Giannoti reported that her team's data suggests that the most likely mass region for the Higgs lies between about 116-130 gigaelectron volts, or GeV, which corresponds very roughly to 116-130 times the mass of the hydrogen atom.
She reported an excess of collision events at around 126 GeV, but could not conclusively declare a discovery. Guido Tonelli, spokesperson for the CMS experiment, also reported what he called "intriguing, tantalizing hints" of the particle. His team reported a most likely mass range for the Higgs at between 115-127 GeV, with their results most compatible with a mass of 124 GeV. Both teams do not have enough statistics to declare a discovery.
Together, these two groups have independently found intriguing collision events between 124 and 126 GeV, suggesting that the Higgs may have been produced at the LHC.
The team recently built a smaller hardware version of the brain simulation, one with just 256 neurons, 262,000 programmable synapses, and 65,000 learning synapses. The good news is that this machine runs at within an order of magnitude of the power that a real brain consumes.
and we used SNP-based relatedness calculations to replicate estimates that about half of the variance in g is accounted for by common genetic variation among individuals.We conclude that different approaches than candidate genes are needed in the molecular genetics of psychology and social science.
High-throughput sequencing of small RNA populations allows the locations of the double-stranded RNA precursors to be inferred. We have developed methods to analyse small RNA sequencing data from mutliple biological sources, taking into account replicate information, to identify robust sets of siRNA precursors. Our methods show good performance on both a set of small RNA sequencing data in Arabidopsis thaliana and simulated data sets.
The creation of a “special OA” for the developing world runs the risk of perpetuating a view in which 85% of the world will always be catching up. Yes we need to try and build systems that ensure access to all scholarship, primary and derived.
How to do that is an important debate, and one I hope will be at the centre of the Berlin10 conference to be held in Stellenbosch in South Africa next year. To not use that meeting to address the issues and challenges of business models and safeguards that help preserve access and optimise impact for the developing world would be a terrible loss.
Whether or not bacterial species exist remains an unresolved issue of paramount theoretical as well as practical consequences. Here we review and synthesize the findings emerging from metagenomic surveys of natural microbial populations and argue that microbial communities are predominantly organized in genetically and ecologically discernible populations, which possess the attributes expected for species.
These sequence-discrete populations represent a major foundation for beginning high-resolution investigations on how populations are organized, interact, and evolve within communities. We also attempt to reconcile these findings with those of previous studies that reported indiscrete species and a genetic continuum within bacterial taxa and discuss the implications for the current bacterial species definition.
"One of the most controversial issues the study team will face is whether to look for and whether to report 'incidental' genetic findings or mutations that suggest previously unsuspected genetic predisposition to cancer, heart disease or other conditions that are found in otherwise healthy individuals," Green said. "Reporting too many incidental results could generate unnecessary and costly medical tests, while reporting too few could deprive patients and doctors of valuable risk information."
Nov. 28-29, 2011, in Abuja, Nigeria
The landmark meeting was sponsored by Ethics and Genomics Research in Africa (EAGER-Africa) (http://eager-africa.com), part of the Human Heredity and Health in Africa (H3Africa) program. NIH and the Wellcome Trust, a global charity based in London, formed H3Africa in 2010 with input from the African Society of Human Genetics.
The goal is to improve African scientists' capacity to solve some of their country's health problems through research on the genomic and environmental causes of common diseases. The National Human Genome Research Institute (NHGRI) administers H3Africa on behalf of the NIH Common Fund.
For instance, recently, the new high-throughput DNA sequencing technologies have produced a huge amount of short read data, and it is known (Hansen et al., 2010) that these data might be biased for unknown reasons. In some studies, it is necessary a reference-free validation of short read data, and novel methodologies have already been proposed (Schroder et al., 2011) to address this problem.
Article VII deals with the provision of ‘assistance’ by States Parties if a State Party is ‘exposed to danger’ because of a breach of the Convention. It was noted that neither ‘assistance’ nor ‘exposed to danger’ had been clarified by any Review Conference.
