Constructing adverse outcome pathway for per- and polyfluoroalkyl substances and retinoblastoma based on PI3K-AKT/MAPK signaling pathway by Yuyan GUI, Tingji WANG, Minghao WANG, Yaqi XU, Yunhui ZHANG

“…MethodsChemical-gene interactions and disease-gene interactions from the Comparative Toxicogenomics Database were retracted to identify key toxicological disruption pathways using Kyoto Encyclopedia of Genes and Genomes (KEGG) and a priori knowledge. The Pathview package in R was employed to predict molecular initiating events, key events, and their associated phenotypes, for further understanding the relevant gene-molecule interaction toxicity pathway network. …”
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Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both No-Antibiotics-Ever (NAE) and conventional broiler complexes by Yagya Adhikari, Dianna V. Bourassa, Sabin Poudel, Matthew A. Bailey, Richard J. Buhr, Kenneth S. Macklin

“…ResFinder was used to identify AMR genes from whole genome sequences while the phenotypic resistance of 14 different antibiotics was determined using broth microdilution method. …”
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The potential of the amaranth collection maintained at VIR in the context of global plant breeding and utilization trends by D. V. Sokolova, A. E. Solovieva, A. M. Zaretsky, T. V. Shelenga

“…Despite the great potential of amaranth, little research has been dedicated to the study of its genomics, concentrating mainly on the identification of its species diversity. …”
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Predicting Outcomes in Esophageal Squamous Cell Carcinoma Using scRNA‐Seq and Bulk RNA‐Seq: A Model Development and Validation Study by Jiaqi Zhang, Shunzhe Song, Yuqing Li, Aixia Gong

“…Methods A total of 8, 99, and 140 individuals from The Gene Expression Omnibus database, The Cancer Genome Atlas database, and the Memorial Sloan Kettering Cancer Center, respectively, were encompassed in the investigation. …”
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Intestinal Microbiome Changes in Fecal Microbiota Transplant (FMT) vs. FMT Enriched with Lactobacillus in the Treatment of Recurrent Clostridioides difficile Infection by Elvira Garza-González, Soraya Mendoza-Olazarán, Rayo Morfin-Otero, Andrea Ramírez-Fontes, Patricia Rodríguez-Zulueta, Samantha Flores-Treviño, Paola Bocanegra-Ibarias, Héctor Maldonado-Garza, Adrián Camacho-Ortiz

“…Fecal microbiota transplant by capsules was clinically and genomically similar between traditional FMT and enriched FMT with Lactobacillus spp. …”
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Gut microbiota, metabolites, and cytokines in relation to the risk of prostate cancer in the Asian population by Zhengshi Wang, Zhengshi Wang, Zhengshi Wang, Zhengshi Wang, Zhengshi Wang, Haotian Chen, Haotian Chen, Yongqiang Liu, Yongqiang Liu, Libin Zou, Libin Zou, Zhijin Zhang, Zhijin Zhang, Zhiqiang Yin, Zhiqiang Yin, Shiyu Mao, Shiyu Mao, Changcheng Guo, Changcheng Guo, Bin Yang, Bin Yang, Pengfei Wu, Pengfei Wu, Pengfei Wu, Xudong Yao, Xudong Yao

“…We aimed to perform a comprehensive analysis of causal associations of gut microbiota, metabolites, and cytokines with prostate cancer in the Asian population.Patients and methodsGenome-wide association study (GWAS) summary datasets were collected from the public databases. …”
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Causal associations between osteoporosis and HBV infection across Asian and European populations: evidence from Mendelian randomization and colocalization analysis by Zhengnan Li, Jiarui Cao, Ke Li, Yixin Wu, Zhanpeng Luo, Rui Cao, Zhiheng Cheng, Zhendong Tian, Yiyang Han, Yuping Lai, Bangqi Wang, Shen Chen

“…The data we utilized were obtained from the genome-wide association studies (GWAS) database. Various MR methods, including inverse variance weighted (IVW), MR Egger, weighted median, simple median and simple mode were employed to estimate the association between HBV infection and osteoporosis. …”
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Proteome‐Wide Mendelian Randomization Identifies Therapeutic Targets for Abdominal Aortic Aneurysm by Ka Zhang, Yuan Liu, Aiqin Mao, Changzhu Li, Li Geng, Hao Kan

“…Genetic associations with AAA were sourced from the AAAgen consortium, a large‐scale genome‐wide association study meta‐analysis involving 37 214 cases and 1 086 107 controls, and the FinnGen study, which included 3869 cases and 381 977 controls. …”
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Selective suppression of influenza A/H5N1 virus replication <i>in vitro</i> using nanocomplexes consisting of siRNA and aminopropylsilanol nanoparticles by Marina N. Repkova, Asya S. Levina, Oleg Yu. Mazurkov, Elena V. Makarevich, Ekaterina I. Filippova, Natalya A. Mazurkova, Valentina F. Zarytova

“…The most effective nanocomplex that contained siRNA targeted at the chosen region of mRNA segment 5 of the viral genome reduced virus replication in the culture by a factor of 630. …”
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Identification and functional analysis of energy metabolism and pyroptosis-related genes in diabetic nephropathy by Shan He, Jian Ye, Yu Wang, Lu yang Xie, Si Yi Liu, Qin kai Chen

“…Subsequent analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) network analysis. …”
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Genetic insights into MIS-C Post-COVID-19 in Kuwaiti children: investigating monogenic factors by Mohammed Dashti, Hessa AlKandari, Hessa AlKandari, Md Zubbair Malik, Rasheeba Nizam, Sumi Elsa John, Sindhu Jacob, Arshad Channanath, Fouzeyah Othman, Safa Al-Sayed, Osama Al-Hindi, Mona Al-Mutari, Thangavel Alphonse Thanaraj, Fahd Al-Mulla

