grandparents of a child with autism. Bob Wright is Senior Advisor at Lee Equity Partners and Chairman and CEO of the Palm Beach Civic Association. He served as Vice Chairman of General Electric; and as the Chief Executive Officer of NBC and NBC Universal for more than twenty years. He also serves on the board of directors of the Polo Ralph Lauren Corporation, Mission Product, EMI Group Global Ltd., and AMC Networks Inc., and is a Trustee of the New York Presbyterian hospital. Suzanne Wright is a Trustee Emeritus of Sarah Lawrence College, her alma mater. Suzanne has received numerous awards, the Women of Distinction Award from Palm Beach Atlantic University, the CHILD Magazine Children’s Champions Award, Luella Bennack Volunteer Award, Spirit of Achievement award by the Albert Einstein College of Medicine's National Women’s Division and The Women of Vision Award from the Weizmann Institute of Science. In 2008, the Wrights were named to the Time 100 Heroes and Pioneers category, a list of the most influential people in the world, for their commitment to global autism advocacy. They have also received the first ever Double Helix Award for Corporate Leadership from Cold Spring Harbor Laboratory, the NYU Child Advocacy Award, the Castle Connolly National Health Leadership Award and the American Ireland Fund Humanitarian Award. In the past couple of years the Wrights have received honorary doctorate degrees from St. John’s University, St. Joseph’s University and UMass Medical School.


          IMB Honours Scholarship for International Student at University of Queensland in Australia, 2017        

This scholarship has been extracted from the BEST SCHOLARSHIP WEB: Scholarships 2017 - 2017 =)

Applications are invited Institute of Molecular Bioscience (IMB) Honours Scholarship at the University of Queensland in Australia. Australian and Permanent Residents or NZ citizens and International student are eligible to apply for this scholarship. IMB is one of Australia’s leading multidisciplinary life sciences research institutes working to pursue discoveries in medical genomics, drug discovery and biotechnology. Ranked in the world’s top 50, the University of Queensland is one of Australia’s leading research and teaching institutions. UQ’s world-class campuses facilitate the best teaching practices and optimal learning experiences. In order to gain entry to an academic program at UQ, applicants will have to

All the complete information in IMB Honours Scholarship for International Student at University of Queensland in Australia, 2017 !


          Fellowship Programme for Medical and Health Science Faculties Long tem & Short term        

Department of Health Research
Ministry of Health and Family Welfare New Delhi
The Department of Health research is developed by Government of India for ‘Human Resource Development for Health Research’. They have various schemes for Health Manpower development. These Schemes of DHR are specially designed for faculties of Medical Colleges / Biomedical Institutes for improving health management and health care.
At present applications are invited for various fellowship schemes as below. The faculty or researcher has to submit application in the prescribed format. The faculty or researcher must be regular employee in Medical Colleges/Research Institutions in India for award of fellowships.  
I.                   Long-term (6-12 months) fellowship/training in foreign Institutes, in identified areas
Areas identified for fellowship:
-          Toxicology specially areas like nano-toxicology
-          Genomics
-          Proteomics
-          Geriatrics
-          Quality Control (QC) and Quality Assurance (QA)
-          Health Informatics
-          Disease Modeling
-          Health Economics
-          Environmental Health
-          Stem cell Research.
-          Any other area relevant for the country (Applicant will have to provide special justification as how it will benefit the country).
Duration:6 to 12 months
 Eligibility:
-          Only Indian citizens are eligible.
-          The faculty employed on a permanent basis in recognized medical college/ research institution and having at least 3 years of teaching/ research experience.
-          Age: not exceeding 45 years.
-          Qualifications: MD/MS/ PhD.
-          The application should be forwarded by the Employer/ Head of the Institution agreeing to the Terms and Conditions of the fellowship.
-          The applicant should submit a concrete plan of proposed training and utilization plan of the training after availing the fellowship.


II.                Short -term (1-3 months) orientation/training in foreign Institutes, in identified areas
Areas identified for fellowship:
-          Toxicology specially areas like nano-toxicology
-          Genomics
-          Proteomics
-          Geriatrics
-          Quality Control (QC) and Quality Assurance (QA)
-          Health Informatics
-          Disease Modeling
-          Health Economics
-          Environmental Health
-          Stem cell Research.
-          Any other area relevant for the country (Applicant will have to provide special justification as how it will benefit the country).
Duration: 1 to 3 months
Eligibility:
-          Only Indian citizens are eligible.
-          The faculty employed on a permanent basis in recognized medical college/ research institution and having at least 3 years ofteaching/ research experience.
-          Age: not exceeding 55 years.
-          Qualifications: MD/MS/ PhD
-          The application should be forwarded by the Employer/ Head of the Institution agreeing to the Terms and Conditions of the fellowship.
-          The applicant should submit a concrete plan of proposed training and utilization plan of the training after availing the fellowship.