Some states indicated that Article VII should be regarded as a sub-set of the Article X issues while others indicated they were a distinct set of issues ? no government is likely to have at its disposal the resources to respond to a severe biological attack and so the concept of receiving assistance applies to developed as well as developing countries.
GenoDiveの共同開発者の西村邦裕さんが分子生物学会のポスター発表を第1日目 1P-0896 でなされています
In this workshop, we would like to discuss and manifest for new challenges on biological databases in terms of their effective developments and research applications from various viewpoints, which lead us to the ideal next generation databases.
五條堀先生 / 問: 今後のデータベース設計のビジョンは？ 答: 置かれている対象物の環境や時系列が大切になる. #2w4ii #mbsj2011
Data quality and relational (multi-) information. データの質とリンク情報が重要. 核酸と臨床情報のリンクがコンパニオン診断の開発には重要になる. / 的場先生（(株) DNAチップ研）#2w4ii #MBSJ2011
メタゲノム解析にとって, NCBIのメタゲノムデータ生物種情報がカオスなのが問題. Uncultured Bacterium, Uncultured organismなど, 生物種の情報として意味をなさないエントリが多い / 中村先生（阪大
解析にはキュレーションされたデータベースを使うことが重要である. silva (http://www.arb-silva.de/) curatedな16S rRNAデータベース
今週の「人工知能学会25周年合同研究会・シンポジウム」は研究会ごとにハッシュタグがあり一覧表示できるサイトがある. 大規模学会の年会は全部こうなればいいのに bit.ly/tpTuEn
BioLODにはBroadly INtegrated Ontological Linked Open Data と Biological Linked Open Data)の2つの意味があるらしい。初めて知った。 #sig_swo
多種多様な生命科学系DB群を上位オントロジーを用いて生物種横断的に統合。理研哺乳類ゲノム総合DB，理研植物フェノーム統合DB，理研タンパク質実験・構造統合DB，生物医学関連および上位オントロジーなど。
スキーマ定義はどうするのか？OWL意味論に従って矛盾をゼロにするのは難しい。WordNetは構造はRDFだけどオントロジーは定義しない。クラス定義はなくてすべてインスタンス。(WordNet日本語化へのLODアプローチ)
中国人と日本人はGWASできれいにわかれる（緑中青日） twitpic.com/7s7za7 源 bit.ly/oGKWUI 欧米人はもっと遠くに分かれる。日本人のゲノムに基づいた研究が欧米人に強い興味をもって評価されるんだろうか
n0rr:
ロシア全土に反政府デモ拡大、ソ連崩壊後で最大規模 | Reuters jp.reuters.com/article/topNew…
rubyやばい http://speakerdeck.com/u/tomstuart/p/programming-with-nothing
Now browsing: "Programming With Nothing" experthuman.com/programming-wi…
「なぜ動物は満月に反応するか？磁気的仮説」 sciencedirect.com/science/articl… 月齢に伴う地磁気変動と、ある種の動物の磁気センサーの感度は光量に依存するため、満月の光によって磁気に対する感度が上がることの2つの効果が合わさって生じる..
野鳥の鳴き声版であれば、ございます(^^; 『ききみみずきん for iPhone』http://t.co/xrjc3meDRT @razoralign: Leafsnapの鳥版はやく
次世代シーケンサのリードを種間で変換するツールRECOT を公開しました: bit.ly/sKoXkR
異種間のゲノム座標変換ツール。SAMを入出力できる。
To goose developers along, Venter?along with the X-Prize Foundation and Medco Health Systems, a health care firm?has put a bounty on the achievement: $10 million to the first team that can meet a standard for accuracy that Venter calls “medical grade.” The task is to sequence the genomes of 100 centenarians, providing a baseline to which other genomes can be compared.
