Neutrophil prime unique transcriptional responses in intestinal organoids during infection with nontyphoidal Salmonella enterica serovars by Anna-Lisa E. Lawrence, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Jason S. Knight, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Basel H. Abuaita, Mary X. O'Riordan

“…Here, we used a co-culture model of human intestinal organoids with human primary PMNs to study the role of PMNs during infection of human intestinal epithelium. Using a transcriptomics approach, we define PMN-dependent reprogramming of the host response to Salmonella, establishing a clear role in amplifying pro-inflammatory gene expression. …”
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The Role of Potassium and KUP/KT/HAK Transporters in Regulating Strawberry (<i>Fragaria</i> × <i>ananassa</i> Duch.) Fruit Development by José A. Mercado-Hornos, Claudia Rodríguez-Hiraldo, Consuelo Guerrero, Sara Posé, Antonio J. Matas, Lourdes Rubio, José A. Mercado

“…Furthermore, the slope of change in E_D at increasing external K⁺ concentration indicated a lower K⁺ permeability of the plasma membrane in white fruits, aligning with transcriptomic data. This study provides critical insights into the regulatory mechanisms of K⁺ transport during strawberry ripening and identifies potential targets for genetic modifications aimed at enhancing fruit firmness and shelf life.…”
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Novel Gene expression-based Risk Stratification tool predicts recurrence in Non-muscle invasive Bladder cancer by Srivatsa N, Hari PS, Rahul P, Lista Paul, Durgadevi Veeraiyan, Ambili Narikot, Vidya Veldore, Nishtha Tanwar, Peddagangannagari Sreekanthreddy, Hitesh Goswami, Rekha V. Kumar, B S Srinath, Aruna Korlimarla

“…Conclusions This retrospective analysis confirms that mRNA expression-based risk stratification provides superior predictive accuracy compared to conventional clinicopathologic risk tools. …”
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Molecular mechanisms underlying age-dependent effects of rearing system on the goose testicular development and semen quality by Shenqiang Hu, Xiaopeng Li, Enhua Qing, Junqi Wang, Qingliang Chen, Yang Song, Jiasen Chen, Jiwei Hu, Liang Li, Jiwen Wang

“…In the present study, the testicular morphological, histological, and transcriptomic responses of three goose breeds to the two dryland rearing systems (i.e., cage rearing system, CRS and net-floor mixed rearing system, MRS) were systematically analyzed and compared. …”
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Insights into high-altitude adaptation and meat quality regulation by gastrointestinal metabolites in Tibetan and black pigs by Xue Bai, Xue Bai, Zhiying Huang, Helin Tan, Yiren Gu, Xun Wang, Long Jin, Peng Shang, Keren Long, Diyan Li, Mingzhou Li

“…Distinct patterns of microbial metabolites were observed in the digestive tract, influencing protein digestion and purine metabolism, and correlating with muscle glycine levels. Transcriptomic data showed varied gene expression in metabolic pathways related to salivary and pancreatic secretion, as well as carbohydrate and fatty acid metabolism. …”
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Mitochondrial dysfunction fuels drug resistance in adult T-cell acute lymphoblastic leukemia by Shanshan Guo, Ekaterina Bourova-Flin, Sophie Rousseaux, Florent Chuffart, Lijun Peng, Duohui Jing, Jian-Qing Mi, Saadi Khochbin, Jin Wang

“…These findings enhance our understanding of the biology of aggressive T-ALL and provide insight into mechanisms of resistance to conventional chemotherapy. …”
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Dual RNA-seq reveals the complement protein C3-mediated host-pathogen interaction in the brain abscess caused by Staphylococcus aureus by Qiyuan Jin, Yaxuan Zhai, Rui Qiang, Xin Ma, Chenhao Zhao, Jinqi Zhong, Jijie Li, Qi Chen, Mingxiao Han, Hong Du, Qifei Cong, Haifang Zhang

“…In the S. aureus-induced brain abscess mouse model, the transcriptomic analysis revealed significant changes in bacterial virulence factors, such as hemolysin. …”
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Medical Hemorrhoid Gel Ameliorates Croton Oil-Induced Hemorrhoids by Suppressing the NLRP3 Inflammasome Activation via NF-&amp;kappa;B Signaling Pathway by Ai Z, Yuan D, Li Y, Cai J, Zhou D, Liu W

“…This mechanistic insight provides scientific validation for clinical application of MHG in HD management.Keywords: medical hemorrhoid gel, hemorrhoidal disease, inflammation, NLRP3 inflammasomes, NK-κB signaling pathway…”
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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

“…We found that different host biological pathways were activated during infection, including those related to inflammation and immune responses. These results provide insights into how NTHi and Mcat contribute to COPD progression and suggest potential targets for new treatments.…”
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Development of a machine learning-based predictive risk model combining fatty acid metabolism and ferroptosis for immunotherapy response and prognosis in prostate cancer by Zhenwei Wang, Zhihong Dai, Yuren Gao, Zhongxiang Zhao, Zhen Li, Liang Wang, Xiang Gao, Qiuqiu Qiu, Xiaofu Qiu, Zhiyu Liu

