UBE2J1 is identified as a novel plasma cell-related gene involved in the prognosis of high-grade serous ovarian cancer by Yunjie Tian, Ruoyu Dong, Yingxia Guan, Ying Wang, Wei Zhao, Jun Zhang, Shan Kang

“…The effects of immune cell markers on prognosis were analyzed via univariate Cox regression, least absolute shrinkage and selection operator (LASSO) and gene set variation analysis (GSVA) of bulk sequencing data from The Cancer Genome Atlas (TCGA)-HGSOC cohort. Finally, the effects of key markers on HGSOC cells were evaluated via Cell Counting Kit-8 (CCK-8), Transwell, colony formation, wound healing, immunofluorescence and in vivo tumor growth assays. …”
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Screening and validation of tsRNAs associated with lung adenocarcinoma by LU Chunli, SHAN Yifan, XIE Weijia

“…The effects of tsRNAs expression levels on the prognosis of lung adenocarcinoma patients were analyzed based on the Cancer Genome Atlas （TCGA） database （TCGA-LUAD）. The target genes were predicted based on TRFtarget2.0 and tRFTar databases. …”
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Analysing DNA methylation and transcriptomic signatures to predict prostate cancer recurrence risk by Fahad M. Aldakheel, Hadeel Alnajran, Shatha A. Alduraywish, Ayesha Mateen, Mohammed S. Alqahtani, Rabbani Syed

“…This study employs a machine learning approach to identify DNA methylation and RNA expression biomarkers predictive of PCa recurrence using datasets from The Cancer Genome Atlas (TCGA). We analyzed 49,133 genes, identifying 684 differentially methylated genes (DMGs) and 691 differentially expressed genes (DEGs) between recurrence and non-recurrence groups. …”
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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

“…The transcriptome profiling and clinical data of melanoma were downloaded from The Cancer Genome Atlas database, and their matched normal samples were obtained from the Genotype-Tissue Expression database. …”
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Feasibility of implementing family-integrated newborn care for hospitalised preterm and low birthweight infants in newborn care units of Ethiopia: a mixed-methods design by Hege Langli Ersdal, Araya Abrha Medhanyie, Damen Haile Mariam, Siren Rettedal, Znabu Hadush Kahsay

“…Despite the WHO’s call for family engagement in newborn care, evidence of the feasibility of implementation remains scarce.Design An observational feasibility study employing a mixed-methods design comprising a quantitative cross-sectional survey among 157 healthcare providers (HCPs) and a qualitative Participatory Rural Appraisal.Setting The study was conducted in 30 neonatal care units (NCUs) of hospitals in Tigray, Northern Ethiopia.Participants HCPs who were on duty in NCUs during the data collection period were included in the study.Analysis Descriptive statistics were obtained for the quantitative data using STATA V.16, while qualitative data were coded and analysed using a framework analysis approach with qualitative data analysis software (Atlas.ti V.9).Results In total, 157 HCPs were enrolled with a mean (SD) age of 32 (±6.8) years. …”
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Mapping Drug-Resistant Tuberculosis Treatment Outcomes in Hunan Province, China by Temesgen Yihunie Akalu, Archie C. A. Clements, Zuhui Xu, Liqiong Bai, Kefyalew Addis Alene

“…Sociodemographic, economic, healthcare, and environmental variables were obtained from various sources, including the WorldClim database, the Malaria Atlas Project, and the Hunan Bureau of Statistics. …”
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Deciphering the heterogeneity and plasticity of the tumor microenvironment in liver cancer provides insights for prognosis by Yihao Sun, Yihao Sun, Guojuan Shi, Jian Yang, Chun-Zhong Zhou, Chuhan Peng, Yu-Hong Luo, Ying Pan, Rui-Qi Wang

“…Using genomic and clinical data from The Cancer Genome Atlas, we identified specific cell components linked to tumor characteristics and genetics. …”
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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…Method mRNA (messenger RNA) data and clinical records pertaining to colon cancer were retrieved from The Cancer Genome Atlas (TCGA) database. The analysis of NR3C2 expression discrepancies between normal colon and tumor tissues was conducted using R software. …”
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Comprehensive Analysis of Competing Endogenous RNA Network Focusing on Long Noncoding RNA Involved in Cirrhotic Hepatocellular Carcinoma by Yuli Zhang, Dinggui Chen, Miaomiao Yang, Xianfeng Qian, Chunmei Long, Zhongwei Zheng

“…The lncRNA, miRNA, and mRNA expression datasets were obtained from Gene Expression Omnibus and The Cancer Genome Atlas. Based on miRanda and TargetScan, the HCC-specific ceRNA network was constructed to illustrate the coexpression regulatory relationship of lncRNAs, miRNAs, and mRNAs. …”
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Seven Immune-Related Genes’ Prognostic Value and Correlation with Treatment Outcome in Head and Neck Squamous Cell Carcinoma by Rui Mu, Yuehong Shen, Chuanbin Guo, Xinyun Zhang, Hongyu Yang, Huijun Yang

