Thailand cave: Medics reach boys as rescuers weigh options (BBC NEWS July 4) Seven divers, including a doctor and a nurse, joined the group inside the caves in the north of the country after they were discovered alive on Monday. Rescuers are now considering how best to bring the group to safety. More heavy rain could see water levels rise and threaten the air pocket where the group has taken refuge.
Thai authorities deciding how to rescue soccer team from flooded cave (abc.net.au July 3) We know all of the group are “safe” with “signs of life” but now the massive international rescue effort has turned its attention to the next challenge — getting the group out of the cave.
Thai cave rescue: Who are the British divers who found the missing boys? (Channel News Asia 03 Jul 2018 02:42PM Updated: 03 Jul 2018 07:36PM) Two cave divers who found 12 Thai boys and their football coach on Monday (Jul 2) were neither military personnel nor professional divers, but volunteers from Britain.
タイの洞窟で少年ら行方不明 水位上昇でダイバー捜索中断 (BBC NEWS JAPAN 2018年06月28日)タイ北部の洞窟で、サッカーチームに所属する少年12人とコーチ1人が23日から行方不明になっている。雨水により洞窟内の水位が上昇し、ダイバーによる潜水が中断に追い込まれるなど、捜索は難航している。ポンプによる排水は中断され、洞窟の入り口が浸水すると、タイ海軍のダイバーは捜索中断に追い込まれた。11歳から16歳の少年12人と25歳のコーチは23日、洞窟に入った。それ以来このグループと連絡が取れていない。
Thai officials believe 12 boys missing in cave are alive (By TASSANEE VEJPONGSA. AP NEWS Jun. 25, 2018) MAE SAI, Thailand (AP) — Anguished parents of 12 members of a boys’ soccer team missing in a flooded cave in northern Thailand were spending a third night without their children Monday as water continued to rise in the sprawling caverns, forcing rescuers led by elite navy divers to suspend their search.
12 missing youth soccer players feared trapped in Thai cave (ST.LOUIS POST-DISPATCH Jun 24, 2018) BANGKOK (AP) — Search and rescue teams were looking Sunday for a dozen members of a youth soccer team who were missing and believed to be trapped in a cave in northern Thailand. Police said that local authorities, police and rescue workers were working with divers to find the 12 boys, aged 11-15, and their coach, who are believed to have entered the Tham Luang Nang Non cave in Chiang Rai province late Saturday afternoon. The group were apparently trapped when a heavy rainstorm flooded a stream at the cave’s entrance.
大阪府立 生野高等学校 東大0名、京大10名 合計10名 ☆2 授業・講習・模試による学力育成 ① 生徒の進路目標実現するため、入試に対応できる質の高い授業、授業中心の「予習→授業→復習」の自学自
習力の向上により学力育成を図る ② 校内・外部模試を活用して学力測定、学習課題の発見とその補強、進路意識向上を図る ③ 授業に加えて、進路指導部が中心となって希望者講習を企画・実施し、学力の向上を図る(進路指導の方針より)
Japan go through but final group game ends in ‘mind-boggling farce’ (BBC 28 June 2018)
What do you expect? Any nation will do the same including England. So get off your high horse (24. Posted by rstlau7 on 28 Jun 2018 19:54)
Japanese coach took a risk and it paid off. Had they tried to score and got caught on the break he d probably lost his job. Qualifying rounds is about getting through and they did. I’ll be pretty sure all the Japanese fans will be happy with at least one more game and keeping alive in the competition. (17. Posted by vern on 28 Jun 2018 19:36)
What is the difference between this and England vs Belgium game now…? Haha (15. Posted by Hurdinho on 28 Jun 2018 19:31)
Japan lost more than just its match against Poland A FRESH “disgrace” has rocked the World Cup, as former players from around the globe lashed out in anger. (James Matthey@jamesmatthey news.com.au JUNE 29, 2018 1:36PM)
