tbuckley/cabot-search huggingface dataset:
Defining lipedema's molecular hallmarks by multi-omics approach for disease prediction in women
Authors: Leon G Straub, Jan-Bernd Funcke, Nolwenn Joffin, Chanmin Joung, Sara Al-Ghadban, Shangang Zhao, Qingzhang Zhu, Ilja L Kruglikov, Yi Zhu, Paul R Langlais, Ruth Gordillo, Karen L Herbst, Philipp E Scherer
Journal: Metabolism (2025)
Early occurrence of hepatic encephalopathy following TIPS-insertion is linked to impaired survival: a multicenter cohort study
Authors: Martin A Kabelitz, Lisa Sandmann, Michael Praktiknjo, Jim B Mauz, Timo Alexander Auer, Tony Bruns, Johannes Chang, Uli Fehrenbach, Jan Hinrichs, Christian Jansen, Roman Klöckner, Johannes Kluwe, Michael Köhler, Carsten Meyer, Felix Piecha, Maike Rebecca Pollmanns, Cristina Ripoll, Michael Schultheiss, Leon Louis Seifert, Fabian Stöhr, Lukas Sturm, Jonel Trebicka, Alexander Zipprich, Christian Labenz, Dominik Bettinger, Benjamin Maasoumy
Journal: Clinical Gastroenterology and Hepatology (2025)
Ion-paired moxifloxacin nanocrystal formulation improves treatment and prevention of ocular infection
Authors: Matthew B Appell, Kiersten Malmberg, Ashwin Pasupathy, Aditya Josyula, Jairo Ortiz, Peter J McDonnell, Nakul Shekhawat, Kunal S Parikh, Laura M Ensign
Journal: Journal of Controlled Release (2025)
Association Between Supplemental Nutrition Assistance Program (SNAP) and Cost-Related Medical Care Delays in Pediatric Atopic Dermatitis: A Cross-Sectional Analysis of the National Health Interview Survey, 1999-2018
Authors: Christopher G Youn, Arash Pour Mohammad, Ann L Marqueling, Dawn H Siegel, Justin M Ko, Gordon H Bae
Journal: Journal of the American Academy of Dermatology (2025)
Erratum to: ‘Inhibition of the renal apical sodium dependent bile acid transporter prevents cholemic nephropathy in mice with obstructive cholestasis’ [J Hepatol (2024) 80:268-281]
Authors: Ahmed Ghallab, Daniela González, Ellen Strängberg, Ute Hofmann, Maiju Myllys, Reham Hassan, Zaynab Hobloss, Lisa Brackhagen, Brigitte Begher-Tibbe, Julia C Duda, Carolin Drenda, Franziska Kappenberg, Joerg Reinders, Adrian Friebel, Mihael Vucur, Monika Turajski, Abdel-Latief Seddek, Tahany Abbas, Noha Abdelmageed, Samy A F Morad, Walaa Morad, Amira Hamdy, Wiebke Albrecht, Naim Kittana, Mohyeddin Assali, Nachiket Vartak, Christoph van Thriel, Ansam Sous, Patrick Nell, Maria Villar-Fernandez, Cristina Cadenas, Erhan Genc, Rosemarie Marchan, Tom Luedde, Peter Åkerblad, Jan Mattsson, Hanns-Ulrich Marschall, Stefan Hoehme, Guido Stirnimann, Matthias Schwab, Peter Boor, Kerstin Amann, Jessica Schmitz, Jan H Bräsen, Jörg Rahnenführer, Karolina Edlund, Saul J Karpen, Benedikt Simbrunner, Thomas Reiberger, Mattias Mandorfer, Michael Trauner, Paul A Dawson, Erik Lindström, Jan G Hengstler
Journal: Journal of Hepatology (2025)
Widespread antibiotic heterotolerance in bacteria remains undetected by resistance assays
Authors: Bram Van den Bergh, Philip Ruelens, Lieze Agten, Laurence Van Moll, Nele Geerts, Laure Verstraete, Sang Nguyen, Linda De Vooght, Natalie Verstraeten, Paul Cos, Jan Michiels
Journal: Drug Resistance Updates (2025)
Epidemiology, Natural History and Treatment of IBD in Africa: A Scoping Review
Authors: Mmeyeneabasi Omede, Asa Itam-Eyo, Albert Park, Joanah Ikobah, Maryam K Ibrahim, Evaristus Chukwudike, Awab Ali-Ibrahim, Melis Lydston, Akwi W Asombang, Ashwin N Ananthakrishnan
Journal: Clinical Gastroenterology and Hepatology (2025)
Linking levels of polyunsaturated fatty acids to acne risk
Authors: Luba Milena Pardo
Journal: British Journal of Dermatology (2025)

