DNA base flipping by a base pair-mimic nucleoside

On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The [Formula: see text] values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol(−1) while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol(−1), respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology

Super-Kamiokande IVを用いた8B太陽ニュートリノスペクトラム測定

学位の種別: 課程博士審査委員会委員 : （主査）東京大学准教授 瀧田 正人, 東京大学准教授 川本 辰男, 東京大学准教授 三代木 伸二, 東京大学准教授 佐川 宏行, 東京大学准教授 濱口 幸一University of Tokyo(東京大学

Atypical gaze patterns in children and adults with autism spectrum disorders dissociated from developmental changes in gaze behaviour

Eye tracking has been used to investigate gaze behaviours in individuals with autism spectrum disorder (ASD). However, traditional analysis has yet to find behavioural characteristics shared by both children and adults with ASD. To distinguish core ASD gaze behaviours from those that change with development, we examined temporo-spatial gaze patterns in children and adults with and without ASD while they viewed video clips. We summarized the gaze patterns of 104 participants using multidimensional scaling so that participants with similar gaze patterns would cluster together in a two-dimensional plane. Control participants clustered in the centre, reflecting a standard gaze behaviour, whereas participants with ASD were distributed around the periphery. Moreover, children and adults were separated on the plane, thereby showing a clear effect of development on gaze behaviours. Post hoc frame-by-frame analyses revealed the following findings: (i) both ASD groups shifted their gaze away from a speaker earlier than the control groups; (ii) both ASD groups showed a particular preference for letters; and (iii) typical infants preferred to watch the mouth rather than the eyes during speech, a preference that reversed with development. These results highlight the importance of taking the effect of development into account when addressing gaze behaviours characteristic of ASD

TCP/IP スタック ニ オケル チェックサムケイサン ノ GPU オフロード ニ ヨル セイノウ コウジョウ シュホウ

Ethernet Jumbo Frameの登場により、特にデータセンタなどの閉じたネットワーク環境において送受信されるフレームサイズが増大している。フレームサイズの増大に伴い、TCP/IPスタックにおけるチェックサム計算に要するCPU負荷が増大する。本報告では、大きな帯域幅のメモリをもつGraphics Processing Unit (GPU)にチェックサム計算をオフロードすることにより、CPU負荷を削減し、データ転送スループットを向上させる手法を提案する。具体的には、CPU-GPU間のパケット転送効率を向上させるためのパケットキューイング手法、及び、GPU上で複数のパケットを同時処理するためのGPUマルチプロセッサを用いたパケット分散処理手法の2つを提案する。ユーザランドで動作するチェックサム計算の簡易実装により性能を評価し、チェックサム計算のGPUオフロードによって、データ転送性能が最大で13%向上することを示す。The size of ethernet frames is becoming larger and larger due to the utilization of Ethernet Jumbo Frame option, especially in closed network environment such as data center networks. Increasing frame size would cause the large overhead for checksum calculation in TCP /IP protocol processing, that increase the CPU load. In this report we propose the scheme for decreasing CPU load and improving data transmission throughput by offloading checksum calculation to Graphics Processing Unit (GPU). Our scheme consists of the following two methods: packet queueing method to improve the packet transmission throughput between CPU and GPU, and the packet processing method exploiting the advantage of GPU's multiprocessor architecture. We evaluate the performance of the proposed scheme by simple experiments using the user-land implementation and confirm that the proposed scheme can improve the TCP data transmission throughput by 13 %, that is almost the same as the case when the checksum calculation is canceled.坪内佑樹, 長谷川剛, 谷口義明, 中野博隆, 松岡茂登「TCP/IPスタックにおけるチェックサム計算のGPUオフロードによる性能向上手法」『電子情報通信学会技術研究報告』Vol.113, No.244、pp.67-72、電子情報通信学会、201

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

Search for Neutrinos in Super-Kamiokande Associated with Gravitational Wave Events †

We report the results from a search in Super-Kamiokande for neutrino signals coincident with gravitational-wave events using a neutrino energy range from 3.5 MeV–100 PeV. We searched for coincident neutrino events within a time window of ± 500 s around the gravitational-wave detection time. In this work, we report the number of events within the search-window and the 90 % confidence level upper limits on the neutrino fluence for each gravitational-wave event

Narrative or Logical? The Effects of Information Format on Pro-Environmental Behavior

To build a sustainable society, the provision of information is very important. This study examines the different methods by which providing a narrative and logical information on climate change affects pro-environmental behavior. Narrative information is defined as expressions describing the process of someone experiencing an event, and logical information refers to straightforward representations composed of only central facts. According to the dual-process theory, these two formats of information seem to be processed in different ways: the former is processed automatically and intuitively, and the latter is processed deliberatively and logically. This study aims to reveal the potential of narrative information to encourage behavioral intentions and policy acceptance in energy and environmental fields. In an experiment conducted via the internet, participants either read the narrative or logical information on climate change and completed the questionnaires before and after reading. The results indicate that narrative evokes stronger emotions, such as anxiety and fear, and leads to higher behavioral intentions and policy acceptance of climate change than logical information. They further infer that this tendency is more pronounced when the participants tend to be absorbed into narratives or have little interest in climate change. Our results suggest that the narrative approach can be effective for providing information on energy and environmental issues