World Cup 2018: Japan go through but final group game ends in ‘mind-boggling farce’ (BBC 28 June 2018)
出会いのパターンは大きく分けてこの二つ。 ① 大学時代に出会う。この場合、相手は同じ学問分野(同学科の同級生)、同趣味(サークルで出会う)、あるいは別学部や別学部(教養科目や友人を介して)だと考えられる。 ② 研究室で出会う。相手は同じ分野の研究者。あるいは研究補助員・テクニカルスタッフ・秘書。(研究者同士の結婚について。 aprilone78 2010-09-06 )
未婚状態から結婚状態への移行を検討する際、交際へ移行する過程と交際から結婚へ移行する過程では意思決定に影響を及ぼす要因が異なることが明らかになりつつある。(結婚の意思決定に関する分析~「結婚の意思決定に関する意識調査」の個票を用いて~ 佐藤博樹、三輪哲、高見具広、高村静、石田絢子 September 2016 内閣府 ESRI Discussion Paper Series No.332 PDF)
結婚前に分かる「長続きしない結婚の8つの兆候」(Amanda Scherker The Huffington Post 2015年01月13日 19時26分 JST) 1.はじめから金銭感覚が合わなかった。カンザス州立大学が行なった研究は、新婚旅行の最中にお金のことでケンカになってしまったら、末永く幸せには暮らせそうにない、と示している。研究者らは、関係の初期段階における金銭絡みのケンカと、将来の結婚生活における不満には相関性がみられるとし、お金は「離婚を予測する最大の判断材料」であるとしている。興味深いことに、この相関性は、収入レベルや裕福度を問わず見られるという。
a new technique called “t-SNE” that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map. (Maaten and Hinton, 2008 PDF)
Most researchers are already familiar with another dimensionality reduction algorithm, Principle Components Analysis (PCA) also available in R2 and explained in more detail in the Principle Components Analysis tutorial. Both PCA and t-SNE reduce the dimension while maintaining the structure of high dimensional data, however, PCA can only capture linear structures. t-SNE on the other hand captures both linear and non-linear relations and preserves local distances in high dimensions while reducing the information to 2 dimensions (an XY plot). (16. t-SNE: high dimensionality reduction in R2 How to find groups in your dataset using t-SNE. r2-tutorials.readthedocs.io)
そもそもなぜ次元削減をする必要があるの?
Computers have no problem processing that many dimensions. However, we humans are limited to three dimensions. Computers still need us (thankfully), so we often need ways to effectively visualize high-dimensional data before handing it over to the computer. (An illustrated introduction to the t-SNE algorithm By Cyrille Rossant March 3, 2015)
(上記サイトはヴィジュアルに非常にわかりやすくt-SNEの説明をしています)
遺伝子解析にはなぜPCAよりもt-SNEが適しているの?
First, although PCA minimizes global reconstruction error, it may not preserve local proximities of points. In visualizing gene expression data, we are typically more interested in resolving nearby clusters than in preserving the correct distance relationships between genes with very different patterns of expression. But the optimization criterion of PCA results in the opposite priority: the relationship of distant points is depicted as accurately as possible, while small inter-point distances can be distorted. Second, there may be no single linear projection that gives a good view of the data: in such a case, all linear projection methods will fail. (An intuitive graphical visualization technique for the interrogation of transcriptome data. Bushati et al., 2011. Nucleic Acids ResearchVolume 39, Issue 17,Pages 7380–7389)
t-SNEの使い方の注意は?
Following are a few common fallacies to avoid while interpreting the results of t-SNE:
For the algorithm to execute properly, the perplexity should be smaller than the number of points. Also, the suggested perplexity is in the range of (5 to 50)
Sometimes, different runs with same hyper parameters may produce different results.