Journal Article Accepted manuscript Linking levels of polyunsaturated fatty acids to acne risk Get access Luba Milena Pardo Luba Milena Pardo Department of Dermatology, Erasmus MC Universitair Medisch Centrum Rotterdam, Rotterdam, the Netherlands Corresponding author: Email: [email protected] https://orcid.org/0000-0003-0684-3175 Search for other works by this author on: Oxford Academic Google Scholar British Journal of Dermatology, ljaf094, https://doi.org/10.1093/bjd/ljaf094 Published: 15 March 2025 Article history Received: 09 March 2025 Accepted: 10 March 2025 Published: 15 March 2025
Characteristics and predictors of central nervous system relapse in newly diagnosed acute promyelocytic leukemia in the era of arsenic: a 13-year monocenter cohort study
Authors: Bingqian Jiang, Hongyan Tong, Haitao Meng, Wanzhuo Xie, Wenjuan Yu, Jian Huang, Huafeng Wang, Liangshun You, Liping Mao, Min Yang, Jiejing Qian, Yanling Ren, Chunmei Yang, Liya Ma, Jie Jin, Yinjun Lou
Journal: Blood Cancer Journal (2025)
Superior preclinical efficacy of co-treatment with BRG1/BRM and FLT3 inhibitor against AML cells with FLT3 mutations
Authors: Warren Fiskus, Christopher P. Mill, Jessica Piel, Mike Collins, Murphy Hentemann, Branko Cuglievan, Christine E. Birdwell, Kaberi Das, Hanxi Hou, John A. Davis, Antrix Jain, Anna Malovannaya, Tapan M. Kadia, Naval Daver, Koji Sasaki, Koichi Takahashi, Danielle Hammond, Patrick K. Reville, Lauren B. Flores, Sanam Loghavi, Xiaoping Su, Courtney D. DiNardo, Kapil N. Bhalla
Journal: Blood Cancer Journal (2025)

Although treatment with standard frontline therapies, including a FLT3 inhibitor (FLT3i) reduces AML burden and achieves clinical remissions, most patients with AML with FLT3 mutation relapse due to therapy-resistant stem/progenitor cells. The core ATPases, BRG1 (SMARCA4) and BRM (SMARCA2) of the canonical (c) BAF (BRG1/BRM-associated factor) complex is a dependency in AML cells, including those harboring FLT3 mutations. We have previously reported that treatment with FHD-286, a BRG1/BRM ATPases inhibitor, induces differentiation and loss of viability of AML stem/progenitor cells. Findings of present studies demonstrate that treatment with FHD-286 induces lethality in AML cells, regardless of sensitivity or resistance to FLT3i. This efficacy is associated with the induction of gene-expression perturbations responsible for growth inhibition, differentiation, as well as a reduced AML-initiating potential of the AML cells. Additionally, co-treatment with FHD-286 and FLT3i exerts superior pre-clinical efficacy against AML cells and patient-derived (PD) xenograft (PDX) models of AML with FLT3 mutations.
Contemporary Topics in Myeloproliferative Neoplasms and Myelodysplastic Syndromes: <i>American Journal of Hematology</i> 100th Volume Anniversary Symposium
Authors: Carlo Brugnara, Alessandro Maria Vannucchi, Ayalew Tefferi
Journal: American Journal of Hematology (2025)

