tbuckley/cabot-search huggingface dataset:
High-throughput proteomics identifies inflammatory proteins associated with disease severity and genetic ancestry in patients with hidradenitis suppurativa
Authors: Peter M Dimitrion, Rachel Krevh, Jesse Veenstra, James Ge, Aamir Siddiqui, Deangelo Ferguson, Aakash Hans, Bobby Zuniga, Kermanjot Sidhu, Steven Daveluy, Iltefat Hamzavi, Li Zhou, Indra Adrianto, Qing-Sheng Mi
Journal: British Journal of Dermatology (2025)

Abstract Background Hidradenitis Suppurativa (HS) is a chronic inflammatory skin condition with a greater prevalence and disease burden in patients who identify as African American and those with a family history of HS, suggesting a strong genetic component to its pathogenesis. Objective To evaluate the relationship between plasma inflammatory protein expression, HS disease severity, and genetic ancestry in a diverse cohort of patients with Hidradenitis Suppurativa. Methods We performed a case-control study of patients with HS compared to age-, sex-, and ethnicity-matched healthy controls. We profiled circulating inflammatory proteins using Olink High-throughput proteomics and determined genetic ancestry from whole-genome sequencing data. Results Using linear regression, we identified novel proteins associated with HS after adjusting for age, sex, and ethnicity. Our analysis also revealed differences in the inflammatory proteome linked to disease severity. Specifically, we found that plasma IL6 levels can distinguish between different Hurley stages, indicating that IL6 may serve as a marker of disease severity. Additionally, we observed variations in inflammatory protein levels based on genetic ancestry: patients with predominantly African ancestry exhibited higher levels of inflammatory proteins associated with neutrophilic inflammation, while those with predominantly European ancestry showed increased levels of Th1-related inflammatory proteins. Limitations Single-center study. Limited sample size. Unable to account for treatment status or comorbidities that may influence the level of inflammatory cytokines. Conclusion Genetic ancestry and disease severity influence the plasma inflammatory profile in patients with HS.
Can ICD Electrograms Help Ventricular Tachycardia Ablation?
Authors: José Luis Ibáñez Criado, Mercedes Ortiz, Javier García-Fernández, Jesús Daniel Martínez-Alday, Enrique Rodríguez Font, Javier Moreno, Miguel Álvarez López, Julio Martí Almor, María López Gil, Dolores García Medina, Ricardo Ruiz Granell, Rafael Peinado Peinado, Victor Bazán Gelizo, Juan José Sánchez Muñoz, Olga Medina, Santiago Angulo Díaz-Parreño, Alicia Ibáñez Criado, Javier Martin Gonzalez, José Miguel Ormaetxe Merodio, Jesús Almendral
Journal: Journal of the American College of Cardiology (2025)
3D bioprinted dynamic bioactive living construct enhances mechanotransduction-assisted rapid neural network self-organization for spinal cord injury repair
Authors: Jia Yang, Kunkoo Kim, Yaosai Liu, Xiaobin Luo, Chao Ma, Weitao Man, Yating Zhao, Zheng Cao, Peilun Hu, Junlin Chen, Yu Wang, Xiaodan Sun, Lingyun Zhao, Guihuai Wang, Kaiyuan Yang, Xiumei Wang
Journal: Bioactive Materials (2025)
Device based monitoring in digital care and its impact on hospital service use
Authors: Anne-Jet S. Jansen, Guido M. Peters, Laura Kooij, Carine J. M. Doggen, Wim H. van Harten
Journal: npj Digital Medicine (2025)

This systematic review examines four themes of device-based remote monitoring (DRM): technology, patient monitoring and support, integration of DRM into clinical care, and patient engagement, and their impact on hospital service use. We included randomized controlled trials (RCTs) until 2024 comparing hospital service use in DRM with usual care. Hospital service use decreased in DRM in 72% of the 116 included RCTs. Non-implantable devices were most commonly used to measure data, but showed a lower decrease in hospital service use than implanted or mobile devices (69% vs 89% and 76%). Providing 24/7 support for patients led to a decrease (81% of the studies). DRM replacing usual care, involving designated healthcare providers, and patient-performed data transmission led to a greater decrease in hospital service use. DRM has the potential to further reduce hospital service use with additional factors such as sufficient support, automated processes, and optimized care redesign.