“…The findings highlight the critical role of genetic predispositions in MIS-C and suggest that further functional genomics work is necessary to explore the mechanistic contributions of these genes, facilitating the development of targeted diagnostic strategies.…”
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Genotype-driven sensitivity of mice to tick-borne encephalitis virus correlates with differential host responses in peripheral macrophages and brain by Michaela Berankova, Jiri Holoubek, Vaclav Hönig, Zuzana Matusova, Martin Palus, Jiri Salat, Imtissal Krayem, Jarmila Vojtiskova, Pavel Svoboda, Veronika Pranclova, Lukas Valihrach, Peter Demant, Marie Lipoldova, Daniel Ruzek

“…BALB/c mice have intermediate susceptibility to TBE virus (TBEV) and STS mice are highly resistant, whereas the recombinant congenic strain CcS-11, which carries 12.5% of the STS genome on the BALB/c background, is more susceptible than BALB/c mice. …”
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Synergistic interaction between wheat streak mosaic virus and Triticum mosaic virus modulates wheat transcriptome to favor disease severity by Haritha Nunna, Nathan A. Palmer, Gautam Sarath, Stephen N. Wegulo, Satyanarayana Tatineni, Satyanarayana Tatineni

“…Gene ontology, protein domain and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis revealed that genes specifically related to photosynthesis, growth, stress, senescence, and defense were differentially enriched. …”
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Traces of Paleolithic expansion in the Nivkh gene pool based on data on autosomal SNP and Y chromosome polymorphism by V. N. Kharkov, N. A. Kolesnikov, L. V. Valikhova, A. A. Zarubin, A. L. Sukhomyasova, I. Yu. Khitrinskaya, V. A. Stepanov

“…The gene pool of the Nivkhs and other Far Eastern and Siberian populations was characterized using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y chromosome haplogroups. …”
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Creation of body color mutants by CRISPR/Cas9 gene editing in largemouth bass, Micropterus salmoides by Lina Sun, Tian Gao, Zhiqiang Li, Xiaolong Yang, Zuliang Qin, Mingxiao Ye, Ying Li, Feilong Wang, Deshou Wang

“…The efficiency of mutation was gRNA and Cas9 mRNA concentration dependent, and 400 ng/μl gRNA and 800 ng/μl Cas9 mRNA were recommended as the appropriate injection dose for genome editing in LMB. Enzyme-digestion and sanger-sequencing demonstrated that the CRISPR/Cas9 system is available for the gene editing of LMB. …”
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How does gut microbiota affect the vaginitis axis? The mediating role of plasma metabolites by Mo Li, Qianyu Zhang, Tong Wu, Lanfang Ma, Dianxing Hu, Zixuan Yuan, Shixuan Wang, Aiyue Luo, Jinjin Zhang

“…Here, we explored whether the gut microbiota influences the risk of vaginitis by performing a two-sample Mendelian randomization analysis using the largest genome-wide association studies to date. Four gut taxa in genus levels were identified related to vaginitis: Candidatus Soleaferrea (inverse-variance weighted [IVW] odds ratio [OR] = 2.20, P = 0.026), Dialister (IVW OR = 2.62, P = 0.029), Lachnospiraceae UCG-008 (IVW OR = 0.41, P = 0.0067), and Ruminiclostridium 5 (IVW OR = 0.080, P = 1.42 × 10−5). …”
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A Network Pharmacology-Based Strategy for Unveiling the Mechanisms of Tripterygium Wilfordii Hook F against Diabetic Kidney Disease by Yuyang Wang, Tongtong Liu, Fang Ma, Xiaoguang Lu, Huimin Mao, Weie Zhou, Liping Yang, Ping Li, Yongli Zhan

“…Finally, all the targets of clusters were subjected for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses via DAVID. …”
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CD2AP deficiency aggravates Alzheimer’s disease phenotypes and pathology through p38 MAPK activation by Yan-Yan Xue, Zhe-Sheng Zhang, Rong-Rong Lin, Hui-Fen Huang, Ke-Qing Zhu, Dian-Fu Chen, Zhi-Ying Wu, Qing-Qing Tao

“…Abstract Background Alzheimer’s disease (AD) is the most common form of neurodegenerative disorder, which is characterized by a decline in cognitive abilities. Genome-wide association and clinicopathological studies have demonstrated that the CD2-associated protein (CD2AP) gene is one of the most important genetic risk factors for AD. …”
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Copy number variations at the Rhg1 locus and their relationship with resistance to soybean cyst nematode (Heterodera glycines) by Dinesh Poudel, Guiping Yan, Carrie Miranda, Gustavo Fernando Kreutz, Intiaz Amin Chowdhury

“…The qPCR assay demonstrated 94.36% efficiency for the target gene at Rhg1 locus, Glyma18g02590, with copy number detected by the assay correlating strongly (r=0.994) with whole genome sequencing data in previous study. Copy number of each line was determined using 2−ΔΔCq method relative to Williams 82 (single copy) and correlated with the resistance response. …”
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Polytrauma in Older Adults Leads to Significantly Increased TIMP-1 Levels in the Early Posttraumatic Period by Mareen Braunstein, Thomas Kusmenkov, Wolf Mutschler, Christian Kammerlander, Wolfgang Böcker, Viktoria Bogner-Flatz

“…MMP-9 and TIMP-1 have been found to play a major role in posttraumatic immune disorder in a previous genome-wide mRNA analysis. Objective. The aim of this study was to evaluate the differences in serum protein dynamics in older and younger polytraumatized adults. …”
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