Determinants of response to daratumumab in Epstein-Barr virus-positive natural killer and T-cell lymphoma by Jennifer Yang, Anand D Jeyasekharan, Joanne Lee, Wee Joo Chng, Tae-Hoon Chung, Nurulhuda Mustafa, Adina Huey Fang Nee, Jing Yuan Chooi, Sabrina Hui Min Toh, Viknesvaran Selvarajan, Shuangyi Fan, Siok Bian Ng, Michelle Poon, Esther Chan, Yen Lin Chee, Longen Zhou

“…Furthermore, elucidation of factors which sensitize the complement-mediated response provides an alternative approach toward optimizing therapeutic efficacy of daratumumab where CDC remains a known limiting factor. …”
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Combination of HDAC inhibition and cytokine enhances therapeutic HPV vaccine therapy by Jeffrey Schlom, James L Gulley, Caroline Jochems, Sofia R Gameiro, Wiem Lassoued, Daniel Burnett, Lisa K Poppe, Nicholas Roller, Miriam Marlene Medina-Enríquez, Katherine E Lothstein, Asma S Khelifa, Masaya Miyamoto

“…These effects were paralleled by strong differentiation of tumor-associated macrophages (TAMs) towards pro-inflammatory, antitumor M1-like cell states. Single-cell transcriptomic analysis indicated all three agents were required for highest modulation of both CD8+ T cells and TAMs conducive to tumor control. …”
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Baseline predictors for 28-day COVID-19 severity and mortality among hospitalized patients: results from the IMPACC study by Jintong Hou, Benjamin Haslund-Gourley, Joann Diray-Arce, Annmarie Hoch, Nadine Rouphael, Patrice M. Becker, Alison D. Augustine, Al Ozonoff, Leying Guan, Steven H. Kleinstein, Bjoern Peters, Elaine Reed, Matt Altman, Charles R. Langelier, Holden Maecker, Seunghee Kim, Ruth R. Montgomery, Florian Krammer, Michael Wilson, Walter Eckalbar, Steven E. Bosinger, Ofer Levy, Hanno Steen, Lindsey B. Rosen, Lindsey R. Baden, Esther Melamed, Lauren I. R. Ehrlich, Grace A. McComsey, Rafick P. Sekaly, Joanna Schaenman, Albert C. Shaw, David A. Hafler, David B. Corry, Farrah Kheradmand, Mark A. Atkinson, Scott C. Brakenridge, Nelson I. Agudelo Higuita, Jordan P. Metcalf, Catherine L. Hough, William B. Messer, Bali Pulendran, Kari C. Nadeau, Mark M. Davis, Ana Fernandez Sesma, Viviana Simon, Monica Kraft, Chris Bime, Carolyn S. Calfee, David J. Erle, IMPACC Network, Lucy F. Robinson, Charles B. Cairns, Elias K. Haddad, Mary Ann Comunale

“…The Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study collected clinical, demographic, blood cytometry, serum receptor-binding domain (RBD) antibody titers, metabolomics, targeted proteomics, nasal metagenomics, Olink, nasal viral load, autoantibody, SARS-CoV-2 antibody titers, and nasal and peripheral blood mononuclear cell (PBMC) transcriptomics data from patients hospitalized with COVID-19. …”
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Long noncoding RNA LINC00339 promotes osteoporosis development via modulating of regulator CDC42 by binding PARP1 by Dong-Li Zhu, Yan Zhang, Xiao-Yu Zhang, Zi-Han Qiu, Ke Li, Xiao-Rong Zhou, Zhen-Zhen He, Xiao-Feng Chen, Shan-Shan Dong, Wen Tian, Ya-Kang Wang, Tie-Lin Yang, Bo Yang, Yan Guo

“…Notably, integrated transcriptomic and rescue experiments revealed that LINC00339 and PARP1 coregulate CDC42 expression through post-transcriptional regulatory mechanisms. …”
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Identification and role of CmLhcb2.1 in regulating low-light stress resistance in Chinese chestnut (Castanea mollissima) by Yong Yang, Yong Yang, Xuan Wang, Xuan Wang, Jing Liu, Meng Wang, Liyang Yu, Dongsheng Wang, Jingshi Li, Yi Lu, Jingzheng Zhang, Haie Zhang, Haie Zhang

“…CmLhcb2.1 and CmLhcb2.2 were grouped on the same branch with GhLhcb2.3 of upland cotton that involved in chlorophyll synthesis.The chestnut leaves exhibited phenotypic and transcriptomic differences under low and normal light conditions. …”
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Identification of key proteins and pathways in myocardial infarction using machine learning approaches by Chang Liu, Xing Zhang, Qian Xie, Binbin Fang, Fen Liu, Junyi Luo, Gulandanmu Aihemaiti, Wei Ji, Yining Yang, Xiaomei Li