The authors have nothing to report. The authors declare no conflicts of interest. The authors have nothing to report.
Silicified curcumin microspheres Combats cardiovascular diseases via Nrf2/HO-1 pathway
Authors: Tianwang Guan, Zhenxing Lu, Rundong Tai, Shuai Guo, Zhaowenbin Zhang, Shaohui Deng, Jujian Ye, Kaiyi Chi, Binghua Zhang, Huiwan Chen, Zhilin Deng, Yushen Ke, Andong Huang, Peier Chen, Chunming Wang, Caiwen Ou
Journal: Bioactive Materials (2025)
Voxel-level radiomics and deep learning for predicting pathologic complete response in esophageal squamous cell carcinoma after neoadjuvant immunotherapy and chemotherapy
Authors: Zhen Zhang, Tianchen Luo, Meng Yan, Haixia Shen, Kaiyi Tao, Jian Zeng, Jingping Yuan, Min Fang, Jian Zheng, Inigo Bermejo, Andre Dekker, Dirk De Ruysscher, Leonard Wee, Wencheng Zhang, Youhua Jiang, Yongling Ji
Journal: Journal for ImmunoTherapy of Cancer (2025)

Background Accurate prediction of pathologic complete response (pCR) following neoadjuvant immunotherapy combined with chemotherapy (nICT) is crucial for tailoring patient care in esophageal squamous cell carcinoma (ESCC). This study aimed to develop and validate a deep learning model using a novel voxel-level radiomics approach to predict pCR based on preoperative CT images. Methods In this multicenter, retrospective study, 741 patients with ESCC who underwent nICT followed by radical esophagectomy were enrolled from three institutions. Patients from one center were divided into a training set (469 patients) and an internal validation set (118 patients) while the data from the other two centers was used as external validation sets (120 and 34 patients, respectively). The deep learning model, Vision-Mamba, integrated voxel-level radiomics feature maps and CT images for pCR prediction. Additionally, other commonly used deep learning models, including 3D-ResNet and Vision Transformer, as well as traditional radiomics methods, were developed for comparison. Model performance was evaluated using accuracy, area under the curve (AUC), sensitivity, specificity, and prognostic stratification capabilities. The SHapley Additive exPlanations analysis was employed to interpret the model’s predictions. Results The Vision-Mamba model demonstrated robust predictive performance in the training set (accuracy: 0.89, AUC: 0.91, sensitivity: 0.82, specificity: 0.92) and validation sets (accuracy: 0.83–0.91, AUC: 0.83–0.92, sensitivity: 0.73–0.94, specificity: 0.84–1.0). The model outperformed other deep learning models and traditional radiomics methods. The model’s ability to stratify patients into high and low-risk groups was validated, showing superior prognostic stratification compared with traditional methods. SHAP provided quantitative and visual model interpretation. Conclusions We present a voxel-level radiomics-based deep learning model to predict pCR to neoadjuvant immunotherapy combined with chemotherapy based on pretreatment diagnostic CT images with high accuracy and robustness. This model could provide a promising tool for individualized management of patients with ESCC.
Novel insights into carbohydrate utilisation, antimicrobial resistance, and sporulation potential in <i>Roseburia intestinalis</i> isolates across diverse geographical locations
Authors: Indrani Mukhopadhya, Jennifer C. Martin, Sophie Shaw, Martin Gutierrez-Torrejon, Nikoleta Boteva, Aileen J. McKinley, Silvia W. Gratz, Karen P. Scott
Journal: Gut Microbes (2025)

Roseburia intestinalis is one of the most abundant and important butyrate-producing human gut anaerobic bacteria that plays an important role in maintaining health and is a potential next-generation probiotic. We investigated the pangenome of 16 distinct strains, isolated over several decades, identifying local and time-specific adaptations. More than 50% of the genes in each individual strain were assigned to the core genome, and 77% of the cloud genes were unique to individual strains, revealing the high level of genome conservation. Co-carriage of the same enzymes involved in carbohydrate binding and degradation in all strains highlighted major pathways in carbohydrate utilization and reveal the importance of xylan, starch and mannose as key growth substrates. A single strain had adapted to use rhamnose as a sole growth substrate, the first time this has been reported. The ubiquitous presence of motility and sporulation gene clusters demonstrates the importance of these phenotypes for gut survival and acquisition of this bacterium. More than half the strains contained functional, potentially transferable, tetracycline resistance genes. This study advances our understanding of the importance of R. intestinalis within the gut ecosystem by elucidating conserved metabolic characteristics among different strains, isolated from different locations. This information will help to devise dietary strategies to increase the abundance of this species providing health benefits.
Long-term exposure to low-level crystalline silica and risk assessment of silicosis: a cohort study
Authors: Dongming Wang, Wenzhen Li, Min Zhou, Jixuan Ma, Yanjun Guo, Weihong Chen
Journal: Thorax (2025)