Consolidation ALK Tyrosine Kinase Inhibitor in Definitively Treated Unresectable Stage III ALK+ NSCLC: Can Real-World Data Inform Clinical Decision in the Absence of a LAURA-Type Designed Trial?
Authors: Zhaohui Liao Arter, Sai-Hong Ignatius Ou, Misako Nagasaka
Journal: Journal of Thoracic Oncology (2025)
Response to the Letters to the Editor by Jing Peng and Colleagues and by Lauren C Leiman Regarding the Manuscript “Terminology Issues in Screening and Early Detection of Lung Cancer—International Association for the Study of Lung Cancer Early Detection and Screening Committee Expert Group Recommendations”
Authors: Rudolf M Huber, Stephen Lam, Milena Cavic, Haval Balata, Andrea Borondy Kitts, John K Field, Claudia Henschke, Ella A Kazerooni, Anna Kerpel-Fronius, Emanuela Taioli, Luigi Ventura, David Yankelevitz, Martin Tammemägi
Journal: Journal of Thoracic Oncology (2025)
Formation of I2+III2 supercomplex rescues respiratory chain defects
Authors: Chao Liang, Abhilash Padavannil, Shan Zhang, Sheryl Beh, David R L Robinson, Jana Meisterknecht, Alfredo Cabrera-Orefice, Timothy R Koves, Chika Watanabe, Miyuki Watanabe, María Illescas, Radiance Lim, Jordan M Johnson, Shuxun Ren, Ya-Jun Wu, Dennis Kappei, Anna Maria Ghelli, Katsuhiko Funai, Hitoshi Osaka, Deborah Muoio, Cristina Ugalde, Ilka Wittig, David A Stroud, James A Letts, Lena Ho
Journal: Cell Metabolism (2025)
T cell malignancies after CAR T cell therapy in the DESCAR-T registry
Authors: Remy Dulery, Vincent Guiraud, Sylvain Choquet, Catherine Thieblemont, Emmanuel Bachy, Stéphane Barete, Ève Todesco, Bertrand Arnulf, Nicolas Boissel, André Baruchel, Jacques-Olivier Bay, Steven Le Gouill, Roch Houot
Journal: Nature Medicine (2025)
A distinct hypothalamus–habenula circuit governs risk preference
Authors: Dominik Groos, Anna Maria Reuss, Peter Rupprecht, Tevye Stachniak, Christopher Lewis, Shuting Han, Adrian Roggenbach, Oliver Sturman, Yaroslav Sych, Martin Wieckhorst, Johannes Bohacek, Theofanis Karayannis, Adriano Aguzzi, Fritjof Helmchen
Journal: Nature Neuroscience (2025)
Structural polymorphism and diversity of human segmental duplications
Authors: Hyeonsoo Jeong, Philip C. Dishuck, DongAhn Yoo, William T. Harvey, Katherine M. Munson, Alexandra P. Lewis, Jennifer Kordosky, Gage H. Garcia, Feyza Yilmaz, Pille Hallast, Charles Lee, Tomi Pastinen, Evan E. Eichler
Journal: Nature Genetics (2025)

Abstract Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies (from 85 samples representing 38 Africans and 47 non-Africans) in which the majority of autosomal SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms and sex chromosomes, we identify 173.2 Mb of duplicated sequence (47.4 Mb not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable, with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy numbers than non-African samples. Comparison to a resource of 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.