III.             Long-term (6-12 months) fellowship/training in Indian Institutes, in identified areas

Area identified for fellowship:
-          Toxicology,
-          Genomics
-          Proteomics
-          Geriatrics
-          Stem cell research.
-          Clinical Trials
-          Good Clinical Practices (GCP)
-          Good laboratory Practices (GLP)
-          Quality Control (QC) and Quality Assurance (QA)
-          Modern Biology
-          Biotechnology
-          Genetics
-          Drugs Chemistry
-          Operational Research
-          Health Informatics
-          Medical Ethics
-          Disease Modeling
-          Health Economics
-          Environmental Health
-          Any other area relevant for the country (Applicantwill have to provide special justification as how it will benefit the country).
 Duration: 6 to 12 months
Eligibility:
-          Only Indian citizen are eligible.
-          The faculty employed on permanent basis in recognized medical college/ research institution and having atleast 3 years of research experience.
-          Qualifications: MD/MS/ PhD
-          Age: not exceeding 45 years
-          The application should be forwarded by the Employer/ Head of the Institution agreeing to the Terms and Conditions of the fellowship.
-          The applicant should submit a concrete plan of training and utilization plan of the training after availing the fellowship.



IV. Short-term (1-3 months) orientation/training in Indian Institutes, in identified areas

The number of fellowships in each category may vary but expected to be 30 in each category. The applicants who want to apply may send 15 copies (print) and a soft-copy of application in the prescribed format by 31st Decedmber 2012to
Dr. K. Satyanarayana,
Scientist ‘G’ & Coordinator -Department of Health Research,
Indian Council of Medical Research,        
V. Ramanlingaswami Bhawan Ansari Nagar
New Delhi–110029.
(Tel: 011-26589258,  011-26589699)

The envelope containing the application must clearly be marked as:
Application for HRD scheme of DHR and the category of fellowship. The soft copy of the application may be sent to kanikaram_s@yahoo.com, or rasikbg@gmail.com , or ashoogrover@gmail.com .
Application for each category of fellowship should be separately sent.
More details available on http://www.icmr.nic.in/icmrnews/dhr_fellowship/dhr_fellowship.htm



          Minnesota Partnership Awards Six New Research Grants        
New treatments and diagnostics for Alzheimer’s and cancer dominate the 2017 research awards recently announced by the Minnesota Partnership for Biotechnology and Medical Genomics. The state-supported funding…
          Minnesota Partnership Announces Seven New Research Awards        
ROCHESTER, Minn. — New treatments and diagnostics for Alzheimer’s and cancer dominate the 2016 research awards recently announced by the Minnesota Partnership for Biotechnology and Medical Genomics. The state-supported…
          Minnesota Partnership Awards Six New Research Grants        
MINNEAPOLIS/ROCHESTER, Minn. — New treatments for cancer and heart disease dominate the 2015 research awards recently announced by the Minnesota Partnership for Biotechnology and Medical Genomics. The…
          Minnesota Partnership Announces Scientific Infrastructure Awards        
ROCHESTER and MINNEAPOLIS, Minn. — The Minnesota Partnership for Biotechnology and Medical Genomics has awarded $2.5 million to four teams of researchers to support scientific infrastructure used…
          Unwinding from HIMSS16        
I'm finally unwinding after having a great time at HIMSS 2016 (#HIMSS16). My personal highlight was participating in two Dell Healthcare Tweetups with @MandiBPro and @drnic1 as we chatted about some of the evolving trends in health care. We discussed how data-driven care can improve patient outcomes as long as clinicians have access to the right data at the right time and the right place. We still live in a world where interoperability remains a major barrier, but perhaps 2016 will be the year where we make some significant strides in this area through broader collaborations and partnerships across the health IT industry.


At HIMSS this year, you couldn't walk around the conference without seeing signs about population health, data analytics, and precision medicine. We discussed these topics at the Dell Healthcare Tweetups and heard different perspectives on cancer care, mental health, team-based care, and the practice of medicine in community-based settings. More patients are getting engaged in their own health care and we are generating so much health data, but clinicians need to know how to effectively tap into all this data to get meaningful and actionable information that will improve patient outcomes. We're seeing a lot of exciting advances in cancer care, especially around precision medicine and genomics. We also heard about how Dell's Cloud Clinical Archive services are integrating genomics into their core offerings. Speaking of genomics and big data, Dell has a longstanding collaboration with Translational Genomics Research Institute (TGen) and they are empowering clinicians and researchers to fight pediatric cancer. 


