Helicobacter mastomyrinus infection induces autoimmune hepatitis in mice by Liqi Zhu, Yuanyuan Liang, Linghan Yang, Qihui Yang, Jun Yin, Tao Wang, Xiangming Xu, Quan Zhang

“…The role of the gut microbiome in the pathogenesis and progression of AIH is of considerable significance. …”
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Retinoblastoma-binding Protein 9 Suppresses Intestinal Inflammation and Inflammation-induced Tumorigenesis in MiceSummary by Kensuke Hamada, Yuki Nakanishi, Yu Muta, Mayuki Omatsu, Kosuke Iwane, Munehiro Ikeda, Jiayu Chen, Yoko Masui, Naoki Aoyama, Nobukazu Agatsuma, Go Yamakawa, Takahiro Utsumi, Hiroki Kitamoto, Makoto Okabe, Yoshiro Itatani, Takumi Adachi, Koubun Yasuda, Shuji Yamamoto, Akihisa Fukuda, Etsushi Kuroda, Masaki Ohmuraya, Kazutaka Obama, Seiichi Hirota, Hiroki Ikeuchi, Kenji Nakanishi, Hiroshi Seno

“…A positive feedback loop involving epithelial cell apoptosis, commensal microbiome invasion, and activation of submucosal immune activity was identified in Rbbp9-/- mouse intestines through enhanced JAK/STAT1 signaling in RBBP9-deficient epithelial cells and macrophages. …”
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Inter-rater reliability and prognostic value of baseline Radiographic Assessment of Lung Edema (RALE) scores in observational cohort studies of inpatients with COVID-19 by Andrew I Kim, William Bain, Alison Morris, Barbara Methe, Bryan J McVerry, Georgios D Kitsios, Daniel Kotok, Janet S Lee, Nameer Al-Yousif, Christine E Girard, Jana J Jacobs, Konstantin Golubykh, Hafiz Qurashi, Michael Lu, Saketram Komanduri, Anatoliy Korzhuk, Halimat O Lawal, Nicholas Abourizk, Caitlin Schaefer, Kevin J Mitchell, Catherine M Dietz, Ellen K Hughes, Clara S Brandt, Georgia M Fitzgerald, Robin Joyce, Asmaa S Chaudhry, Jose D Rivera, Shruti Shettigar, Allen Lavina, Samantha R Gillenwater, Anas Hadeh, Faraaz A Shah, Matthew Bittner, Niall Prendergast, John Evankovich, Navitha Ramesh, Cathy Kessinger

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Association of exposure to second-hand smoke during childhood with blood DNA methylation by Marta Cosin-Tomas, Thanh Hoang, Cancan Qi, Giulietta S. Monasso, Ryan Langdon, Simon Kebede Merid, Lucinda Calas, Paula de Prado-Bert, Rebecca Richmond, Vincent VW Jaddoe, Liesbeth Duijts, John Wright, Isabella Annesi-Maesano, Regina Grazuleviciene, Marianna Karachaliou, Gerard H. Koppelman, Erik Melén, Olena Gruzieva, Martine Vrijheid, Paul Yousefi, Janine F. Felix, Stephanie J. London, Mariona Bustamante

