tbuckley/cabot-search huggingface dataset:
Incidence, prevalence, and mortality of sarcoidosis in England: a population-based study
Authors: Katie Bechman, Mark D Russell, Kathryn Biddle, Mark Gibson, Maryam Adas, Zijing Yang, Samir Patel, Alex Dregan, Sarah Walsh, Peter Brex, Amit Patel, Katherine J Myall, Sam Norton, Surinder S Birring, James Galloway
Journal: The Lancet Regional Health - Europe (2025)
Strengthening resilience to emerging vector-borne diseases in Europe: lessons learnt from countries facing endemic transmission
Authors: Gina E C Charnley, Tilly Alcayna, Alex Almuedo-Riera, Christiana Antoniou, Athanase Badolo, Frederic Bartumeus, Laura-Lee Boodram, Rubén Bueno-Marí, Claudia Codeço, Flavio Codeço Coelho, Federico Costa, Horace Cox, Nabil Haddad, Nurulhusna Ab Hamid, Pattamaporn Kittayapong, Gülay Korukluoğlu, Antonios Michaelakis, Rafael Maciel-de-Freitas, Tomas Montalvo, Jose Muñoz, Silvia Sauleda Oliveras, John R B Palmer, Carlos Jesús Barboza Pizard, Guilherme S Ribeiro, Rachel Lowe
Journal: The Lancet Regional Health - Europe (2025)
Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study
Authors: Ouli Xie, Rebecca H Chisholm, Leo Featherstone, An N T Nguyen, Andrew J Hayes, Magnus G Jespersen, Cameron Zachreson, Nefel Tellioglu, Gerry Tonkin-Hill, Ravindra Dotel, Stephanie Spring, Alice Liu, Alexander Rofe, Sebastian Duchene, Norelle L Sherry, Robert W Baird, Vicki L Krause, Deborah C Holt, Lachlan J M Coin, Neela Joshi Rai, Matthew V N O'Sullivan, Katherine Bond, Jukka Corander, Benjamin P Howden, Tony M Korman, Bart J Currie, Steven Y C Tong, Mark R Davies
Journal: The Lancet Microbe (2025)
Early-Life Wheeze Trajectories Are Associated with Distinct Asthma Transcriptomes Later in Life
Authors: Kieran J Phelan, Krishna M Roskin, Jeffrey W Burkle, Wan-Chi Chang, Lisa J Martin, Jocelyn M Biagini, Latha Satish, David B Haslam, Daniel Spagna, Seth Jenkins, Elsie Parmar, Leonard B Bacharier, Tebeb Gebretsadik, Michelle Gill, Diane R Gold, Daniel J Jackson, Christine C Johnson, Susan V Lynch, Kathryn E McCauley, Chris G McKennan, Rachel Miller, Carole Ober, Dennis R Ownby, Patrick H Ryan, Nathan Schoettler, Sweta Singh, Cynthia M Visness, Matthew C Altman, James E Gern, Gurjit K Khurana Hershey
Journal: Journal of Allergy and Clinical Immunology (2025)
Cisplatin-induced Disruption of Mitochondrial Divisome Leads to Enhanced Cisplatin Resistance in Cholangiocarcinoma
Authors: Guo-Yue Lv, Wen-Tao Mu, Yan-Nan Cao, Xiao-Dong Sun, Feng Wei, Kai-Yuan Chai, Bo Huang, Jian-Peng Zhou, Chuan-Lei Wang, Ming-Yue Li, Xiao-Hong Du, Wei Qiu, Meng Wang, Xiao-Ju Shi, Jun-Feng Ye, Xing-Kai Liu, He-Yu Huang, Yu-Guo Chen, Zhao-Ming Gou, Ping Zhang, Ya-Hui Liu, Guang-Yi Wang, Zhong-Qi Fan
Journal: Journal of Hepatology (2025)
Minoxidil toxicosis in cats and dogs: a scoping review and call to action
Authors: Eric McMullen, Grace Xiong, Daniel G Rayner, Shakira Brathwaite, Dea Metko, Shanti Mehta, Sana Gupta, Maria-Victoria Walker-Genovese, Stephanie W Rayner, Izabella Witelus, Shireen Dumont, Ilya Mukovozov, Cathryn Sibbald, Jeffrey Donovan
Journal: Journal of the American Academy of Dermatology (2025)
Effect, tolerability, and safety of exclusive palatable elemental diet in patients with intestinal microbial overgrowth
Authors: Ali Rezaie, Bianca W Chang, Juliana de Freitas Germano, Gabriela Leite, Ruchi Mathur, Krystyna Houser, Ava Hosseini, Daniel Brimberry, Mohamad Rashid, Sepideh Mehravar, M J Villanueva-Millan, Maritza Sanchez, Stacy Weitsman, Cristina M Fajardo, Ignacio G Rivera, Joo Lijin, Yin Chan, Gillian M Barlow, Pimentel Mark
Journal: Clinical Gastroenterology and Hepatology (2025)