Make sure to follow @DellHealth for the latest in health IT and don't miss the 2016 #DoMoreHIT Healthcare Think Tank on Tue, Mar 15 2016 2:00 PM EDT -  5:00 PM EDT
http://livestream.com/Dell/2016DoMoreHIT



          Election 2013: Day 16 (or, Frankly my dear, I don’t think they giver a damn)        

Today was an odd one of the election. There were a couple new policies released, but it wasn’t much of a big deal.

It was such a bit of a nothing day that ABC’s 7:30 Report didn’t even get round to recapping the day’s events till after its expose on the Cronulla Sharks. Twitter - ellinghausen- Opposition Leader Tony Abbott ...

It was a day that reinforced that there’s not a lot of money going around. The old days of needing a policy in the billions to get the wow factor are gone. And so today we had Tony Abbott on the Great Ocean Road looking at potholes.

He was there to hand out $25 million over 5 years to help repair the road on the ocean that is so great.

Cripes. Back in 2004 or 2007 such a thing would have been lucky to make it onto a media release.

But when the budget is in an “emergency” you can’t very well go spending hand over fist.

Of course however the Liberal Party is handing out a a fair bit of money for one policy – it’s PPL. And for the third day is was the most talked about policy. And not in a :gee this thing is a great vote winner way.

Robert Gottliebsen picked up on the fact that for the Libs policy to be fully paid for by hitting not businesses, but shareholders. And not indirectly – but directly:

But then comes Tony and Joe’s sleight of hand attack on retirees. Many big corporate taxpayers, like banks, pay around three quarters of their profits out in dividends and there is constant pressure from retirees for companies to payout more, especially now interest rates on bank deposits have been reduced. Most dividends (but not all) are fully franked because they come out of tax paid profits.

So a superannuation fund obtains a franking credit equal to the tax paid by the company. Those franking credits are currently calculated at a tax rate of 30 cents in the dollar. When the Abbott-Hockey plan is introduced the franking credits will be calculated on the basis of 28.5 cent in the dollar. They are worth less and so the retirees and those saving to pay for retirement cop the bill because Abbott and Hockey have simply swapped a tax for a levy aiming to lower the franking credit.

In other words, while big businesses will end up paying an effective 30% tax rate, what is happening is they first get the cut to 28.5% then they get the levy to go back to 30%. But the franking credit will be calculated on the 28.5% rate not the 30%. And thus it is worth less.

Sweet eh?

The Liberal Party, who so loudly and boldly defend self-funded retirees, is now getting them to help pay for a paid parental leave scheme which they won’t get any possible benefit from and which is also a dud of a scheme because it won’t deliver the productivity benefits Abbott and Hockey claim it will.

Wow that’s great policy and outstanding politics!

Lenore Taylor in Guardian Australia went back to the Parliamentary Budget Office’s costings of the Greens’ PPL scheme. The Greens’ scheme cuts out at $100,000 rather than $150,00 but otherwise is much the same.

As Taylor writes:

The costings show that the Coalition’s decision not to allow shareholders to claim franking credits, which reduce their income tax bill, on the 1.5% levy reduces the cost of the scheme to the government by $3.2bn over the first four years. The saving amounts to about $1.6bn per year once the scheme is fully up and running.

Now back in May when the PBO’s costing of the Libs scheme were apparently leaked to the AFR the Lib’s rejected both the leaked costings and those by the Australia Institute

Senator Cormann also rejected calculations by The Australia Institute that suggest a Coalition government would have to double its planned levy on business from 1.5 per cent to 3 per cent to adequately fund the scheme, because 46 per cent of the extra company tax raised under the scheme as proposed would be lost in franking credits returned to shareholders.

It seems the reason why it might not be losing the franking credit is because they’re not going to be returned to shareholders.

Perhaps the best response the ALP can have is that of Joe Hockey back when interest rates were cut in May:

We express concerns for those people that rely on income from savings accounts. Let’s think about all of those people for the moment who are facing lower income from their savings – particularly self-funded retirees.

Today Tony Abbott, was shall we say, a tad effusive on the figures of how it was all going to be paid. Yesterday Joe Hockey in an interview with Neil Mitchell put the amount that the levy would cover from 50% to 60% to 70%. Today a journalist in the press gallery tried to get something a bit more narrow out of Tony Abbott:

QUESTION: Joe Hockey did have a stab yesterday at putting a figure on a share of the PPL would be covered by the levy. It ranged between 50 per cent and 70 per cent, but he did have a go at it. Can you have a go at it and tell us what the figure is and how concerned should you be that your Treasury spokesman can’t put a figure on it within a 20 per cent point range?

TONY ABBOTT: Well I saw the debate, or aspects of the debate last night, between Joe Hockey and the Treasurer and I think anyone watching the debate on Q&A last night would say that the stewardship of our nation’s finances will be in much better shape under Joe Hockey than under the Treasurer. Now, the fact is it’s been fully costed by the Parliamentary Budget Office. It is fully funded. It’s fully funded by the company levy, the levy on large companies, the discontinuation of the existing scheme and by ending double dipping. Now it is fully funded, fully costed, it’s a very important economic advance.