Die Frage nach dem Leben erhielt eine neue Bedeutung, als der amerikanische Biochemiker Craig Venter ein Bakterium aus künstlich hergestelltem Erbgut schuf. Gert Scobel wird mit seinen Gästen darüber diskutieren, wie bahnbrechend die Forschungen der synthetischen Biologie wirklich sind und welche Gefahren damit einher gehen.
Melanie Swan - Genomic Self Hacking from Gary Wolf on Vimeo.
Melanie Swan of DIY Genomics describes the results of sequencing her own genome in the hopes of developing her own personalized preventive medicine strategies. She developed a mobile app that permits exporting of personalized sequencing data more easily.
A series of small nucleotide polymorphisms (SNPs) were identified by Melanie in her own genome relating to cancer, immunity and aging. Importantly, she has made available the results of her own deep sequencing results to be combined and compared with those of other individuals.
2. For the clinician, it would provide a new avenue of investigation to be taken when all other treatment strategies have failed. A guided shot in the dark is better than no shot in the dark at all.
By 2017, quantum physics will help reduce the energy consumption of our computers and cellular phones by up to a factor of 100. For research and industry, the power consumption of transistors is a key issue.
The next revolution will likely come from tunnel-FET, a technology that takes advantage of a phenomenon referred to as "quantum tunneling." At the EPFL, but also in the laboratories of IBM Zurich and the CEA-Leti in France, research is well underway. As part of a special issue of Nature devoted to silicon, Adrian Ionescu, an EPFL researcher, has written an article on the topic.
Now browsing: "クラウド ガール 技術解説マンガ | MSDN" msdn.microsoft.com/ja-jp/windowsa…
”ありがとう、ジョブス”で、科学論文の作成環境に、ジョブスが引き起こした革命について書かれてますな。確かに、その通りだね。Nature ダイジェスト 2011年12月号 : NPG Nature Asia-Pacific: bit.ly/sJr1AO via
遺伝子検査と保険 bit.ly/snCwcn
1985年に米国でHIV抗体検査を保険契約のときに使うようになる→州が禁止に→すでに病気で保険に入れない人とどう違うの？→抗体検査禁止の州から保険会社撤退→1988年末までに抗体検査禁止の州なくなる。
米の保険会社マジこえー…こんなんが日本の医療保険と同じ市場なわけないわ
20 Hz from Semiconductor on Vimeo.
20 Hz observes a geo-magnetic storm occurring in the Earth's upper atmosphere. Working with data collected from the CARISMA radio array and interpreted as audio, we hear tweeting and rumbles caused by incoming solar wind, captured at the frequency of 20 Hertz.
Generated directly by the sound, tangible and sculptural forms emerge suggestive of scientific visualisations. As different frequencies interact both visually and aurally, complex patterns emerge to create interference phenomena that probe the limits of our perception.
機械学習の会議 IBIS 2011で，次世代シーケンサへの招待的なトークを行いました．スライド公開します．「次世代シーケンサ解析で新たに求められる機械学習」 slidesha.re/w3N6LE #ibis2011 #ngsfield
We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observed regions of accumulated wrong base calls. Only 3% of all error positions accounted for 24.7% of all substitution errors.
Analyzing the forward and reverse strand separately revealed error rates of up to 18.7%. Insertions and deletions occurred at very low rates on average but increased to up to 2% in homopolymers. A positive correlation between read coverage and GC content was found depending on the GC content range.
The BGI@CHOP partnership will bring together the unique strengths of two world-class institutions. BGI's capabilities and expertise in whole genome sequencing and analysis, combined with Children's Hospital's extensive biobank and expertise in clinical phenotyping, will allow scientists and clinicians to harness the power of large, detailed data sets to improve the lives of patients and families.
BGIの人と話して、シーケンスする前の準備がもの凄く大事なのが分かった。とくにDe nove のproject
PCRは目につくレベルで複製ミスしてる
シーケンス設備と計算設備と人的リソースに加えて、ゲノムペーパーを書くノウハウが蓄積されているのもBGIの強みになっていると感じます。各プロジェクトごとに試行錯誤するのでは大変（これを補うためのNGS現場の会ですね）
Can scientists raise money for their research by convincing the general public to open their wallets for small-amount donations? The process is called crowdfunding. You can think of it as the model charities have always used (bundling lots of donations to do good works), with an internet/social media twist.
