The immune microenvironment in non‐small cell lung cancer is predictive of prognosis after surgery by Åsa Kristina Öjlert, Ann Rita Halvorsen, Daniel Nebdal, Marius Lund‐Iversen, Steinar Solberg, Odd Terje Brustugun, Ole Christian Lingjærde, Åslaug Helland

“…Here, we examined gene expression in 399 surgically derived NSCLC samples and 47 samples from normal lung, using Agilent microarray and RNA sequencing. In 335 of the tumor samples, programmed death‐ligand 1 (PD‐L1) expression was evaluated by immunohistochemistry. …”
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Enhancing human phenotype ontology term extraction through synthetic case reports and embedding-based retrieval: A novel approach for improved biomedical data annotation by Abdulkadir Albayrak, Yao Xiao, Piyush Mukherjee, Sarah S. Barnett, Cherisse A. Marcou, Steven N. Hart

“…With the increasing utilization of exome and genome sequencing in clinical and research genetics, accurate and automated extraction of human phenotype ontology (HPO) terms from clinical texts has become imperative. …”
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Analysis of the transcriptional profile of mononuclear cells from e-cigarette users by Carlos Camero, María José Peña, Camila Bernal, Daniel González, Litzy Gisella Bermudez, Zully Pulido, David Padilla, Alexis Infante, Alejandra Cañas, Liliana Lopez-Kleine, Adriana Rojas

“…A cross-sectional observational study was conducted in which transcriptomes of peripheral blood mononuclear cells from e-cigarette users were sequenced, analyzed and classified according to their use into exclusive users (n = 4), mixed users (n = 4), and controls (n = 7). …”
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Co-Infection of Lophomonas blattarum and Pneumocystis jirovecii in Patients with Respiratory Disorders in Northeastern Iran by Fariba Berenji, Hossein Zarrinfar, Ali Gholizadeh, Fatemeh Sargazi, Jamshid Jamali, Mahmoud Parian Noghabi, Ghodratollah Salehi Sangani, Bibi Razieh Hosseini Farash

“…PCR amplification targeting L. blattarum and P. jirovecii was performed, with subsequent sequencing for molecular identification. The presence of Pneumocystis was identified using a 346-bp PCR band. …”
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PPDPF promotes the progression of esophageal squamous cell carcinoma via c-Myc/CD24 axis by Ning Ma, Wei Chen, Yu Chen, Xiang Wang, Bing Zhu, Kai Ding, Lin Qiu, Jing-jing Li, Jing-Yi Huang, Xin Liang, Yan-Jun Xiang, Qian-Zhi Ni, Zhi-Chao Liu, Qian-Wen Zheng, Yi-Kang Wang, Hui-Jun Cao, Ji Xia, Sheng Xu, Xiao-Song Qiu, Xi-Ran Zhang, Lingyun Long, Zhi-Gang Li, Fan Yao

“…This study aims to identify novel targets for immunotherapy in ESCC.Experimental design ESCC cell lines and mouse models were used to identify the tumor-promoting function of pancreatic progenitor cell differentiation and proliferation factor (PPDPF) and evaluate the effect of blockade of CD24. RNA sequencing was performed to profile transcriptomic changes upon PPDPF deficiency. …”
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The role of Fusobacterium nucleatum in macrophage M2 polarization and NF-κB pathway activation in colorectal cancer by Wei Zheng, Wei Zheng, Yuxin Wang, Yuxin Wang, Haoyang Sun, Haoyang Sun, Surina Bao, Surina Bao, Shuai Ge, Shuai Ge, Chunshan Quan, Chunshan Quan

“…Macrophage polarization was evaluated using scanning electron microscopy (SEM), real-time quantitative PCR (RT-qPCR), and immunofluorescence staining. …”
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MG53 deficiency mediated skeletal muscle dysfunction in chronic obstructive pulmonary disease via impairing mitochondrial fission by Liwei Liao, Ziwen Zheng, Mingming Deng, Weidong Xu, Qin Zhang, Zilin Wang, Chang Li, Jiaye Li, Yiding Bian, Kai Wang, Jinrui Miao, Ruixia Li, Yan Yin, Xiaoming Zhou, Gang Hou

“…The underlying mechanisms were investigated using multi-omics sequencing, live-cell imaging, and histological and molecular experiments. …”
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Gandouling ameliorates Wilson’s disease-associated liver fibrosis in mice with associated faecal microbiome and metabolome remodeling by Lulu Tang, Wei Dong, Danqing Liu, Chenling Zhao, Jie Chen, Yuya Wen, Jingyu Zeng, Ting Dong, Wenming Yang, Wenming Yang

“…Histological analyses and immunohistochemistry staining, were performed to evaluate the histopathological changes and collagen deposition in mouse liver tissues. …”
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Prognostic and immune modulatory effects of ammonia-induced cell death in head and neck squamous cell carcinoma by Qian Chengqun, Wang Xijun, Fan Yangyang, Yang Xiaoqin, Cheng Min, Xu Jun

“…Methods A prognostic model was developed using random survival forests (RSF), with performance evaluated through concordance index (C-index) and survival analysis. …”
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Correlation between daily physical activity and intestinal microbiota in perimenopausal women by Yanqiu Zheng, Junyu Ke, JinBin Song, Xuyu Li, Rongman Kuang, Haiyan Wang, Shuang Li, Yanwu Li

