tbuckley/cabot-search huggingface dataset:
Feasibility of traction-band-assisted endoscopic closure for mucosal defects after colorectal endoscopic submucosal dissection: a multicenter, prospective, single-arm, pilot study
Authors: Mitsuru Esaki, Kosuke Maehara, Yorinobu Sumida, Yosuke Minoda, Hitoshi Homma, Taisuke Inada, Kazuo Shiotsuki, Shin-ichiro Fukuda, Hirotada Akiho, Norimoto Nakamura, Yusuke Suzuki, Xiaopeng Bai, Yoshimasa Tanaka, Yoshitaka Hata, Haruei Ogino, Takatoshi Chinen, Eikichi Ihara, Yoshihiro Ogawa
Journal: Endoscopy (2025)

Background and Aims: The complete closure of mucosal defects following colorectal endoscopic submucosal dissection (ESD) is often challenging. We invented a traction-band-assisted endoscopic closure (TBEC) technique using clips with an integrated traction band. We aimed to evaluate the feasibility of TBEC for closing mucosal defects following colorectal ESD. Methods: This multicenter, prospective, single-arm, pilot study was conducted at three institutions from June 2022 to March 2023. Thirty-four patients with colorectal neoplasms measuring 20-50 mm scheduled for ESD were enrolled. TBEC was performed at each mucosal defect after ESD. The primary outcome was the complete closure rate by TBEC. Secondary outcomes included the number of clips used, procedure time, and adverse events (AEs). Results: TBEC yielded a 100.0% [95% confidence interval: 89.8%-100.0%] complete closure rate, with a median closure time of 14.5 min (interquartile range: 12.9). The median number of clips used was 10.0 (3.3). One case of delayed bleeding and one of post-ESD coagulation syndrome (both 2.9% [0.5%-14.9%]) occurred following TBEC. Conclusions: This study demonstrated the feasibility of TBEC for closing mucosal defects following colorectal ESD. TBEC is a simple and easily applicable technique for endoscopic closure. Further studies are required to evaluate its efficacy in reducing delayed AEs.
Corrigendum to “International Union of Basic and Clinical Pharmacology. CXIX. Fundamental insights and clinical relevance regarding the carnitine palmitoyltransferase family of enzymes” [Pharmacological Reviews 77 (2025) 100051]
Authors: Rosalía Rodríguez-Rodríguez, Miguel Baena, Sebastián Zagmutt, West Kristian Paraiso, Ana Cristina Reguera, Rut Fadó, Núria Casals
Journal: Pharmacological Reviews (2025)
Shaping the future of inflammatory bowel disease: a global research agenda for better management and public health response
Authors: Virginia Solitano, Charles N Bernstein, Iris Dotan, Axel Dignass, Rhondell Domilici, Marla C Dubinsky, Richard B Gearry, Ailsa Hart, Gilaad G Kaplan, Christopher Ma, Fernando Magro, Joyce Wing Yan Mak, Siew C Ng, Remo Panaccione, Sreecanth Raja, David T Rubin, Corey A Siegel, Vipul Jairath, Laurent Peyrin-Biroulet, Silvio Danese
Journal: Nature Reviews Gastroenterology & Hepatology (2025)
Amphiphilic Lipid-Peptide Engineered Placenta-Derived Mesenchymal Stem Cells for Liver Fibrosis Treatment
Authors: Hee Won Park, Dae Hyun Lee, Sungjun Kim, Hyeri Park, Ashok Kumar Jangid, Chae Eun Lee, Jaewon Park, Gyu Tae Park, Ha Yeon Park, HyunJin Kim, Jae Ho Kim, Gi Jin Kim, Kyobum Kim
Journal: Asian Journal of Pharmaceutical Sciences (2025)
ALKBH3-regulated m1A of ALDOA potentiates glycolysis and doxorubicin resistance of triple negative breast cancer cells
Authors: Yuhua Deng, Zhiyan Chen, Peixian Chen, Yaming Xiong, Chuling Zhang, Qiuyuan Wu, Huiqi Huang, Shuqing Yang, Kun Zhang, Tiancheng He, Wei Li, Guolin Ye, Wei Luo, Hongsheng Wang, Dan Zhou
Journal: Acta Pharmaceutica Sinica B (2025)
Orchestration of human multi‐lineage hematopoietic cell development by humanized in vivo bone marrow models
Authors: Laurent Renou, Wenjie Sun, Chloe Friedrich, Klaudia Galant, Cecile Conrad, Anne Consalus, Evelia Plantier, Katharina Schallmoser, Linda Krisch, Vilma Barroca, Saryami Devanand, Nathalie Dechamps, Andreas Reinisch, Jelena Martinovic, Alessandra Magnani, Lionel Faivre, Daniel Lewandowski, Julien Calvo, Leila Perie, Olivier Kosmider, Françoise Pflumio
Journal: HemaSphere (2025)

