Human menstrual blood-derived stem cells secreted ECM1 directly interacts with LRP1α to ameliorate hepatic fibrosis through FoxO1 and mTOR signaling pathway by Yangxin Fang, Lin Chen, Yin Yuan, Sining Zhou, Jiamin Fu, Qi Zhang, Ning Zhang, Yuqi Huang, Yifei Li, Li Yuan, Lijun Chen, Charlie Xiang

“…The downstream molecular mechanisms were characterized by non-target metabolomics and multiplex immunohistochemical staining. RNA sequencing was performed to evaluate the genetic alterations in various genes within the MenSCs. …”
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Speeding up drug susceptibility testing in Mycobacterium tuberculosis using RNA biomarkersResearch in context by Amandine Sury, Margo Maex, Alain Baulard, Roby P. Bhattacharyya, Stéphanie Depickère, Deborah T. Hung, Paul Cos, Fadel Sayes, Wafa Frigui, Roland Brosch, Vanessa Mathys, Elizabeth M. Streicher, Frederik De Keersmaeker, Leen Rigouts, Pieter-Jan Ceyssens, An Van den Bossche

“…Methods: To develop TRACeR-TB, target genes were first identified through RNA sequencing experiments conducted on two drug-exposed, susceptible strains for four antitubercular drugs. …”
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SP140 inhibits STAT1 signaling, induces IFN-γ in tumor-associated macrophages, and is a predictive biomarker of immunotherapy response by Richard Carvajal, Akiva Mintz, Fatemeh Momen-Heravi, Alison Taylor, Kranthi Kiran Kishore Tanagala, Joshua Morin-Baxter, Maryum Cheema, Sunil Dubey, Angela Yoon, Yi-Shing L Cheng, Jeffrey Nickerson

“…Chromatin immunoprecipitation and analysis of assay of transposase accessible chromatin sequencing data were used to demonstrate the direct binding of SP140 on the promoters of STAT1. …”
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Comprehensive genetic variant analysis reveals combination of KRAS and LRP1B as a predictive biomarker of response to immunotherapy in patients with non-small cell lung cancer by Ella A. Eklund, Johanna Svensson, Louise Stauber Näslund, Maria Yhr, Sama I. Sayin, Clotilde Wiel, Levent M. Akyürek, Per Torstensson, Volkan I. Sayin, Andreas Hallqvist, Sukanya Raghavan, Anna Rohlin

“…Methods In this prospective bi-center clinical study, we performed next-generation sequencing (NGS) of 597 cancer-associated genes in a prospective cohort of 49 patients as the final cohort analyzed, with stage III or IV NSCLC, followed by establishment of an in-house developed bioinformatics-based molecular classification method that integrates, interprets and evaluates data from multiple databases and variant prediction tools. …”
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Immunomodulatory gene networks predict treatment response and survival to de-escalated, anthracycline-free neoadjuvant chemotherapy in triple-negative breast cancer in the WSG-ADAP... by Darren Korbie, Clare Stirzaker, Oleg Gluz, Christine zu Eulenburg, Ulrike Nitz, Matthias Christgen, Sherko Kuemmel, Eva-Maria Grischke, Helmut Forstbauer, Michael Braun, Mathias Warm, John Hackmann, Christoph Uleer, Bahriye Aktas, Claudia Schumacher, Rachel Wuerstlein, Enrico Pelz, Hans Heinrich Kreipe, Susan J. Clark, Matt Trau, Monika Graeser, Nadia Harbeck

“…The primary endpoint was pCR (ypT0/is, ypN0), and the secondary endpoints included survival and translational research. AmpliSeq RNA sequencing, allowing simultaneous analysis of the expression of > 20,000 genes, was performed in 135 patients. …”
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Associations of HLA-G 3’UTR polymorphisms and increased HLA-G expression with gastric cancer susceptibility and prognosis by Ines Zemni, Daria Bortolotti, Sabrine Dhouioui, Sana Baroudi, Malek Ferjani, Inès Nasri, Yosr Zenzri, Md Ataur Rahman, Abdel Halim Harrath, Roberta Rizzo, Nadia Boujelbene, Inès Zidi

“…Immunohistochemistry was used to evaluate the expression of HLA-G in tumor tissues. …”
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The expression profile analysis and functional prediction of lncRNAs in peripheral blood mononuclear cells in maintenance hemodialysis patients developing heart failure by Xing Qi, Lin Yu, Shuai Liu, Yujiao Zhou, Wenqing Liu, Wei Liao, Qin Guo, Xuhui Song, Jifeng Li, Sheng Lin, Chuanqiang Dai, Lin Yan, Tao Li, Li Zhang, Shucheng Zhao, Juan Tang, Jian Cai, Zejiang Liu, Ran Zhu, Q.-Y. Long, Huaguo Wang

