Novel immune cross-talk between inflammatory bowel disease and IgA nephropathy by Qianqian Yan, Zihao Zhao, Dongwei Liu, Jia Li, Shaokang Pan, Jiayu Duan, Zhangsuo Liu

“…Kyoto Encyclopedia of Genes and Genomes analysis showed 15 mutual pathways between the two diseases, with lipid metabolism playing a vital role in the cross-talk. …”
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Caution when using network partners for target identification in drug discovery by Dandan Tan, Yiheng Chen, Yann Ilboudo, Kevin Y.H. Liang, Guillaume Butler-Laporte, J. Brent Richards

“…We used the IntAct database to find physically interacting proteins of genes identified by exome-wide association studies (ExWASs), genome-wide association studies (GWASs) combined with a locus-to-gene mapping algorithm called the Effector Index, and Genetic Priority Score (GPS), which integrated eight genetic features with drug indications from the Open Targets and SIDER databases. …”
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Unraveling ankylosing spondylitis: Exploring the genetic and immunological factors and latest treatment innovations by Nilasree Hazra, Sudeshna Sengupta, Dipannita Burman, Jyoti Sekhar Banerjee, Malavika Bhattacharya

“…Over 100 genes related to AS were identified in genome-wide association studies, many connected to IL-23-driven inflammation and antigen processing. …”
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Bioinformatics and Expression Profiling of the DHHC-CRD S-Acyltransferases Reveal Their Roles in Growth and Stress Response in Woodland Strawberry (<i>Fragaria vesca</i>) by Si Gu, Xinghua Nie, Amal George, Kyle Tyler, Yu Xing, Ling Qin, Baoxiu Qi

“…S-acylation plays important roles in plant growth, development, and stress responses. Here, we report the genome-wide analysis of the <i>PAT</i> family genes in the woodland strawberry (<i>Fragaria vesca</i>), a model plant for studying the economically important Rosaceae family. …”
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Emergence and polyclonal dissemination of NDM-5/OXA-181 carbapenemase-producing Escherichia coli in the French Indian Ocean territories by Thibaut Vedani, Matthieu Pot, Thomas Garrigos, Loïk Sababadichetty, Marion Daniel, David Wilkinson, Thierry Benoit-Cattin, Olivier Belmonte, Patrick Mavingui, Laurent Dortet, Guillaume Miltgen

“…Results A total of 92 isolates of NDM-5 (n = 67) and OXA-181 (n = 25) CPEc was collected from Reunion (n = 55) and Mayotte (n = 37) islands. Whole-genome sequencing identified 4 majors STs (ST58, ST167, ST405 and ST410). …”
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Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness by Patricia Nabisubi, Stephen Kanyerezi, Grace Kebirungi, Ivan Sserwadda, Mike Nsubuga, Grace Kisitu, Patricia Ntege Nahirya, Bonny Mulindwa, George P. Akabwai, Sylvia Nantongo, Adeodata Kekitiinwa, Edgar Kigozi, Nsubuga Moses Luutu, Fred Ashaba Katabazi, Leymon Kalema, Andrew Katabalwa, Daudi Jjingo, Gerald Mboowa

“…Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. …”
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A Five-Year Retrospective Study of Foot-and-Mouth Disease Outbreaks in Southern Africa, 2014 to 2018 by Elliot Mpolokang Fana, Sununguko Wata Mpoloka, Melvin Leteane, LaToya Seoke, Kelebogile Masoba, Mokganedi Mokopasetso, Aobakwe Rapharing, Tshephang Kabelo, Patricia Made, Joseph Hyera

“…Foot-and-mouth disease (FMD) virus (FMDv), like other ribonucleic acid (RNA) genome viruses, has a tendency to mutate rapidly. …”
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The association of cigarette smoking with the development and progression of diabetic retinopathy: based on cross-sectional survey and mendelian randomization by Bin Wang, Hui Li, Huafeng Ma, ZaiHong Chen

“…Subsequently, we implemented Mendelian randomization (MR) to explore the causal relationship between smoking and DR, as well as its specific categories, leveraging genome-wide association study data. Results The cross-sectional study found an inverse association between smoking and DR risk across three analytical models (fully adjusted OR = 0.50, P < 0.001) that still persisted after propensity score matching (OR = 0.56, P = 0.011), and MR analysis also supported this finding (OR = 0.50, P = 0.024). …”
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Genetic association of lipid and lipid-lowing drug targets with uterine fibroids by Mei Wu, Qiannan Lin, Siyu Li, Huiyan Wang, Wenbo Zhou

“…Methods: Genetic variants from genome-wide association studies (GWAS) of lipid traits and variants in genes encoding lipid-lowering drug targets were extracted, and two independent UF GWAS were set as the outcome. …”
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Identification of retinol dehydrogenase 10 as a shared biomarker for metabolic dysfunction-associated steatotic liver disease and type 2 diabetes mellitus by Fangyu Li, Rui Li, Hongjun Deng