This was a whole day after Hockey’s flub. You would think they could come up with a better answer than that!

Do they care that they’re being hounded about the costing? It seems not at this point.

My feeling however – and it is mostly based on the attitude of the QANA audience last night to both Hockey and Bowen –  is that people are getting tired of the ”in good time” line.

This is Tony Abbott’s “signature policy”. This is the one he has had hanging around his neck the longest. It is his baby and he is either too embarrassed to explain how it is paid for, or he is too ignorant of the details. Take you pick. It ain’t good for him

In an election where big numbers are thin on the ground and the details of this policy are coming apart bit by bit, I expect to see this once again be a topic for questions tomorrow. Especially as state governments are involved so there’s plenty of places to get quotes of Premiers saying they’re not sure about it.

Importantly tomorrow night Rudd and Abbott are having their “people forum” debate in Brisbane. If Abbott hasn’t announced all the costings for it by then, expect Rudd to go in very hard. And given last night on QANDA the audience was frequently yelling out to both sides for “the numbers”, saying “It’s fully funded” won’t be enough, no matter how often he says it.

***

Kevin Rudd’s day started at a school in the electorate of Graeme Perrett (he who once vowed to resign if Rudd came back). He was fired up, but as Katharine Murhpy noted, it did remind one a bit of John Hewson in 1993.  Passion is great, but you don’t want to be seen shouting and leading a chorus too much; it starts to look desperate.

His big policy today was $250 million for medical research – $125m from the govt, $125m from the private sector. 

He announced:

The Government will contribute $125 million to be matched at least dollar for dollar by private sector investors, generating a total investment of $250 million, a major injection of investment capital into our emerging biotechnology sector.

In addition, Labor will implement around $70 million of investments and reforms as part of its initial response to the 2013 McKeon Review of Health and Medical Research.

This includes delivering $47.5 million in funding for 19 Centres for Research Excellence to encourage research in fields identified as national priorities.

This also includes establishing four new Centres that will focus on Indigenous health, national clinical trials, international health and genomics.

Kevin Rudd to unveil $125m fund for health and medical research - World news - theguardian.com

It comes off the back of the Strategic Review of Health and Medical Research, and geez policy is so much better when it actually comes after some actual research into what should be done. And because the $125m is an equity based investment – ie not a grant – it is in effect “off budget” – because there are expected returns from the investment.

Sound policy based on a report, coupled with $70m in announcement of things already funded by the government. That’s who you do policy during an election campaign when you;re the government.

The Libs have also used the so-called McKeon Review to come up with e medical research policy. Their policy is about streamlining funding grant processes, rather than giving more money. So it will be interesting to see if Peter Dutton pops up his head to respond in any meaningful way.

Thus far all I’ve seen is a comment. I wonder if he’ll ever get to stand next to Abbott in a press conference and answer some questions?

We wait.. and wait.. and wait… (ok let’s be honest, no one would ever really wait to hear Peter Dutton speak) 

***

Today Tony Abbott also announced he would change the name of Disability Care back to the National Disability Insurance Scheme. Now I know some have suggest the current name is a bit demeaning, but I’ve never been too hung up about it.

But it is interesting that Kevin Rudd hasn’t campaigned on the NDIS at all. It has received a bit of a mention, but only in a list of things the ALP has done.

It is clearly Julia Gillard’s policy, but Rudd should be able to swallow the pride and run hard on it.

***

Bill Shorten turned up at the National Press Club for a debate on education. Only problem is Chris Pyne was a no show. Not a shock. But it was a blessing for anyone who had tuned in to watch.

I know Shorten gets some grief, and he was full of passion today (perhaps too full of passion) but I think when he leaves the factional argy bargy alone and talks policy he speaks well.l I still recall the speech he gave at the ALP National Conference in support on the NDIS that was as good as you’ll see in Australian politics.

***

A Liberal Party candidate in Greg Combet’s old seat was dumped after reports came out that he had run a web forum for of all things Mini Coopers, which had a lot of sexist, racist, jokes on it.

I realise because he ran it he has extra responsibility but I’m predicting this will not be the last time a candidate will be kicked off because of something he (it’ll most likely be a he) said on the internet. As Barrack Obama said to a of school kid who asked him what he could do to become President one day:

“I want everybody here to be careful about what you post on Facebook, because in the YouTube age whatever you do, it will be pulled up again later somewhere in your life. That’s number one.”

Yep.


           Molecular cloning and tissue expression of FAT, the human homologue of the Drosophila fat gene that is located on chromosome 4q34-q35 and encodes a putative adhesion molecule.