“…Finally, the hub gene’s differential mRNA expression levels were evaluated by means of the Gene Expression Profiling Interactive Analysis (GEPIA), and the Human Protein Atlas (HPA) was utilized for the validation of their translational levels. …”
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Identification and Verification of Novel Biomarkers Involving Rheumatoid Arthritis with Multimachine Learning Algorithms: An In Silicon and In Vivo Study by Fucun Liu, Juelan Ye, Shouli Wang, Yang Li, Yuhang Yang, Jianru Xiao, Aimin Jiang, Xuhua Lu, Yunli Zhu

“…We retrieved RA-related and pan-cancer information datasets from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. Six gene expression profiles and corresponding clinical information of GSE12021, GSE29746, GSE55235, GSE55457, GSE77298, and GSE89408 were adopted to perform differential expression gene analysis, enrichment, and immune component difference analyses of RA. …”
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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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The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution by Eleftheriadi, Klara, Guiglielmoni, Nadège, Salces-Ortiz, Judit, Vargas-Chavez, Carlos, Martínez-Redondo, Gemma I., Gut, Marta, Flot, Jean-François, Schmidt-Rhaesa, Andreas, Fernández, Rosa

“…As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensis Schmidt-Rhaesa & Fernández sp. nov.). …”
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Studies on the Removal of Cadmium Toxic Metal Ions by Natural Clays from Aqueous Solution by Adsorption Process by Rajaa Bassam, Achraf El hallaoui, Marouane El Alouani, Maissara Jabrane, El Hassan El Khattabi, Malika Tridane, Said Belaaouad

“…The aim of this study is the valorization of the Moroccan clays (QC-MC and QC-MT) from the Middle Atlas region as adsorbents for the treatment of water contaminated by cadmium Cd (II) ions. …”
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Identification of Five m6A-Related lncRNA Genes as Prognostic Markers for Endometrial Cancer Based on TCGA Database by Li Shan, Ye Lu, Cheng-Cheng Xiang, Xiaoli Zhu, Er-Dong Zuo, Xu Cheng

“…Gene expression and clinical data were extracted from The Cancer Genome Atlas. Coexpression analysis was performed to identify m6A-related lncRNAs, which were entered into univariate Cox regression models for evaluating the prognosis of UCEC. …”
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Identification of HOXA9 methylation as an epigenetic biomarker predicting prognosis and guiding treatment choice in acute myeloid leukemia by Fei Xie, Ting-juan Zhang, Xin-long Zhang, Zi-jun Xu, Liang Qiao, Yun Wang, Yang-jing Zhao, Jun Qian, Jing-dong Zhou

“…Methods We systematically first screened the prognostic value of HOXA cluster genes methylation in AML from The Cancer Genome Atlas (TCGA) datasets. Afterwards, the candidate prognosis-related gene HOXA9 were selected for clinical relevance analysis and were further validated in another independent cohort from our research center. …”
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Chromosome-level reference genome assembly for the mountain hare (Lepus timidus) by Fekete, Zsófia, Absolon, Dominic E., Michell, Craig, Wood, Jonathan M. D., Goffart, Steffi, Pohjoismäki, Jaakko L. O.

“…Following the previously published brown hare reference genome assembly, the mountain hare is the second Finnish pilot species for the European Reference Genome Atlas (ERGA) initiative, a collaborative effort to generate reference genomes for European biodiversity. …”
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Eficacia del sistema de retroalimentación en tiempo real en la práctica profesional de estudiantes de educación física by Claudio Hinojosa-Torres, Juan Pablo Zavala-Crichton, Macarena Hurtado-Guerrero, Sebastián Espoz-Lazo, Claudio Farías-Valenzuela, Pedro Valdivia-Moral, Anthony Araya-Hernández, Rodrigo Yáñez-Sepúlveda

“…Con el objetivo de conocer la percepción de los estudiantes sobre la eficacia del sistema de retroalimentación se aplicó una entrevista semiestructurada con cuatro preguntas, cuyo análisis se llevó con el software Atlas.ti 24. Resultados: Se generaron cuatro grupos de códigos que muestran: a) el valor de la retroalimentación en tiempo real; b) la importancia de la comunicación para mejorar la praxis pedagógica; c) las tensiones generadas por el Sistema de retroalimentación en la práctica; y d) el reconocimiento de aspectos positivos y áreas de mejora para la implementación del sistema de retroalimentación. …”
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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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Genetic and neurochemical profiles underlying cortical morphometric vulnerability to Parkinson’s disease by Su Yan, Jun Lu, Bingfang Duan, Hongquan Zhu, Tian Tian, Yuanyuan Qin, Yuanhao Li, Wenzhen Zhu

“…Then we performed gene-category enrichment and spatial correlation analyses to evaluate the specific correspondence between cortical alteration in PD and genetic expression from the Allen Human Brain Atlas and normative neurotransmitter atlases from Neuromaps. …”
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