“…This study integrated bulk RNA sequencing, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics to construct a prognostic model based on genes shared between ferroptosis and fatty acid metabolism (FAM). …”
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A haplotype-resolved genome assembly and gene expression map of Cushion willow by Jindan Wang, Kaiyun Chen, Rengang Zhang, Yuan Huang, Jiahui Chen

“…Here, we updated the genome of Cushion willow to be haplotype-resolved and near telomere-to-telomere, and obtained a high-quality transcriptomic map. Our research provides a potential model species for alpine adaptive research, sex determination evolution studies, and improving willow crops.…”
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Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model. by Peter A C Wing, Maria Prange-Barczynska, Amy Cross, Stefania Crotta, Claudia Orbegozo Rubio, Xiaotong Cheng, James M Harris, Xiaodong Zhuang, Rachel L Johnson, Kathryn A Ryan, Yper Hall, Miles W Carroll, Fadi Issa, Peter Balfe, Andreas Wack, Tammie Bishop, Francisco J Salguero, Jane A McKeating

“…Nasal and lung epithelia showed a reduction in SARS-CoV-2 RNA and nucleocapsid expression in treated animals. Transcriptomic and pathological analysis showed reduced epithelial damage and increased expression of ciliated cells. …”
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Establishment of bovine extraembryonic endoderm stem cells enables efficient blastoid formation by Hao Ming, Giovanna Nascimento Scatolin, Oscar Alejandro Ojeda-Rojas, Zongliang Jiang

“…Summary: Extraembryonic endoderm stem cells (XENs) resemble the primitive endoderm of blastocyst and provide valuable alternatives for understanding hypoblast development and building stem cell-based embryo models. …”
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Autophagy disruption and mitochondrial stress precede photoreceptor necroptosis in multiple mouse models of inherited retinal disorders by Fay Newton, Mihail Halachev, Linda Nguyen, Lisa McKie, Pleasantine Mill, Roly Megaw

“…Using single-cell transcriptomics, we identify common transcriptional signatures in degenerating photoreceptors. …”
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Construction of prognostic scoring model for ovarian cancer based on deep learning algorithm by Xiaolin Zhong, Hongyang Xiao, Weihong Lu, Jiayuan Chen, Fan Chao, Ruiqin Tu

“…In addition, the prediction model was analysed in combination with patients’ clinical characteristics and transcriptomic data. The results showed a significant prognostic difference between high and low risk groups. …”
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Time-dependent RNA transcriptional profiling of abomasal mucosa in cattle infected with Ostertagia ostertagi by Clarissa Boschiero, Ethiopia Beshah, Mariam Bakshi, Peter Thompson, Xiaoping Zhu, George E. Liu, Wenbin Tuo

“…Bioinformatics analyses were performed to profile the transcriptomic changes over time as well as between cattle abomasal tissues. …”
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Improved radicchio seedling growth under CsPbI3 perovskite rooftop in a laboratory-scale greenhouse for Agrivoltaics application by Carlo Spampinato, Salvatore Valastro, Gaetano Calogero, Emanuele Smecca, Giovanni Mannino, Valentina Arena, Raffaella Balestrini, Fabiano Sillo, Lucio Ciná, Antonino La Magna, Alessandra Alberti

“…Eu-enriched CsPbI3 layers are chosen to provide semi-transparency and phase stability while radicchio has limited size and grows in pots. …”
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Ocular immune privilege in action: The living eye imposes unique regulatory and anergic gene signatures on uveitogenic T cells by Zixuan Peng, Vijayaraj Nagarajan, Reiko Horai, Yingyos Jittayasothorn, Mary J. Mattapallil, Rachel R. Caspi

“…Here, single-cell transcriptomics and functional validation revealed distinct phenotypes in both populations: ocular Tregs were highly suppressive, whereas non-Tregs expressed suppression- and anergy-associated genes and lacked regulatory function. …”
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Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC by Qian Zhu, Akhila Balasubramanian, Jaya Ruth Asirvatham, Megha Chatterjee, Badrajee Piyarathna, Jaspreet Kaur, Nada Mohamed, Ling Wu, Stacy Wang, Niloufar Pourfarrokh, Paula Danika Binsol, Mahak Bhargava, Uttam Rasaily, Yitian Xu, Junjun Zheng, Deborah Jebakumar, Arundhati Rao, Carolina Gutierrez, Angela R. Omilian, Carl Morrison, Gokul M. Das, Christine Ambrosone, Erin H. Seeley, Shu-hsia Chen, Yi Li, Eric Chang, Xiaoxian Li, Elizabeth Baker, Ritu Aneja, Xiang H.-F. Zhang, Arun Sreekumar

“…To investigate these disparities, we employed a multi-omic approach integrating imaging mass cytometry and spatial transcriptomics to characterize the tumor microenvironment (TME) in self-identified Black American (BA) and White American (WA) TNBC patients. …”
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Scalable topic modelling decodes spatial tissue architecture for large-scale multiplexed imaging analysis by Xiyu Peng, James W. Smithy, Mohammad Yosofvand, Caroline E. Kostrzewa, MaryLena Bleile, Fiona D. Ehrich, Jasme Lee, Michael A. Postow, Margaret K. Callahan, Katherine S. Panageas, Ronglai Shen

“…We benchmarked SpatialTopic across diverse single-cell spatial transcriptomic and proteomic imaging platforms spanning multiple tissue types. …”
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