A day after teaming up with the storage concern NetApp, Cloudera announced today that it has landed a $40 million series D round of venture capital funding from Ignition Partners, in a round led by its partner, Frank Artale. Previous investors include Accel Partners, Greylock Partners, Meritech Capital Partners and In-Q-Tel. Cloudera says it will use the funds to expand its marketing and sales operations. By my count, the round brings Cloudera’s total capital raised so far to $76 million.
Accel Partners, which led Cloudera’s last round, is launching a $100 million “Big Data Fund,” with Cloudera as a partner. / in infrastructure like storage or security or management, or building applications that run on Hadoop. And the opportunities for that are multiplying
GigaOm reports that one of the key attributes of the NetApp Open Solution is its separation of the compute and storage layers of a Cloudera Hadoop installation. Separating the compute and storage layers enables enhanced performance, scalability and reduced downtime in the event of the failure of a disk within either the compute or storage layer.
“研究キャリアを成功へと導くには 若手研究者者（Early Career Researcher: ECR) のためのガイド 第二版 アラン・M・ジョンソン教授 オーストラリア名誉勲章AM受章 文学修士（優等）、教育管理学修” htn.to/6ad3x4
We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource.
The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe.
The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe.
We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.
Spartan Bioscience today announced data from the RAPID GENE study showing that point-of-care DNA testing successfully identified patients carrying the CYP2C19*2 gene at the time of cardiac catheterization. Cardiologists were then able to prescribe antiplatelet therapy according to the patient's genotype. This personalized medicine approach completely eliminated high on-treatment platelet reactivity (HPR) in CYP2C19*2 carriers.
RAPID GENE is the first randomized prospective clinical trial to demonstrate the utility of point-of-care DNA testing for personalized medicine.
Cancer cell-selective in vivo near infrared photoimmunotherapy targeting specific membrane molecules go.nature.com/4NoUZw これすごい
In the paper, LGB and JCM make the point that an exome costs about 1/6th what a whole genome costs. That seems pretty accurate to me. And that does demonstrate how much more valuable we consider the exome compared to the other regions. Because of that I would not say that exome-seq has been driven by cost alone, but also because it is considered more valuable per base than whole genome.
気が付いたらはてブが伸びてた。先日も呟いたけど、文科省内部での認識としては研究開発投資はずーっと右肩上がり。なのに日本発論文の総被引用数はずーっと横這い。 viking-neurosci.sakura.ne.jp/blog-wp/?p=6442 「いくら金をかけようが日本発の研究はインパクトに乏しいまま」らしい。
Fischer Journal Archives on SciVerse ScienceDirect: bit.ly/udLoLT
Elsevier, a world-leading provider of scientific, technical and medical information products and services, today announced the availability of Elsevier Urban & Fischer Journal Archives, three new backfile collections in the life and health sciences, on SciVerse ScienceDirect.
The new backfiles, published in English under the renowned German imprint Urban & Fischer, contain journals concerning immunology and microbiology, medicine, and biochemistry
This paper argues that the distribution of global poverty has changed and that most of the world’s poor no longer live in countries officially classified as low-income countries (LICs). It is estimated that the majority of the world’s poor, or up to a billion people, live in middle-income countries (MICs).
競争的PCRによるバーコード増幅過程にはいくつか改善案がありそうです。ひとつの簡単な手法は、すべてのバーコードを例えば[G/C][A/T]のリピートで構築してDNAの融解温度を似たようなものに保つことです。
もうひとつは、ゲノムやプラスミドにバーコードをエンコードする際にイルミナのシーケンスアダプターで挟んだ配列ごとエンコードしてしまうことが考えられるかもしれません。
In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons.
Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling.