“…We also analyzed the enriched pathways of shared genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Next, hub gene validation was performed using the least absolute shrinkage and selection operator (LASSO) and receiver operating characteristic (ROC) curves. …”
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Virus adaptation to heparan sulfate comes with capsid stability tradeoff by Han Kang Tee, Simon Crouzet, Arunima Muliyil, Gregory Mathez, Valeria Cagno, Matteo Dal Peraro, Aleksandar Antanasijevic, Sophie Clément, Caroline Tapparel

“…In this study, we used enterovirus A71 (EV-A71) as the model and demonstrated that, unlike the parental MP4 variant, the cell-adapted strong HS-binder MP4-97R/167 G does not require acidification for uncoating and releases its genome in the neutral or weakly acidic environment of early endosomes. …”
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Seedling resistance of winter and spring bread wheat cultivars to <i>Pyrenophora tritici-repentis</i> by N. V. Mironenko, N. M. Kovalenko, O. A. Baranova, A. G. Khakimova, O. P. Mitrofanova

“…The disclosed diversity of bread wheat cultivars in their responses to the infection with isolates of different Ptr populations may be due to their differences in the alleles of Ptr resistance/susceptibility genes as well as the presence of still unknown effector genes in the pathogen’s genome. Cultivars resistant to two or three Ptr populations can be used by breeders as sources of seedling resistance.…”
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Associations and potential epigenetic changes between air pollution and osteoarthritis risk and survival: Insights from a prospective cohort study by Jing Qian, Jiahao Zhu, Yifan Wang, Ruoqi Dai, Jingyou Miao, Ye Yang, Wenxia Zhao, Jing Wang, Lilu Ding, Dan Zhou, Min Yu, Yingjun Li

“…Cox models assessed associations between air pollution exposure and OA incidence, joint replacement, and survival. Additionally, using genome-wide association statistics, we examined the potential causal associations between air pollution-related DNA methylation (DNAm) and OA risk. …”
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A Nodulation-Proficient Nonrhizobial Inhabitant of Pueraria phaseoloides by W. M. M. Wedage, A. H. M. N. R. Aberathne, I. N. Harischandra, D. Gunawardana

“…When a nifH fragment from the genome of this bacterium was amplified using a pair of nifH primers, it yielded an amplicon of 360 bp that, when sequenced, helped us identify the bacterium, as belonging to a species of Pseudacidovorax intermedius, at 99% sequence identity. …”
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The role of MRO as an M2 macrophage-associated gene in non-small cell lung cancer: insights into immune infiltration, prognostic significance, and therapeutic implications by Yue Gu, Miaosen Zheng, Jing Xie

“…Methods NSCLC samples from The Cancer Genome Atlas (TCGA) were analyzed using the CIBERSORT algorithm to quantify immune cell compositions. …”
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Direct and Indirect Methods for Studying Human Gut Microbiota by V. T. Ivashkin, O. S. Medvedev, E. A. Poluektova, A. V. Kudryavtseva, I. R. Bakhtogarimov, A. E. Karchevskaya

“…Integration of the data obtained by gut microbiota studies at the genome, transcriptome and metabolome levels would allow a comprehensive analysis of microbial community function and its interaction with the human organism. …”
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Association of Visceral Adipose Tissue With Hypertension: Results From the NHANES 2011–2018 and Mendelian Randomization Analyses by Jia Liao, Miaohan Qiu, Jing Li, Yi Li, Yaling Han

“…Independent genetic variants related to VAT mass were derived from genome‐wide association studies (GWAS) in 325 153 UK Biobank participants. …”
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Effects of hypoxia on the heart of the juvenile four-finger threadfin (Eleutheronema tetradactylum) based on physiological indicators and transcriptome analysis by Yi Lu, Eric Amenyogbe, Ye- Yang, Zhong-liang Wang, Zhong-liang Wang, Zhong-liang Wang, Jing-hui Jin, Rui-tao Xie, Eric Kwabena Droepenu, Jian-sheng Huang, Jian-sheng Huang, Jian-sheng Huang

“…Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis highlighted key pathways such as mitogen-activated protein kinase (MAPK), hypoxia-inducible factor-1 (HIF-1), endocytosis, and phagosome formation. …”
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DOCK4 Is a Platinum-Chemosensitive and Prognostic-Related Biomarker in Ovarian Cancer by Qianqian Zhao, Jie Zhong, Ping Lu, Xiao Feng, Ying Han, Chenqi Ling, Wenke Guo, Weijin Zhou, Fudong Yu

“…The gene expression profiles were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) database. A total of 4 genes (AP2A2, DOCK4, HSDL2, and PDK4) were the candidate differentially expressed genes (DEGs) of PPAR-TRGs with platinum chemosensitivity. …”
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Causal Effects of PM2.5, NOx, and NO2 on Cognitive Function: A Two-sample Mendelian Randomization Study by Yilin Tang, Zhenyu Li, Yicheng Fu, Mingyi Zhao

“…We conducted a two-sample Mendelian randomization (MR) study using pooled statistics from publicly available genome-wide association study (GWAS) data to show the association between air pollutants and cognitive decline in the European population. …”
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