Connecting the Sun and the Solar Wind: The First 2.5 Dimensional Self-consistent MHD Simulation under the Alfv\'en Wave Scenario

The solar wind emanates from the hot and tenuous solar corona. Earlier studies using 1.5 dimensional simulations show that Alfv\'{e}n waves generated in the photosphere play an important role in coronal heating through the process of non-linear mode conversion. In order to understand the physics of coronal heating and solar wind acceleration together, it is important to consider the regions from photosphere to interplanetary space as a single system. We performed 2.5 dimensional, self-consistent magnetohydrodynamic simulations, covering from the photosphere to the interplanetary space for the first time. We carefully set up the grid points with spherical coordinate to treat the Alfv\'{e}n waves in the atmosphere with huge density contrast, and successfully simulate the solar wind streaming out from the hot solar corona as a result of the surface convective motion. The footpoint motion excites Alfv\'{e}n waves along an open magnetic flux tube, and these waves traveling upwards in the non-uniform medium undergo wave reflection, nonlinear mode conversion from Alfv\'{e}n mode to slow mode, and turbulent cascade. These processes leads to the dissipation of Alfv\'{e}n waves and acceleration of the solar wind. It is found that the shock heating by the dissipation of the slow mode wave plays a fundamental role in the coronal heating process whereas the turbulent cascade and shock heating drive the solar wind.Comment: 7 pages, 7 figures, accepted for publication in Ap

Overexpression and gene amplification of both ERBB2 and EGFR in an esophageal squamous cell carcinoma revealed by fluorescence in situ hybridization, multiplex ligation-dependent probe amplification and immunohistochemistry

EGFR and ERBB2 belong to the EGFR gene family. In esophageal squamous cell carcinomas (SCCs), amplification of EGFR or ERBB2 is usually mutually exclusive. EGFR amplification occurs in approximately 15% of SCCs, ERBB2 occurs in less than 5%. Here, we report the co-amplification of EGFR and ERBB2 in an ulcerative and infiltrating-type SCC that measured approximately 4.2 × 2.7 × 1.2cm with a superficial lesion occurring in the thoracic esophagus of a 72-year-old man. Multiplex ligation-dependent probe amplification using representative tumor sections showed gain of CCND1 and coincident amplification of ERBB2 or EGFR or neither. Immunohistochemistry and fluorescence in situ hybridization revealed that the tumor comprised three cancer-cell populations: well-differentiated SCC with high-level ERBB2 amplification and ERBB2 overexpression, more infiltrative poorly-differentiated SCC with high-level EGFR amplification and EGFR overexpression, and poorly-differentiated SCC lacking any ERBB2 or EGFR abnormality. These three populations each had low-level CCND1 amplification and nuclear cyclin D1 overexpression. This histological topology and gene amplification combinations suggested that genetic instability first produced CCND1 amplification, and then ERBB2 or EGFR gene amplification occurred. It is further speculated that during cancer progression and clonal selection indecisive predominance of either clone caused the rare co-amplification of ERBB2 and EGFR in a single chimeric tumor. © 2015 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.発行後1年より全文公

Fast WDM provisioning with minimal probing: the first field experiments for DC exchanges

We propose an approach to estimate the end-to-end GSNR accurately in a short time when a data center interconnect (DCI) network operator receives a service request from users, not by measuring the GSNR at the operational route and wavelength for the End-End optical path but by simply applying a QoT probe channel link by link, at a convenient wavelength/modulation-format for measurement. Assuming connections between coherent transceivers of various frequency ranges, modulators, and modulation formats, we propose a new device software architecture in which the DCI network operator optimizes the transmission mode between user transceivers with high accuracy using only standard parameters such as Bit Error Rate. In this paper, we first experimentally built three different routes of 32 km/72 km/122 km in the C-band to confirm the accuracy of this approach. For the operational end-to-end GSNR measurements, the accuracy estimated from the sum of the measurements for each link was 0.6 dB, and the wavelength-dependent error was about 0.2 dB. Then, using field fibers deployed in the NSF COSMOS testbed (deployed in an urban area), a Linux-based transmission device software architecture, and coherent transceivers with different optical frequency ranges, modulators, and modulation formats, the fast WDM provisioning of an optical path was completed within 6 minutes (with a Q-factor error of about 0.7 dB).Comment: 9 pages, 11 figures, 3 table

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

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

動的スケジューリングライブラリを用いたPythonにおける分散コレスキー分解の実装と評価

identifier:oai:t2r2.star.titech.ac.jp:5068624

Segmental gastrectomy with radical lymph node dissection for early gastric cancer

AIM: To describe a new surgical technique and evaluate the early results of segmental gastrectomy (SG) with modified D2 lymph node (LN) dissection for early gastric cancer (EGC)