tbuckley/cabot-search huggingface dataset:
Meta-analysis of shotgun sequencing of gut microbiota in obese children with MASLD or MASH
Authors: Thomas Zöggeler, Anna Maria Kavallar, Adam Robert Pollio, Denise Aldrian, Cornelia Decristoforo, Sabine Scholl-Bürgi, Thomas Müller, Georg Friedrich Vogel
Journal: Gut Microbes (2025)

Alterations in the gut microbiome affect the development and severity of metabolic dysfunction-associated steatotic liver disease (MASLD) or metabolic dysfunction-associated steatohepatitis (MASH). We analyzed microbiomes of obese children with and without MASLD, MASH, and healthy controls. Electronic databases were searched for studies on the gut microbiome in children with obesity with/without MASLD or MASH, providing shotgun-metagenomic-sequencing data. Nine studies and an additionally recruited cohort were included. Fecal microbiomes of children with MASLD (n = 153) and MASH (n = 70) were significantly different in alpha- and beta-diversity (p < 0.001) compared to obese (n = 58) and healthy (n = 132). Species Faecalibacterium_prausnitzii and Prevotella_copri are differentially abundant between obese, MASLD and MASH groups. XGBoost and random forest-models accurately predict MASLD over obesity with an AUROC of 87% and MASH over MASLD with 89%. Pathway-abundance-based models accurately predict MASLD over obesity with an AUROC of 81% and MASH over MASLD with 88%. The composition of the gut microbiome is altered with increasing hepatic fibrosis and concomitant species-abundance increase of Prevotella_copri (p = 0.0082). Machine-learning models discriminate pediatric from adult MASH with an AUROC of 97%. The gut microbial composition is increasingly altered in children with the progression of MASLD toward MASH. This can be utilized as a fecal biomarker and highlights the impact of diet on the gut microbiome for disease intervention.
Activin A‐activated ALK4 induces pathogenic Th17 involved endothelial–mesenchymal transition in systemic lupus erythematosus‐associated pulmonary arterial hypertension
Authors: Shuliang Jing, Junyan Qian, Hongjie Ying, Pei Mao, Mingxin Yao, Zhihong Wu, Harm J Bogaard, Lie Wang, Mengtao Li, Jun Yang
Journal: Arthritis & Rheumatology (2025)

Objective Autoimmune diseases, such as systemic lupus erythematosus (SLE), are associated with pulmonary arterial hypertension (PAH), a condition that can lead to heart failure. However, whether T cells also contribute to the occurrence of PAH in SLE, has not been clarified. The objective of this study was to elucidate the role of Activin A and activated receptor signaling in SLE‐PAH. Methods CyTOF analysis was performed to identify the major affected immune cell population in SLE‐PAH patients. Serum Activin A and IL‐17 levels in patients with SLE‐PAH, SLE and healthy donors were determined by ELISA. Cocultures of Th17 cells with pulmonary microvascular endothelial cells (PMECs) and relevant rodent models were used to identify the converged target. Results The reduced CD4 + T cell number was detected in SLE‐PAH patients after treatment with immunosuppressant and vasodilator. Increased Th17 cells population, higher serum Activin A and IL‐17 levels were found in patients with SLE‐PAH compared to SLE or Donor. Activin A signals via ALK4 in both Th17 cells and PMECs. Overexpressing ALK4 in Th17 cells increased IL‐6 and endothelial–mesenchymal transition (EndoMT) marker levels in cocultured PMECs. We found severe SLE‐PH in mice by overexpressing ALK4, and alleviated hemodynamic changes in CD4 + T cells depletion mice. ALK4 inhibitor TEW effectively treated SLE‐PH mice by repressing CTGF transcription, which was induced by ALK4 activated pSmad2 and pSTAT3. Conclusion Our findings suggest that Activin A activates ALK4 in Th17 cells, thereby inducing IL‐17 secretion. Concurrently, activated ALK4 induces EndoMT in hPMECs via CTGF upregulation. It suggests that ALK4 is a promising therapeutic target for SLE‐PAH.
<scp>FGL</scp>‐1 Modulates Inter‐Organ Communication by Controlling T Cell Homeostasis during the Onset of Sjögren's Disease
Authors: Kunihiro Otsuka, Aya Ushio, Ruka Nagao, Shigefumi Matsuzawa, Rieko Arakaki, Kazuki Fukuta, Yasuhiro Mouri, Takaaki Tsunematsu, Naozumi Ishimaru
Journal: Arthritis & Rheumatology (2025)

