Integrated Analysis Reveals Genetic Basis of Growth Curve Parameters in an F₂ Designed Pig Population Based on Genome and Transcriptome Data by Zhaoxuan Che, Jiakun Qiao, Fangjun Xu, Xinyun Li, Yunxia Zhao, Mengjin Zhu

“…Based on genome and transcriptome data, the integrated analyses identified five putative SNPs (including INRA0056566 on chromosome X, DRGA0004151 on chromosome 3, INRA0056460 on chromosome X, H3GA0049324 on chromosome 17, and H3GA0037747 on chromosome 13) and 15 candidate genes (<i>PDGFA</i>, <i>VEGFD</i>, <i>CSPP1</i>, <i>EFHC1</i>, <i>PIK3C3</i>, <i>ZZZ3</i>, <i>GCC2</i>, <i>MAPK14</i>, <i>ZPR1</i>, <i>ISG15</i>, <i>ANG</i>, <i>CEBPD</i>, <i>ZHX3</i>, <i>CTBP2</i>, and <i>MYNN</i>). The functional analysis indicated that these candidate genes played important roles in cell division and differentiation, development and aging, and skeletal muscle and fat formation. …”
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Weighted Gene Co-Expression Network Analysis Uncovers Critical Genes and Pathways Involved in Soybean Response to Soybean Mosaic Virus by Hanhan Zhu, Ruiqiong Li, Yaoyao Fang, Xue Zhao, Weili Teng, Haiyan Li, Yingpeng Han

“…KEGG pathway enrichment analysis of the 9809 DEGs revealed significant enrichment of genes involved in resistance-related pathways such as plant–pathogen interaction, linoleic acid metabolism, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signaling transduction. Functional analysis using MapMan software identified multiple DEGs that were associated with pathways such as jasmonate synthesis and phenylpropanoid biosynthesis. …”
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CRYPTO-RESISTANT METHODS AND RANDOM NUMBER GENERATORS IN INTERNET OF THINGS (IOT) DEVICES by Petro Klimushyn, Tetiana Solianyk, Oleksandr Mozhaiev, Yurii Gnusov, Oleksandr Manzhai, Vitaliy Svitlychny

“…Research methods: method of structural and functional analysis of RNG and IoT devices, cryptographic methods of information protection, methods of random sequence generation, method of stability analysis of systems, methods of construction of autonomous Boolean networks and Boolean chaos analysis, methods of quality assessment of random sequences. …”
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Identification of the CBF Gene Family in Wheat and <i>TaCBF14B</i> Could Enhance the Drought Tolerance of <i>Arabidopsis thaliana</i> by Zubaidai Abudukerimu, Yitu Xu, Shengjing Chen, Yuliu Tan, Caihong Li, Nan Niu, Yuxin Xie, Zihan He, Xiangyu Liu, Junwei Xin, Jiafei Yu, Junrong Li, Ximei Li, Huifang Wang, Ming Wang, Nataliia Golub, Yumei Zhang, Weiwei Guo

“…According to the high expression after drought stress, <i>TaCBF14B</i> was selected for further functional analysis. Subcellular localization and transcriptional activation activity analysis indicated that <i>TaCBF14B</i> likely functions as a transcription factor involved in drought stress tolerance. …”
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Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model by Philip M. Ashton, Leonardos Mageiros, James E. Meiring, Angeziwa Chunga-Chirambo, Farhana Khanam, Sabina Dongol, Happy Banda, Abhilasha Karkey, Lorena Preciado-Llanes, Helena Thomaides-Brears, Malick Gibani, Nazmul Hasan Rajib, Nazia Rahman, Prasanta Kumar Biswas, Md Amirul Islam Bhuiyan, Sally Kay, Kate Auger, Olivier Seret, Nicholas R. Thomson, Andrew J. Pollard, Stephen Baker, Buddha Basnyat, John D. Clemens, Christiane Dolecek, Sarah J. Dunstan, Gordon Dougan, Robert S. Heyderman, Virginia E. Pitzer, Firdausi Qadri, Melita A. Gordon, Kathryn E. Holt, Thomas C. Darton, STRATAA Study Group

“…Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. …”
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Reconstruction of a lncRNA-Associated ceRNA Network in Endothelial Cells under Circumferential Stress by Zhuhui Huang, William Adiwignya Winata, Kui Zhang, Yang Zhao, Yang Li, Ning Zhou, Shaoyou Zhou, Wei Fu, Bokang Qiao, Guoqi Li, Yihui Shao, Jubing Zheng, Ran Dong

“…The nodes with most degrees in three kinds of RNAs are hsa-miR-4739, NEAT1, and MAP3K2. Functional analysis showed that different biological processes enriched in biological regulation, response to stimulus and cell communication. …”
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Metabolomic signatures in liquid biopsy are associated with overall survival in metastatic melanoma patients treated with immune checkpoint inhibitor therapy by Susan Costantini, Gabriele Madonna, Mariaelena Capone, Elena Di Gennaro, Palmina Bagnara, Federica Renza, Domenico Mallardo, Roberta Affatato, Carlo Vitagliano, Marilena Romanelli, Marilena Tuffanelli, Ester Simeone, Gennaro Ciliberto, Paolo A. Ascierto, Alfredo Budillon

“…Peripheral metabolomics was performed using baseline sera from 132 patients via 600 MHz Nuclear Magnetic Resonance (NMR) spectroscopy. Enriched functional analysis was conducted to identify the metabolic pathways in which significant metabolites were involved. …”
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Therapeutic Targeting of Decr1 Ameliorates Cardiomyopathy by Suppressing Mitochondrial Fatty Acid Oxidation in Diabetic Mice by Qing‐Bo Lu, He‐Ting Sun, Kuo Zhou, Jia‐Bao Su, Xin‐Yu Meng, Guo Chen, Ao‐Yuan Zhang, An‐Jing Xu, Chen‐Yang Zhao, Yuan Zhang, Yao Wang, Hong‐Bo Qiu, Zhuo‐Lin Lv, Zheng‐Yang Bao, Jian Zhu, Feng Xiao, Xue‐Xue Zhu, Hai‐Jian Sun

“…Furthermore, RNA sequencing and functional analysis showed that Decr1 interacted with and upregulated pyruvate dehydrogenase kinase 4 (PDK4) in injured cardiomyocytes, and overexpression of PDK4 eliminated the benefits of Decr1 downregulation in DCM (−20% for EF, p = 0.0071; −28% for FS, p = 0.0022). …”
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Insights into the Stearoyl-Acyl Carrier Protein Desaturase (SAD) Family in Tigernut (<i>Cyperus esculentus</i> L.), an Oil-Bearing Tuber Plant by Zhi Zou, Xiaowen Fu, Chunqiang Li, Xiaoping Yi, Jiaquan Huang, Yongguo Zhao

“…These findings highlight lineage-specific evolution of the <i>SAD</i> family and putative roles of <i>CeSAD</i> genes in tuber oil accumulation, which facilitate further functional analysis and genetic improvement in tigernut and other species.…”
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Metagenomic analysis reveals distinct patterns of gut microbiota features with diversified functions in C. difficile infection (CDI), asymptomatic carriage and non-CDI diarrhea by Lamei Wang, Xinhua Chen, Nira R. Pollock, Javier A. Villafuerte Gálvez, Carolyn D. Alonso, Dangdang Wang, Kaitlyn Daugherty, Hua Xu, Junhu Yao, Yulin Chen, Ciaran P. Kelly, Yangchun Cao

“…Downstream statistical analyses (including alpha and beta diversity analysis, differential abundance analysis, correlation network analysis, and potential functional analysis) were then performed. The gut microbiota in the Control group showed higher Chao1 index (p < 0.05), while Shannon index at KEGG module level was higher in CDI than in Carrier and Control (p < 0.05). …”
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1α,25(OH)2D3 reverses exhaustion and enhances antitumor immunity of human cytotoxic T cells by Peng Li, Hua Zhang, Xiao Wang, Biyun Chen, Ke Li, Zhinan Yin, Xinhai Zhu, Guangchao Cao, Ruan Wu, Wenhui Yuan, Guodong Sun, Xichun Xia, Ligong Lu, Yunfei Gao

“…We performed phenotypical and functional analysis of T-cell through flow cytometry. Vitamin D receptor (VDR) knockout and overexpression CD8+ and Vδ2+ T cells were constructed using Cas9-gRNA targeted and overexpressing approaches to identify 1α,25(OH)2D3/VDR-mediated transcription regulation for ICRs or antitumor activity in T cells.Results We show that serum level of vitamin D is negatively correlated with expression of programmed cell death-1 (PD-1), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3), but positively correlated with CD28 expression on CD8+ and Vγ9Vδ2+ T cells in patients with NSCLC. 1α,25(OH)2D3, the active form of vitamin D, promotes the nuclear translocation of VDR, which binds to the promoter region of Pdcd1, Tim3, and Tigit genes and inhibits their expression. …”
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Metabolism-associated marker gene-based predictive model for prognosis, targeted therapy, and immune landscape in ovarian cancer: an integrative analysis of single-cell and bulk RN... by Lele Ling, Bingrong Li, Boliang Ke, Yinjie Hu, Kaiyong Zhang, Siwen Li, Te Liu, Peng Liu, Bimeng Zhang

“…The MRG-based prognostic model was further utilized for functional analysis of the model gene set, pan-cancer analysis of genomic variations, spatial transcriptomics analysis, as well as GO and KEGG enrichment analysis. …”
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Exploring the additive antibacterial potential of Cinnamomum cassia volatile oil and imipenem against Acinetobacter baumannii: a multi-omics investigation by Youyuan Lu, Youyuan Lu, Wanlin Xu, Jiahui Xue, Mingxia Xie, Haotian Liu, Ruilin Wang, Gang Li, Hanqing Wang, Hanqing Wang

“…CBV and IPM also induced significant changes at both the transcriptomic and proteomic levels in A. baumannii. Functional analysis revealed that the differentially expressed genes (DEGs) and proteins (DEPs) were involved in multiple pathways. …”
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Bioinformatics identification and validation of m6A/m1A/m5C/m7G/ac4 C-modified genes in oral squamous cell carcinoma by Cheng-Hui Lu, Xue-Lai Yin, Zhuo-Deng Huang, Si-Ang Lv, Jun Wu, Jie Wei

“…The four most significantly differentially expressed genes were selected for further functional analysis, and small interfering RNA (siRNA) vectors targeting these genes were transfected into OSCC CAL27 cells. …”
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Serum extracellular vesicle microRNAs as potential biomarkers to predict pembrolizumab response and prognosis in metastatic non-small cell lung cancer patients by Daniela Lamorte, Luciana De Luca, Alfredo Tartarone, Stefania Trino, Irene Giulivo, Angelo De Stradis, Maddalena Maietti, Antonella Caivano, Ilaria Laurenzana

“…All data were associated with immunotherapy response, Progression Free Survival (PFS), Overall Survival (OS), Eastern Cooperative Oncology Group Performance Status (ECOG-PS) and metastases.ResultsTwelve NSCLC-related microRNAs have been found, for the first time, in serum cEVs from a specific cohort of metastatic advanced stage NSCLC patients. Through a functional analysis, these microRNAs are found to be connected to each other and involved in the pathology of NSCLC, particularly in IGF/P53/VEGF/NOTCH/PI3K pathways, in cytokine/interleukin signaling and in the immune system. …”
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Mechanism of electroacupuncture on rats with primary dysmenorrhea based on microRNA expression spectrum and PI3K/Akt/mTOR signaling pathway by Si-an PAN, Shao-hua WANG, Han-yu YUAN, Juan LI, Xiao XUE, Zeng-hui YUE, Yu LIU

“…After EA intervention, the expression of miR-144–3p was significantly up-regulated. GO functional analysis of differentially expressed miRNAs in PDM rats after EA showed that the biological functions involved calcium transmembrane transporter activity, mitogen-activated protein kinase binding, epithelial cell migration, tissue migration, etc. 3. …”
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The transcription factor PbeNAC83 positively regulates the Valsa canker resistance in apple and pear by DOU Zhiqi, CAI Minrui, DU Chenglong, HU Huanhuan, ZUO Cunwu

“…PbeNAC83 was transfected into the DuliG03 suspension cells, and three wellgrown overexpression cell lines were obtained. Functional analysis demonstrated that PbeNAC83-OE cells were more resistant to Vp and VpM compared to the control. …”
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