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Cohort profile: the multigeneration Respiratory Health in Northern Europe, Spain and Australia (RHINESSA) cohort by Thorarinn Gislason, Torben Sigsgaard, Vivi Schlünssen, Joachim Heinrich, Jesús Martínez-Moratalla, Øistein Svanes, Mathias Holm, Bertil Forsberg, Dan Norbäck, Rain Jogi, Kjell Torén, Deborah Jarvis, Magnus Ekström, Adrian Lowe, Caroline J Lodge, Michael Abramson, Shyamali Dharmage, Kathrine Pape, Cecilie Svanes, Gita Mishra, Caroline Lodge, Lyle Gurrin, Bruce Thompson, Eva Lindberg, Christer Janson, Simone Accordini, Ane Johannessen, Bryndis Benediktsdottir, Karl Franklin, Andrei Malinovschi, Anna Oudin, Francisco Gómez Real, José Luis Sánchez-Ramos, Lennart Bråbäck, Torgeir Storaas, Shanshan Xu, Julia Dratva, John Holloway, Jorunn Kirkeleit, Christine Cramer, Gro Tjalvin, Anne Mette Lund Würtz, Randi Jacobsen Bertelsen, Oskar Jõgi, Signe Timm, Francisco Javier Callejas, Raúl Godoy, Trude Duelien Skorge, Christine Drengenes, Nils Oskar Jõgi, Maryia Khomich, Toril Mørkve Knudsen, Ingrid Kuiper, Juan Pablo López-Cervantes, Marianne Lønnebotn, Shokouh Makvandi-Nejad, Antonio Pérez, Anders Røsland, Rajesh Shigdel, Svein Magne Skulstad, Kai Triebner, Hilde Vindenes, Jose Luis Sanchez, Jose Maldonado, David Martino, Jennifer Perret, Lucia Calciano, William Horsnell, Susanne Krauss-Etchmann

“…Study protocols are harmonised across generations.Findings to date Collected data include spirometry, skin prick tests, exhaled nitric oxide, anthropometrics, bioimpedance, blood pressure; questionnaire/interview data on respiratory/general/reproductive health, indoor/outdoor environment, smoking, occupation, general characteristics and lifestyle; biobanked blood, urine, gingival fluid, skin swabs; measured specific and total IgE, DNA methylation, sex hormones and oral microbiome. Research results suggest that parental environment years before conception, in particular, father’s exposures such as smoking and overweight, may be of key importance for asthma and lung function, and that there is an important susceptibility window in male prepuberty. …”
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An assessment of breast cancer HER2, ER, and PR expressions based on mammography using deep learning with convolutional neural networks by Shun Zeng, Hongyu Chen, Rui Jing, Wenzhuo Yang, Ligong He, Tianle Zou, Peng Liu, Bo Liang, Dan Shi, Wenhao Wu, Qiusheng Lin, Zhenyu Ma, Jinhui Zha, Yonghao Zhong, Xianbin Zhang, Guangrui Shao, Peng Gong

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Evaluating Methods for Aflatoxin B1 Monitoring in Selected Food Crops Within Decentralized Agricultural Systems by Haadia Tanveer, Hannah Glesener, Blake Su, Brooke Bolsinger, Rosa Krajmalnik-Brown, Lee E. Voth-Gaeddert

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Known and novel parvoviruses identified in domestic pigeons by Ewa Łukaszuk, Daria Dziewulska, Anthony Khalifeh, Joy M. Custer, Simona Kraberger, Arvind Varsani, Tomasz Stenzel

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Endometrial Receptivity–Lessons from “Omics” by Louie Ye, Evdokia Dimitriadis

“…Drawing on findings from various branches of “omics”, including genomics, epigenomics, transcriptomics, proteomics, lipidomics, metabolomics, and microbiomics, this narrative review aims to (1) discuss mechanistic insights on endometrial receptivity and its implication in infertility; (2) highlight advances in investigations for endometrial receptivity; and (3) discuss novel diagnostic and therapeutic strategies that may improve reproductive outcomes.…”
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Environmental Metagenomic Analysis of "ESKAPE" Pathogens in the Pediatric Intensive Care Unit of General Hospital Yogyakarta Indonesia by Ludhang Pradipta Rizki, Indah Kartika Murni, Abu Tholib Aman, Titik Nuryastuti