…
(Comprehensive Guide on t-SNE algorithm with implementation in R & Python
SAURABH.JAJU2, JANUARY 22, 2017)
t-SNEの短所は?
t-SNE has three potential weaknesses: (1) it is unclear how t-SNE performs on general dimensionality reduction tasks, (2) the relatively local nature of t-SNE makes it sensitive to the curse of the intrinsic dimensionality of the data, and (3) t-SNE is not guaranteed to converge to a global optimum of its cost function. (Maaten and Hinton, 2008 PDF)
ゲノムデータ(遺伝子発現プロファイルの解析)にt-SNEが使われるようになったのはいつ頃から?
自分が調べた限り、下記の論文よりも古い論文が見つかりませんでした。
Here, we test the recently developed nonlinear dimensionality reduction algorithm, t -statistic Stochastic Neighbor Embedding ( t -SNE) ( 8 ), on a variety of real-world transcriptome data sets. (An intuitive graphical visualization technique for the interrogation of transcriptome data. Nucleic Acids Res. 2011 Sep 1;39(17):7380-9.
We tested seven DRTs applied to four microarray cancer datasets and ran four clustering algorithms using the original and reduced datasets. … On the other hand, t-distributed Stochastic Embedding (t-SNE) and Laplacian Eigenmaps (LE) achieved good results for all datasets. (Comparative study on dimension reduction techniques for cluster analysis of microarray data. Date of Conference: 31 July-5 Aug. 2011 ieeexplore.ieee.org)
どんなデータに使えるの?
Question: why PCA for RNA-Seq but tSNE for scRNA-seq? (biostars.org)
Question: What to use: PCA or tSNE dimension reduction in DESeq2 analysis? (support.bioconductor.org)
t-SNEを実際に使うには?(生物学研究者向け)
Rを用いてt-SNE
A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor (bioconductor.org)
A step-by-step workflow for low-level analysis of single-cell RNA-seq data Aaron T.L. Lun, et al. F1000Research Software tool article
The Rtsne module in Array Studio will allow the user to cluster different cells with UMI counts, using the Rtsne package in R (arrayserver.com)
Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. (satijalab.org)
Identifying and Characterizing Subpopulations Using Single Cell RNA-seq Data (hms-dbmi.github.io)
シングルセルRNA-seqガイド
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications (Haque et al., Genome Med. 2017; 9: 75)
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Bo Wang, Junjie Zhu, Emma Pierson, Daniele Ramazzotti & Serafim Batzoglou Nature Methods volume 14, pages 414–416 (2017) 新手法の提案 We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. 既存の手法との比較 On seven published data sets, we benchmark SIMLR against state-of-the-art methods.
CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data. Lin P, Troup M, Ho JW. Genome Biol. 2017 Mar 28;18(1):59. 新手法の提案 Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling and computational machinery. Here, we introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of dropouts in scRNA-seq data in a principled manner. 従来の手法t-SNEなどとの比較 Using a range of simulated and real data, we show that CIDR improves the standard principal component analysis and outperforms the state-of-the-art methods, namely t-SNE, ZIFA, and RaceID, in terms of clustering accuracy. 代表的な結果の図
Visualization and cellular hierarchy inference of single-cell data using SPADE. Anchang B, Hart TD, Bendall SC, Qiu P, Bjornson Z, Linderman M, Nolan GP, Plevritis SK. Nat Protoc. 2016 Jul;11(7):1264-79. 新たなデータ可視化手法の提案 we describe the use of Spanning-tree Progression Analysis of Density-normalized Events (SPADE), a density-based algorithm for visualizing single-cell data and enabling cellular hierarchy inference among subpopulations of similar cells. 別のデータ可視化手法であるt-SNEとの比較 We compare SPADE with recently developed single-cell visualization approaches based on the t-distribution stochastic neighborhood embedding (t-SNE) algorithm.
