Developing and validating a drug recommendation system based on tumor microenvironment and drug fingerprint by Yan Wang, Xiaoye Jin, Rui Qiu, Bo Ma, Sheng Zhang, Xuyang Song, Jinxi He

“…Clinical application was assessed using The Cancer Genome Atlas (TCGA) dataset, with Best Overall Response (BOR) serving as the clinical efficacy measure. …”
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Key regions aberrantly connected within cerebello-thalamo-cortical circuit and their genetic mechanism in schizophrenia: an fMRI meta-analysis and transcriptome study by Yarui Wei, Ziyu Wang, Kangkang Xue, Xiaoyu Niu, Longyao Ma, Shaoqiang Han, Baohong Wen, Yong Zhang, Huafu Chen, Jingliang Cheng

“…Gene annotation analysis was performed to identify genes over-expressed in these regions by using the Allen Human Brain Atlas, followed by a set of gene functional feature analyses. 19 studies (1333 patients and 1174 healthy controls) were included in this meta-analysis. …”
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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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Single-cell sequencing uncovers the mechanistic role of DAPK1 in glioma and its diagnostic and prognostic implications by Tian-Hang Yu, Yan-Yu Ding, Yan-Yu Ding, Si-Guo Zhao, Jie-Hui Zhao, Yu Gu, Dong-Hui Chen, Fang Zhang, Wen-Ming Hong, Wen-Ming Hong

“…However, the precise role and underlying mechanisms of DAPK1 in gliomas remain inadequately understood.MethodsWe performed analyses on RNA-seq and microarray datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), in addition to single-cell RNA sequencing (scRNA-seq) data from glioma patients available in GEO. …”
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Comprehensive Analysis of the Mechanism of Anoikis in Hepatocellular Carcinoma by Dongqian Li, Qian Bao, Shiqi Ren, Haoxiang Ding, Chengfeng Guo, Kai Gao, Jian Wan, Yao Wang, MingYan Zhu, Yicheng Xiong

“…This paper’s data (TCGA-HCC) were retrieved from the database of the Cancer Genome Atlas (TCGA). Differential gene expression with prognostic implications for anoikis was identified by performing both the univariate Cox and differential expression analyses. …”
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Providing an Anti-Marketing Model to Prevent Criminal Behaviors in Online and Digital Businesses by Ghasem Zarei, Younes Nikkhah

“…Ultimately, employing ATLAS.ti software, “the anti-marketing model aimed at preventing criminal behaviors in the online business environment” was derived.   …”
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Single-cell transcriptomics reveals novel chondrocyte and osteoblast subtypes and their role in knee osteoarthritis pathogenesis by Yuan Liu, Wacili Da, Ming-Jie Xu, Chao-Xin Xiao, Tao Deng, Sheng-Liang Zhou, Xiao-Ting Chen, Yao-Jia Zhou, Li Tang, Yong Nie, Yi Zeng, Hui-Qi Xie, Bin Shen

“…Therefore, this study constructed a bipedal postmenopausal KOA mouse model to better understand how the interplay between subchondral bone remodeling and cartilage degeneration contributes to KOA development. A single-cell atlas of the osteochondral composite tissue was established. …”
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Basal-Supported Oral Therapy with Sitagliptin Counteracts Rebound Hyperglycemia Caused by GLP-1 Tachyphylaxis by Shu Meguro, Toshihide Kawai, Tomohiro Matsuhashi, Motoaki Sano, Keiichi Fukuda, Hiroshi Itoh, Yoshihiko Suzuki

“…Their GLP-1 analog-based therapy was switched to BOT with insulin glargine plus sitagliptin and other medications. The primary outcomes were whether switching of therapy was associated with a change of hemoglobin A1c (HbA1c) and whether weight gain occurred. …”
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Activin levels correlate with lymphocytic infiltration in epithelial ovarian cancer by Elizabeth T. Evans, Emily F. Page, Alex Seok Choi, Zainab Shonibare, Andrea G. Kahn, Rebecca C. Arend, Karthikeyan Mythreye

“…Immune gene expression profile was further explored within the TCGA‐OV cohort derived from The Cancer Genome Atlas (TCGA). Immunohistochemical analysis was performed to evaluate activin A and T‐cell markers CD8 and FoxP3 at the protein level. …”
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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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Identification of Survival Risk and Immune-Related Characteristics of Kidney Renal Clear Cell Carcinoma by Xiaobin Wu, Yonghui Liang, Xian Chen, Xiangyang Long, Wujun Xu, Li Liu, Binhui Wang, Xiong Zou

“…A series of information such as RNA sequence, clinical data, and tumor mutation burden (TMB) of KIRC patients were downloaded through The Cancer Genome Atlas (TCGA). Next, combining the survival information and gene expression data of TCGA and Gene Expression Omnibus (GEO), we established an immune gene-related prognosis model (IGRPM) and analyzed it. …”
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Single-cell transcriptomes of dissecting the intra-tumoral heterogeneity of breast cancer microenvironment by Peixian Chen, Kaifeng Liang, Xiaofan Mao, Qiuyuan Wu, Zhiyan Chen, Yabin Jin, Kairong Lin, Tiancheng He, Shuqing Yang, Huiqi Huang, Guolin Ye, Juntao Gao, Dan Zhou, Zhihao Zeng

