Integrated Transcriptome Analysis Reveals Novel Molecular Signatures for Schizophrenia Characterization by Tong Ni, Yu Sun, Zefeng Li, Tao Tan, Wei Han, Miao Li, Li Zhu, Jing Xiao, Huiying Wang, Wenpei Zhang, Yitian Ma, Biao Wang, Di Wen, Teng Chen, Justin Tubbs, Xiaofeng Zeng, Jiangwei Yan, Hongsheng Gui, Pak Sham, Fanglin Guan

“…Their genetic contributions are comparable to genome‐wide polygenic risk scores. The DREG‐based SVM model demonstrated high performance (AUC 85% for SCZ characterization, 79% for specificity). …”
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Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response by Lisa Teichmann, Sam Luitwieler, Johan Bengtsson-Palme, Benno ter Kuile

“…Ciprofloxacin, enrofloxacin, and moxifloxacin exposures led to the most evident reliance on the SOS response for resistance, whereas levofloxacin exposed cultures showed less dependency. Whole genome analysis indicated distinct genetic changes associated with each fluoroquinolone, highlighting potential different pathways and mechanisms involved in resistance. …”
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Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores by Karen Barmettler, Sara Boss, Michael Biggel, Roger Stephan

“…The 11 isolates identified by matrix-assisted laser desorption ionization-time of flight were whole-genome sequenced with Illumina technology to confirm the identity of the pathogen, determine its toxin gene profile, and perform panC typing. …”
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Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma by Fan Yang, Xiaodong Jia, Zihuan Ma, Siyao Liu, Chunzi Liu, Dan Chen, Xiuju Wang, Niansong Qian, Hui Ma

“…LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. …”
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The Role of Gut Microbiota in Tumor Immunotherapy by Miao Wu, Jiawei Bai, Chengtai Ma, Jie Wei, Xianjin Du

“…With the maturity of genomics and metabolomics technologies, the effect of intestinal microbiota in tumor development and treatment has gradually been recognized. …”
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Mendelian randomization analysis does not support a causal influence between lipoprotein(A) and immune-mediated inflammatory diseases by Yun Ti, Dan Xu, Xiaoning Qin, Yang Hu, Yuru Xu, Qingzhao Zhao, Peili Bu, Jingyuan Li

“…We performed a bidirectional two-sample mendelian randomization analyses based on genome-wide association study (GWAS) summary statistics of Lp(a) and nine IMIDs, specifically celiac disease (CeD), Crohn’s disease (CD), ulcerative colitis (UC), inflammatory bowel disease (IBD), multiple sclerosis (MS), psoriasis (Pso), rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), and summary-level data for lipid traits. …”
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VCAM-1 Promotes Angiogenesis of Bone Marrow Mesenchymal Stem Cells Derived from Patients with Trauma-Induced Osteonecrosis of the Femoral Head by Regulating the Apelin/CCN2 Pathway by Yiming Shao, Lei Sun, Baodong Ma, Ranran Jin, Yueyao Ban, Ruibo Li, Jianfa Wang, Hongkai Lian, Han Yue

“…Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that upregulated DEGs were engaged in the Apelin signaling pathway. …”
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A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice,Wiki and Databases by Tesson, Florian, Planel, Rémi, Egorov, Artyom A, Georjon, Héloïse, Vaysset, Hugo, Brancotte, Bryan, Néron, Bertrand, Mordret, Ernest, Atkinson, Gemma Catherine, Bernheim, Aude, Cury, Jean

“…To overcome these challenges, we present a hub of resources on defense systems, including: 1) an updated version of DefenseFinder with a web-service search function, 2) a community-curated repository of knowledge on the systems, and 3) precomputed databases, which include annotations done on RefSeq genomes and structure predictions generated by AlphaFold. …”
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Computational identification and experimental validation of novel Saccharum officinarum microRNAs along with their targets through RT-PCR approach by Abdul Baqi, Samiullah, Jadoon Khan, Asma Sadiq, Yousaf Khan, Shahid Ali, Syed Nadeem ul Hassan Mohani, Naqeebullah Khan, Tawaf Ali Shah, Khalid S. Almaary, Youssouf Ali Younous, Mohammed Bourhia

“…This was accomplished by predicting novel conserved miRNAs in sugarcane plants using a variety of genomics-based techniques like BLASTn, MFOLD, psRNA Target, sequence logo, Weblogo, primer-3, etc. and annotated using miRBase and NCBI. …”
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Systematic screening and dynamic profiling of germline regulatory pathways and spermatogonial surface markers in a bivalve mollusc by Liangjie Liu, Ya Shu, Tian Liu, Huilan Wei, Yaxin Yang, Lijing Zhang, Xiaohui Ma, Guoqing Li, Yajuan Li, Shi Wang, Lingling Zhang

“…A single copy of Fgfr (PyFgfr) was confirmed in the P. yessoensis genome, which exhibited the canonical functional domains of FGFRs. …”
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Causality between insulin use and malignant tumors of the digestive system: a two-sample mendelian randomized study by DengZhuo Chen, YongLi Ma, JingHui Li, Liang Wen, GuoSheng Zhang, ChengZhi Huang, XueQing Yao

“…However, further MR studies with larger sample sizes from genome-wide association study (GWAS) data are needed to verify this association.…”
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Brown Rot-Type Fungal Decomposition of Sorghum Bagasse: Variable Success and Mechanistic Implications by Gerald N. Presley, Bongani K. Ndimba, Jonathan S. Schilling