We describe a statistical framework for QTL mapping using bulk segregant analysis (BSA) based on high throughput, short-read sequencing. Our proposed approach is based on a smoothed version of the standard statistic, and takes into account variation in allele frequency estimates due to sampling of segregants to form bulks as well as variation introduced during the sequencing of bulks.
Visa has filed a patent application for a process that would use, among other sources, DNA databases to identify potential customers.
The application, published in April, is titled "Systems and Methods to Deliver Targeted Advertisements to Audience," and covers generating transaction profiles based on the transaction data, the account data, and/or other data, such as non-transactional data, wish lists, merchant provided information, address information, information from social network websites, information from credit bureaus, information from search engines, information about insurance claims, information from DNA databanks, and other examples.
What's needed, the report says, is for patient's health records to be combined with layers of genomic and other molecular measurements, such as blood proteins and the microbes in a patient's gut. Like the GPS data used to make Google maps, these data could be plumbed in detail by researchers and used more superficially by others, such as doctors to treat patients, the report says. Separate databases would be combined to form a single network.
We present a method for gene expression profiling called EDGE, or EcoP15I-tagged Digital Gene Expression, based on ultra-high-throughput sequencing of 27-bp cDNA fragments that uniquely tag the corresponding gene, thereby allowing direct quantification of transcript abundance.
そういや、こないだシンガポールの研究集会のプロブレムセッションで、Downeyが、物理的なランダムと計算論的ランダムの関連性は今後の課題だ的な発言をしていたけど、一応何らかの繋がりが見出せそうなのかどうなのかは気になるところ。
というより「物理的なランダム」というのが人間とは独立に存在するという見方に賛同できない。だからこの２つを対等に見て「関連性」という表現を使うのも適切ではないのではと個人的に思っている。“RT @tri_iro: Downeyが、物理的なランダムと計算論的ランダムの関連性”
Increasing scholarly use of Web 2.0 tools like CiteULike, Mendeley, Twitter, and blogs presents an opportunity to create new filters. Metrics based on a diverse set of social sources could yield broader, richer, and timelier assessments of current and potential scholarly impact.
Realizing this, many authors have begun to call for investigation of these metrics under the banner of “altmetrics.” Specifically, altmetrics is the creation and study of new metrics based on the Social Web for analyzing and informing scholarship.
Google Codeでグラフ理論の本を作ってる。 graph-theory-algorithms-book code.google.com/p/graph-theory…
第１２回 IPABシンポジウム ～超並列スパコンとバイオ計算～ 並列生物情報処理イニシアティブ ? IPAB ipab.org
バイオインフォマティクスではパブリックなサービスが好まれる文化があるけれど、パブリックでグラントのサポートがなくなるのは深刻な問題で、public private partnershipをどう構築してゆくかということ
方針転換の結果E-Cell 3の継続開発が手薄になり新規機能は追加していません。てこ入れ出来たかもしれないけどIABがリスクを取る研究を嫌い先進的なユーザー母体の供給が細ったのがかなり痛かった。従来的なシステム生物学業界での存在感低下は当然と言えます。
でも、細胞シミュレーションもシステム生物学もまだ黎明期なのだから、10年も同じ事を続けていてどこに行き着くのか？ ブランドを守る事も大事ですが、本質を見据えて先に向かう事はもっと大事だと思います。未来を作りましょう。 http://www.riken.jp/r-world/research/results/2010/100129/index.html @gaou_ak
短期的にはともかく、真のブランドは革新を続ける事によってしか維持できないものだ。ブランドを守ることが目的かするのはくだらなく、あくまで革新を行うことが大事なわけだが、単純に短期的なブランドすら維持できなかったのはマネージメントの問題だよなぁ、というのが僕のポイント。
ベックマン・コールターが買収されたけど、あれは経営難とかそういうことではないから部門の切り売りは阻止したんだよね。一括買収のみ応じた。でも、オリンパスはそうもいかないだろうね。
Whether you purchase a CD, digitally download the album, or stream our music on your favorite service, we are thankful for your enthusiastic support of our artistic efforts, and hope that "Break From This World" is as inspiring to you the listener as it was to us who created it.
