A Generalized Flow-Based Method for Analysis of Implicit Relationships on Wikipedia

We focus on measuring relationships between pairs of objects in Wikipedia whose pages can be regarded as individual objects. Two kinds of relationships between two objects exist: in Wikipedia, an explicit relationship is represented by a single link between the two pages for the objects, and an implicit relationship is represented by a link structure containing the two pages. Some of the previously proposed methods for measuring relationships are cohesion-based methods, which underestimate objects having high degrees, although such objects could be important in constituting relationships in Wikipedia. The other methods are inadequate for measuring implicit relationships because they use only one or two of the following three important factors: distance, connectivity, and cocitation. We propose a new method using a generalized maximum flow which reflects all the three factors and does not underestimate objects having high degree. We confirm through experiments that our method can measure the strength of a relationship more appropriately than these previously proposed methods do. Another remarkable aspect of our method is mining elucidatory objects, that is, objects constituting a relationship. We explain that mining elucidatory objects would open a novel way to deeply understand a relationship

Finding Neighbor Communities in the Web Using an Inter-Site Graph

In this paper, we present Neighbor Community Finder (NCF, for short), a tool for finding Web communities related to given URLs. While existing link-based methods of finding communities, such as HITS, trawling, and Companion, use algorithms running on a Web graph whose vertices are pages and edges are links on the Web, NCF uses an algorithm running on an inter-site graph whose vertices are sites and edges are global-links (links between sites). Since the phrase "Web site" is used ambiguously in our daily life and has no unique definition, NCF uses directory-based sites proposed by the authors as a model of Web sites. NCF receives URLs interested in by a user and constructs an inter-site graph containing neighbor sites of the given URLs by using a method of identifying directory-based sites from URL and link data obtained from the actual Web on demand. By computational experiments, we show that NCF achieves higher quality than Google\u27s "Similar Pages" service for finding pages related to given URLs corresponding to various topics selected from among the directories of Yahoo! Japan.PAPE

Compact Encoding of the Web Graph Exploiting Various Power Distributions

Compact encodings of the web graph are required in order to keep the graph on the main memory and to perform operations on the graph efficiently. In this paper, we propose a new compact encoding of the web graph. It is 10% more compact than Link2 used in the Connectivity Server of Altavista and 20% more compact than the encoding proposed by Guillaume et al. in 2002 and is comparable to it in terms of extraction time.Special Section LETTER (Special Section on Discrete Mathematics and Its Applications

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