SAIC: an iterative clustering approach for analysis of single cell RNA-seq data. Yang L, Liu J, Lu Q, Riggs AD, Wu X. BMC Genomics. 2017 Oct 3;18(Suppl 6):689. 解析の重要性 An important step in the single–cell transcriptome analysis is to identify distinct cell groups that have different gene expression patterns. 従来の手法の問題点 Many studies rely on principal component analysis (PCA) with arbitrary parameters to identify the genes that will be used to cluster the singlecells. 新手法の提案 We have developed a novel algorithm, called SAIC (Singlecell Analysis via Iterative Clustering), that identifies the optimal set of signature genes to separate singlecells into distinct groups. データ可視化のステップでのt-SNEの利用 We applied the SAIC algorithm to one simulated dataset and two published single cell datasets. After signature genes selection, the results were evaluated by Davies-Bouldins index and then visualized using both a t-SNE 2D–plot and an unsupervised hierarchical clustering heatmap.
Specific loci in the mouse genome that allow stable, reliable, and ubiquitous transgene expression in the absence of adverse effects like Rosa26, Hprt1, or Col1A1, have become essential tools in the performance of genetic studies. Safe harbor loci allow comparable analysis between different lines of mice in isogenic contexts. ((Rapid and Efficient Generation of Recombinant Human Pluripotent Stem Cells by Recombinase-mediated Cassette Exchange in the AAVS1 Locus Ordovas et al. JoVE)
Expression of a randomly integrated transgene is unpredictable and tends to be unstable over time due to epigenetic effects. Further, random integration often yields multiple integrants per cell, and this can result in the disruption or activation of host cell genes. Such unintended side effects produce a non-isogenic experimental setting, and this can confound data analysis and interpretation. (DeKelver et al., Genome Res. 2010. 20: 1133-1142)
ヒト細胞においてもトランス遺伝子を挿入できる、類似のセーフ・ハーバー部位が報告されました(DeKelver, et al., 2010)。これはアデノ随伴ウイルス(AAV)が通常、第19染色体上のPP1R12Cという特定のゲノム座位に組込まれるとの報告に端を発しています。AAVS1としても知られる本座位へAAVを組み込んだ場合でも、初代培養細胞や不死化細胞、人工多能性幹細胞(iPSC)および胚性幹細胞などをはじめとする種々の細胞に目に見える表現型の変化を生じることはありません。 (セーフ・ハーバー部位への目的遺伝子組込み用ゲノム編集ツール 実験検証 コスモ・バイオ GeneCopoeia 技術情報)
用例
Here we describe a strategy to genetically modify human iPS cells at ‘safe harbor’ sites in the genome, which fulfill five criteria based on their position relative to contiguous coding genes, microRNAs and ultraconserved regions. (Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells. Nat Biotechnol. 2011 Jan;29(1):73-8.)
Nuclease, and using these nucleases, secretory tissues which they derived, cloned, and a method of expressing a transgene from the safe harbor locus in animals. (The methods and compositions for controlling transgene expression Google Patents JP2014526279A)
Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. DeKelver et al., Genome Res. 2010. 20: 1133-1142)
Disruption of overlapping transcripts in the ROSA βgeo 26 gene trap strain leads to widespread expression of β-galactosidase in mouse embryos and hematopoietic cells. Brian P. Zambrowicz, Akira Imamoto, Steve Fiering, Leonard A. Herzenberg, William G. Kerr, and Philippe Soriano. PNAS April 15, 1997. 94 (8) 3789-3794; https://doi.org/10.1073/pnas.94.8.3789
Green fluorescent protein – calmodulin protein – (GCaMP)-type GECI are based on a circularly permutated EGFP molecule (cpEGFP) flanked at the N and C termini by the smooth muscle myosin light chain kinase derived calmodulin binding peptide (RS20) and calmodulin (CaM), respectively. (Helassa et al., Scientific Reports volume 5, Article number: 15978 (2015))
In our laboratory, we have focused our efforts to improve genetically encoded calcium indicator proteins (GECIs), specifically the green fluorescent protein (GFP)-Calmodulin fusion protein (GCaMP).(Badura et al., 2014 doi: 10.1117/1.NPh.1.2.025008)
Here we report the development of a high-affinity Ca(2+) probe composed of a single GFP (named G-CaMP). (Nakai et al., Nat Biotechnol. 2001 Feb;19(2):137-41.)