Background High-level exposure to crystalline silica dust is the key factor in silicosis. Long-term exposure to low-level silica dust, for example, lower than that in occupational exposure limits, still needs to be studied for their risk of silicosis. Methods A total of 30 697 workers were included from a cohort in China. Low-level silica dust exposure was defined as those having a lifetime mean silica dust concentration equal to or under permissible exposure limits, including 0.05 mg/m 3 , 0.10 mg/m 3 and 0.35 mg/m 3 . Cumulative respirable silica dust exposure (CDE) for individual workers was assessed by linking a job-exposure matrix to personal work history. Results Among those with average exposure level equal to or lower than 0.05 mg/m 3 , compared with the lowest quartile CDE (Q1), the HRs of silicosis were 1.32 (95% CI 0.82 to 2.10) for Q2, 1.87 (95% CI 1.22 to 2.88) for Q3 and 2.00 (95% CI 1.30 to 3.09) for Q4. Among those exposed to 0.10 mg/m 3 or less exposure level, compared with Q1, the HRs were 2.52 (95% CI 1.88 to 3.38) for Q2, 4.08 (95% CI 3.09 to 5.39) for Q3 and 4.02 (95% CI 3.04 to 5.32) for Q4. Among those exposed to 0.35 mg/m 3 or less exposure level, compared with Q1, the HRs were 2.80 (95% CI 2.38 to 3.28) for Q2, 5.76 (95% CI 4.93 to 6.73) for Q3 and 7.14 (95% CI 6.07 to 8.40) for Q4, respectively. Stratified analysis showed that the results and trends did not change with facilities and smoking status. Conclusion Long-term exposure to low-level silica dust is still associated with a higher risk of silicosis. Control measurements and personal protective equipment should be emphasised to protect the health of workers.
Adding insult to injury: the spectrum of tubulointerstitial responses in acute kidney injury
Authors: Megan L. Baker, Lloyd G. Cantley
Journal: Journal of Clinical Investigation (2025)

Acute kidney injury (AKI) encompasses pathophysiology ranging from glomerular hypofiltration to tubular cell injury and outflow obstruction. This Review will focus on the tubulointerstitial processes that underlie most cases of AKI. Tubular epithelial cell (TEC) injury can occur via distinct insults, including ischemia, nephrotoxins, sepsis, and primary immune-mediated processes. Following these initial insults, tubular cells can activate survival and repair responses or they can develop mitochondrial dysfunction and metabolic reprogramming, cell-cycle arrest, and programmed cell death. Developing evidence suggests that the fate of individual tubular cells to survive and proliferate or undergo cell death or senescence is frequently determined by a biphasic immune response with initial proinflammatory macrophage, neutrophil, and lymphocyte infiltration exacerbating injury and activating programmed cell death, while alternatively activated macrophages and specific lymphocyte subsets subsequently modulate inflammation and promote repair. Functional recovery requires that this reparative phase supports proteolytic degradation of tubular casts, proliferation of surviving TECs, and restoration of TEC differentiation. Incomplete resolution or persistence of inflammation can lead to failed tubular repair, fibrosis, and chronic kidney disease. Despite extensive research in animal models, translating preclinical findings to therapies remains challenging, emphasizing the need for integrated multiomic approaches to advance AKI understanding and treatment.
Oncostatin M silence and neopeptide: the value of exploring patients with rare inherited bone marrow failure
Authors: Selket Delafontaine, Isabelle Meyts
Journal: Journal of Clinical Investigation (2025)