Objective Autoimmunity occurs due to the tactics between pathogenic and regulatory factors in systemic organs. Although inter‐organ communication has been demonstrated in various diseases, the effects of the crosstalk between the immune system and other organs on autoimmune disease is unknown. Methods We analyzed the influence of inter‐organ communication on the cellular or molecular mechanism of autoimmunity using a mouse model of primary Sjögren's disease (pSjD) and patients with pSjD by integrative genomic, bioinformatics, pathological, and immunological analyses. Results Fibrinogen‐like protein‐1 (FGL‐1) was identified as a potent factor for inter‐organ communication between the liver and immune system in pSjD model mice. The production of FGL‐1 of the liver is induced by IL‐6 from CD4 + T cells in these mice. The onset of autoimmune lesions in Fgl1 ‐deficient pSjD model mice was earlier than that in the WT‐pSjD model mice. FGL‐1 produced in the liver regulates naïve/memory T cell homeostasis. Further, FGL‐1 was significantly upregulated in patients with pSjD compared to the controls. Moreover, its concentration was closely related to the serum IL‐6 levels in patients with pSjD. Conclusion FGL‐1 plays a key role in the onset of autoimmunity by suppressing T cell activation in pSjD. Our results will facilitate the development of novel diagnostic or therapeutic strategies targeting the inter‐organ communication for autoimmune diseases. image
Mucosal‐associated invariant T cells in rheumatic diseases.
Authors: Manon Lesturgie‐Talarek, Virginie Gonzalez, Lucie Beaudoin, Noémie Sénot, Corinne Miceli‐Richard, Yannick Allanore, Agnès Lehuen, Jerôme Avouac
Journal: Arthritis & Rheumatology (2025)

Mucosal‐associated invariant T (MAIT) cells are innate‐like T cells defined by their semi‐invariant T cell receptor (TCR) and restriction by the MHC class I‐related molecule (MR1). These cells are primarily activated by microbial‐derived metabolites presented by MR1 or by cytokines. Upon activation, MAIT cells rapidly produce pro‐inflammatory cytokines, including IFN‐γ, TNF‐α, and IL‐17, and secrete cytotoxic molecules such as granzyme B. Due to their ability to interact with microbiota and accumulate in inflamed tissues, MAIT cells have attracted great interest in autoimmune and inflammatory diseases. In this review, we summarize recent findings on MAIT cells in major rheumatic diseases, including rheumatoid arthritis, spondyloarthritis, psoriatic arthritis, systemic lupus erythematosus, systemic sclerosis, primary Sjögren syndrome, and dermatomyositis. Circulating MAIT cells frequency is reduced in these diseases. Interestingly, the residual MAIT cells exhibit an activated profile and increased cytokine‐producing capacity in some conditions. Moreover, an enrichment of MAIT cells in inflamed tissues is described in rheumatoid arthritis, spondyloarthritis, psoriatic arthritis, and primary Sjögren syndrome. This pattern suggests that MAIT cells may migrate from the circulation to inflamed tissues, contributing to local immune responses. Furthermore, they have been shown to play a critical role in disease progression in two mouse models. All these findings suggest an involvement of MAIT cells in inflammatory rheumatologic diseases and their potential therapeutic target.
Light‐Responsive Oxygen Generation from <i>Chlorella</i> Hydrogels for Facial Nerve Injury Recovery: Crosstalk between M1/M2 Macrophages and Schwann Cells
Authors: Guihua Wei, Xi Li, Mengqi Huang, Haoyan Wang, Zaiqi Li, Shuxin Qu
Journal: Advanced Healthcare Materials (2025)