Elemental diets (EDs) have desirable safety and efficacy profiles in several clinical settings partly due to modulation of gut microbiome. Palatability of EDs remains the main barrier to compliance/adherence, and their effect has not been prospectively explored in microbiome-driven disorders such as small intestinal bacterial overgrowth (SIBO) and intestinal methanogen overgrowth (IMO). We aimed to assess the effect, tolerance, and safety of a novel palatable ED (PED) in subjects with IMO and/or SIBO. Adult subjects with positive lactulose breath tests (LBT) for SIBO and/or IMO completed one week of screening, 2 weeks of exclusive oral PED, and 2 weeks of follow-up during reintroduction of regular diet. Primary endpoint was changes in stool microbiome after PED and reintroduction of regular diet. Secondary endpoints included tolerability, rate of normalization of LBT, change in stool form based on daily diary and artificial intelligence-analyzed images, symptomatic response, and adverse events. All 30 enrolled subjects tolerated the PED and completed the trial. Several taxonomic differences were detected including decreased relative abundance of Prevotella_9 and Fusobacterium. Abundance of Methanobrevibacter smithii decreased at the end of the trial and correlated with average daily methane levels (p=0.024, r=0.489). Maximum methane levels (41±35 to 12±15 ppm, p<0.001) and hydrogen rise (43±42 to 12±11 ppm, p<0.001) dropped significantly, with 73% normalizing their LBT. Adequate global relief of symptoms was reported in 83% of subjects. No serious or severe adverse events were observed. PED significantly impacts the gut microbiome. Tolerance to EDs improve with enhanced palatability. Larger studies with longer follow-up are needed to assess response durability. (ClinicalTrials.gov ID: NCT05978973).
A proximity-induced chimera platform for targeted protein arginine methylation
Authors: Yanlin Jian, Tianyang Zhou, Chendong Guo, Yibo Gao, Chen Yao, Zixi Wang, Xuehan Jiang, Ke Wang, Jian Ma, Yang Gao, Yizeng Fan, Jing Liu, Bohan Ma, Lei Li
Journal: Acta Pharmaceutica Sinica B (2025)
RBM14 enhances transcriptional activity of p23 regulating CXCL1 expression to induce lung cancer metastasis
Authors: Wen Zhang, Yulin Peng, Meirong Zhou, Lei Qian, Yilin Che, Junlin Chen, Wenhao Zhang, Chengjian He, Minghang Qi, Xiaohong Shu, Manman Tian, Xiangge Tian, Yan Tian, Sa Deng, Yan Wang, Xiaokui Huo, Zhenlong Yu, Xiaochi Ma
Journal: Acta Pharmaceutica Sinica B (2025)
Nanomedicine-driven tumor glucose metabolic reprogramming for enhanced cancer immunotherapy
Authors: Chenwei Jiang, Minglu Tang, Yun Su, Junjie Xie, Qi Shang, Mingmei Guo, Xiaoran An, Longfei Lin, Ruibin Wang, Qian Huang, Guangji Zhang, Hui Li, Feihu Wang
Journal: Acta Pharmaceutica Sinica B (2025)
Deubiquitinase USP13 alleviates doxorubicin-induced cardiotoxicity through promoting the autophagy-mediated degradation of STING
Authors: Liming Lin, Jibo Han, Diyun Xu, Zimin Fang, Bozhi Ye, Jinfu Qian, Xue Han, Julian Min, Xiaohong Long, Gaojun Wu, Guang Liang
Journal: Acta Pharmaceutica Sinica B (2025)
Unveiling the metabolic fate of drugs through metabolic reaction-based molecular networking
Authors: Haodong Zhu, Xupeng Tong, Qi Wang, Aijing Li, Zubao Wu, Qiqi Wang, Pei Lin, Xinsheng Yao, Liufang Hu, Liangliang He, Zhihong Yao
Journal: Acta Pharmaceutica Sinica B (2025)
Psychological stress-activated NR3C1/NUPR1 axis promotes ovarian tumor metastasis
Authors: Bin Liu, Wen-Zhe Deng, Wen-Hua Hu, Rong-Xi Lu, Qing-Yu Zhang, Chen-Feng Gao, Xiao-Jie Huang, Wei-Guo Liao, Jin Gao, Yang Liu, Hiroshi Kurihara, Yi-Fang Li, Xu-Hui Zhang, Yan-Ping Wu, Lei Liang, Rong-Rong He
Journal: Acta Pharmaceutica Sinica B (2025)
Metabolic reprogramming nanomedicine potentiates colon cancer sonodynamic immunotherapy by inhibiting the CD39/CD73/ADO pathway
Authors: Yuanyuan Zhang, Weiwei Jin, Zhichao Deng, Bowen Gao, Yuanyuan Zhu, Junlong Fu, Chenxi Xu, Wenlong Wang, Ting Bai, Lianying Jiao, Hao Wu, Mingxin Zhang, Mingzhen Zhang
Journal: Acta Pharmaceutica Sinica B (2025)
Peroxiredoxin‐4, a marker of systemic oxidative stress, is associated with incident heart failure
Authors: Navin Suthahar, Sanne G.J. Mourmans, Anouk Achten, Joseph Pierre Aboumsallem, Wouter C. Meijers, Nils Bomer, Isabella Kardys, Ron T. Gansevoort, Stephan J.L. Bakker, Jerremy Weerts, Etto C. Eringa, Kevin Damman, Vanessa van Empel, Rudolf A. de Boer
Journal: European Journal of Heart Failure (2025)

