Spatial transcriptomics reveals unique metabolic profile and key oncogenic regulators of cervical squamous cell carcinoma by Limin Zhou, Jiejie Liu, Peipei Yao, Xing Liu, Fei Chen, Yu Chen, Li Zhou, Chao Shen, You Zhou, Xin Du, Junbo Hu

“…We also employed The Cancer Genome Atlas (TCGA) database to examine the analysis results of ST data. …”
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Infarct‐like myocarditis with coronary vasculitis and aneurysm formation caused by Epstein–Barr virus infection by Cristina Chimenti, Romina Verardo, Claudia Grande, Marco Francone, Andrea Frustaci

“…Two additional frozen samples were evaluated by real‐time polymerase chain reaction for the presence of cardiotropic viral genomes. Routine laboratory tests revealed the presence of elevated white blood cells (17 000 103/μL) and increased Troponin T. …”
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Transfer of Cytoplasmic Male Sterility to the Female Parents of Heat- and Drought-Resilient Maize (<i>Zea mays</i> L.) Hybrids by Ayyanagouda Patil, Kushal Gowda, Shivananda T. Lakshman, Prakash H. Kuchanur, Gajanan Saykhedkar, Sudha Krishnan Nair, Kisan B. Jadhav, Sharanabasappa Yeri, Gururaj Sunkad, Jayaprakash M. Nidagundi, Vinayan Madhumal Thayil, Pervez H. Zaidi

“…The present research used Diversity Array Technology (DArTag) and Kompetitive Allele Specific PCR (KASP)-based single-nucleotide polymorphic markers for background selection in backcross populations. Genome recovery percentage ranged from 64.25 to 72.70, 78.94 to 87.69 and 82.28 to 90.77 percent in the BC₁F₁, BC₂F₁ and BC₃F₁ population, respectively, in the CAL1514 population, while it was 63.47 to 73.55, 78.16 to 88.76 and 83.96 to 91.81 percent in the BC₁F₁, BC₂F₁ and BC₃F₁ population, respectively, in the ZL153493 population. …”
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Relationship between vaginal and gut microbiome and pregnancy outcomes in eastern Ethiopia: a protocol for a longitudinal maternal-infant cohort study (the EthiOMICS study) by Piet Cools, Alemseged Abdissa, Abera Kenay Tura, Nega Assefa, Merga Dheresa, Kedir Teji Roba, Tara Wilfong, Tesfaye Assebe Yadeta, Fitsum Weldegebreal, Desalegn Admassu Ayana, Akewok Sime Negesa, Yohannes Mulugeta Demmu, Tewodros Tesfa, Tegbaru Nibrat Alemu, Tadesse Gure Eticha, Abraham Geremew, Abel Abera Negash

“…Clinical study data will be submitted to Data Compass (https://datacompass.lshtm.ac.uk/), and molecular profiles of the microbiome and whole-genome sequences will be submitted to the European Nucleotide Archive (https://www. ebi.ac.uk/ena). …”
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Impact of prior SARS-CoV-2 infection and COVID-19 vaccination on the subsequent incidence of COVID-19: a multicentre prospective cohort study among UK healthcare workers – the SIRE... by Nick Andrews, Mary Ramsay, Maria Zambon, Victoria Hall, Sarah Wallace, Susan Hopkins, Jean Timeyin, Tim J G Brooks, Amoolya Vusirikala, Meera Chand, Andre Charlett, Sakib Rokadiya, Colin S Brown, Madhumita Shrotri, Peter D Kirwan, Michele Cole, Natalie Gillson, Ana Atti, Sarah Foulkes, Andrew Taylor-Kerr, Blanche Oguti, Jasmin Islam

“…Secondary outcomes include incidence and prevalence (both RNA and antibody) of SARS-CoV-2, viral genomics, viral culture, symptom history and antibody/neutralising antibody titres.Ethics and dissemination The study was approved by the Berkshire Research Ethics Committee, Health Research Authority (IRAS ID 284460, REC reference 20/SC/0230) on 22 May 2020; the vaccine amendment was approved on 12 January 2021. …”
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Investigating POU3F4 in cancer: Expression patterns, prognostic implications, and functional roles in tumor immunity by Weiwei Chen, Yaya Ji, Rui Wang, Ruijie Ji, Yujian Lin, Yuhang Wu, Lehan Liu, Tianle Sha, Wen Li, Lei Zhang, Longfei Yang, Xinhua Zhang, Jianxiang Song

“…Based on data from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE), Genotype-Tissue Expression (GTE), and Gene Set Cancer Analysis (GSCA), we employed various bioinformatics approaches to investigate the potential carcinogenic effects of POU3F4. …”
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Autophagy activation in response to cigarette smoke: Exploring the disparity in laryngeal cancer incidence and outcomes between sexes in South Korea by Min Ji Kim, Jisu Hong, Hyo Won Chang, Yun-Hee Lee, Jun-Pyo Myong, Ah Ra Jung, Yoon Se Lee, Minsu Kwon

“…In addition, to explore the relationship between the level of autophagy-related gene expression and clinical features, female LC patients were compared with male patients through an analysis of data from The Cancer Genome Atlas (TCGA). Results: In the NHIS data analyses, male LC patients had an 11 times higher incidence than female patients, even after adjusting for smoking and age. …”
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Heterogeneity of avian infectious bronchitis virus population by Ye. V. Ovchinnikova, L. O. Scherbakova, S. N. Kolosov, A. N. Andriyasova, N. G. Zinyakov, Z. B. Nikonova, A. A. Kozlov, P. B. Akshalova, D. A. Altunin, D. B. Andreychuk