Transplantation of a genetically modified porcine heart into a live human
Authors: Bartley P. Griffith, Alison Grazioli, Avneesh K. Singh, Andy Tully, Javier Galindo, Kapil K. Saharia, Aakash Shah, Erik R. Strauss, Patrick N. Odonkor, Brittney Williams, Henry J. Silverman, Allen Burke, Cinthia B. Drachenberg, Chris L. Wells, Timm Dickfeld, Susie N. Hong, Albert J. Hicks, Manjula Ananthram, Anuj Gupta, Robert H. Christenson, Lo Tamburro, Tianshu Zhang, Alena Hershfeld, Billeta Lewis, Erika D. Feller, Kasinath Kuravi, Lori Sorrells, Erwan Morgand, Fariza Mezine, Valentin Goutaudier, Martine Rothblatt, Christine L. Lau, Bradley Taylor, Steve Perrin, Alexandre Loupy, David Ayares, Muhammad M. Mohiuddin
Journal: Nature Medicine (2025)
A multi-kinase inhibitor screen identifies inhibitors preserving stem-cell-like chimeric antigen receptor T cells
Authors: Feifei Song, Ourania Tsahouridis, Simone Stucchi, Tara Walhart, Sophie Mendell, P. Brian Hardy, Matthew Axtman, Shiva K. R. Guduru, Thomas S. K. Gilbert, Lee M. Graves, Laura E. Herring, Barbara Savoldo, Xingcong Ma, Mark Woodcock, Justin J. Milner, Anastasia Ivanova, Kenneth H. Pearce, Yang Xu, Gianpietro Dotti
Journal: Nature Immunology (2025)

Chimeric antigen receptor T cells (CAR T cells) with T stem (TSCM) cell-like phenotypic characteristics promote sustained antitumor effects. We performed an unbiased and automated high-throughput screen of a kinase-focused compound set to identify kinase inhibitors (KIs) that preserve human TSCM cell-like CAR T cells. We identified three KIs, UNC10225387B, UNC10225263A and UNC10112761A, that combined in vitro increased the frequency of CD45RA+CCR7+TCF1hi TSCM cell-like CAR T cells from both healthy donors and patients with cancer. KI-treated CAR T cells showed enhanced antitumor effects both in vitro and in vivo in mouse tumor models. The KI cocktail maintains TSCM cell-like phenotype preferentially in CAR T cells originating from naive T cells and causes transcriptomic changes without arresting T cell activation or modulating the chromatin organization. Specific kinases, ITK, ADCK3, MAP3K4 and CDK13, targeted by the KI cocktail in a dose-dependent manner are directly associated with the preservation of TSCM cell-like CAR T cells. Knockdown of these kinases individually or in combination enriches for TSCM cell-like CAR T cells, but only CAR T cells generated in the presence of the KI cocktail show robust expansion and differentiation on stimulation with tumor cells. Overall, transient pharmacological inhibition of strategically targeted kinases maintains stem-like features in CAR T cells and improves their antitumor activity. Dotti and colleagues performed an unbiased, high-throughput screen of kinase inhibitors to identify a three-kinase inhibitor cocktail capable of preserving a stem-cell-like subset in chimeric antigen receptor T cells.
Intestinal TM6SF2 protects against metabolic dysfunction-associated steatohepatitis through the gut–liver axis
Authors: Xiang Zhang, Harry Cheuk-Hay Lau, Suki Ha, Chuanfa Liu, Cong Liang, Hye Won Lee, Queena Wing-Yin Ng, Yi Zhao, Fenfen Ji, Yunfei Zhou, Yasi Pan, Yang Song, Yating Zhang, Jennie Ching Yin Lo, Alvin Ho Kwan Cheung, Jianfeng Wu, Xiaoxing Li, Hongzhi Xu, Chi Chun Wong, Vincent Wai-Sun Wong, Jun Yu
Journal: Nature Metabolism (2025)

Transmembrane-6 superfamily member 2 (TM6SF2) regulates hepatic fat metabolism and is associated with metabolic dysfunction-associated steatohepatitis (MASH). TM6SF2 genetic variants are associated with steatotic liver disease. The pathogenesis of MASH involves genetic factors and gut microbiota alteration, yet the role of host–microbe interactions in MASH development remains unclear. Here, we discover that mice with intestinal epithelial cell-specific knockout of Tm6sf2 (Tm6sf2ΔIEC) develop MASH, accompanied by impaired intestinal barrier and microbial dysbiosis. Transplanting stools from Tm6sf2ΔIEC mice induces steatohepatitis in germ-free recipient mice, whereas MASH is alleviated in Tm6sf2ΔIEC mice co-housed with wild-type mice. Mechanistically, Tm6sf2-deficient intestinal cells secrete more free fatty acids by interacting with fatty acid-binding protein 5 to induce intestinal barrier dysfunction, enrichment of pathobionts, and elevation of lysophosphatidic acid (LPA) levels. LPA is translocated from the gut to the liver, contributing to lipid accumulation and inflammation. Pharmacological inhibition of the LPA receptor suppresses MASH in both Tm6sf2ΔIEC and wild-type mice. Hence, modulating microbiota or blocking the LPA receptor is a potential therapeutic strategy in TM6SF2 deficiency-induced MASH. Intestinal TM6SF2 is found to interact with fatty acid-binding protein 5 to modulate the secretion of fatty acids and the composition of the gut microbiota, thereby protecting against metabolic dysfunction-associated steatohepatitis.