Inherited bone marrow failure syndromes (IBMFSs) encompass a diverse group of hematological disorders characterized by a progressive single-lineage cytopenia or pancytopenia. Despite their heterogeneity, these syndromes often result from genetic errors affecting key biological mechanisms, including telomere maintenance, DNA repair and chromosomal stability, and ribosome assembly, generally leading to accelerated apoptosis of hematopoietic cells. Nevertheless, a genetic diagnosis remains elusive in more than half of the cases. The increased risk of myelodysplastic syndrome (MDS), acute leukemia, and solid tumors associated with IBMFS frequently prompts early hematopoietic stem cell transplantation (HSCT). In this issue of the JCI, Garrigue, Kermasson, and colleagues identified a homozygous variant in Oncostatin M (OSM) in 3 children from a consanguineous family presenting with IBMFS characterized by profound anemia, thrombocytopenia, and neutropenia. The findings suggest that the loss-of-function OSM variant affected hematopoietic stem cell function through changes to the bone marrow microenvironment (BMM).
Immune-related events in individuals with solid tumors on immunotherapy associate with Th17 and Th2 signatures
Authors: Chester J. Kao, Soren Charmsaz, Stephanie L. Alden, Madelena Brancati, Howard L. Li, Aanika Balaji, Kabeer Munjal, Kathryn Howe, Sarah Mitchell, James Leatherman, Ervin Griffin, Mari Nakazawa, Hua-Ling Tsai, Ludmila Danilova, Chris Thoburn, Jennifer Gizzi, Nicole E. Gross, Alexei Hernandez, Erin M. Coyne, Sarah M. Shin, Jayalaxmi Suresh Babu, George W. Apostol, Jennifer Durham, Brian J. Christmas, Maximilian F. Konig, Evan J. Lipson, Jarushka Naidoo, Laura C. Cappelli, Aliyah Pabani, Yasser Ged, Marina Baretti, Julie Brahmer, Jean Hoffman-Censits, Tanguy Y. Seiwert, Rachel Garonce-Hediger, Aditi Guha, Sanjay Bansal, Laura Tang, Elizabeth M. Jaffee, G. Scott Chandler, Rajat Mohindra, Won Jin Ho, Mark Yarchoan
Journal: Journal of Clinical Investigation (2025)
The FoxO4/DKK3 axis represses IFN-γ expression by Th1 cells and limits antimicrobial immunity
Authors: Xiang Chen, Jia Hu, Yunfei Wang, Younghee Lee, Xiaohong Zhao, Huiping Lu, Gengzhen Zhu, Hui Wang, Yu Jiang, Fan Liu, Yongzhen Chen, Byung-Seok Kim, Qinghua Zhou, Xindong Liu, Xiaohu Wang, Seon Hee Chang, Chen Dong
Journal: Journal of Clinical Investigation (2025)
Sensing mycobacteria through unconventional pathways
Authors: Catarina F. Almeida, Jennifer A. Juno
Journal: Journal of Clinical Investigation (2025)

Approximately one-quarter of the global population is estimated to be infected with Mycobacterium tuberculosis. New developments in vaccine design and therapeutics are urgently needed, particularly in the face of multidrug-resistant tuberculosis (TB). In this issue of the JCI, Sakai and colleagues used a multidisciplinary approach to determine that trehalose-6-monomycolate (TMM), a mycobacterial cell wall lipid, serves as a T cell antigen presented by CD1b. CD1b-TMM–specific T cells were characterized by conserved T cell receptor features and were present at elevated frequencies in individuals with active TB disease. These findings highlight the dual role of TMM in stimulating both innate and adaptive immunity and broaden our understanding of CD1-mediated lipid recognition by unconventional T cells.
Nonvesicular cholesterol transport in physiology
Authors: Alessandra Ferrari, Peter Tontonoz
Journal: Journal of Clinical Investigation (2025)