NASA-funded researchers have evidence that some building blocks of DNA, the molecule that carries the genetic instructions for life, found in meteorites were likely created in space. The research gives support to the theory that a "kit" of ready-made parts created in space and delivered to Earth by meteorite and comet impacts assisted the origin of life.
An article in the Joyce Laboratory newsletter called it “The Immortal Molecule.” Dr. Joyce’s molecule is a form of RNA, or ribonucleic acid, which plays Robin to DNA’s Batman in Life As We Do Know It, assembling proteins in accordance with the blueprint encoded in DNA. Neither RNA nor DNA is alive by itself, any more than any other chemical, like bleach, or a protein. But in Dr. Joyce’s test tube, his specially engineered RNA molecule comes close, copying itself over and over, and evolving.
Genetic barcodes are a sequence of a particular segment of DNA that has just the right amount of variability to identify what species it came from. When an unknown creature -- or part of a creature -- is found, its tissue can be barcoded. If the sequence matches another barcode in one of several international databases, the creature's identity is revealed.
Ecologists are starting to wire such detailed predator and prey linkages into ecosystem models to test how such resource partitioning might support the resilience of the reef, especially when faced with stressors such as climate change and recent increases of invasive species.
The technique, they say, could give biologists "atom-by-atom control" over the molecules in living organisms.
Sebastian Greiss and Jason Chin have re-engineered the nematode worm's gene-reading machinery to include a 21st amino acid, not found in nature.
Field recordings play an integral role in all of my works. I always try to incorporate this whenever I can. I always feel it can bring a natural human element to any project. I usually will do raw recording for client projects, and often-record additional sounds for my own sound effects releases. I like to record sounds and divide them into categories, objects, debris, impacts, textures, movements, and ambiences.
RNA-seq may replace gene expression microarrays in the near future. Using RNA-seq, the expression of a gene can be estimated using the total number of sequence reads mapped to that gene, known as the total read count (TReC).
In this article, we show that eQTL mapping, by directly modeling TReC using discrete distributions, has higher statistical power than the two-step approach: data normalization followed by linear regression.
現代の計算技術の基盤となっている磁気データビットは、強い磁気異方性を示す高保磁力材料でできているため、情報がしっかり保持される。しかし、この特性によって、情報を磁気ビットに書き込むことが困難になっている。磁気的書き込みは依然として、配線やコイルによって誘導される磁場を用いて広く行われており、この方法はスケーラビリティーと効率の面で大きく制約される。
今回Mironたちは、コバルト薄層面内に注入した電子電流によってこの薄層の磁化が容易に反転できるという、スケーラブルな磁気的書き込み法を実証している。この新しい手法は、標準的な磁気記録技術に簡単に組み入れることができる。
アフリカ系アメリカ人1万8,000人のデータを使って遺伝子地図が作製された。ヨーロッパ人の遺伝子地図との比較により、西アフリカ系の人々では組み換えが頻発するがヨーロッパ人の大半では組み換えがあまり起こらないホットスポットが2,000か所以上見つかった。
The RNAi Center's four initial projects were funded as part of the NIH grant and will draw on the La Jolla Institute's immunology expertise. The projects aim to make key discoveries about how the body recognizes bacteria and viruses and fights infections.
The projects also aim to understand how the immune system can sometimes hurt the body, and what genes cause these problems, which underlie the development of autoimmune diseases like multiple sclerosis, type 1 diabetes and rheumatoid arthritis. These immune system diseases are areas for which the La Jolla Institute's scientific research is particularly renowned.
"Natural intermediate degree"と言っても、次数の理論の人は「自然な中間次数の具体例」とか言いながら、「D上の一様次数普遍写像が云々」とか「ZF+ADを仮定してマーティン測度が云々」とか言い出すので、次数の理論の人の言う『自然』を真に受けちゃダメだよ！