“…Due to the lack of mechanisms to correct errors during genome replication, the virus can quickly mutate and generate new strains. …”
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A disintegrin and metallopeptidase domain (ADAM) 12, ADAM 17 mRNA and ADAM10 protein hold potential as biomarkers for detection of early gastric cancer by Sooyeon Oh, Sang-Soo Lee, Hoeyoung Jin, Seo-Hyeon Choi, Choong-Keun Cha, Jooho Lee, KyuBum Kwack, Sang Gyun Kim, Sang-Woon Choi

“…As a proof-of-concept pilot study, the expression of ADAM8, ADAM9, ADAM10, ADAM12, ADAM17, and major histocompatibility complex (MHC) class I chain-related sequence A (MICA), a ligand for NKG2D, in gastric cancer was investigated in silico using The Cancer Genome Atlas (TCGA) database. Subsequently, the mRNA and protein expression levels of these markers except ADAM8 were tested in blood samples from patients with EGC and healthy controls. …”
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Identification of Co-Expression Modules of Cotton Plant Height-Related Genes Based on Weighted Gene Co-Expression Network Analysis by Qian Huang, Li Liu, Hang Li, Xuwen Wang, Aijun Si, Liangrong He, Yu Yu

“…Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these modules are associated with biologically significant pathways, including oxidoreductase activity, transcriptional regulator activity, catalytic activity, and phosphate hydrolase activity. …”
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Assessment of genetic polymorphism in sea buckthorn (Hippophae L.) of different environmentally-geographical origin by ISSR-markers by A. Y. Zemtsova, Y. A. Zubarev, A. V. Gunin, M. S. Ivanova

“…The absence of an approved procedure of genome definition for Siberian sea buckthorn makes the above task quite complicated. …”
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A Metabolic Gene Signature to Predict Overall Survival in Head and Neck Squamous Cell Carcinoma by Zeng-Hong Wu, Yun Tang, Yue Zhou

“…In this study, we used RNA sequencing (RNA-seq) data from the cancer genome atlas (TCGA), with validation in the GEO dataset to profile the metabolic microenvironment and define potential biomarkers for metabolic therapy. …”
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Integrating bioinformatics and machine learning to identify AhR-related gene signatures for prognosis and tumor microenvironment modulation in melanoma by Qianru Li, Qianru Li, Heli Li

“…However, the specific downstream targets and mechanisms by which AhR influences melanoma remain insufficiently understood.MethodsMelanoma samples from The Cancer Genome Atlas (TCGA) and normal skin tissues from the Genotype-Tissue Expression (GTEx) database were analyzed to identify differentially expressed genes, which were intersected with a curated list of AhR-related pathway genes. …”
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Integrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis by Guanyou Huang, Yong Yu, Heng Su, Hongchuan Gan, Liangzhao Chu

“…Objective This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.Methods Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes. …”
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The heterogeneity of NOTCH1 to tumor immune infiltration in pan-cancer by XiaoJun Duan, Rihan Wu, Mingyang Zhang, Kexin Li, Lei Yu, Huirong Sun, Xingxia Hao, Changshan Wang

“…In this study, the data originated from the Genotype-Tissue Expression (GTEx) and the Cancer Genome Atlas (TCGA) databases were input into multiple online bioinformatic tools to study the characteristics of NOTCH1 in pan-cancer. …”
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Deficiency of the palmitoyl acyltransferase ZDHHC7 modulates depression-like behaviour in female mice after a mild chronic stress paradigm by Christa Hohoff, Nicole Kerkenberg, Mingyue Zhang, Weronika Palkowska, Lydia Wachsmuth, Maja Peng, Lena Stiehl, Christiane Schettler, Johannes C. S. Zang, Andreas Huge, Evgeni Ponimaskin, Cornelius Faber, Bernhard T. Baune, Weiqi Zhang

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Revisiting human language and speech production network: A meta-analytic connectivity modeling study by Chun-Wei Hsu, Chu-Chung Huang, Chih-Chin Heather Hsu, Yanchao Bi, Ovid Jyh-Lang Tzeng, Ching-Po Lin

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Unhealthy Phenotype as Indicated by Salivary Biomarkers: Glucose, Insulin, VEGF-A, and IL-12p70 in Obese Kuwaiti Adolescents by Mor-Li Hartman, J. Max Goodson, Ping Shi, Jorel Vargas, Tina Yaskell, Danielle Stephens, Maryann Cugini, Hatice Hasturk, Roula Barake, Osama Alsmadi, Sabiha Al-Mutawa, Jitendra Ariga, Pramod Soparkar, Jawad Behbehani, Kazem Behbehani, Francine Welty

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Detection of Mycobacterium tuberculosis DNA in intraocular fluid of 11 suspected tuberculous uveitis patients by multiplex PCR by Huirong Xu, Min Xu, Fang Chen, Hong Chen, Wei Du, Jing Yu

“…Methods Primers targeting three specific genes (MPB64, CYP141, and IS6110) within the MTBC genome were designed. Multiplex PCR was conducted using DNA from the H37Rv strain as well as DNA extracted from fluids of confirmed tuberculosis patients to assess primer specificity and method feasibility. …”
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Causal Effects of Air Pollution, Noise, and Shift Work on Unstable Angina and Myocardial Infarction: A Mendelian Randomization Study by Qiye Ma, Lin Chen, Hao Xu, Yiru Weng

“…Summary statistics were derived from large genome-wide association studies (GWASs) from the UK Biobank and the FinnGen consortium (Helsinki, Finland), with replication using an independent GWAS data source for myocardial infarction. …”
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