Generation and Imaging of Transgenic Mice that Express G-CaMP7 under a Tetracycline Response Element. (Sato et al., 2015 PLoS One 10(5):e0125354)
Designed and random alterations in the previously described, circularly permutated eGFP-based, Ca2+-sensing molecule, which we now term GCaMP1 (11), were undertaken to improve brightness and stability. (Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2. Yvonne N. Tallini, Masamichi Ohkura, Bum-Rak Choi, Guangju Ji, Keiji Imoto, Robert Doran, Jane Lee, Patricia Plan, Jason Wilson, Hong-Bo Xin, Atsushi Sanbe, James Gulick, John Mathai, Jeffrey Robbins, Guy Salama, Junichi Nakai, and Michael I. Kotlikoff. PNAS March 21, 2006. 103 (12) 4753-4758)
Howard Hughes Medical Institute/Janelia Research Campusの研究者らはGCaMPとハイフンを入れない表記をしています。
Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL. Nat Methods. 2009 Dec;6(12):875-81.
PNAS : Calcium waves occur as Drosophila oocytes activate
(In vivo imaging at dissection scope resolution of Ca2+ flux in activating oocytes from transgenic flies expressing GCaMP3 in their oocytes. See text and the legend to Fig. 1A for details. 論文 https://doi.org/10.1073/pnas.1420589112)
Ca2+ dynamics in body wall muscles of wild-type C. elegans
(Genetic crosses were made to transfer the genetically encoded Ca2+ indicator GCaMP3.35 (Schwarz et al., 2011) into the vps-36 (gk427) background. 論文リンク http://jcs.biologists.org/content/129/7/1490)
Neuronal Activity during Visual Perception 脳に映る視覚世界をリアルタイムで観察
(The gSA2AzGFF49A;UAS:GCaMP7a double-transgenic zebrafish used for imaging were also homozygous for the nacre pigmentation mutation [24] to eliminate melanophores. 論文リンク https://doi.org/10.1016/j.cub.2012.12.040)
(Here, we report a method for long-term imaging of a GECI, GCaMP6f, expressed from adeno-associated virus vectors in cortical neurons of the adult common marmoset (Callithrix jacchus), a small New World primate. 論文リンク https://doi.org/10.1016/j.celrep.2015.10.050)
High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.HodDana, YiSun, BoazMohar, BradHulse, Jeremy PHasseman, GetahunTsegaye, ArthurTsang, AllanWong, RonakPatel, John JMacklin, YangChen, ArthurKonnerth, VivekJayaraman, Loren LLooger, Eric RSchreiter, KarelSvoboda, Douglas SKim https://www.biorxiv.org/content/early/2018/10/03/434589
Using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo.
Based on screening in cultured neurons (Fig. 1), we chose three ultrasensitive GCaMP6 sensors (GCaMP6s, 6m, 6f; for slow, medium and fast kinetics, respectively) for characterization in vivo. These sensors vary in kinetics, with the more sensitive sensors having slower kinetics. (Chen et al., 2013 Nature 499, 295-300)
G-CaMP6, G-CaMP7, G-CaMP8およびそのヴァリアント (中井博士らのグループ)
The dynamic range of G-CaMP7 (Fmax/Fmin = 36.6±4.10, n = 3) was ∼3-fold greater than that of G-CaMP6, even though this variant showed a lower Ca2+ affinity (Kd = 243±14 nM, n = 3) than G-CaMP6 (Fig. 1B and C). By performing further random mutagenesis on G-CaMP7, we obtained a more sensitive variant of G-CaMP7 termed G-CaMP8, (Ohkura et al., 2012 PLOS ONE https://doi.org/10.1371/journal.pone.0051286)
we introduced amino acid substitutions into GCaMP-HS, tested their activities, and developed a new version, which we named GCaMP7a (Muto, Ohkura et al., 2013. Curr Biol. 23(4):307-311)
【ジャネリア GCaMP6シリーズ】Ultrasensitive fluorescent proteins for imaging neuronal activity. Chen et al.,2013. Nature 499:295–300. “we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo.” “Based on screening in cultured neurons (Fig. 1), we chose three ultrasensitive GCaMP6 sensors (GCaMP6s, 6m, 6f; for slow, medium and fast kinetics, respectively) for characterization in vivo.”