Abstract Aims Oxidative stress is known to be involved in the pathophysiology of heart failure (HF). To assess oxidative stress, direct quantification of reactive oxygen species would be ideal but this is not feasible due to their short half‐lives. Antioxidant enzymes such as peroxiredoxins, produced as a direct response to oxidative stress, mirror the process and can be more easily quantified. The aim of this study was to examine whether circulating peroxiredoxin‐4 (Prx4), a marker of systemic oxidative stress, associates with incident HF and its subtypes. Methods and results We included a total of 8199 individuals from the Prevention of REnal and Vascular End‐stage Disease (PREVEND) community‐based cohort (mean age: 49.8 years; 50.1% women). During a median follow‐up of 12.6 years, 349 (4.3%) HF events occurred of which 118 (33.8%) had HF with preserved ejection fraction. In a Cox proportional hazards model adjusting for age, sex, smoking, diabetes, hypertension, obesity, total and high‐density lipoprotein cholesterol, cholesterol‐lowering medication and renal disease, Prx4 was significantly associated with incident HF (hazard ratio [HR] per 1 standard deviation increase in log‐Prx4: 1.22; 95% confidence interval [CI] 1.09–1.36; p &lt; 0.001). Among HF subtypes, Prx4 remained associated with incident HF with preserved (HR 1.27; 95% CI 1.05–1.53) as well as reduced ejection fraction (HR 1.19; 95% CI 1.04–1.37), with no significant difference between the subtypes ( p = 0.64). Conclusion Circulating Prx4 associates with the risk of developing HF, both with preserved and reduced ejection fraction. Future studies should examine whether Prx4 can serve as a real‐time marker of oxidative stress status.
Efficacy and safety of ultrasound combined with microbubbles for treating retinal artery occlusion in rats
Authors: Sen Fan, Yonghong Tang, Xinying Hu, Mingmin Qin, Yuancheng Zhao, Xiaofan Chen, Huan Zou, Hui Gao, Peijing Li, Haiwei Xu, Rongdi Yuan
Journal: Journal of Controlled Release (2025)
Tranexamic acid contamination and bloodstream infections due to Burkholderia cepacia complex and Pseudomonas aeruginosa: implications for clinical trials and good manufacturing processes for investigational products
Authors: Trisha Peel, Jessica Wisniewski, Jane Hawkey, Ravali Theegala, Katherine Pragastis, Anton Y Peleg, Sophia Wallace, Paul Myles
Journal: Clinical Microbiology and Infection (2025)
A scoping review of OMOP CDM adoption for cancer research using real world data
Authors: Liwei Wang, Andrew Wen, Sunyang Fu, Xiaoyang Ruan, Ming Huang, Rui Li, Qiuhao Lu, Heather Lyu, Andrew E Williams, Hongfang Liu
Journal: npj Digital Medicine (2025)

