Screening and validation of tsRNAs associated with lung adenocarcinoma by LU Chunli, SHAN Yifan, XIE Weijia

“…Gene ontology （GO） enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis were performed based on DAVID and KOBA KEGG online websites. …”
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Exploration of the Immune-Related Signatures and Immune Infiltration Analysis in Melanoma by Ai-lan Li, Yong-mei Zhu, Lai-qiang Gao, Shu-yue Wei, Ming-tao Wang, Qiang Ma, You-you Zheng, Jian-hua Li, Qing-feng Wang

“…After merging the genome expression data using Perl, the limma package was used for data normalization. …”
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Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression by D. F. Santoro, G. Marconi, S. Capomaccio, M. Bocchini, A. W. Anderson, A. Finotti, M. Confalonieri, E. Albertini, D. Rosellini

“…Abstract Whole genome duplication (WGD) is a powerful evolutionary mechanism in plants. …”
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Immune regulatory genes impact the hot/cold tumor microenvironment, affecting cancer treatment and patient outcomes by Mengmeng Sang, Jia Ge, Juan Ge, Juan Ge, Gu Tang, Qiwen Wang, Jiarun Wu, Liming Mao, Liming Mao, Xiaoling Ding, Xiaorong Zhou

“…Kyoto Encyclopedia of Genes and Genomes and Hallmark pathway enrichment were evaluated through gene set variation analysis. …”
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An association between type A porcine endogenous retrovirus copy number and hematological parameters and gender in miniature pigs by R. B. Aitnazarov, S. V. Nikitin, G. V. Kontsevaya, M. I. Voevoda, N. S. Yudin

“…Selection for animals with low copy number of retroviruses in the genome using simple phenotypic indications is required for the widespread implementation of xenotransplantation. …”
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Neurotrophin-3 as a mediator in the link between PM2.5 exposure and psychiatric disorders: A Mendelian randomization study by Yuan Zhang, Wei Wang, Xuening Zhang, Ran Jing, Xin Wen, Peng Xiao, Xinjie Liu, Zengle Zhao, Tongmin Chang, Yufei Li, Wen Liu, Chenxi Sun, Xiaorong Yang, Lejin Yang, Ming Lu

“…Background: The causal relationship between PM2.5 (particulate matter with an aerodynamic diameter ≤2.5 μm) and common mental disorders, along with its neuropathological mechanisms, remains unclear. Methods: We used genome-wide association study datasets from the UK Biobank and Psychiatric Genomics Consortium to systematically investigate the causal relationship between PM2.5 and nine common psychiatric disorders using two-sample Mendelian randomization (TSMR) methods. …”
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Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs by Anargyros Skoulakis, Anargyros Skoulakis, Giorgos Skoufos, Giorgos Skoufos, Armen Ovsepian, Armen Ovsepian, Artemis G. Hatzigeorgiou, Artemis G. Hatzigeorgiou

“…Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. …”
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Exploring the role of inflammatory biomarkers in trigeminal neuralgia by Shenglong Lai, Haiyang Li, Yazhou Xing, Du Wu, Lin Wang, Qinghua Liang

“…Instrumental variables (IVs) were selected based on genome-wide significance and clumping thresholds to avoid linkage disequilibrium. …”
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Pharmacological activity of OST-01, a natural product from baccharis coridifolia, on breast cancer cells by HyunJun Kang, Dinh Hoa Hoang, Melissa Valerio, Khyatiben Pathak, William Graff, Alexis LeVee, Jun Wu, Mark A. LaBarge, David Frankhouser, Russell C. Rockne, Patrick Pirrotte, Bin Zhang, Joanne Mortimer, Le Xuan Truong Nguyen, Guido Marcucci

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Key Drivers of Consumption, Conceptual, Sensory, and Emotional Profiling of Cheeses Based on Origin and Consumer Familiarity: A Case Study of Local and Imported Cheeses in Greece by Malamatenia Panagiotou, Efstathios Kaloudis, Danai Ioanna Koukoumaki, Vasiliki Bountziouka, Evangelia Giannakou, Margarita Pandi, Konstantinos Gkatzionis