Abstract Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune‐deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post‐natal (P‐N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34 + cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single‐cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross‐talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P‐N/hOss, uncovering ontogeny‐related impact of the BM on human hematopoietic cell production.
Polyploidy in potatoes: challenges and possibilities for climate resilience
Authors: Helen H Tai, Laura M Shannon, Martina V Strömvik
Journal: Trends in Genetics (2025)

Solanum section Petota Dumort. consists of tuber-bearing species (i.e., the cultivated potatoes and their wild relatives) that have both asexual and sexual propagation, variation in ploidy, and reproductive isolation. These species have undergone adaptation to a diversity of climates, altitudes, photoperiods, and geographical range. The section defies characterization with the biological species concept due to interspecies hybridization, allo- and auto-polyploidy, and phenotypic plasticity. Genetic studies, and more recently genome sequencing and pangenome analyses, are fostering a greater understanding of genetic processes that shape genome evolution and speciation in the section, shedding light on the phylogeny and providing insights on utilization of potato crop wild relatives in breeding for climate-resilient potato varieties.
The future of phage therapy in the USA
Authors: Brandon A Berryhill, Teresa Gil-Gil, Andrew P Smith, Bruce R Levin
Journal: Trends in Molecular Medicine (2025)

Fueled by the increasing abundance of antibiotic-resistant pathogens, there has been a resurrection in the use of bacterial viruses (bacteriophages or 'phage') for therapeutic applications. Phage therapy was used in the early 20th century to limited success, which we attribute to its haphazard employment. To avoid repeating the mistakes of the past, this Opinion first evaluates the historical reasons for the failure of phage therapy, analyzes the current state of the field, and ultimately makes recommendations for how to proceed with contemporary phage therapy. Despite many advances in phage biology, crucial gaps in our knowledge persist. Our recommendations require physicians, scientists, and public-policy leaders to cooperate to bridge the outstanding gaps around phage therapy to develop phage into a useful therapeutic tool.
Pre-diagnostic serum concentrations of per- and polyfluoroalkyl substances and risk of endometrial cancer in a US cohort
Authors: Jessica M. Madrigal, Britton Trabert, Danielle N. Medgyesi, Jared A. Fisher, Antonia M. Calafat, Julianne Cook Botelho, Kayoko Kato, Paul S. Albert, Debra T. Silverman, Jonathan N. Hofmann, Rena R. Jones
Journal: Environmental Health Perspectives (2025)
ADAGIO: A Phase IIb, Open-Label, Single-Arm, Multicenter Study Assessing the Efficacy and Safety of Adavosertib (AZD1775) as Treatment for Recurrent or Persistent Uterine Serous Carcinoma
Authors: Joyce F. Liu, Nicoletta Colombo, Amit M. Oza, Jean-Sebastien Frenel, Bradley R. Corr, Maria M. Rubinstein, Nicole S. Nevadunsky, Stephanie Lheureux, Lydia Gaba, Lucía González Cortijo, Vanda Salutari, Benoit You, Sarah Chiang, Mark J. O'Connor, Lenka Oplustil O'Connor, Didier Meulendijks, Mahmuda Khatun, Dana Ghiorghiu, Ana Oaknin
Journal: Journal of Clinical Oncology (2025)

PURPOSE This phase IIb, single-arm, multicenter, global study (ADAGIO; ClinicalTrials.gov identifier: NCT04590248 ) assessed the efficacy and safety of adavosertib in patients with recurrent/persistent uterine serous carcinoma (USC) who had previously received platinum-based chemotherapy. METHODS Eligible patients were age 18 years and older and had histologically confirmed recurrent/persistent USC, previously treated with at least one platinum-based chemotherapy regimen, and with evidence of measurable disease. Adavosertib was administered orally at 300 mg once daily on days 1-5 and 8-12 of a 21-day cycle until discontinuation criteria were met. The primary end point was objective response rate (ORR) by blinded independent central review (BICR). Secondary end points included duration of response (DoR), progression-free survival (PFS), safety, and tolerability. Biomarkers previously associated with adavosertib response in other settings were assessed in archival tissue samples. RESULTS In 104 evaluable patients, one complete response and 26 partial responses were observed, for an ORR by BICR of 26.0% (95% CI, 17.9 to 35.5). Median DoR was 4.7 months (95% CI, 3.8 to 8.3); median PFS was 2.8 months (95% CI, 2.6 to 3.9). Biomarker analysis identified no single predictive alteration for adavosertib response, although a trend was observed for CCNE1 amplification or high cyclin E1 protein expression. Most patients (97.2%) experienced treatment-related adverse events (TRAEs), most frequently diarrhea (59.6%), nausea (59.6%), and anemia (58.7%). Grade ≥3 TRAEs occurred in 60.6% of patients, with neutropenia (21.1%) and fatigue (13.8%) most common. 17.4% of patients discontinued adavosertib due to AEs (treatment-related in 14.7%). CONCLUSION Adavosertib showed some antitumor activity in patients with recurrent/persistent USC. However, at 300 mg once daily dosing, it was not well tolerated in this population. Exploratory biomarker studies suggest CCNE1 /cyclin E1 expression may enrich for response to Wee1 inhibition in USC.
Age-related mesenchymal stromal cell senescence is associated with progression from MGUS to multiple myeloma
Authors: Natalya Plakhova, Vasilios Panagopoulos, Melissa D Cantley, Laura J Trainor, Duncan R Hewett, Kimberley C Clark, Jo Gardiner, Angelina Yong, Cindy Lee, Noemi Horvath, Peter I Croucher, Dimitrios Cakouros, Sheila A Stewart, Stan Gronthos, Andrew C W Zannettino, Krzysztof M Mrozik, Kate Vandyke
Journal: Leukemia (2025)
Gut microbiota and associated metabolites: key players in high-fat diet-induced chronic diseases
Authors: Wei Du, Zhen-Ping Zou, Bang-Ce Ye, Ying Zhou
Journal: Gut Microbes (2025)