“…This study combines proteomics, transcriptomics and machine learning (ML) to identify key proteins and pathways associated with AMI. …”
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Circulating proteins and metabolites panel for noninvasive preoperative diagnosis of epithelial ovarian cancer by Yan Jia, Li Yuan, Weijia Wen, Linna Chen, Xueyuan Zhao, Qiong Wu, Yan Liao, Caixia Shao, Chaoyun Pan, Chunyu Zhang, Shuzhong Yao

“…Conclusions Our findings provide novel insights into the EOC metabolic and protein landscape. …”
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Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques by Hayden N. Brochu, Elise Smith, Sangmi Jeong, Michelle Carlson, Scott G. Hansen, Jennifer Tisoncik-Go, Lynn Law, Louis J. Picker, Michael Gale, Xinxia Peng

“…A promising pre-clinical HIV vaccine based on rhesus cytomegalovirus (RhCMV) expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) provides sustained, durable protection against SIV challenge in ~59% of vaccinated rhesus macaques. …”
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Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle by Bruna Maria Salatta, Maria Malane Magalhães Muniz, Larissa Fernanda Simielli Fonseca, Lucio Flavio Macedo Mota, Caio de Souza Teixeira, Gabriela Bonfá Frezarim, Marta Serna-García, Danielly Beraldo dos Santos Silva, Angélica Simone Cravo Pereira, Fernando Baldi, Lucia Galvão de Albuquerque

“…These findings offer new insights into the biological mechanisms underlying the gene regulation of FA composition in beef and may provide a valuable foundation for further investigations regarding the interactions between lncRNAs and mRNAs, as well as their potential impact on meat quality.…”
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Single-cell profiling reveals a reduced epithelial defense system, decreased immune responses and the immune regulatory roles of different fibroblast subpopulations in chronic atro... by Lin Lin, Tingxuan Huang, Lizhi Li, Yang Lin, Feng Chen, Ziyi Zheng, Jie Zhou, Yizhe Wang, Weihao You, Yujie Duan, Yawen An, Shiwei He, Weimin Ye

“…Results We generated a single-cell transcriptomic atlas from 3 CAG biopsy samples and paired adjacent normal tissues. …”
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Weighted Gene Co-Expression Network Analysis Uncovers Critical Genes and Pathways Involved in Soybean Response to Soybean Mosaic Virus by Hanhan Zhu, Ruiqiong Li, Yaoyao Fang, Xue Zhao, Weili Teng, Haiyan Li, Yingpeng Han

“…To explore the defense mechanisms of soybean against SMV, we performed comparative transcriptomic sequencing of the leaves between the Dongnong 93-046 inoculated with SMV at 8 h (T) and the non-inoculated control (C) on the HiSeq2000 platform. …”
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Differential gene expression of tumor-infiltrating CD8+ T cells in advanced versus early-stage colorectal cancer and identification of a gene signature of poor prognosis by Reem Saleh, Varun Sasidharan Nair, Salman M Toor, Rowaida Z Taha, Khaled Murshed, Mahmood Al-Dhaheri, Mahwish Khawar, Mahir Abdulla Petkar, Mohamed Abu Nada, Fares Al-Ejeh, Eyad Elkord

“…Due to tumor intrinsic and/or extrinsic factors, the density and function of CD8+ tumor-infiltrating lymphocytes (TILs) could be compromised, leading to poor prognosis and survival.Methods Using RNA-Seq, transcriptomes of sorted CD3+CD8+ TILs from treatment-naïve colorectal cancer (CRC) patients at advanced stages (III and IV) were compared with those from patients with early stages (I and II). …”
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Identification of intratumoral microbiome-driven immune modulation and therapeutic implications in diffuse large B-cell lymphoma by Zheng Yijia, Xiaoyu Li, Lina Ma, Siying Wang, Hong Du, Yun Wu, Jing Yu, Yunxia Xiang, Daiqin Xiong, Huiting Shan, Yubo Wang, Zhi Wang, Jianping Hao, Jie Wang

“…This study aims to identify microbiome-related subtypes in DLBCL and assess their impact on prognosis, immune infiltration, and therapeutic sensitivity. Methods Transcriptomic and microbiome data from 48 DLBCL patients were obtained from public databases. …”
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Exploring the Potential of Coix Seeds to Mitigate High Humidity-Induced Gut Inflammation via Microbiota and Metabolite Modulation by Zhao P, Xiao C, Xuan M, Yan S, Yu X, Li W, Han L, Wang H, Zhao J, Zhang S, Zhong X