“…The expression profile analysis of lncRNAs was performed by using Illumina Novaseq 6000 sequencer. Quantitative real time polymerase chain reaction (qRT-PCR) was used to verify the expression of representative differentially expressed lncRNAs. …”
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Antioxidant and stress-adaptive properties of putative probiotic bacteria in Pakistani fermented buffalo milk by Gulnaz Saleem, Gulnaz Saleem, Bisma Rao, Gul Bahar Khaskheli, Hengxian Qu, Hengxian Qu, Md Shabuddin Ahamed, Muhammad Qasim, Ruixia Gu, Ruixia Gu, Xia Chen, Xia Chen

“…Molecular identification (16S rRNA sequencing) classified isolates into LAB and non-LAB taxa. …”
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Emodin promotes GSK-3β-mediated PD-L1 proteasomal degradation and enhances anti-tumor immunity in hepatocellular carcinoma by Xuemei Yang, Weiguang Chen, Haitao Sun, Weicong Chen, Wei Xu, Chunyu He, Yang Liu, Ying Kuang, Yanhao Ma, Binglian Zhong, Chaojie Li, Guohuan Li, Qingfeng Du, Songqi He

“…In vivo anti-tumor effects were evaluated in H22 subcutaneous tumor model, and CD8+ T cells and RNA-seq data were analyzed. …”
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Pseudomonas aeruginosa Detection Using Conventional PCR and Quantitative Real-Time PCR Based on Species-Specific Novel Gene Targets Identified by Pangenome Analysis by Chufang Wang, Chufang Wang, Qinghua Ye, Aiming Jiang, Jumei Zhang, Yuting Shang, Fan Li, Baoqing Zhou, Xinran Xiang, Qihui Gu, Rui Pang, Yu Ding, Shi Wu, Moutong Chen, Qingping Wu, Qingping Wu, Juan Wang, Juan Wang

“…Pangenome analysis was used to analyze the whole genomic sequences of 2017 strains (including 1,000 P. aeruginosa strains and 1,017 other common foodborne pathogen strains) downloaded from gene databases to obtain novel species-specific genes, yielding a total of 11 such genes. …”
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Myeloid Zinc Finger 1: insights into its oncogenic potential, prognostic value, and impact on immune microenvironment across cancers by Wenze Tian, Chun Yu, Xin Xu, Jiaqi Li, Shuangfu Peng, Aijun Sun, Shasha Zhang, Chao Jiang

“…A univariate Cox regression analysis was performed to evaluate MZF1’s prognostic value. The cBioPortal database helped explore potential MZF1 mutations across cancer types. …”
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PARP inhibitors enhance antitumor immune responses by triggering pyroptosis via TNF–caspase 8–GSDMD/E axis in ovarian cancer by Ping Jin, Qi Zhang, Xin Li, Yu Xia, Yong Fang, Xiong Li, Ning Jin, Xiang-Ping Yang, Qing-Lei Gao, Zhengmao Zhang, Pu Huang, Yi-yu Qian, Zanhong Wang, Wen Pan, Si-Yuan Wang, Emmanuel Kwateng Drokow, Pingfei Li, Zhiqiang Han

“…However, it remains not fully understood whether and how PARPis trigger tumor-targeting immune responses.Methods To decode the immune responses reshaped by PARPis, we conducted T-cell receptor (TCR) sequencing and immunohistochemical (IHC) analyses of paired clinical specimens before and after niraparib monotherapy obtained from a prospective study, as well as ID8 mouse ovarian tumors. …”
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Identification of glycolysis-related gene signatures for prognosis and therapeutic targeting in idiopathic pulmonary fibrosis by Han Gao, Zhongyi Sun, Xingxing Hu, Weiwei Song, Yuan Liu, Menglin Zou, Menglin Zou, Minghui Zhu, Zhenshun Cheng, Zhenshun Cheng, Zhenshun Cheng

“…A prognostic signature was developed using LASSO regression, and time-dependent receiver operating characteristic (ROC) curves were generated to evaluate predictive performance. Single-cell RNA sequencing (scRNA-seq) data were analyzed to examine GRG expression across various cell types. …”
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Assessment of Antibiotic Resistance Among Isolates of <i>Klebsiella</i> spp. and <i>Raoultella</i> spp. in Wildlife and Their Environment from Portugal: A Positive Epidemiologic Ou... by Carolina Sabença, Rani de la Rivière, Paulo Barros, João Alexandre Cabral, Roberto Sargo, Luís Sousa, Maria de Lurdes Enes Dapkevicius, Filipe Silva, Filipa Lopes, Ana Carolina Abrantes, Madalena Vieira-Pinto, Manuela Caniça, Gilberto Igrejas, Carmen Torres, Patrícia Poeta

