Synovial macrophage diversity and activation of M-CSF signaling in post-traumatic osteoarthritis by Alexander J Knights, Easton C Farrell, Olivia M Ellis, Michelle J Song, C Thomas Appleton, Tristan Maerz

“…In summary, we defined different synovial macrophage subpopulations present in healthy and injured mouse synovium. …”
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Panoramic spatial enhanced resolution proteomics (PSERP) reveals tumor architecture and heterogeneity in gliomas by Ziyan Xu, Yunzhi Wang, Tao Xie, Rongkui Luo, Heng-Li Ni, Hang Xiang, Shaoshuai Tang, Subei Tan, Rundong Fang, Peng Ran, Qiao Zhang, Xiaomeng Xu, Sha Tian, Fuchu He, Wenjun Yang, Chen Ding

“…Through integrative analysis with single-cell transcriptomic data, we elucidated the cellular composition and cell–cell communications in a spatial context. …”
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Metallosphaera sedula bifurcates into two sizes when it is cultured mixotrophically on soluble iron by Robert C. Blake, Richard G. Painter, Nghi Pham, Olivia Griswold, Brooke White, Richard A. White, Richard A. White, Richard A. White

“…These functional data were consistent with the transcriptomic evidence presented by others, that the proteins presumably responsible for aerobic respiration on soluble iron are expressed constitutively in M. sedula. …”
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Mechanisms of Impact of <i>Alnus ferdinandi-coburgii</i> Odor Substances on Host Location of <i>Tomicus yunnanensis</i> by Jingyi Bo, Wen Li, Xiangyi Li, Zongbo Li, Xiangzhong Mao, Bin Yang, Ning Zhao

“…This study identified and analyzed chemosensory-related genes from the transcriptomes of different tissues of male and female adults of <i>Tomicus yunnanensis</i>. …”
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Linking preclinical models to clinical realities: VEGF/VEGFR inhibitors and thrombotic microangiopathy in cancer therapy by Aimin Jiang, Zhanzhi Li, Ying Liu, Junyi Shen, Quan Cheng, Anqi Lin, Peng Luo, Linhui Wang

“…The results underscore the enhanced risk of TMA posed by these inhibitors, particularly noting the timelines and mechanisms through which different inhibitors trigger TMA, and recommend regular monitoring of biochemical markers for early risk assessment and management.…”
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Identification of matrix stiffness-related molecular subtypes in HCC via integrating multi-omics analysis and machine learning algorithms by Hanqi Li, Jiayi Zhang, Yu Shi, Huanhuan Wang, Ruida Yang, Shaobo Wu, Yue Li, Xue Yang, Qingguang Liu, Liankang Sun

“…Single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) analyses assessed matrix stiffness activity scores across different cell subgroups and examined PPARG spatial localization within tissues. …”
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Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells by Adonis D’Mello, Timothy F. Murphy, Martina Wade, Charmaine Kirkham, Yong Kong, Hervé Tettelin, Melinda M. Pettigrew

“…Several biological pathways were differentially regulated across all conditions (31, NTHi; 22, Mcat; and 169, human). NTHi transcriptomic profiles differed during mono-infection and coinfection; examples included downregulation of iron-sulfur metabolism (IscR regulon) and differential regulation of quorum sensing in coinfection compared to mono-infection. …”
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Myocardial Proteome in Human Heart Failure With Preserved Ejection Fraction by Vivek P. Jani, Edwin J. Yoo, Aleksandra Binek, Alina Guo, Julie S. Kim, Jennifer Aguilan, Mohammad Keykhaei, Sydney R. Jenkin, Simone Sidoli, Kavita Sharma, Jennifer E Van Eyk, David A. Kass, Virginia S. Hahn

“…Recent human myocardial transcriptomics and metabolomics have identified major differences between HFpEF and controls. …”
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In silico evaluation of the immunogenic profile of lung cancers with SMARCA4 genetic alterations by Cristina Nieto-Jiménez, Esther Garcia-Lorenzo, Cristina Diaz-Tejeiro, Lucía Paniagua-Herranz, Adrián Sanvicente, Bernard Doger, Irene Moreno, Manuel Pedregal, Jorge Bartolomé, Arancha Manzano, Gyöngyi Munkácsy, Balázs Győrffy, Pedro Pérez-Segura, Emiliano Calvo, Victor Moreno, Alberto Ocana

“…In the present work, we explore the transcriptomic landscape and immunologic profile of NSCLC with molecular alterations in SMARCA4. …”
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Molecular effects of clinically relevant chemotherapeutic agents on choline phospholipid metabolism in triple negative breast cancer cells by Caitlin M. Tressler, Kanchan Sonkar, Menglin Cheng, Vinay Ayyappan, Ruoqing Cai, Kristine Glunde

“…We sought to further investigate these clinical observations at the molecular level by combining metabolic and transcriptomic studies in two human TNBC cell lines treated with six different chemotherapeutic agents. …”
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Adaptive attenuation of virulence mediated by Wzc mutation in ST11-KL47 Carbapenem-resistant Klebsiella pneumonia by Yufeng Dai, Yufeng Dai, Qiang Zhao, Huanhuan Yan, Huanhuan Yan, Kun Ye, Lifeng Wang, Ling Guo, Na Guo, Na Guo, Wenwen Li, Wenwen Li, Jiyong Yang