“…In this study, daily physical activity was assessed using the ActiGraph wGT3X-BT wearable sensor, and 16S rRNA sequencing was employed to analyze gut microbiota diversity and composition. …”
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Prior chemotherapy deteriorates T-cell quality for CAR T-cell therapy in B-cell non-Hodgkin’s lymphoma by Annette Künkele, Andrea Stroux, Olaf Penack, Lars Bullinger, Benedikt Obermayer, Charlotte Junkuhn, Phillip Schiele, Anna Luzie Walter, Frederik Hamm, David Busch, Mareike Frick, Frederik Damm, Julia Polansky, Marco Frentsch, Il-Kang Na, Jonas Kath, Dimitrios L Wagner

“…Since CAR T-cell therapy is currently only approved for advanced cancers after at least one line of chemotherapy, we evaluated the potential negative effects of prior exposure to chemotherapy on T-cell functionality.Methods We studied T cells of two B-cell non-Hodgkin’s lymphoma patient cohorts, one collected before treatment (pre-therapy) and the other after one or more (median 3) lines of chemotherapy (post-therapy). …”
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NGS coverage accurately predicts MET and HER2 (ERBB2) gene amplifications in a real-world non-small cell lung cancer cohort by Adam Kowalewski, Adam Kowalewski, Adam Kowalewski, Janna Siemanowski-Hrach, Thomas Stehle, Jan Rehker, Udo Siebolts, Sabine Merkelbach-Bruse, Carina Heydt

“…BackgroundFluorescence in situ hybridization (FISH) is the current standard for detecting gene amplifications, yet its low throughput and practical constraints call for alternative methods. This study evaluates next-generation sequencing (NGS) as a potential tool for accurately predicting gene amplifications.MethodsWe analyzed 66 primary non-small cell lung cancer (NSCLC) samples, tested by both NGS and FISH. …”
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DNA methylation of ACADS promotes immunogenic cell death in hepatocellular carcinoma by Ze Qian, Yifan Jiang, Yacong Wang, Yu Li, Lin Zhang, Xiaofeng Xu, Diyu Chen

“…Methods and results Using RNA sequencing data from different tumours in The Cancer Genome Atlas database, we observed that ACADS was downregulated and hypermethylated in HCC. …”
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Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production by Narisa Rueangsri, Sittiruk Roytrakul, Chawanphat Muangnoi, Kullanart Tongkhao, Sudathip Sae-Tan, Khemmapas Treesuwan, Jintana Sirivarasai

“…We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (<i>Lactobacillus</i> and <i>Weissella</i>) and species (<i>Lacticaseibacillus rhamnosus</i> and <i>Levilactobacillus brevis</i>) of lactic acid bacteria (LAB). …”
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ADAR1 expression is associated with tumour-infiltrating lymphocytes in triple-negative breast cancer by In Hye Song, Young-Ae Kim, Sun-Hee Heo, In Ah Park, Miseon Lee, Won Seon Bang, Hye Seon Park, Gyungyub Gong, Hee Jin Lee

“…In addition to DNA mutations, RNA editing can be related to neoantigens; hence, we need to explore non-synonymous mutations exclusively found using RNA sequencing data to identify clinically relevant neoantigens.…”
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Current methods in the diagnosis of invasive meningococcal disease by Ergin Ciftci, Duygu Ocal, Ayper Somer, Hasan Tezer, Dilek Yilmaz, Sirac Bozkurt, Oldac Uras Dursun, Şeyhmus Merter, Ener Cagri Dinleyici

“…The goal of this review was to evaluate the current methods for diagnosing IMD and to discuss diagnostic challenges in practice.…”
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Isorhamnetin Attenuates Isoproterenol-Induced Myocardial Injury by Reducing ENO1 (Alpha-Enolase) in Cardiomyocytes by Zhenli Guo, Shizhong Liu, Xianghong Hou, Xin Zhou, Yan Wang, Yi Rong, Xinzhi Li, Rui Yang, Ketao Ma

“…Additionally, an ISO-induced H9c2 cell injury model was established to evaluate the impact of isorhamnetin on cellular damage. …”
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miR-146b/Btg2 axis as a potential inducer of islet beta-cell decline during the progression of obesity to T2DM by Weixuan Wang, Dan Ma, Yong Chen, Rui Cheng, Ting Zhang, Qian Ge, Xi Li

“…We evaluated the potential mechanisms responsible for inducing beta-cell decline during the progression of obesity to type 2 diabetes mellitus (T2DM). …”
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Exposure of perfluorohexane sulfonate alters platelet homeostasis: From epidemiological evidence to mechanistic insights by Juxiao Li, Yue Luo, Xinrong Guo, Wenzheng Zhuo, Li Li, Ming Shi, Juan Ma, Lining Xu, Jiahuang Qiu

“…Using a combined experimental and epidemiological approach, this study comprehensively evaluated the relationship of PFAS with platelet levels and explored potential mechanisms. …”
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Fecal carriage of multidrug-resistant organisms increases the risk of hepatic encephalopathy in patients with cirrhosis: insights from gut microbiota and metabolite features by Pei-Shan Wu, Pei-Chang Lee, Tien-En Chang, Yun-Cheng Hsieh, Chi-Wei Huang, Chao-Hsiung Lin, Yi-Long Huang, Yi-Tsung Lin, Teh-Ia Huo, Bernd Schnabl, Kuei-Chuan Lee, Ming-Chih Hou

“…The fecal bacterial and fungal composition was assessed using 16S ribosomal RNA and internal transcribed spacer sequencing, whereas plasma metabolomic analysis was evaluated via untargeted liquid chromatography-mass spectrometry. …”
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