EBP1 potentiates amyloid β pathology by regulating γ-secretase
Authors: Byeong-Seong Kim, Inwoo Hwang, Hyo Rim Ko, Young Kwan Kim, Hee Jin Kim, Sang Won Seo, Yujung Choi, Sungsu Lim, Yun Kyung Kim, Shuke Nie, Keqiang Ye, Jong-Chan Park, Yunjong Lee, Dong-Gyu Jo, Seung Eun Lee, Daesik Kim, Sung-Woo Cho, Jee-Yin Ahn
Journal: Nature Aging (2025)
Modulating mTOR-dependent astrocyte substate transitions to alleviate neurodegeneration
Authors: Liansheng Zhang, Zhengzheng Xu, Zhiheng Jia, Shicheng Cai, Qiang Wu, Xingyu Liu, Xinde Hu, Tao Bai, Yongyu Chen, Tianwen Li, Zhen Liu, Bin Wu, Jianhong Zhu, Haibo Zhou
Journal: Nature Aging (2025)
β-Glucan reprograms neutrophils to promote disease tolerance against influenza A virus
Authors: Nargis Khan, Kim A. Tran, Raphael Chevre, Veronica Locher, Mathis Richter, Sarah Sun, Mina Sadeghi, Erwan Pernet, Andrea Herrero-Cervera, Alexandre Grant, Ahmed Saif, Jeffrey Downey, Eva Kaufmann, Shabaana Abdul Khader, Philippe Joubert, Luis B. Barreiro, Bryan G. Yipp, Oliver Soehnlein, Maziar Divangahi
Journal: Nature Immunology (2025)

Disease tolerance is an evolutionarily conserved host defense strategy that preserves tissue integrity and physiology without affecting pathogen load. Unlike host resistance, the mechanisms underlying disease tolerance remain poorly understood. In the present study, we investigated whether an adjuvant (β-glucan) can reprogram innate immunity to provide protection against influenza A virus (IAV) infection. β-Glucan treatment reduces the morbidity and mortality against IAV infection, independent of host resistance. The enhanced survival is the result of increased recruitment of neutrophils via RoRγt+ T cells in the lung tissue. β-Glucan treatment promotes granulopoiesis in a type 1 interferon-dependent manner that leads to the generation of a unique subset of immature neutrophils utilizing a mitochondrial oxidative metabolism and producing interleukin-10. Collectively, our data indicate that β-glucan reprograms hematopoietic stem cells to generate neutrophils with a new 'regulatory' function, which is required for promoting disease tolerance and maintaining lung tissue integrity against viral infection.
Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing
Authors: Tsion Abay, Robert R. Stickels, Meril T. Takizawa, Benan N. Nalbant, Yu-Hsin Hsieh, Sidney Hwang, Catherine Snopkowski, Kenny Kwok Hei Yu, Zaki Abou-Mrad, Viviane Tabar, Brooke E. Howitt, Leif S. Ludwig, Ronan Chaligné, Ansuman T. Satpathy, Caleb A. Lareau
Journal: Nature Genetics (2025)
Budesonide, Added to <scp>PTCy</scp>‐Based Regimen, for Prevention of Acute <scp>GI GVHD</scp> After Allogeneic Stem Cell Transplantation
Authors: Piyanuch Kongtim, Piyatida Chumnumsiriwath, Pongthep Vittayawacharin, Deepa Jeyakumar, Benjamin J. Lee, Jean Doh, Shawn P. Griffin, Richard A. Van Etten, Stefan Ciurea
Journal: American Journal of Hematology (2025)

Oral budesonide exerts local effects with negligible systemic glucocorticoid activity, due to rapid first-pass metabolism, therefore, could potentially be efficacious in preventing gastrointestinal (GI) acute GVHD (aGVHD). We explored the use of budesonide, added to posttransplant cyclophosphamide (PTCy), tacrolimus, and mycophenolate mofetil, for prevention of GI aGVHD after allogeneic hematopoietic stem cell transplantation (AHSCT) in a prospective observational study and treated 80 patients with a median age of 53 years (range 19-74). Results were compared with a publicly available CIBMTR dataset of 646 patients who received PTCy-based GVHD prophylaxis (CIBMTR Study # GV17-02) (control). Cumulative incidence (CI) of 3-month grade 2-4 and grade 3-4 aGVHD in the budesonide and control groups were 3.8% vs. 34.4% (p < 0.001) and 1.3% vs. 9.8% (p = 0.029), respectively. One-year GRFS (70.5% vs. 31.5%, p < 0.001), PFS (73.4% vs. 52.8%, p = 0.003), and OS (80.1% vs. 64.2%, p = 0.038) were significantly higher in the budesonide group compared with control group. Propensity score-adjusted analyses showed that the addition of budesonide significantly decreased risk of aGVHD grade 2-4 (HR 0.29, p < 0.001), grade 3-4 (HR 0.12, p = 0.045), and cGVHD (HR 0.22, p < 0.001), which resulted in better GRFS (HR 0.38, p < 0.001), PFS (HR 0.58, p = 0.012), and OS (HR 0.72, p = 0.044). Similar results were found when using propensity score-matched analysis restricted to recipients of haploidentical transplantation. In conclusion, addition of budesonide to PTCy-based GVHD prophylaxis is safe and effective in preventing severe acute GI GVHD with significantly improved GRFS. These results could facilitate transition to peripheral blood grafts for all allogeneic transplant recipients.
The gut–brain axis underlying hepatic encephalopathy in liver cirrhosis
Authors: Xiaolong He, Mengyao Hu, Yi Xu, Fangbo Xia, Yang Tan, Yuqing Wang, Huiling Xiang, Hao Wu, Tengfei Ji, Qian Xu, Lei Wang, Zhenhe Huang, Meiling Sun, Yu Wan, Peng Cui, Shaocong Liang, Yuan Pan, Siyu Xiao, Yan He, Ruixin Song, Junqing Yan, Xin Quan, Yingge Wei, Changze Hong, Weizuo Liao, Fuli Li, Emad El-Omar, Jinjun Chen, Xiaolong Qi, Jie Gao, Hongwei Zhou
Journal: Nature Medicine (2025)
Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness
Authors: Ling-Yun Luo, Hui Wu, Li-Ming Zhao, Ya-Hui Zhang, Jia-Hui Huang, Qiu-Yue Liu, Hai-Tao Wang, Dong-Xin Mo, He-Hua EEr, Lian-Quan Zhang, Hai-Liang Chen, Shan-Gang Jia, Wei-Min Wang, Meng-Hua Li
Journal: Nature Genetics (2025)
Tandem kinase proteins across the plant kingdom
Authors: Tamara Reveguk, Andrii Fatiukha, Evgenii Potapenko, Ivan Reveguk, Hanan Sela, Valentyna Klymiuk, Yinghui Li, Curtis Pozniak, Thomas Wicker, Gitta Coaker, Tzion Fahima
Journal: Nature Genetics (2025)
Novel antibiotics against <i>Staphylococcus aureus</i> without detectable resistance by targeting proton motive force and FtsH
Authors: She Pengfei, Yang Yifan, Li Linhui, Li Yimin, Xiao Dan, Guo Shaowei, Huang Guanqing, Wu Yong
Journal: MedComm (2025)

Abstract The increased prevalence of methicillin‐resistant Staphylococcus aureus (MRSA) and its biofilms poses a great threat to human health. Especially, S. aureus ‐related osteomyelitis was hardly cured even by conventional antibiotics combined with surgical treatment. The development of novel structural antibiotics is urgently needed. By high‐throughput screening and rational design, we identified a small molecule C218‐0546 and its optimized analog STK848198 with great antimicrobial potential against MRSA avoiding resistance occurrence. And significant synergistical antimicrobial effects were found between the molecules and conventional antibiotics. Mechanisms studies by transcriptomics, fluorescent probes, molecule dynamics, and plasma surface resonance indicated that the proton motive force as well as FtsH are the main potential targets of these molecules. The compounds exhibited excellent in vivo pharmacokinetics, toxicity profiles, and antimicrobial activities in the abscess model as well as the peritonitis‐sepsis model. In addition, STK848198 was found to be effective against MRSA biofilms by interacting with the quorum sensing system. STK848198 also showed in vivo efficacy in the periprosthetic joint infection model. In all, our study identified a class of antimicrobials with novel scaffolds that could be potential alternatives for the treatment of MRSA and its biofilm‐related infections.