“…Shigella spp.) and correcting sphingolipid metabolism (eg sphingomyelin, ceramide). Metabolomic and transcriptomic analyses revealed that CD suppressed immune-related pathways (eg T/B cell receptor signalling, Th1/Th2 differentiation), consistent with reduced serum levels of proinflammatory cytokines (TNF-α, IL-6, IL-17). …”
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Resolvin D1-mediated cellular crosstalk protects against MASH by Amaia Navarro-Corcuera, Yiwei Zhu, Fanglin Ma, Neha Gupta, Haley Asplund, Bruno Cogliati, Jerry E. Chipuk, Oren Rom, Scott L. Friedman, Brian E. Sansbury, Xin Huang, Bishuang Cai

“…Our study provides a new mechanistic insight into the role of RvD1 in MASH and highlights its therapeutic potential to treat this condition.…”
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In-depth characterization of vaccine-induced neoantigen-specific T cells in patients with IDH1-mutant glioma undergoing personalized peptide vaccination by Martin Glas, Florian Battke, Dirk Hadaschik, Martin Schulze, Saskia Biskup, David Reardon, Christina Kyzirakos, Simone Kayser, Oliver Bartsch, Armin Rabsteyn, Henning Zelba, Borong Shao, Annekathrin Reinhardt, Carsten Greve, Lisa Oenning, Pauline Latzer, Tabea Riedlinger, Julian Wünsche, Johannes Harter, Magdalena Feldhahn, Yannick Bantel, Janina Johänning, Jiri Ködding, Olga Maksimovic, Veit Scheble, Alexandra M Miller, Michael Castro, Deborah T Blumenthal

“…The obtained TCRβ sequences could be tracked in autologous ex-vivo single-cell transcriptomic data. Our results provide a rationale for pursuing vaccination and T cell transfer strategies targeting IDH1. …”
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Cellular effects of splenectomy on liver regeneration after 70% resection by Andrey Elchaninov, Andrey Elchaninov, Polina Vishnyakova, Polina Vishnyakova, Elena Gantsova, Elena Gantsova, Miroslava Chirkova, Victoria Karyagina, Larkin Anatoliy, Evgeniya Kananykhina, Maria Kuznetsova, Ibrahim Atabekov, Evgeny Karpulevich, Silachev Denis, Dmitry Trofimov, Dmitry Goldshtein, Timur Fatkhudinov, Timur Fatkhudinov, Gennady Sukhikh

“…The hepatic portal vein system provides a direct anatomical connection between the liver and the spleen ― the largest lymphoid organ in mammals. …”
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SLIT3-mediated intratumoral crosstalk induces neuroblastoma differentiation via a spontaneous regression-like program by Meiling Liu, Dekang Lv, Wenjing Yan, Yi Wu, Shulan Wang, Luoxuan Wang, Jie Lei, Deshun Zeng, Zifeng Wang, Fang Liu, Bing Deng, Quentin Liu, Bin He, Min Yan

“…Methods Single-nucleus transcriptomics (snRNA-seq) data of neuroblastoma samples were obtained from the Synapse repository to investigate the composition of heterogeneous tumor cell clusters. …”
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Relevance of Cellular Homeostasis-Related Gene Expression Signatures in Distinct Molecular Subtypes of Breast Cancer by Sharda P. Singh, Chathurika S. Dhanasekara, Michael W. Melkus, Chhanda Bose, Sonia Y. Khan, Flavia Sardela de Miranda, Maria F. Mahecha, Prrishti J. Gukhool, Sahil S. Tonk, Se-Ran Jun, Sahra Uygun, Rakhshanda Layeequr Rahman

“…<b>Conclusions:</b> This study identified gene expression signatures associated with breast cancer risk and molecular subtypes. These findings provide insights into the biological processes that may drive breast cancer progression and could inform the development of prognostic biomarkers and personalized therapeutic strategies.…”
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Screening of reference genes in Callosobruchus maculatus (Coleoptera: Bruchidae) fourth-instar larvae under high-temperature and antibiotic treatments(高温及抗生素处理下四纹豆象四龄幼虫内参基因的筛选)... by 耿加美(GENG Jiamei), 何云川(HE Yunchuan), 陈秋霖(CHEN Qiulin), 高扬(GAO Yang), 周瀛(ZHOU Ying), 祝增荣(ZHU Zengrong)

“…Therefore, RpL39_1 is recommended as a single reference gene for gene expression analysis in C. maculatus larvae under high-temperature and antibiotic treatments. This study provides methodological insights into the gut microbiota-mediated regulation of heat tolerance-related genes in the host. . …”
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