【中井博士ら GCaMP7a】Real-Time Visualization of Neuronal Activity during Perception. Muto, Ohkura et al., 2013.Curr Biol. 23(4):307-311. “we introduced amino acid substitutions into GCaMP-HS, tested their activities, and developed a new version, which we named GCaMP7a”
【中井博士ら G-CaMP6, G-CaMP7, G-CaMP8】Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals. Ohkura et al., 2012. PLOS ONE 7(12): e51286. “As expected, G-CaMP6, a variant of G-CaMP5.09 bearing an M36L substitution in the CaM domain (Fig. 1A), showed a higher Ca2+ affinity (Kd = 158±4.0 nM, n = 3) than G-CaMP5.09 or the previously reported G-CaMP2 variants G-CaMP-HS [17] and G-CaMP3 [4] (Fig. 1B and C).” ” Next we performed random mutagenesis on G-CaMP6 by using an error-prone PCR [15] and were able to screen a highly responsive variant termed G-CaMP7, which differs from G-CaMP6 by a deletion of histidine (ΔH) in the RSET domain and an S205N mutation in the circularly permutated EGFP domain (Fig. 1A). The dynamic range of G-CaMP7 (Fmax/Fmin = 36.6±4.10, n = 3) was ∼3-fold greater than that of G-CaMP6, even though this variant showed a lower Ca2+ affinity (Kd = 243±14 nM, n = 3) than G-CaMP6 (Fig. 1B and C). By performing further random mutagenesis on G-CaMP7, we obtained a more sensitive variant of G-CaMP7 termed G-CaMP8,”
【ジャネリア GCaMP5シリーズ】Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging. Akerboom et al., 2012.J Neurosci 32 (40) 13819-13840 “Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of “GCaMP5” sensors.” “Consequently, the Asp380Tyr mutation raises the brightness of the calcium-bound state of GCaMP3 for both GCaMP5A and GCaMP5G; in addition, calcium affinity and cooperativity (Hill coefficient) are increased by ∼25% for GCaMP5A (Table 1).”
【中井博士ら G-CaMP 4.1】Tissue-Tissue Interaction-Triggered Calcium Elevation Is Required for Cell Polarization during Xenopus Gastrulation. Shindo et al., 2010. PLoS ONE 5(2): e8897. “G-CaMP 4.1, which is an improved form of a previously reported calcium indicator,”
【中井博士ら GCaMP-HS】Genetic visualization with an improved GCaMP calcium indicator reveals spatiotemporal activation of the spinal motor neurons in zebrafish. Muto, Ohkura et al., 2011. PNAS 108 (13) 5425-5430. “we developed GCaMP-HS (GCaMP-hyper sensitive), an improved version of the genetically encoded calcium indicator GCaMP,” “Kd and Hill coefficient of GCaMP-HS were 102 nM and 5.0, respectively (Fig. 1D). Kd and Hill coefficient of GCaMP2 were 146 nM and 3.8, respectively, indicating that GCaMP-HS has a higher affinity to Ca2+ ions and a higher cooperativity”
【ジャネリア GCaMP3】Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Tian et al., 2009. Nat Methods. 6(12):875-81.”We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials”
【ジャネリア GCaMP2結晶構造解析】Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design. Akerboom et al., 2009. J Biol Chem. 284, 6455-6464
【ジャネリア&中井博士ら GCaMP2】Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2.