“…Extended-spectrum β-lactamase (ESBL) production was tested by the double-disc synergy test, and one ESBL-producing <i>K. pneumoniae</i> isolate was screened by PCR and whole-genome sequencing. Biofilm production was analyzed using the microtiter plate method. …”
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Macrophage GSK3β-deficiency inhibits the progression of hepatocellular carcinoma and enhances the sensitivity of anti-PD1 immunotherapy by Li Liu, Jie Zhao, Jinyu Zhang, Guoqiang Sun, Yongxiang Xia, Xuehao Wang, Hanyuan Liu, Siqi Zhao, Zihao Zhang, Tian Huang, Xiangyi Kong, Weiwei Tang, Guangshun Sun, Hengsong Cao, Dawei Rong, Qinghua Ji

“…The in vitro and in vivo assays assisted in evaluating how GSK3β in TAMs affected HCC in terms of proliferation, invasion and migration. …”
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Impact of POU3F4 mutation on cochlear development and auditory function by Jiong Dang, Panpan Bian, Chao Chen, Chi Chen, Wenqi Shan, Luhang Cai, Yong Li, Huan Tan, Baicheng Xu, Minxin Guan, Yufen Guo

“…Cochlear structure was analyzed through histology, immunohistochemistry, scanning electron microscopy, and transmission electron microscopy. RNA sequencing, qPCR and Western blot were conducted to evaluate gene expression and mitochondrial function. …”
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The impact of de novo lipogenesis on predicting survival and clinical therapy: an exploration based on a multigene prognostic model in hepatocellular carcinoma by Xin Zhou, Guangzu Cui, Erya Hu, Xinwen Wang, Diya Tang, Xiangyang Zhang, Jiayao Ma, Yin Li, Haicong Liu, Qingping Peng, Ying Han, Yihong Chen, Shan Zeng, Yan Zhang, Hong Shen

“…Comprehensive validation included immunohistochemical analysis and Western blotting to assess expression levels of key model genes, along with multiplex immunofluorescence staining and single-cell RNA sequencing(scRNA-seq) to characterize immune microenvironmental differences between risk groups. …”
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Combination of spatial transcriptomics analysis and retrospective study reveals liver infection of SARS-COV-2 is associated with clinical outcomes of COVID-19Research in context by Shiqi Chen, Yi Zhang, Asha Ashuo, Shu Song, Lunzhi Yuan, Weixia Wang, Cong Wang, Zunguo Du, Yangtao Wu, Dan Tan, Chenlu Huang, Jingna Chen, Yaming Li, Jinjin Bai, Huilin Guo, Zehong Huang, Yi Guan, Ningshao Xia, Zhenghong Yuan, Jiming Zhang, Quan Yuan, Zhong Fang

“…The 10x Genomics Visium CytAssist Spatial Gene Assay was designed to analyze liver transcriptomics. TCR CDR3 sequences were analyzed in DNA from liver tissues. …”
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Utility of quantitative measurement of T 2 using restriction spectrum imaging for detection of clinically significant prostate cancer by Mariluz Rojo Domingo, Christopher C. Conlin, Roshan Karunamuni, Courtney Ollison, Madison T. Baxter, Karoline Kallis, Deondre D. Do, Yuze Song, Joshua Kuperman, Ahmed S. Shabaik, Michael E. Hahn, Paul M. Murphy, Rebecca Rakow-Penner, Anders M. Dale, Tyler M. Seibert

“…Data includes two cohorts scanned for csPCa with 3T multi-b-value diffusion-weighted sequences acquired at multiple TEs. cT 2 values were computed from multi-TE RSI data and compared by compartment. …”
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circFTO binding with IGF2BP2 regulates trophoblast cells proliferation, migration, and invasion while mediating m6A modification of CCAR1 mRNA in spontaneous abortion by Yiwen Zhang, Meiyao Wu, Xiaoling Lin, Bingfeng Lu, Xi Chen, Qianhui Li, Yinan Jiang, Baixue Li, Dongmei Zhou, Xiujie Sheng

“…Furthermore, colorimetric examinations were used to evaluate the m6A methylation levels of trophoblast cells, and meRIP-qPCR assays confirmed the m6A modification of CCAR1 mRNA. …”
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