The Observational Medical Outcomes Partnership (OMOP) common data model (CDM) supports large-scale research by enabling distributed network analyses. However, the breadth of its adoption in cancer research is not well understood. We conducted a scoping review to describe the adoption of the OMOP CDM in cancer research. A total of 49 unique articles were included in the review, with 30 on the data analysis theme, and 20 on the infrastructure theme. This review highlighted that while the OMOP CDM ecosystem has enabled successful data support for cancer research, particularly for collaborative studies, ongoing model development and iterative improvement remain needed to fulfill additional research data needs. Expanding disease sites, specifically for rare cancers, integrating more diverse types of data sources, improving data quality, adopting advanced analytics methodology, and increasing multisite evaluations serve as important opportunities to facilitate secondary usage of observational data in future cancer research.
A methodological systematic review of validation and performance of sepsis real-time prediction models
Authors: Zichen Wang, Wen Wang, Che Sun, Jili Li, Shuangyi Xie, Jiayue Xu, Kang Zou, Yinghui Jin, Siyu Yan, Xuelian Liao, Yan Kang, Craig M Coopersmith, Xin Sun
Journal: npj Digital Medicine (2025)

Sepsis real-time prediction models (SRPMs) provide timely alerts and may improve patient outcomes but face limited clinical adoption due to inconsistent validation methods and potential biases. Comprehensive evaluation, including external full-window validation with model- and outcome-level metrics, is crucial for real-world effectiveness, yet performance evidence remains scarce. This study systematically reviewed SRPM performance across validation methods, analyzing 91 studies from multiple databases. Only 54.9% applied full-window validation with both metric types. Performance decreased under external and full-window validation, with median AUROCs of 0.886 and 0.861 at 6- and 12-hours pre-onset, dropping to 0.783 in full-window external validation. Median Utility Scores declined from 0.381 in internal to -0.164 in external validation. Combining AUROC and Utility Score identified top-performing SRPMs in 18.7% of studies. Hand-crafted features significantly improved performance. Future research should focus on multi-center datasets, hand-crafted features, multi-metric full-window validation, and prospective trials to support clinical implementation.
An engineered M2 macrophage-derived exosomes-loaded electrospun biomimetic periosteum promotes cell recruitment, immunoregulation, and angiogenesis in bone regeneration
Authors: Zhuohao Wen, Shuyi Li, Yi Liu, Xueyan Liu, Huiguo Qiu, Yuejuan Che, Liming Bian, Miao Zhou
Journal: Bioactive Materials (2025)
The impact of gut microbial short-chain fatty acids on colorectal cancer development and prevention
Authors: Boobalan Thulasinathan, Kanve N. Suvilesh, Sumanas Maram, Erik Grossmann, Yezaz Ghouri, Emma Pernas Teixeiro, Joshua Chan, Jussuf T. Kaif, Satyanarayana Rachagani
Journal: Gut Microbes (2025)

Cancer is a long-term illness that involves an imbalance in cellular and immune functions. It can be caused by a range of factors, including exposure to environmental carcinogens, poor diet, infections, and genetic alterations. Maintaining a healthy gut microbiome is crucial for overall health, and short-chain fatty acids (SCFAs) produced by gut microbiota play a vital role in this process. Recent research has established that alterations in the gut microbiome led to decreased production of SCFA's in lumen of the colon, which associated with changes in the intestinal epithelial barrier function, and immunity, are closely linked to colorectal cancer (CRC) development and its progression. SCFAs influence cancer progression by modifying epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNA functions thereby affecting tumor initiation and metastasis. This suggests that restoring SCFA levels in colon through microbiota modulation could serve as an innovative strategy for CRC prevention and treatment. This review highlights the critical relationship between gut microbiota and CRC, emphasizing the potential of targeting SCFAs to enhance gut health and reduce CRC risk.
Caveolin-1: an ambiguous entity in breast cancer
Authors: Naveen Chintalaramulu, Dhirendra Pratap Singh, Biplov Sapkota, Dayanidhi Raman, Suresh Alahari, Joseph Francis
Journal: Molecular Cancer (2025)

Breast cancer (BC) is the most frequently diagnosed cancer in women and the second leading cause of death from cancer among women. Metastasis is the major cause of BC-associated mortality. Accumulating evidence implicates Caveolin-1 (Cav-1), a structural protein of plasma membrane caveolae, in BC metastasis. Cav-1 exhibits a dual role, as both a tumor suppressor and promoter depending on the cellular context and BC subtype. This review highlights the role of Cav-1 in modulating glycolytic metabolism, tumor-stromal interactions, apoptosis, and senescence. Additionally, stromal Cav-1's expression is identified as a potential prognostic marker, offering insights into its contrasting roles in tumor suppression and progression. Furthermore, Cav-1's context-dependent effects are explored in BC subtypes including hormone receptor-positive, HER2-positive, and triple-negative BC (TNBC). The review further delves into the role of Cav-1 in regulating the metastatic cascade including extracellular matrix interactions, cell migration and invasion, and premetastatic niche formation. The later sections discuss the therapeutic targeting of Cav-1 by metabolic inhibitors such as betulinic acid and Cav-1 modulating compounds. While Cav-1 may be a potential biomarker and therapeutic target, its heterogeneous expression and context-specific activity necessitates further research to develop precise interventions. Future studies investigating the mechanistic role of Cav-1 in metastasis may pave the way for effective treatment of metastatic BC.
Telehealth virtual reality intervention reduces chronic pain in a randomized crossover study
Authors: Luana Colloca, Anna Han, Rachel Massalee, Nandini Raghuraman, Rachel L Cundiff-O'Sullivan, Giancarlo Colloca, Yang Wang
Journal: npj Digital Medicine (2025)