Excessive intake of dietary fats is strongly associated with an increased risk of various chronic diseases, such as obesity, diabetes, hepatic metabolic disorders, cardiovascular disease, chronic intestinal inflammation, and certain cancers. A significant portion of the adverse effects of high-fat diet on disease risk is mediated through modifications in the gut microbiota. Specifically, high-fat diets are linked to reduced microbial diversity, an overgrowth of gram-negative bacteria, an elevated Firmicutes-to-Bacteroidetes ratio, and alterations at various taxonomic levels. These microbial alterations influence the intestinal metabolism of small molecules, which subsequently increases intestinal permeability, exacerbates inflammatory responses, disrupts metabolic functions, and impairs signal transduction pathways in the host. Consequently, diet-induced changes in the gut microbiota play a crucial role in the initiation and progression of chronic diseases. This review explores the relationship between high-fat diets and gut microbiota, highlighting their roles and underlying mechanisms in the development of chronic metabolic diseases. Additionally, we propose probiotic interventions may serve as a promising adjunctive therapy to counteract the negative effects of high-fat diet-induced alterations in gut microbiota composition.
Impact of environmental factors on the distribution patterns of nephropathia epidemica cases in western Europe
Authors: Diana Erazo, Maria Fernanda Vincenti-Gonzalez, Guillaume Ghisbain, Mirko Faber, Chantal Reusken, Virginie Sauvage, William Wint, Herwig Leirs, Simon Dellicour, Katrien Tersago
Journal: Environmental Health Perspectives (2025)

Environmental factors, such as fluctuations of climatic conditions and land cover, play a pivotal role in driving infectious disease epidemics, particularly those originating from wildlife reservoirs. Orthohantavirus puumalaense, hosted by bank voles in Europe, is the causative agent of a form of haemorrhagic fever and renal syndrome called nephropathia epidemica. Despite two decades of consistent presence in western Europe, nephropathia epidemica outbreaks still pose challenges due to localised periodic occurrences and a lack of understanding of its environmental drivers. Our study aims to bridge this gap by investigating the specific ecological and climatic factors influencing nephropathia epidemica outbreaks in western Europe. We compiled monthly, serologically confirmed nephropathia epidemica case data obtained from public health authorities in Belgium, France, Germany, and the Netherlands for the period 2004-2012. Cases were geo-referenced to the finest available administrative unit. We selected 28 covariates, including climatic variables, land cover, tree species distributions, and human population, and implemented a Bayesian spatio-temporal model using integrated nested Laplace approximation (INLA) with zero-inflated Poisson distribution, including fixed effects and spatial, temporal, and non-structured random effects. We identified key triggers for nephropathia epidemica outbreaks, particularly climate-mediated changes in all seasons up to two years before, favouring tree mast impacting bank vole abundance. Our findings revealed that while land cover factors mostly determine hotspots locations, climatic fluctuation patterns rather tend to modulate outbreak intensity. Crucially, our model allows for the generation of yearly maps showcasing nephropathia epidemica incidence and risk factors, aiding in public health preparedness against climate change-induced disease emergence. This work represents a significant step towards developing targeted forecasting tools for Orthohantavirus puumalaense outbreaks, offering valuable insights for epidemic control strategies. https://doi.org/10.1289/EHP15457.
Genetic diversity of <i>Salmonella enterica</i> during acute human infections
Authors: Alexandra Grote, Natav Hendin, Sharon Amit, Boaz Adani, Galia Rahav, Amos Adler, Jonathan Livny, Ohad Gal-Mor, Ashlee M. Earl
Journal: Gut Microbes (2025)