In mammalian cells cholesterol can be synthesized endogenously or obtained exogenously through lipoprotein uptake. Plasma membrane (PM) is the primary intracellular destination for both sources of cholesterol, and maintaining appropriate membrane cholesterol levels is critical for cellular viability. The endoplasmic reticulum (ER) acts as a cellular cholesterol sensor, regulating synthesis in response to cellular needs and determining the metabolic fates of cholesterol. Upon reaching the ER, cholesterol can be esterified to facilitate its incorporation into lipoproteins and lipid droplets or converted into other molecules such as bile acids and oxysterols. In recent years, it has become clear that the intracellular redistribution of lipids, including cholesterol, is critical for the regulation of various biological processes. This Review highlights physiology and mechanisms of nonvesicular (protein-mediated) intracellular cholesterol trafficking, with a focus on the role of Aster proteins in PM to ER cholesterol transport.
Genomic and transcriptomic profiling reveals distinct molecular subsets associated with outcomes in mantle cell lymphoma
Authors: Shuhua Yi, Yuting Yan, Meiling Jin, Supriyo Bhattacharya, Yi Wang, Yiming Wu, Lu Yang, Eva Gine, Guillem Clot, Lu Chen, Ying Yu, Dehui Zou, Jun Wang, An T. Phan, Rui Cui, Fei Li, Qi Sun, Qiongli Zhai, Tingyu Wang, Zhen Yu, Lanting Liu, Wei Liu, Rui Lyv, Weiwei Sui, Wenyang Huang, Wenjie Xiong, Huijun Wang, Chengwen Li, Zhijian Xiao, Mu Hao, Jianxiang Wang, Tao Cheng, Silvia Bea, Alex F. Herrera, Alexey Danilov, Elias Campo, Vu N. Ngo, Lugui Qiu, Lili Wang
Journal: Journal of Clinical Investigation (2025)
Macrophages: key conductors behind perivascular inflammation and vascular remodeling in hypoxia-induced pulmonary hypertension
Authors: Edda Spiekerkoetter
Journal: Journal of Clinical Investigation (2025)

Pulmonary hypertension (PH) encompasses a heterogenous group of disorders with the common feature of increased pulmonary arterial pressures. Patients with PH associated with lung disease and/or hypoxia undergo immune-mediated vascular remodeling that includes thickening of the muscular layer surrounding arteries and arterioles. In this issue of the JCI, Kumar and colleagues examined the role of interstitial macrophages in a model of high-altitude PH. Resident interstitial macrophages increased, proliferated, and expressed CCL2, a monocyte chemoattractant ligand. There was also a rise in CCR2+ macrophages expressing thrombospondin-1, which is known to activate vascular remodeling through TGF-β. Blocking monocyte recruitment partially reduced hypoxic PH, and corticosteroid treatment effectively reduced CCL2 expression and CCR2+ monocyte recruitment. Further, plasma samples collected from individuals ascending from low to high altitudes showed increased thrombospondin-1 and TGF-β levels, which were reduced with dexamethasone. These findings reveal interstitial macrophage populations as potential therapeutic targets in hypoxic PH.
Identification of lysosomal lipolysis as an essential noncanonical mediator of adipocyte fasting and cold-induced lipolysis
Authors: Yu-Sheng Yeh, Trent D. Evans, Mari Iwase, Se-Jin Jeong, Xiangyu Zhang, Ziyang Liu, Arick Park, Ali Ghasemian, Borna Dianati, Ali Javaheri, Dagmar Kratky, Satoko Kawarasaki, Tsuyoshi Goto, Hanrui Zhang, Partha Dutta, Francisco J. Schopfer, Adam C. Straub, Jaehyung Cho, Irfan J. Lodhi, Babak Razani
Journal: Journal of Clinical Investigation (2025)

Adipose tissue lipolysis is the process by which triglycerides in lipid stores are hydrolyzed into free fatty acids (FFAs), serving as fuel during fasting or cold-induced thermogenesis. Although cytosolic lipases are considered the predominant mechanism of liberating FFAs, lipolysis also occurs in lysosomes via lysosomal acid lipase (LIPA), albeit with unclear roles in lipid storage and whole-body metabolism. We found that adipocyte LIPA expression increased in adipose tissue of mice when lipolysis was stimulated during fasting, cold exposure, or β-adrenergic agonism. This was functionally important, as inhibition of LIPA genetically or pharmacologically resulted in lower plasma FFAs under lipolytic conditions. Furthermore, adipocyte LIPA deficiency impaired thermogenesis and oxygen consumption and rendered mice susceptible to diet-induced obesity. Importantly, lysosomal lipolysis was independent of adipose triglyceride lipase, the rate-limiting enzyme of cytosolic lipolysis. Our data suggest a significant role for LIPA and lysosomal lipolysis in adipocyte lipid metabolism beyond classical cytosolic lipolysis.