Abstract Facial nerve injury (FNI), hindered by hypoxic microenvironments limiting Schwann cell (SCs) repair potential, remains a therapeutic challenge. We developed light‐responsive Chlorella hydrogels (C‐Gel) to modulate oxygen release and inflammation. In vitro, light‐activated C‐Gel enhanced RSC96 SC proliferation, migration, and secretion while reducing reactive oxygen species (ROS), hypoxia‐inducible factor‐1α (HIF‐1α), tumor necrosis factor‐alpha (TNF‐α), and interleukin‐6 (IL‐6). It also shifted macrophage polarization from pro‐inflammatory M1 (inducible nitric oxide synthase (iNOS) + /TNF‐α + ) to anti‐inflammatory M2 (arginase‐1 (Arg‐1) + /IL‐10 + ), with M2‐conditioned mediumboosting SCs production of neurotrophic factors (nerve growth factor, NGF; glial cell line‐derived neurotrophic factor, GDNF), adhesion molecules (neural cell adhesion molecule‐1, NCAM‐1), regeneration‐associated proteins (c‐JUN), and myelin components (myelin basic protein, MBP; myelin‐associated glycoprotein, MAG). In vivo, C‐Gel‐light therapy improved behavioral recovery in FNI rats, suppressed inflammation (ROS/HIF‐1α/TNF‐α), and enhanced SC‐mediated remyelination (S100 calcium‐binding protein, S100; neurofilament 200, NF200). RNA sequencing identified upregulated phosphoinositide 3‐kinase‐protein kinase (PI3K‐Akt) and calcium ion (Ca² + ) signaling pathways. This oxygen‐regulating, immunomodulatory biomaterial offers a dual‐action strategy to advance FNI rehabilitation by synergistically optimizing the regenerative microenvironment.
NIR‐II‐Responsive Chainmail Nanocatalysts for Spatiotemporally Controlled Enzymatic Tumor Therapy
Authors: Hongji Liu, Zhenxing Wang, Xinyue Hu, Shanshan Rao, Hui Wang, Hui Xie
Journal: Advanced Healthcare Materials (2025)

Abstract The clinical translation of metal‐based peroxidase‐like nanozymes for antitumor therapy faces two critical challenges: off‐target catalytic activation and suboptimal hydroxyl radical (•OH) generation efficiency. To address these limitations, an innovative chainmail nanocatalyst featuring nitrogen‐doped carbon‐encapsulated nanoceria is developed, which combines spatial confinement effects with photo‐trigger catalytic enhancement. The graphitic carbon shell serves as a physical barrier that effectively isolates metallic cerium from the biological environment, reducing nonspecific catalytic activation by 100% compared to bare nanoceria. Remarkably, under 1064 nm laser irradiation, electrons of cerium species can penetrate the carbon confinement through quantum tunneling effects, activating multiple enzymatic pathways. Vacancy engineering further optimizes the Ce 3+ /Ce 4+ redox pair ratio (1.75 vs 0.44 in pristine nanoceria), establishing an electron reservoir that facilitates catalytic amplification of H 2 O 2 ‐to‐•OH conversion and glutathione oxidase‐mimicking activity for tumor microenvironment remodeling. This dual mechanism synergistically elevates intracellular oxidative stress while preserving normal tissue viability. In vivo evaluations demonstrate that the photoactivated nanocatalyst exhibits remarkable tumor suppression efficacy, prolonging the survival duration of tumor‐bearing mice from 33 days to 70 days. The light‐gated chainmail architecture provides a paradigm for spatiotemporally controlled catalytic therapy, resolving the critical dilemma between catalytic potency and biological specificity in nanozyme design.
A 3D Co‐Culture System Inspired by Fracture Healing Cell Interactions for Bone Tissue Engineering
Authors: Jicenyuan Wu, Yuxuan Wang, Liang Wang, Wenjia Xie, Qianbing Wan, Jian Wang, Junyu Chen, Xibo Pei, Zhou Zhu
Journal: Advanced Healthcare Materials (2025)