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Radiomic prediction for durable response to high‐dose methotrexate‐based chemotherapy in primary central nervous system lymphoma by Haoyi Li, Mingming Xiong, Ming Li, Caixia Sun, Dao Zheng, Leilei Yuan, Qian Chen, Song Lin, Zhenyu Liu, Xiaohui Ren

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Rice–Potato Rotation Pattern Affects 2-Acetyl-1-Pyrroline Biosynthesis and Productivity in Aromatic Rice Grains by Fengqin Hu, Congcong Shen, Dehao Feng, Shuangbing Zhu, Jian Lu, Jianqiang Zhu, Xianjin Qiu, Kai Chen, Bin Du, Jianlong Xu

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Colorectal cancer in Lynch syndrome families: consequences of gene germline mutations and the gut microbiota by Xuexin Wang, Zhijun Zheng, Dongliang Yu, Xiaojue Qiu, Ting Yang, Ruoran Li, Jing Liu, Xin Wang, Peng Jin, Jianqiu Sheng, Nan Qin, Na Li, Junfeng Xu

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Effects of Sitagliptin Treatment on Dysmetabolism, Inflammation, and Oxidative Stress in an Animal Model of Type 2 Diabetes (ZDF Rat) by Liliana Ferreira, Edite Teixeira-de-Lemos, Filipa Pinto, Belmiro Parada, Cristina Mega, Helena Vala, Rui Pinto, Patrícia Garrido, José Sereno, Rosa Fernandes, Paulo Santos, Isabel Velada, Andreia Melo, Sara Nunes, Frederico Teixeira, Flávio Reis

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Heterochrony in orthodenticle expression is associated with ommatidial size variation between Drosophila species by Montserrat Torres-Oliva, Elisa Buchberger, Alexandra D. Buffry, Maike Kittelmann, Genoveva Guerrero, Lauren Sumner-Rooney, Pedro Gaspar, Georg C. Bullinger, Javier Figueras Jimenez, Fernando Casares, Saad Arif, Nico Posnien, Maria D. S. Nunes, Alistair P. McGregor, Isabel Almudi

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<i>Botrytis cinerea</i> PMT4 Is Involved in <i>O</i>-Glycosylation, Cell Wall Organization, Membrane Integrity, and Virulence by Verónica Plaza, Alice Pasten, Luz A. López-Ramírez, Héctor M. Mora-Montes, Julia Rubio-Astudillo, Evelyn Silva-Moreno, Luis Castillo

“…Using bioinformatics analysis within the <i>Botrytis cinerea</i> genome database, an ortholog to <i>Saccharomyces cerevisiae</i> Pmt4 and other fungal species was identified. …”
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Deep learning in microbiome analysis: a comprehensive review of neural network models by Piotr Przymus, Krzysztof Rykaczewski, Adrián Martín-Segura, Jaak Truu, Enrique Carrillo De Santa Pau, Mikhail Kolev, Mikhail Kolev, Irina Naskinova, Aleksandra Gruca, Alexia Sampri, Alexia Sampri, Marcus Frohme, Alina Nechyporenko, Alina Nechyporenko

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Identification and validation of prognostic biomarkers in ccRCC: immune-stromal score and survival prediction by Fang Lyu, Yuxin Zhong, Qingliu He, Wen Xiao, Xiaoping Zhang

“…Methods Data from the Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) were subjected to analysis to compute immune and stromal scores utilizing the ESTIMATE algorithm. …”
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Age-related changes in DNA methylation in a sample of elderly Brazilians by Hayley Welsh, Caio M. P. F. Batalha, Weili Li, Nadja C. Souza-Pinto, Yeda A. O. Duarte, Michel S. Naslavsky, Esteban J. Parra

“…Both aDMPs and aDMRs exhibited age-related hypermethylation within CpG islands and promoter regions of the genome, whereas hypomethylation predominantly occurred in interCGI and intergenic regions and introns. …”
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Accuracy of Large Language Models for Infective Endocarditis Prophylaxis in Dental Procedures by Paak Rewthamrongsris, Jirayu Burapacheep, Vorapat Trachoo, Thantrira Porntaveetus

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