Tallini, Ohkura, et al., 2006. PNAS 103 (12) 4753-4758. “previously described sensors have proved to be of limited use to report cell signaling in vivo in mammals. Here, we describe an improved Ca2+ sensor, GCaMP2,”
【中井博士ら 元祖G-CaMP】A high signal-to-noise Ca2+ probe composed of a single green fluorescent protein. Nakai et al., 2001. Nat Biotech. 19:137–141.
中教審は「英語教育の早期化」という諮問を慎重に検討せよ Tweet ThisSend to Facebook | by suzumura 2014/11/25 政策の決定に携わる者の狭隘な視野が前途有為な児童や生徒の将来に悪影響を及ぼすことは避けられなければなりませんし、英語の教育を早期から行うという計画が新たな利権を生み出すための措置となることも、断固として排除されなければなりません。その意味でも、下村文科相による中教審への諮問は実態を伴わないものであるばかりでなく、英語を含む今後の日本の教育界に禍根を残すことになりかねないといえます。
Getting your research into an influential journal is certain to give a healthy boost to both academic standing and future career prospects. (How to get published in high-impact journals: Big research and better writing. Posted by Julie Gould, Nature Jobs Blog 03 Nov 2014)
1 本件対象文書について不開示とした理由について
本件対象文書は「「インターネット上で指摘のあった論文の画像データに係る調査結果について」として調査結果が平成27年7月31日付けで公表されている,研究行動規範委員会の調査に関わる資料の一切。具体的には,調査にかかる会議に提出された資料,会議の議事次第,調査委員が示された資料,会議の議事録,調査報告書とその案,調査対象者から提出された実験データなどの資料,その他調査に使われた資料,調査で行われた関係者のヒアリングの記録,外部機関に調査や分析を行っていればその報告書。加えて,調査にかかった費用とその使途がわかる資料(外部調査委員への支払なども含む)」である。本学では,研究不正の事案については,科学研究行動規範委員会において調査を行っているが,請求にかかる文書は以下の5つの理由に該当する部分について不開示とする決定を行った。
① 個人名その他個人を識別できる情報であって法5条1号ただし書イ,ロ,ハのいずれにも該当しないものが記されている部分を不開示とする。
② 審議,検討又は協議に関する情報であって,公にすることにより,率直な意見の交換若しくは意志決定の中立性が不当に損なわれるおそれがあるものについては,法5条3号に該当するため不開示とする。
③ 公にすることにより,当該事務又は事業の適正な遂行に支障を及ぼすおそれがあるものについては,法5条4号柱書きに該当するため不開示
とする。
④ 公にすることにより,正確な事実の把握を困難にするおそれ,若しくはその発見を困難にするおそれがあるものについては,法5条4号ハに該当するため不開示とする。
⑤ 公にすることにより,人事管理に係る事務に関し,その公正かつ円滑な人事の確保に支障を及ぼすおそれがある部分については,法5条4号
ヘに該当するため不開示とする。よって,本件対象文書を平成26年度~27年度科学研究行動規範委員会資料並びに支給調書として,部分開示決定を行ったものである。これについて,審査請求人は,平成29年4月4日受付の審査請求書のなかで,原処分の取消しを求めている。
私:「来週のラボミーティングは自分の番なんですが、データがないんですけど。」
ボス:「それはあなたの問題ね。」
Me: “I’m supposed to present at lab meeting next week, but I have no data.”