Abstract Peri‐bone fibroblasts play a crucial role in regulating bone regeneration during early fracture healing. Inspired by the synergy between osteoblasts and fibroblasts at fracture sites, a biomimetic three‐dimensional (3D) indirect co‐culture system is developed, comprising a 3D scaffold and co‐cultured cells. To mimic cellular interactions in the fracture healing zone, the scaffold features an inner–outer ring structure with communication channels that support indirect cell co‐culture. This setup provides fibroblasts and osteoblasts with a 3D culture environment resembling the in vivo extracellular matrix, enhancing intercellular signaling while minimizing risks of direct contact. Mechanically tunable bioinks are formulated by incorporating hyaluronic acid methacrylate (HAMA) hydrogel into gelatin methacryloyl (GelMA) hydrogel to construct the scaffold. The optimal co‐culture ratio is established in vitro, where fibroblasts are found to regulate the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) via zinc ion transport mechanisms. In vivo validations are conducted, including ectopic bone formation in nude mice and bone regeneration in rat cranial defect and tooth extraction socket models. This 3D indirect co‐culture system enhances osteogenesis by promoting functional fibroblast–osteoblast interactions, offering a novel platform for co‐culture studies and a promising strategy for clinical bone regeneration applications.
A NIR‐Responsive Deep Penetration Phototherapy Strategy for Treating Infected Skin Defect via Antibacterial Effect and Inflammation Elimination
Authors: Jinze Song, Wenxin Liu, Li Yang, Xiao Sun, Liangliang Xie, Jiawei Li, Ling Xu, Alideertu Dong
Journal: Advanced Healthcare Materials (2025)

Abstract The increasing severity of antibiotic resistance and the delayed healing of infected wounds have triggered an arduous challenge that threatens human health. Instantly, quiet a few novel, efficient, and safe antibacterial strategies are urgently needed to be explored. In this study, a NIR‐activated antibacterial nanocomposite (RB/UCNPs@BP) integrating rose bengal‐sensitized upconversion nanoparticles (RB/UCNPs) and black phosphorus (BP) is developed for promoting infection wound healing. The photodynamic therapy (PDT) and photothermal therapy (PTT) are employed here for synergistic antibacterial action, while UCNPs further improve the penetration depth of irradiation and treatment efficiency. More importantly, the typical biodegradability of BP confers reduced resistance on nanocomposites through residual‐free antimicrobial methods. The results show that RB/UCNPs@BP significantly inhibits the growth of both Escherichia coli (E.coli) and Staphylococcus aureus (S.aureus) via enhanced PDT and PTT. Besides, the infected wounds achieve better healing by accelerating fibroblast proliferation and migration, reducing inflammatory cell infiltration, and promoting neuronal regeneration and angiogenesis. This study provides a promising and anti‐resistant strategy with light‐triggered antibacterial and anti‐inflammatory activities that can promote the regeneration of infected skin tissue.
Polymer‐Conjugated SOD‐Pt⁰ Micelles Enhance ROS Cascade Scavenging to Alleviate Ischemia‐Reperfusion Injury During Kidney Transplantation
Authors: Shengzhou Li, Fei Duan, Zhiwen Qiu, Zhuofan Nan, Xiangqian Cao, Chenkai Yang, Wei Li, Bing Shen
Journal: Advanced Healthcare Materials (2025)

