Phase shift spectra of a fiber-microsphere system at the single photon level

We succeeded in measuring phase shift spectra of a microsphere cavity coupled with a tapered fiber using a weak coherent probe light at the single photon level. We utilized a tapered fiber with almost no depolarization and constructed a very stable phase shift measurement scheme based on polarization analysis using photon counting. Using a very weak probe light (\bar{n} = 0:41), we succeeded in observing the transition in the phase shift spectrum between undercoupling and overcoupling (at gap distances of 500 and 100 nm, respectively).We also used quantum state tomography to obtain a 'purity spectrum'. Even in the overcoupling regime, the average purity was 0.982 \pm 0.024 (minimum purity: 0.892), suggesting that the coherence of the fiber-microsphere system was well preserved. Based on these results, we believe this system is applicable to quantum phase gates using single light emitters such as diamond nitrogen vacancy centers.Comment: 8 pages, 3 figure

A Dipeptidyl Peptidase-4 Inhibitor, Des-Fluoro-Sitagliptin, Improves Endothelial Function and Reduces Atherosclerotic Lesion Formation in Apolipoprotein E–Deficient Mice

ObjectivesThe aim of this study was to investigate the antiatherogenic effects of the dipeptidyl peptidase-4 inhibitor, des-fluoro-sitagliptin (DFS).BackgroundThe new class of anti–type 2 diabetes drugs, dipeptidyl peptidase-4 inhibitors, improves glucose metabolism by increasing levels of active glucagon-like peptide (GLP)-1.MethodsEndothelial function was examined by acetylcholine-induced endothelium-dependent vasorelaxation using aortic rings and atherosclerotic lesion development in the entire aorta in apolipoprotein E–deficient mice fed a high-fat diet with or without DFS, and the antiatherogenic effects of DFS were investigated in cultured human macrophages and endothelial cells. Plasma levels of active GLP-1 were measured in patients with or without coronary artery disease.ResultsDFS significantly improved endothelial dysfunction (89.9 ± 3.9% vs. 79.2 ± 4.3% relaxation at 10−4 mol/l acetylcholine, p < 0.05) associated with increased endothelial nitric oxide synthase phosphorylation and reduced atherosclerotic lesion area (17.7% [15.6% to 25.8%] vs. 24.6% [19.3% to 34.6%], p < 0.01) compared with vehicle treatment. In cultured human macrophages, DFS significantly increased GLP-1-induced cytosolic levels of cyclic adenosine monophosphate compared with GLP-1 alone, resulted in inhibiting phosphorylation of c-jun N-terminal kinase and extracellular signal-regulated kinase 1/2 and nuclear factor-kappa B p65 nuclear translocation through the cyclic adenosine monophosphate/protein kinase A pathway, and suppressed proinflammatory cytokines (i.e., interleukin-1-beta, interleukin-6, and tumor necrosis factor-alpha) and monocyte chemoattractant protein-1 production in response to lipopolysaccharide. DFS-enhanced GLP-1 activity sustained endothelial nitric oxide synthase phosphorylation and decreased endothelial senescence and apoptosis compared with GLP-1 alone. In the human study, fasting levels of active GLP-1 were significantly lower in patients with coronary artery disease than those without (3.10 pmol/l [2.40 to 3.62 pmol/l] vs. 4.00 pmol/l [3.10 to 5.90 pmol/l], p < 0.001).ConclusionsA DPP-4 inhibitor, DFS, exhibited antiatherogenic effects through augmenting GLP-1 activity in macrophages and endothelium

脳科学と教育

シンポジウム　企画者：河合優年・田中俊也　司会者：田中俊也　話題提供者：小西行郎・小泉英明・川島隆太・八田武志　指定討論者：河合優

Students’ self-directed learning activities during the OSCE preparation period

This study aimed to clarify the self-directed learning activities of students in preparation for the OSCE, while examining the influences of such an examination on all students’ recognition of learning. A questionnaire survey was conducted, involving students who took the OSCE. The questionnaire consisted of 15 questions; the first one regarded <students’ recognition of their own self-directed learning activities>, followed by those regarding cognitive domain, aff ective domain, psychomotor domain, and self-effi cacy. Based on responses to the first question, students who were not sufficiently performing selfdirected learning activities were identifi ed at the beginning, and, focusing on changes in their self-directedness, they were classifi ed into the following 2 groups at the end of the OSCE preparatory period: those who maintained a passive attitude; and those whose selfdirectedness was enhanced. At the beginning of the period, 48.1% of all students recognized that they were not sufficiently performing self-directed learning activities. While self-directedness was subsequently enhanced in the majority of such students, 16.2% （7.8% of all students） maintained a passive attitude until the end. On comparison between the beginning and end of the period, the recognition of learning was signifi cantly enhanced in all questions in all those whose self-directedness increased during the period. In contrast, in those who maintained a passive attitude toward learning, such improvement was observed for 4 questions, excluding the <recognition of self-directed learning activities>. Furthermore, in all students who took the OSCE, a significant enhancement of recognition was observed for all questions regarding the knowledge and skills necessary for clinical training at the end of the period.本研究の目的は、OSCEの実施準備期間に学習活動の主体性が低い学生に着目しその傾向を把握することと、OSCEの実施が受講学生全体の学習自覚にどう影響しているかについて明らかにすることである。対象と方法は、OSCEを受講した77名の学生に対するアンケート調査とした。質問は15項目で、最初に主体的な学習活動の自覚を質問し、以降、「認知領域」「情意領域」「精神運動領域」に関する項目と自己効力感について質問した。また、全対象学生から学習活動の主体性が低い学生に対象を絞り、さらに、終了時まで主体性が低く留まった学生と終了時には主体性が上昇した学生に分け、分析対象とした。開始時に主体性が低いと自覚していた学生は全体の48.1％であり、そのうちの多くは終了時に主体性が上昇したが、16.2％（全体の7.8％）の学生は継続して主体性が低く留まった。それぞれの学生の学習期間の開始時と終了時の比較では、主体性が上昇した学生は全ての項目で有意に自覚の上昇が認められ、主体性が低く留まった学生では「主体的な学習活動の自覚」を除き4 項目で有意に自覚の上昇が認められた。また、OSCE受講全学生における学習期間前後の比較では、臨床実習に必要な知識や技術を反映する項目の全てにおいて有意に自覚の上昇が認められた

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

<p>Abstract</p> <p>Background</p> <p>The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009.</p> <p>Results</p> <p>Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs.</p> <p>Conclusions</p> <p>Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.</p

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection