Prognostic models of immune-related cell death and stress unveil mechanisms driving macrophage phenotypic evolution in colorectal cancer by Hao Liu, Chuhan Zhang, Sanfei Peng, Yuhan Yin, Yishi Xu, Sihan Wu, Liping Wang, Yang Fu

“…Furthermore, we performed enrichment analyses and deconvolution algorithms to elucidate the complex interactions between immune cell infiltration and the processes of PCD and stress within a substantial array of transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data base (GEO) related to CRC. …”
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Single nucleotide polymorphism rs110861313 in the intergenic region of chromosome 23 is associated with the development of leukosis in the Russian Black Pied cattle by R. B. Aitnazarov, E. V. Ignatieva, T. A. Agarkova, N. G. Dvoeglazov, N. A. Osipova, V. V. Khramtsov, N. S. Yudin

“…In recent years, using a genome-wide association study (GWAS), a number of single nucleotide polymorphisms (SNPs) have been suggested to be associated with susceptibility to leukemia in cattle. …”
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Identification of core biomarkers for tuberculosis progression through bioinformatics analysis and in vitro research by Zhanpeng Chen, Qiong Wang, Quan Ma, Jinyun Chen, Xingxing Kong, Yuqin Zeng, Lanlan Liu, Shuihua Lu, Xiaomin Wang

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that these genes are primarily associated with fatty acid degradation, pyruvate metabolism, arginine and proline metabolism, as well as cholesterol metabolism signaling pathways. …”
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Vic9 mycobacteriophage: the first subcluster B2 phage isolated in Russia by Marina Zaychikova, Maja Malakhova, Dmitry Bespiatykh, Maria Kornienko, Ksenia Klimina, Aleksandra Strokach, Roman Gorodnichev, Arina German, Mikhail Fursov, Dmitry Bagrov, Dmitry Bagrov, Anna Vnukova, Alexandra Gracheva, Anastasia Kazyulina, Margarita Shleeva, Egor Shitikov

“…No lysis was observed in other tested mycobacterial species. The genome of Vic9 comprises 67,543 bp of double-stranded DNA and encodes 89 open reading frames. …”
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Identification of critical biomarkers and immune landscape patterns in glioma based on multi-database by Hanzhang Yuan, Jingsheng Cheng, Jun Xia, Zeng Yang, Lixin Xu

“…Patients and methods Differentially expressed genes (DEGs) of glioma were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. …”
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Collection of microorganisms of ICG SB RAS as a genetic resource for biotechnology by A. V. Bryanskaya, Y. E. Uvarova, A. S. Rozanov, N. M. Slynko, V. N. Shlyakhtun, K. V. Starostin, E. A. Demidov, E. V. Lazareva, O. P. Taran, S. E. Peltek

“…The value of the collection of microorganisms of the FRC ICG SB RAS as a genetic resource for biotechnology and bioengineering is determined not only by the species diversity of its strains, but also by a wide range of their area isolation and by the depth of their characterization using the widest arsenal of both classical and modern methods (including methods of genomics, proteomics, transcriptomics and bioinformatics).…”
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Genetic Association and Expression Correlation between Colony-Stimulating Factor 1 Gene Encoding M-CSF and Adult-Onset Still’s Disease by Yi-Ming Chen, Wei-Ting Hung, Wan-Chun Chang, Chia-Wei Hsieh, Wen-Hung Chung, Joung-Liang Lan, Ning-Rong Gung, Yun-Shien Lee, Der-Yuan Chen, Shuen-Iu Hung

“…To assess the genetic susceptibility of AOSD, we conducted a genome-wide association study (GWAS) on a cohort of 70 AOSD cases and 688 controls following a replication study of 36 cases and 200 controls and meta-analysis. …”
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Oncolytic peptide LTX-315 induces anti-pancreatic cancer immunity by targeting the ATP11B-PD-L1 axis by Meng Wang, Xing Huang, Tingbo Liang, Tianyu Tang, Gang Zhang, Minghao Lu, Zhengtao Hong, Junming Huang, Xiao Zhi

“…Both in-house tissue microarray and open accessed The Cancer Genome Atlas data sets were used to evaluate the clinical relevance in pancreatic cancer prognosis.Results LTX-315 treatment inhibited PD-L1 expression and enhanced lymphocyte infiltration in pancreatic tumors. …”
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First detection and molecular characterization of Jingmen tick virus with a high occurrence in Rhipicephalus (Boophilus) microplus collected from livestock in Cameroon (2024) by Paloma Kiwan, Eva Lopez, Morena Gasparine, Geraldine Piorkowski, Agathe Colmant, Achille Paguem, Stephanie Mvodo, Laurence Thirion, Xavier de Lamballerie, Remi Charrel, Alessandra Falchi

“…Positive JMTV pools were sequenced for partial JMTV-Segment 1 and full genome analyses. Results A total of 622 ticks, organized into 251 pools were collected from 155 cattle and nine sheep. …”
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Novel digital droplet inverse PCR assay shows that natural clearance of hepatitis B infection is associated with fewer viral integrations by Dong Li, Vikki Ho, Chiao-Fang Teng, Hung-Wen Tsai, Yuanyuan Liu, Sarah Bae, Harout Ajoyan, Jochen M. Wettengel, Ulrike Protzer, Brian S. Gloss, Rebecca J. Rockett, Rafid Al Asady, Jane Li, Simon So, Jacob George, Mark W. Douglas, Thomas Tu

“…Hepatitis B virus (HBV) DNA integration into the host cell genome is reportedly a major cause of liver cancer, and a source of hepatitis B surface antigen (HBsAg). …”
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Exosomes from LPS-Stimulated hDPSCs Activated the Angiogenic Potential of HUVECs In Vitro by Xiangyu Huang, Wei Qiu, Yuhua Pan, Jianjia Li, Zhao Chen, Kaiying Zhang, Yifei Luo, Buling Wu, Wenan Xu

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to estimate the signaling pathways associated with the inflammation-induced angiogenesis process. …”
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Potential biomarkers and immune infiltration linking endometriosis with recurrent pregnancy loss based on bioinformatics and machine learning by Jianhui Chen, Qun Li, Xiaofang Liu, Fang Lin, Yaling Jing, Jiayan Yang, Lianfang Zhao

“…Moreover, immune cell infiltration was estimated using CIBERSORTx, and the Cancer Genome Atlas (TCGA) database was employed to elucidate the role of key genes in endometrial carcinoma (EC).Results26 common differentially expressed genes (DEGs) were screened in both diseases, three of which were identified as common core genes (MAN2A1, PAPSS1, RIBC2) through the combination of WGCNA, PPI network, and machine learning-based feature selection. …”
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Survival outcome prediction of esophageal squamous cell carcinoma patients based on radiomics and mutation signature by Ting Yan, Zhenpeng Yan, Guohui Chen, Songrui Xu, Chenxuan Wu, Qichao Zhou, Guolan Wang, Ying Li, Mengjiu Jia, Xiaofei Zhuang, Jie Yang, Lili Liu, Lu Wang, Qinglu Wu, Bin Wang, Tianyi Yan

“…The mutation signature was constructed based on whole genome sequencing data and found to be significantly associated with the prognosis of patients with ESCC. …”
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Risk of residual/recurrent cervical diseases in HPV-positive women post-conization depends on HPV integration status by Wenyu Lin, Yuxuan Huang, Yan Zhang, Lixiang Huang, Hongning Cai, Guanxiang Huang, Ye Li, Qiaoyu Zhang, Huifeng Xue, Binhua Dong, Pengming Sun

“…HPV integration test was performed using the high-throughput viral integration detection (HIVID), a sensitive method for genome-wide survey of HPV integration breakpoints. …”
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Effect of the gut microbiome in glaucoma risk from the causal perspective by He Chen, Meng Zhou, Zicheng Zhang, Siqi Bao, Jia Qu, Yaxuan Wu, Ronghua Shi

“…However, the causal effect of GM on glaucoma risk remains to be determined.Methods and analysis We conducted two-sample bidirectional Mendelian randomisation (MR) analyses to explore the causal association between GM and glaucoma. Genome-wide association study summary statistics of 196 GM taxa (n=18 340) and glaucoma (18 902 cases and 358 375 controls) were obtained from MiBioGen and FinnGen Consortium. …”
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WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Pathway enrichment exploration was conducted utilizing gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), and Metascape tools. …”
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Effectiveness of a Novel Liposomal Methylglyoxal–Tobramycin Formulation in Reducing Biofilm Formation and Bacterial Adhesion by Wed Alluhaim, Manal M. Alkhulaifi, Raghad R. Alzahrani, Bahauddeen M. Alrfaei, Alaa Eldeen B. Yassin, Majed F. Alghoribi, Ahlam M. Alsaadi, Ahmed I. Al-Asmari, Ahmed J. Al-Fahad, Rizwan Ali, Naif M. Alhawiti, Majed A. Halwani

“…<b>Methods:</b> Clinical isolates of <i>Pseudomonas aeruginosa</i> and <i>Klebsiella pneumoniae</i> were characterized using whole-genome sequencing. Liposomes (Lip-MGO-TOB) were formulated using Manuka honey as a surfactant and loaded with MGO and TOB. …”
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Expression of CSTF2 in oral squamous cell carcinoma and its relationship with immune infiltration and poor prognosis by Zumulaiti Aierken, Muertiza Muhetaer, Zhang Lei, Ainiwaerjiang Abudourousuli, Ainiwaerjiang Abudourousuli

“…However, its specific association with patient prognosis and immune cell infiltration in OSCC remains insufficiently understood.MethodsTo assess the expression levels and prognostic implications of CSTF2 in OSCC, comprehensive data were acquired from The Cancer Genome Atlas (TCGA) and subsequently normalized. Immunohistochemical staining of tissue microarrays was performed to analyze CSTF2 expression in the OSCC samples. …”
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Mechanistic insights into Y-Box binding protein-1 mediated regulation of lipid metabolism and oxidative stress in NAFLD via INHBE/TNF-β pathway by Zhi Ren, Rui Wang, Jun Wei, Zhenzeng Ma, Xiquan Ke

“…RNA sequencing was performed, followed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and protein-protein interaction (PPI) network analyses to identify differentially expressed genes (DEGs). …”
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Dose-response risks of all-cause, cancer, and cardiovascular disease mortality according to sex-specific cigarette smoking pack-year quantiles by Jieun Hwang, Suyoung Jo, Heewon Kang, Eunsil Cheon, Sung-il Cho

“…Methods The integrated Korean Genome and Epidemiology Study provided data for 209770 individuals who were classified as never, former, or current smokers, based on their current smoking status. …”
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