Abstract Ischemia‐reperfusion injury (IRI) during kidney transplantation is linked to oxidative stress induced by excessive reactive oxygen species (ROS), which causes the injury of transplanted kidney, leading to further intensified organ shortages. Protein‐based antioxidants have been developed for ROS scavenging via cascade biocatalyst. The in situ growth of metal nanozymes on proteins effectively decreases the steric hindrance between active sites, improving the efficiency of cascade biocatalysts. However, the poor stability of protein during the process of preparation and intracellular delivery leads to low therapeutic effects. In this study, three different functional polymers are conjugated to SOD for the formation of micelles. Surprisingly, it is found that the conjugated ultra‐acid sensitive polymer efficiently preserves the enzymatic activity of SOD, due to great endo/lysosomal escape capacity. Subsequently, SOD micelles (SOE) are used as a template to prepare SOE‐Pt 0 (SOEP) through in situ growth of Pt 0 with vicinal enzymatic active sites. The preparation process minimally impacts on the activity of SOD, owing to improved stability. The system exhibits effective cascade ROS scavenging, significantly reducing kidney damage and inflammation caused by IRI. The research offers a novel approach for addressing IRI challenges in organ transplantation and provides a promising strategy to mitigate organ shortages.
An All‐In‐One Dendrobium Ionic Hydrogel with Wound Microenvironment Remodeling for Promoting Diabetic Wound Healing
Authors: Beige Zong, Yongquan Lu, Zhongfu Li, Lian Pan, Peng Zhao, Wei Li, Kaiyong Cai
Journal: Advanced Healthcare Materials (2025)

Abstract Diabetic wounds pose a complex clinical challenge due to their intricate pathological microenvironment and delayed healing process. To address this challenge, this work has developed a multifunctional all‐in‐one ionic hydrogel through dynamic Schiff base and amide bond crosslinking between the aldehyde groups on oxidized sodium alginate (OSA) and the amino groups on 1‐(3‐aminopropyl)‐3‐(4‐vinylbenzyl) imidazole salts, in which Dendrobium officinale polysaccharides (DOP) is embedded via electrostatic interactions in the form of ionic hydrogel (OPP@DOP). The OSA and polyionic liquid enable good biocompatibility, high water containment, high swelling rate, moderate adhesion, antioxidant activity, electrical conductivity, and efficient antibacterial activity against MRSA at early stages. A sustained release of DOP is then realized and exhibits anti‐inflammation, antioxidant, further promoted angiogenesis via AKT signaling pathway. These effects significantly promote re‐epithelialization and collagen deposition and increase angiogenesis in wound tissue. Besides, it regulates the macrophage phenotype from the M1 subtype to the M2 subtype and reduces the expression levels of inflammatory factors, thus accelerating wound healing. The development of this multifunctional ionic hydrogel harnesses the profound potential of traditional Chinese medicine, offering a promising potential for treating diabetic wounds.
Smart Silk‐Based In Situ Sol‐Gel Modulates Rectal Microenvironment for Effective Ulcerative Colitis Alleviation
Authors: Perumal Ramesh Kannan, Liuting Chen, Yudie Lv, Ruibo Zhao, Yeting Hu, M. Zubair Iqbal, Qianqian Han, Xiangdong Kong, Yao Li
Journal: Advanced Healthcare Materials (2025)

Abstract Ulcerative colitis (UC) is a chronic inflammatory bowel disease, with untreated cases often progressing to colorectal cancer. Current treatments aim to induce inflammatory remission but often neglect the surrounding microenvironment, which significantly impairs mucosal healing and contributes to treatment failures. This study presents a novel silk fibroin‐based fucoidan (SFU) in situ rectal gel, with sol‐gel transition confirmed through rheological analysis under physiological pH and temperature conditions. The SFU gel exhibits strong antioxidant activity, achieving a DPPH radical scavenging rate of 73.3 ± 1.52%. The gel efficiently reduces reactive oxygen species (ROS) and nitric oxide (NO) production, demonstrating its reliable antioxidant effects. In a DSS‐induced UC mouse model, SFU effectively alleviates colitis symptoms, including weight loss and disease activity index (DAI) reduction, with improved stool consistency and reduced rectal bleeding. Moreover, SFU therapy reprograms macrophages from proinflammatory M1 to anti‐inflammatory M2 phenotypes, significantly lowering IL‐6 and TNF‐α levels, suggesting anti‐inflammatory properties. Furthermore, SFU increased tight junction proteins Occludin‐1 and ZO‐1, indicating gut mucosal barrier integrity. SFU treatment restores goblet cells and mucin production while preventing fibrosis, demonstrating its potential as a natural therapy for UC treatment.
A Polysaccharide‐Based Self‐Gelling Powder With Antibacterial and Antioxidant Capacities for Acute Hemostasis and Efficient Infected Wound Healing
Authors: Wei Li, Jiahao Yang, Weishi Kong, Peng Fan, Dingding Guan, Yulu Bao, Guosheng Wu, Shige Wang, Yu Sun
Journal: Advanced Healthcare Materials (2025)