“…Unexpectedly, Wzc-mediated HMV CRKp exhibits reduced pathogenicity versus non-mucoviscosity (NMV) strains in different animal models, with competitive disadvantage, decreased biofilm formation, serum resistance, and adhesion, yet higher anti-phagocytic ability in vitro. …”
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Behavioral, physiological and genetic responses of the Yesso scallop Mizuhopecten yessoensis to the predation of sea star by Xuetao Li, Xuetao Li, Xuetao Li, Xian Li, Xian Li, Danyang Li, Danyang Li, Dandan Zhang, Xingyue Zhai, Xubo Wang, Xubo Wang, Junxia Mao, Junxia Mao, Ying Tian, Ying Tian, Ming Liu, Yaqing Chang, Yaqing Chang, Zhenlin Hao, Zhenlin Hao

“…Transcriptomic profiling of adductor muscle in this group identified 514 differentially expressed genes (DEGs), of which 20 remained significant after P - value correction. …”
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Identification of the crucial circ-mi-mRNA interaction networks regulating testicular development and spermatogenesis in ganders by Xiaopeng Li, Xiaoyong He, Guibi Li, Zhujun Wang, Fuli Huang, Jiasen Chen, Yang Song, Tanze Liu, Zhaoyan Chen, Xiangfeng Wang, Jiwei Hu, Hua He, Hehe Liu, Liang Li, Jiwen Wang, Shenqiang Hu

“…In the present study, we firstly compared the morphological and histological differences in the testes of ganders from normozoospermic group (NG) and azoospermic group (AG), and then analyzed the testicular expression patterns of circRNAs, miRNAs, and mRNAs between the two groups by using whole-transcriptome sequencing technology. …”
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High-starchy carbohydrate diet aggravates NAFLD by increasing fatty acids influx mediated by NOX2 by Yuqi Gao, Rui Hua, Kezheng Peng, Yuemiao Yin, Chenye Zeng, Yannan Guo, Yida Wang, Liyuan Li, Xue Li, Ying Qiu, Zhao Wang

“…Our study showed that a high-starch carbohydrate diet (HCD) led to the occurrence and exacerbation of NAFLD in mice. Transcriptomics and metabonomic analyses showed that the increased fatty acid influx mediated by NADPH oxidase 2 (NOX2) exacerbated NAFLD. …”
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Lake Baikal amphipods and their genomes, great and small by P. B. Drozdova, E. V. Madyarova, A. N. Gurkov, A. E. Saranchina, E. V. Romanova, J. V. Petunina, T. E. Peretolchina, D. Y. Sherbakov, M. A. Timofeyev

“…The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. …”
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Natural history, immunological and genetic characteristics of preclinical inflammatory bowel disease (EARLY): study protocol for a prospective cohort study by Iago Rodríguez-Lago, Urko M. Marigorta, Beatriz Mateos, Míriam Mañosa, Lucía Márquez-Mosquera, Luis Menchén, Francisco Rodríguez-Moranta, Inmaculada Alonso, Mariam Aguas, Horacio Alonso-Galán, Pere Borràs, Beatriz Castro, Eugeni Domènech, Rocío Ferreiro-Iglesias, Ruth de Francisco, Francisco Javier García-Alonso, Natalia García, Orlando García-Bosch, Carla Gargallo, Javier P. Gisbert, Eva Iglesias, Francisco Mesonero, Jone Ortiz de Zárate, Laura Ramos, Empar Sáinz, Pablo Ladrón, Carles Suria, Cristina Suárez Ferrer, Coral Tejido, Pilar Varela, Raquel Vicente, Yamile Zabana, Gisela Castany, Eva Rodríguez, Ana Gutiérrez, Manuel Barreiro-de Acosta

“…Samples from patients and controls will undergo genetic, proteomic, transcriptomic, single-cell RNA sequencing, metabolomic, and microbiome analyses, and integration of data between the different omic perspectives will also be performed. …”
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Bioinformatics Analysis of the Expression and Prognostic Significance of Transcription Factor YY1 in Gastric Cancer by Wenliang Chen, Huanhuan Wang, Ntiak Achi, Jinjin Hao, Rui Gong, Qiang Zhao

“…Methods and Results Transcriptomic data and clinical information from GC patients were obtained from the TCGA and UCSC databases. …”
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Deciphering the role of miR-71 in Echinococcus multilocularis early development in vitro. by Matías Gastón Pérez, Markus Spiliotis, Natalia Rego, Natalia Macchiaroli, Laura Kamenetzky, Nancy Holroyd, Marcela Alejandra Cucher, Klaus Brehm, Mara Cecilia Rosenzvit

“…Notably, miR-71-silenced primary cell cultures showed a strikingly different phenotype from control cells and did not develop into fully mature metacestodes. …”
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Unveiling tissue-specific transcriptional adaptations in iPSC-derived fibroblasts via co-culture systems by Amar J. Azad, Alessandro Bentivogli, Henrike Germar, Dana Wörz, Elena Lizunova, Max J. Cumberland, January Weiner, Sarah Hedtrich

“…This study investigates whether iFBs can acquire tissue-specific transcriptional profiles through co-culture with cells from different germ layers, including skin (keratinocytes), heart (cardiomyocytes), gut (intestinal cells), and lung (bronchial epithelial cells). …”
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Chemical quantification of N-acyl alanine methyl ester (NAME) production and impact on temporal gene expression patterns in Roseovarius tolerans EL-164 by Janina Leinberger, Diana Koteska, Judith Boldt, Jörn Petersen, Sahana Shivaramu, Jürgen Tomasch, Stefan Schulz, Thorsten Brinkhoff

“…Expression levels of stress response genes differed between NAME- and AHL-spiked EL-164 cultures in the stationary phase. …”
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