“…Conclusion We constructed a comprehensive single-cell transcriptome atlas of 54,055 cells from 4 malignant and 4 nonmalignant patients, providing insights into the mechanisms underlying breast cancer progression and the development of potential therapeutic strategies in breast cancer.…”
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Predicting Outcomes in Esophageal Squamous Cell Carcinoma Using scRNA‐Seq and Bulk RNA‐Seq: A Model Development and Validation Study by Jiaqi Zhang, Shunzhe Song, Yuqing Li, Aixia Gong

“…Methods A total of 8, 99, and 140 individuals from The Gene Expression Omnibus database, The Cancer Genome Atlas database, and the Memorial Sloan Kettering Cancer Center, respectively, were encompassed in the investigation. …”
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Tumour DNA methylation markers associated with breast cancer survival: a replication study by Elaheh Zarean, Shuai Li, Ee Ming Wong, Enes Makalic, Roger L. Milne, Graham G. Giles, Catriona McLean, Melissa C. Southey, Pierre-Antoine Dugué

“…Candidate methylation sites (N = 22) and signatures (N = 3) potentially associated with breast cancer survival were identified from five prior studies that used The Cancer Genome Atlas (TCGA) methylation dataset, which shares key characteristics with the MCCS: comparable sample size, tissue type (formalin-fixed paraffin-embedded; FFPE), technology (Illumina HumanMethylation450 array), and participant characteristics (age, ancestry, and disease subtype and severity). …”
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Heterogeneous Acupuncture Effects of Taixi (KI3) on Functional Connectivity in Healthy Youth and Elder: A Functional MRI Study Using Regional Homogeneity and Large-Scale Functional... by Linlu He, Guangxiang Chen, Ruwen Zheng, Yan Hu, Xiu Chen, Jianghai Ruan

“…Regional homogeneity (ReHo) and large-scale FC analysis using Power 264 atlas were utilized to analyze the changes of brain spontaneous activity. …”
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Apoptosis antagonizing transcription factor expression and its validation as a potential diagnostic and prognostic biomarker in oral squamous cell carcinoma by Ainiwaerjiang Abudourousuli, Zumulaiti Aierken, Hasiyati Mamuti, Tuxunayi Yimamu, Chengli Da

“…This study aimed to investigate the expression of apoptosis antagonizing transcription factor (AATF) in OSCC, examine its correlation with clinicopathological features, assess its prognostic implications, and explore its potential role in OSCC progression.MethodsExpression profiles and clinical data of OSCC patients were obtained from The Cancer Genome Atlas (TCGA). Immunohistochemical analysis on tissue microarrays was performed to assess AATF expression in OSCC. …”
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Conceptualización y Práctica de la Comunicación Responsable Universitaria: la perspectiva de los DirCOM sobre su ejercicio by Hilda Gabriela Hernández Flores

“…Las categorías y códigos de análisis se definieron a priori mediante una sistematización deductiva aplicada al software Atlas.Ti (v.8). Resultados: Los expertos muestran concordancia respecto a la definición de la Comunicación Responsable y plantean la necesidad de contemplar sus rasgos como parte de la Comunicación Pública que ejercen en la dinámica universitaria. …”
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Single-cell sequencing provides clues about the developmental genetic basis of evolutionary adaptations in syngnathid fishes by Hope M Healey, Hayden B Penn, Clayton M Small, Susan Bassham, Vithika Goyal, Micah A Woods, William A Cresko

“…We created a single-cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. …”
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Efeito da burocracia no custo de transação econômica na Pró-Reitoria de Administração da Universidade Federal Rural do Semi-Árido by Fabianny de Sales Guerra, Luciana Batista Sales, Carlos Alano Soares de Almeida, Adriana Martins de Oliveira, Antônio Erivando Xavier Júnior

“…Os dados foram tratados, atendendo aos preceitos da análise de conteúdo; para isso, primeiramente, transcreveu-se a entrevista, que posteriormente foi importada para o Software Atlas ti 8.0. Logo após, fez-se o trabalho de codificação que, com a finalização, empregou-se a categorização dos dados, com o propósito de criar famílias de acordo com as dimensões estudadas. …”
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Training and onboarding initiatives in high energy physics experiments by Allison Reinsvold Hall, Nicole Skidmore, Gabriele Benelli, Ben Carlson, Ben Carlson, Claire David, Jonathan Davies, Wouter Deconinck, David DeMuth, Peter Elmer, Rocky Bala Garg, Stephan Hageböck, Killian Lieret, Valeriia Lukashenko, Valeriia Lukashenko, Sudhir Malik, Andy Morris, Heidi Schellman, Graeme A. Stewart, Jason Veatch, Michel Hernandez Villanueva

“…In this article we document the current analysis software training and onboarding activities in several High Energy Physics (HEP) experiments: ATLAS, CMS, LHCb, Belle II and DUNE. Fast and efficient onboarding of new collaboration members is increasingly important for HEP experiments. …”
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