Abstract Traumatic wounds with severe bleeding and heavy contamination present significant challenges, including delayed healing and high infection rates. An ideal wound dressing should achieve rapid hemostasis, provide antibacterial activity, and regulate the microenvironment to facilitate tissue regeneration. To address these needs, this work develops a novel selfgelling powder (COT) comprising carboxymethyl chitosan (CMCS), oxidized konjac glucomannan (OKGM), and tannic acid (TA). The COT powder exhibits rapid gelation upon contact with water, forming a COT hydrogel, making it suitable for controlling hemorrhage across diverse wound sites. In vitro and in vivo studies confirm that the COT possesses broad‐spectrum antibacterial activity and potent free radical scavenging capacity. When applied to infected wounds, the COT hydrogel significantly reduces oxidative stress and inflammatory responses while promoting angiogenesis and re‐epithelialization. Transcriptomic analysis suggests that COT modulates wound inflammation, likely by suppressing the NF‐κB signaling pathway. Given its favorable mechanical properties, strong antibacterial/antioxidant effects, ease of application, and rapid hemostatic performance, the COT emerges as a promising translational wound dressing for managing infected wounds.
Quantum machine learning-based electrokinetic mining for the identification of nanoparticles and exosomes with minimal training data
Authors: Abhimanyu Thakur, Pedro Correia Santos Bezerra, None Abhishek, Shihao Zeng, Kui Zhang, Werner Treptow, Alexander Luna, Urszula Dougherty, Akushika Kwesi, Isabella R. Huang, Christine Bestvina, Marina Chiara Garassino, Fuyu Duan, Yash Gokhale, Bin Duan, Yin Chen, Qizhou Lian, Marc Bissonnette, Jianpan Huang, Huanhuan Joyce Chen
Journal: Bioactive Materials (2025)
Text messaging with or without financial incentives versus a waitlist control for weight loss in men: cost-effectiveness analysis of the Game of Stones randomised controlled trial
Authors: Abraham M. Getaneh, Marjon van der Pol, Dwayne Boyers, Alison Avenell, Seonaidh Cotton, Stephan U. Dombrowski, Cindy M. Gray, Frank Kee, Lisa Macaulay, Michelle McKinley, Catriona O’Dolan, James Swingler, Claire Torrens, Katrina Turner, Graeme MacLennan, Pat Hoddinott
Journal: The Lancet Regional Health - Europe (2025)
Corrigendum to “Glands of Moll: history, current knowledge and their role in ocular surface homeostasis and disease” [Progr. Retin. Eye Res. 106 (2025) 101362]
Authors: Michael Stopfer, Ingrid Zahn, Katharina Jüngert, Gerhard Aumüller, Frans L Moll, Martin Schicht, Helen P Makarenkova, Cintia S de Paiva, Friedrich P Paulsen
Journal: Progress in Retinal and Eye Research (2025)
RNA methylation in retrotransposon control
Authors: Basil Barter, Jungnam Cho
Journal: Trends in Genetics (2025)

N6-methyladenosine (m6A) regulates retrotransposon activity, shifting between repression and activation across different species and developmental stages. It promotes RNA decay, sequestration, or stability, influencing genome integrity, adaptation, and disease. This article explores the dual role of m6A in retrotransposon control, highlighting its evolutionary significance in genome regulation and cellular differentiation.