“…These microbiomes encompass a wide array of microbial species, including ESKAPE bacterial pathogens, as well as profiles related to resistome and virulome. …”
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Novel adaptive immune systems in pristine Antarctic soils by Marc W. Van Goethem, Oliver K. I. Bezuidt, Rian Pierneef, Surendra Vikram, David W. Hopkins, Thomas Aspray, Grant Hall, Stephan Woodborne, Ian D. Hogg, Trent R. Northen, Weidong Kong, Daniele Daffonchio, Don A. Cowan, Yves Van de Peer, Manuel Delgado-Baquerizo, Thulani P. Makhalanyane

“…These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.…”
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Microbial keratitis in Southern Malawi: a microbiological pilot study by Timothy Neal, Dean Everett, Stephen B Kaye, Alistair Darby, Moira Gandiwa, Shaffi Mdala, Caroline E Corless, Rose Herbert, Nicholas A V Beare, Tobi F Somerville, Thokozani Zungu, Malcolm J Horsburgh, Petros C Kayange

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African army ants at the forefront of virome surveillance in a remote tropical forest by Fritz, Matthieu, Reggiardo, Bérénice, Filloux, Denis, Claude, Lisa, Fernandez, Emmanuel, Mahé, Frédéric, Kraberger, Simona, Custer, Joy M., Becquart, Pierre, Mebaley, Telstar Ndong, Kombila, Linda Bohou, Lenguiya, Léadisaelle H., Boundenga, Larson, Mombo, Illich M., Maganga, Gael D., Niama, Fabien R., Koumba, Jean-Sylvain, Ogliastro, Mylène, Yvon, Michel, Martin, Darren P., Blanc, Stéphane, Varsani, Arvind, Leroy, Eric, Roumagnac, Philippe

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Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data by Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius, Rob Knight

“…Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.…”
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Impact of a block structure on the Lotka-Volterra model by Clenet, Maxime, Massol, François, Najim, Jamal

“…The Lotka-Volterra (LV) model is a simple, robust, and versatile model used to describe large interacting systems such as food webs or microbiomes. The model consists of n coupled differential equations linking the abundances of n different species. …”
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Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea by Darsha Prabhaharan, Young Wook Go, Hyunjin Kim, Seongcheol Kang, Byoung-In Sang

“…Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. …”
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Probiotics, Prebiotics, and Synbiotics: Gut and Beyond by Usha Vyas, Natarajan Ranganathan

“…Restoration of the gut microbiota may be difficult to accomplish, but the use of probiotics has led to promising results in a large number of well-designed (clinical) studies. Microbiomics has spurred a dramatic increase in scientific, industrial, and public interest in probiotics and prebiotics as possible agents for gut microbiota management and control. …”
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Biomarkers of inflammation and colorectal cancer risk by Yuting Li, Yuting Li, Yuting Li, Yuexin Luo, Yue Ran, Furong Lu, You Qin

“…Multi-omics techniques, including genomics and microbiomics, offer new avenues for CRC diagnosis. Overall, while evidence highlights the significance of inflammatory biomarkers in CRC risk prediction, larger prospective studies are urgently needed to clarify their roles due to existing inconsistencies and methodological limitations.…”
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An atlas of metabolites driving chemotaxis in prokaryotes by Maéva Brunet, Shady A. Amin, Iurii Bodachivskyi, Unnikrishnan Kuzhiumparambil, Justin R. Seymour, Jean-Baptiste Raina

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Unveiling the mechanism of micro-and-nano plastic phytotoxicity on terrestrial plants: A comprehensive review of omics approaches by Asad Jamil, Ambreen Ahmad, Muhammad Moeen-ud-din, Yihao Zhang, Yuxuan Zhao, Xiaochen Chen, Xiaoyu Cui, Yindong Tong, Xianhua Liu

“…Recent advancements in omics technologies such as proteomics, metabolomics, transcriptomics, and microbiomics, coupled with emerging technologies like 4D omics, phenomics, spatial transcriptomics, and single-cell omics, offer unprecedented insight into the physiological, molecular, and cellular responses of terrestrial plants to MNPs exposure. …”
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