“…Linking this information to genome comparisons including other brown rot fungi known to have a similar issue regarding decomposing grasses (Postia placenta, Fomitopsis pinicola) suggested that a lack of CE 1 feruloyl esterases as well as low xylanase activity in S. lacrymans (3x lower than in G. trabeum) may hinder S. lacrymans, P. placenta, and F. pinicola when degrading grass substrates. …”
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The Possible Role of TLR2 in Chronic Hepatitis B Patients with Precore Mutation by Malihe Moradzadeh, Sirous Tayebi, Hossein Poustchi, Kourosh Sayehmiri, Parisa Shahnazari, Elnaz Naderi, Ghodratollah Montazeri, Ashraf Mohamadkhani

“…Fifty-one patients with chronic hepatitis B, negative for HBeAg and detectable HBV DNA, were examined for the presence of mutations in pre-core region of HBV genome by direct sequencing. Serum TLR2 was measured by enzyme-linked immunosorbent assay. …”
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Gut microbial 3α‐hydroxysteroid dehydrogenase promotes depression in males via degrading testosterone by Di Li, Jingru Cheng, Wei Zhang, Pengfei Cheng, Yuan He, Jinghan Jia, Chao Wang, Zhongchun Liu, Zhou Sun, Jinxi Wang

“…We found that A. koreensis administration in mice led to reduced serum testosterone levels and depression‐like behaviors, which were improved by antibiotic treatment. Using whole genome sequencing, the gene mediating testosterone degradation in A. koreensis was identified and annotated as 3α‐hydroxysteroid dehydrogenase (3α‐HSD). …”
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Development and validation of PCR marker array for molecular selection towards spring, vernalization-independent and winter, vernalization-responsive ecotypes of white lupin (Lupin... by Anna Surma, Michał Książkiewicz, Wojciech Bielski, Bartosz Kozak, Renata Galek, Sandra Rychel-Bielska

“…Abstract White lupin (Lupinus albus L.) is an ancient grain legume that is still undergoing improvement of domestication traits, including vernalization-responsiveness, providing frost tolerance and preventing winter flowering in autumn-sowing agriculture, and vernalization-independence, conferring drought escape by rapid flowering in spring-sowing. A recent genome-wide association study highlighted several loci significantly associated with the most contrasting phenotypes, including deletions in the promoter of the FLOWERING LOCUS T homolog, LalbFTc1, and some DArT-seq/silicoDArT loci. …”
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In the coevolution of cotton and pathogenic fungi, resistant cotton varieties lead to an escalation in the virulence of Verticillium dahliae by Yalin Zhang, Lifang Cui, Ruibing Liu, Zili Feng, Hongjie Feng, Jinglong Zhou, Lihong Zhao, Feng Wei, Heqin Zhu

“…Consequently, among the offspring strains, high virulence strains exhibited higher levels of physiological characteristics and genetic diversity compared to moderate and low virulence strains. Moreover, whole genome resequencing revealed that the Ka/Ks ratio of single nucleotide polymorphism (SNPs) in the majority of the offspring strains was about 0.6, indicating an adverse selection impact in the offspring strains. …”
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Bacteriophage LDT325 enhances Pseudomonas syringae tolerance by improving antioxidant defense in tea plant [Camellia sinensis (L.) O. Kuntze] by Li Liu, Anqi Huang, Hua Zhang, Yubao Li, Lei Wang, Lei Wang

“…Using NCBI BLASTn to compare the entire genome with other nucleotide sequences, we found that the phage LDT325 exhibited cross-species characteristics that had not been previously reported. …”
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Impact of Mediterranean Diet Adherence on the Incidence of New‐Onset Hypertension in Adults With Obesity in Korea: A Nationwide Cohort Study by Jung‐Hwan Kim, Ji‐Won Lee, Yaeji Lee, Chung‐Mo Nam, Yu‐Jin Kwon

“…We used data from the Korean Genome and Epidemiology Study, a population‐based prospective cohort study. …”
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Zoonotic transmission of novel Influenza A variant viruses detected in Brazil during 2020 to 2023 by Paola Cristina Resende, Dennis M. Junqueira, Caroline Tochetto, Maria Ogrzewalska, Fernando C. Motta, Jonathan Lopes, Luciana Appolinario, Larissa Macedo, Braulia Caetano, Aline Matos, Thauane Silva, Elisa Cavalcante Pereira, Leticia Ferreira Lima, Irina Riediger, Maria do Carmo Debur, Guilherme Nardi Becker, Aline Andrade, Acácia Maria Lourenço Francisco Nasr, Rosana Aparecida Piler, Ana Carolina Dalla Vecchia, Walquíria Almeida, David Brown, Rejane Schaefer, Marilda M. Siqueira

“…Here, we describe eight human IAV variant infections (6 mild and 2 severe cases, including 1 death) detected in Paraná, Brazil, during 2020–2023. Genomes recovered were closely related to Brazilian swIAVs of three major lineages (1 A.3.3.2/pdm09, 1B/human-like, and H3.1990.5), including three H1N1v, two H1N2v, two H3N2v and one H1v. …”
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Breeding and selection of mini-pigs in the ICG SB RAS by S. V. Nikitin, S. P. Knyazev, K. S. Shatokhin, V. I. Zaporozhets, V. I. Ermolaev

“…We explained the possibility of using similarity indices calculated by using portions of the ancestors’ blood (genome) for the selection of parental pairs and the evaluation of genetic consolidation of the herd. …”
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