Chemical cross‐linking facilitates antigen uptake and presentation and provides improved protection from Mpox with a dual‐antigen subunit vaccine
Authors: Long Chen, Chao Shang, Zihao Wang, Mengzhu Zheng, Cuiling Zhang, Dapeng Li, Zhanqun Yang, Yuchao Dong, Yuru Xu, Yunsheng Yuan, Shiyong Fan, Wu Zhong, Jian Lin, Xiao Li
Journal: MedComm (2025)

Abstract Antigen uptake, processing, and presentation are crucial for the immune responses of protein‐based vaccines. Herein, we introduced a reversible chemical cross‐linking strategy to engineer protein antigens, which can be tracelessly removed upon antigen‐presenting cell (APC) uptake and cellular reduction. The chemically cross‐linked antigen proteins presented significantly enhanced uptake and epitope presentation by APC. We applied this strategy to monkeypox virus antigens A29L and A35R to construct dual‐antigen subunit vaccines. Our results revealed that chemical cross‐linking was robust enough to improve both proteins' APC uptake and lymph node accumulation, with each protein being chemically cross‐linked and administered separately. In vivo validation revealed that the chemical cross‐linking of the two antigen proteins improved immune responses, with increases in antigen‐specific antibody and live virus‐neutralizing antibody production. Monkeypox virus challenge experiments revealed that dual‐antigen vaccines prepared via the chemical cross‐linking strategy mitigated tissue damage, reduced the virus load, and extended mouse survival, which proved that the chemical cross‐linking strategy is valuable for protein‐based subunit vaccine development. In consideration of the current threats from the monkeypox virus and potential future emerging pathogens, the chemical cross‐linking strategy provide powerful tools.
Associations between degree of food processing and all-cause and cause-specific mortality: a multicentre prospective cohort analysis in 9 European countries
Authors: Esther M González-Gil, Michèle Matta, Fernanda Morales Berstein, Manon Cairat, Geneviève Nicolas, Jessica Blanco, Nathalie Kliemann, Renata Bertazzi Levy, Fernanda Rauber, Inarie Jacobs, Aline Al Nahas, Emine Koc Cakmak, Eszter P Vamos, Kiara Chang, Sahar G Yammine, Christopher Millett, Mathilde Touvier, Maria Gabriela Matias Pinho, Konstantinos K Tsilidis, Alicia K Heath, Christina M Lill, Valeria Pala, Conchi Moreno-Iribas, Maria Santucci De Magistris, Christina C Dahm, Niels Bock, Anja Olsen, Anne Tjønneland, Yvonne T van der Schouw, Pilar Amiano, Franziska Jannasch, Matthias B Schulze, Francesca Romana Mancini, Chloé Marques, Claire Cadeau, Catalina Bonet, Daniel Redondo-Sánchez, Kristin Benjaminsen Borch, Magritt Brustad, Guri Skeie, Jesús Humberto-Gómez, Alessandra Macciotta, Pietro Ferrari, Laure Dossus, Marc J Gunter, Inge Huybrechts
Journal: The Lancet Regional Health - Europe (2025)