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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Malignant phyllodes tumors with sarcomatous components: A histopathologic and molecular study by Ting Lei, Yunjie Song, Zhiyi Shen, Yongqiang Shi, Cunyan Xia, Xu Deng, Wenyue Da, Yan Peng, Qing Li

“…The clinicopathological characteristics, prognostic information, and genomic profiles were compared to those of MPTs without sarcomatous components. …”
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Loss of BRCA1 Spontaneously Induces the Tumorigenesis in Lacrimal Gland by Sun Eui Kim, Hye Jung Baek, Eun Jung Park, Sung Chul Lim, Sang Soo Kim

“…These results suggest that BRCA1 is involved in genetic stability of the lacrimal gland, providing new insight into genomic instability in organism maintenance and tumorigenesis of the lacrimal gland.…”
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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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Genetic diversity assessed in Ethiopian highland bamboo [Oldeania alpina (K. Schum) Stapleton] populations revealed by microsatellite markers by Muhamed Adem, Oumer Abdie, Tileye Feyissa, Dereje Beyene

“…Methods The study relied on 150 DNA samples representing 15 O.alpina populations collected across major O.alpina harboring forests of Ethiopia. Following total genomic DNA isolation SSR primer screening was conducted using PCR, gel electrophoreses, gel doc imaging, allele scoring, and statistical analysis. …”
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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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Genetic structure of the collection of ryegrass (<i>Lolium</i>) cultivars: a study based on SSR and SCoT markers by Yu. M. Mavlyutov, E. A. Vertikova, A. O. Shamustakimova, I. A. Klimenko

“…The efficiency of PCR-based SSR and SCoT marker techniques was studied in the context of evaluating the genetic structure of annual and perennial ryegrass accessions and defining DNA-identifying markers.Materials and methods. Genomic DNA was isolated from the aggregate sample of 30 seedlings from each of the 15 analyzed cultivars according to the modified SDS DNA extraction protocol. …”
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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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Long-term maintenance of patient-specific characteristics in tumoroids from six cancer indications by Colin D. Paul, Chris Yankaskas, Pradip Shahi Thakuri, Brittany Balhouse, Shyanne Salen, Amber Bullock, Sylvia Beam, Anthony Chatman, Sybelle Djikeng, Xiaoyu Jenny Yang, Garrett Wong, Isha Dey, Spencer Holmes, Abigail Dockey, Lindsay Bailey-Steinitz, Lina Zheng, Weizhong Li, Vivek Chandra, Jakhan Nguyen, Jason Sharp, Erik Willems, Mark Kennedy, Matthew R. Dallas, David Kuninger

“…Newly derived tumoroid lines (n = 20) were analyzed by targeted genomic profiling and RNA sequencing and were representative of tumor tissue samples. …”
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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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Improving drug repositioning with negative data labeling using large language models by Milan Picard, Mickael Leclercq, Antoine Bodein, Marie Pier Scott-Boyer, Olivier Perin, Arnaud Droit

“…A detailed review of the top 30 revealed 9 promising drugs targeting various mechanisms such as genomic instability, p53 regulation, or TMPRSS2-ERG fusion. …”
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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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A two-sample bidirectional Mendelian randomization analysis between telomere length and hyperthyroidism by Shiben Zhu, Ziyu Hao, Qihang Chen, Xiaoliu Liu, Wenyan Wu, Fang Zhang

“…However, the casual association between telomere length (TL) and hyperthyroidism remains unclear.ObjectiveWe aim to explore the casual relationship between TL and hyperthyroidism.MethodsA two-sample bidirectional Mendelian randomization (MR) analysis employed the inverse variance weighted (IVW) method, supplemented by additional approaches such as Weighted Median (WM), and MR Egger.ResultsThe summary statistics for TL were derived from the UK Biobank, comprising 472,174 individuals, while the data for hyperthyroidism were sourced from the GWAS Catalog and the FinnGen database, encompassing cohorts of 460,499 and 173,938 individuals, respectively. Utilizing 139 genome-wide significant single nucleotide polymorphisms (SNPs) as instrumental variables (IVs) for TL, forward MR analyses indicated a negative causal effect of TL on hyperthyroidism. …”
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Description of a new Ornithodoros (Pavlovskyella) (Ixodida: Argasidae) tick species from Pakistan by Abid Ali, Mehran Khan, Muhammad Numan, Abdulaziz Alouffi, Mashal M. Almutairi, Ronel Pienaar, Minique H. de Castro, Lidia Chitimia-Dobler, Sebastián Muñoz-Leal, Ben J. Mans, Ala Tabor

“…Phylogenetic analyses of the full-length mitochondrial genome and the 18S and 28S ribosomal RNA genes, combined with pairwise nucleotide comparisons of cox1, cox2, atp8, atp6, cox3, nad3, nad5, nad4, nad4L, nad6, cytb, nad1, nad2, 12S rDNA, 16S rDNA, 18S rDNA and 28S rDNA further support that the new species belongs to the Pavlovskyella subgenus, clustering with O. tholozani, Ornithodoros verrucosus and Ornithodoros tartakovskyi.…”
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Molecular Typing of Klebsiella pneumoniae Clinical Isolates by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction by Parinaz Sedighi, Omid Zarei, Kiana Karimi, Mohammad Taheri, Pezhman Karami, Leili Shokoohizadeh

“…Also, the samples were evaluated by PCR method for the detection of aerobactin gene within their genome. Finding. The genetic relatedness among K. pneumoniae isolates was studied, and results established the genetic diversity of the clinical isolates by detecting 25 different ERIC types, including 14 common types and 11 unique types. …”
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An initial exploration of core collection construction and DNA fingerprinting in Elymus sibiricus L. using SNP markers by Xinrui Li, Xinrui Li, Xinrui Li, Daping Song, Mingfeng Li, Daxu Li, Minghong You, Yan Peng, Jiajun Yan, Shiqie Bai

“…Additionally, we identified 290 SNP loci from among the high-quality SNP loci generated by whole-genome sequencing of the 90 E. sibiricus samples as candidate markers. …”
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