Advisor: “That’s your problem.” @sianbehr 14:48 – 2014年2月21日
大学院で最初のラボミーティングだけどデータが無いから休日の写真を1時間見せていよう First lab meeting presentation today as a PhD, no data, just going to show my holiday photos for an hour @Sarah_Bethy_ 0:22 – 2016年2月26日
1. 失敗の過程を話して、ラボからの助言を仰ぐ
2.古いデータを見直してみる 定量的な解析を行うことにより、新しい見方ができるかも
3.解析ソフトウェアを使いこなす バイオインフォマティクスツールなどの利用で新しい発見があるかも
(4.論文紹介の時間にする)
5. 新しいモデル、模式図をつくってみる 手持ちのデータや文献からの知見をあわせて新たなモデルがつくれるかも
6.備えあれば憂いなし 日頃からサ イドプロジェクトを走らせておいて、何もニューデータがないという状態をつくらないようにする (How to present during lab meeting without new data May 25, 2017 BY Brittany Carson)
“I have not failed 10,000 times. I have not failed once. I have succeeded in proving that those 10,000 ways will not work. When I have eliminated the ways that will not work, I will find the way that will work.” (Thomas Edison) (How Failure Taught Edison to Repeatedly Innovate. By Nathan Furr, forbes.com Jun 9, 2011)
Bacon notes that studies can be enjoyable, and they can also be useful (whether for developing critical thinking skills or learning something for one’s profession). But he also notes that if done too much, studying could lead to “sloth”— laziness (in other words, if all you do is study, you won’t make the time to apply what you’ve learned and use your knowledge in a positive way). Bacon also believed that certain subjects could enhance different abilities— for example, mathematics can improve concentration, poetry can enhance one’s “wit” (what we today would call a sense of humor), and studying history can expand one’s wisdom.
Liumbruno et al., How to write a scientific manuscript for publication. Blood Transfus. 2013 Apr; 11(2): 217–226. doi: 10.2450/2012.0247-12 PMCID: PMC3626472
Tips for Academic Writing and Other Formal WritingWrite what you mean, mean what you write For instance, we often speak informally of “going the extra mile”, “at the end of the day”, “hard facts”, things being “crystal clear” … if there was no crystal, do not write about its clarity.
(7:15-) Now, when I show my students the mystery box, they say now show us what’s inside. But, I will never do that. Of course, it’s sealed. Just like science, the mystery box isn’t about the answer. We don’t have access to some sort of universal truth. All we have are the questions. I tell the students, they can go home and make their own mystery box. And, you can do that, too. And, if your mystery box works the same as mine, congratulations, you are successful. But I will never show you the inside of my mystery box. That’s the science demonstration, right?
Teaching science: we’re doing it wrong | Danny Doucette | TEDxRiga
International English Language Testing System(IELTS)
International English Language Testing System(IELTS:アイエルツ)は、海外留学や研修のために英語力を証明する必要のある方、およびイギリス、オーストラリア、カナダなどへの海外移住申請に最適なテストです。イギリス、オーストラリア、カナダ、ニュージーランドのほぼ全ての高等教育機関で認められており、アメリカでも TOEFLに代わる試験として入学審査の際に採用する教育機関が3,000を超え、英語力証明のグローバルスタンダードテストとして世界中で受験者が増え続けています。
International English Language Testing System(IELTS)
Cambridge Assessment English(ケンブリッジ大学英語検定機構)
ケンブリッジ英語検定 [C2 Proficiency, C1 Advanced, B2 First for Schools, B2 First, B1 Preliminary for Schools, B1 Preliminary, A2 Key for Schools, A2 Key]、
Cambridge Englishは、学習者が実生活のさまざまな状況でのコミュニケーションのために英語をどのように使うことができるかを評価できるように設計されています。
Cambridge English はすべて、言語能力評価の国際指標であるヨーロッパ共通参照枠 Common European Framework of Reference for Languages (CEFR) に準拠しています。
世界中の20,000以上の大学、企業 (雇用者)、行政機関が、Cambridge English を認定しています。
Cambridge English の試験の多くが、 ビザや入学申請 のため次の国々で利用できます: 英国, オーストラリア, 米国およびカナダ。 IELTS (Cambridge English が提供) も英国ビザや入国申請に使うことができます。(引用元:http://www.cambridgeenglish.org/jp/why-cambridge-english/)