Abstract The efficacy of telehealth Virtual Reality (VR) for chronic pain, a promising digital intervention, remains underexplored due to methodological challenges. In a 5-week crossover trial, we compared VR to matched audio content control in individuals with chronic pain. VR significantly reduced pain intensity, anxiety, and pain interference while improving mood and sleep quality. Findings highlight the potential of telehealth-based VR for addressing real-world challenges in managing chronic pain. ISRCTN12473220 (07/18/2023).
Reutericyclin, a specialized metabolite of <i>Limosilactobacillus reuteri</i> , mitigates risperidone-induced weight gain in mice
Authors: Fatima A. Aboulalazm, Alexis B. Kazen, Orlando deLeon, Susanne Müller, Fatima L. Saravia, Valery Lozada-Fernandez, Matthew A. Hadiono, Robert F. Keyes, Brian C. Smith, Stephanie L. Kellogg, Justin L. Grobe, Tammy L. Kindel, John R. Kirby
Journal: Gut Microbes (2025)

The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.
The intrinsic expression of NLRP3 in Th17 cells promotes their protumor activity and conversion into Tregs
Authors: Théo Accogli, Christophe Hibos, Lylou Milian, Mannon Geindreau, Corentin Richard, Etienne Humblin, Romain Mary, Sandy Chevrier, Elise Jacquin, Antoine Bernard, Fanny Chalmin, Catherine Paul, Berhard Ryffel, Lionel Apetoh, Romain Boidot, Mélanie Bruchard, François Ghiringhelli, Frédérique Vegran
Journal: Cellular and Molecular Immunology (2025)

Abstract Th17 cells can perform either regulatory or inflammatory functions depending on the cytokine microenvironment. These plastic cells can transdifferentiate into Tregs during inflammation resolution, in allogenic heart transplantation models, or in cancer through mechanisms that remain poorly understood. Here, we demonstrated that NLRP3 expression in Th17 cells is essential for maintaining their immunosuppressive functions through an inflammasome-independent mechanism. In the absence of NLRP3, Th17 cells produce more inflammatory cytokines (IFNγ, Granzyme B, TNFα) and exhibit reduced immunosuppressive activity toward CD8+ cells. Moreover, the capacity of NLRP3-deficient Th17 cells to transdifferentiate into Treg-like cells is lost. Mechanistically, NLRP3 in Th17 cells interacts with the TGF-β receptor, enabling SMAD3 phosphorylation and thereby facilitating the acquisition of immunosuppressive functions. Consequently, the absence of NLRP3 expression in Th17 cells from tumor-bearing mice enhances CD8 + T-cell effectiveness, ultimately inhibiting tumor growth.
Lipid droplets restrict phagosome formation in antifungal immunity
Authors: Wanwei Sun, Han Wu, Guimin Zhao, Qing Shui, Lei Zhang, Xiaoxi Luan, Tian Chen, Feng Liu, Yi Zheng, Wei Zhao, Xiaopeng Qi, Bingyu Liu, Chengjiang Gao
Journal: Cellular and Molecular Immunology (2025)
A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat
Authors: Shoucheng Liu, Kui Li, Xiuru Dai, Guochen Qin, Dongdong Lu, Zhaoxu Gao, Xiaopeng Li, Bolong Song, Jianxin Bian, Da Ren, Yongqi Liu, Xiaofeng Chen, Yunbi Xu, Weimin Liu, Chen Yang, Xiaoqin Liu, Shisheng Chen, Jian Li, Bosheng Li, Hang He, Xing Wang Deng
Journal: Nature Genetics (2025)

The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 rDNA units. Genome-wide rearrangements, centromeric elements, transposable element expansion and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, transposable element insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence protein-coding genes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity and provides insights for future wheat research and breeding.