The ubiquitous bacterial pathogen Salmonella enterica is the causative agent of both enteric fever and gastroenteritis. Despite its significant global health burden, we lack an understanding of its genetic diversity during acute infection, with ramifications for treatment and prevention. Here, we investigated within-host infection diversity of acute salmonellosis using whole-genome sequencing of blood or stool isolates obtained from 23 different patients. We found that intestinal infections exhibited greater genetic variation than blood infections, including in their plasmid content. While same-patient isolates were separated by 10 single nucleotide polymorphisms or less, they often differed in the carriage of genes or alleles, including those associated with antibiotic resistance or virulence. Given the longstanding emphasis on single colony isolation in clinical and laboratory microbiology, these findings have implications for how we both study evolution and transmission and how we treat salmonellosis in an age of increasing antibiotic resistance.
Application of Neoadjuvant Docetaxel Plus Cisplatin in Early-Stage Triple-Negative Breast Cancer (HELEN-001): Results from a Phase II Trial
Authors: Dechuang Jiao, Jianghua Qiao, Xianfu Sun, Chengzheng Wang, Zhenduo Lu, Chongjian Zhang, Lianfang Li, Min Yan, Yueqing Feng, Yong Zhou, Miao Deng, Xinlan Liu, Mingde Ma, Haiquan Jia, Qingxin Xia, Geok Hoon Lim, Naohiro Ishii, Armando Orlandi, Fernado Hernanz, Xiuchun Chen, Zhenzhen Liu
Journal: Clinical Cancer Research (2025)

Abstract Purpose: This study investigated the effects of taxane-cisplatin combinations on pathological complete response (pCR) rates and survival outcomes in triple-negative breast cancer (TNBC). Methods: The HELEN-001 trial enrolled patients aged 18–70 years with stage II–III TNBC, randomly assigning them to receive either docetaxel (75 mg/m²) plus cisplatin (75 mg/m²) (TP) or docetaxel (75 mg/m²), doxorubicin (50 mg/m²), and cyclophosphamide (500 mg/m²) (TAC). Treatments were administered every three weeks for six cycles, with the primary endpoint being pCR (ypT0/isN0) and secondary endpoints including event-free survival (EFS), overall response rate (ORR), breast-conserving surgery rate, and toxicity. Results: From November 2018 to June 2022, 212 Asian female patients were enrolled across six hospitals in China, with 106 patients in each group. The pCR rate was significantly higher for TP (51.9%) than for TAC (35.8%, P=0.028). After a median follow-up of 40 months, EFS was 86.1% in the TP group and 80.0% in the TAC group (HR= 0.639; P=0.196). In germline BRCA1/2 mutation carriers, EFS was significantly higher with TP than with TAC (100% vs. 53.8%, P=0.008). Grade 3 or higher adverse events occurred in 54% of patients in the TP group and 48% in the TAC group. Conclusion: The TP regimen demonstrated significantly improved pCR rates with a manageable toxicity profile, suggesting the potential benefit of taxane plus platinum regimens in patients with TNBC.
Low allele frequency variants identified on germline multi-gene panel testing for cancer predisposition can suggest the presence of constitutional mosaicism
Authors: Adela Rodriguez-Hernandez, Linda M. Polfus, Brittany L. Bychkovsky, Beth Souders, Aleix Prat, Barbara Adamo, Judy E. Garber, Carolyn Horton, Huma Q. Rana
Journal: Clinical Cancer Research (2025)

Abstract Purpose: Enabled by advancements in next-generation sequencing for hereditary cancer conditions, low allele frequency variants (LAFVs) are detected by testing laboratories. This study describes the frequency and clinical factors associated with LAFVs and reports results of follow-up testing when available. Patients and Methods: This retrospective study analyzed LAFV cases identified through multi-gene panel testing (MGPT) at a single high-volume germline genetic testing laboratory. LAFVs were defined as variant allele frequencies (VAF) between 10-30% as confirmed by Sanger sequencing. Comparative analyses were conducted between pathogenic variants (PVs) with a VAF of 30-60% (inferred heterozygous) and LAFV cohorts. Clinical characteristics were analyzed using descriptive statistics and logistic regression models. Ancillary testing was performed on alternative specimens or family members to determine if LAFVs were due to constitutional mosaicism. Results: Among 363,405 individuals undergoing MGPT, 965 (1.8%) had variants with VAF between 10-30%. Sanger sequencing confirmed 463 (0.1%) as LAFVs. Among the confirmed LAFVs, 262 (57.6%) were classified as PVs. The LAFV cohort compared to the control heterozygous cohort was significantly older, with a higher proportion of individuals &amp;gt; 50 years (84.1% vs. 54.9%; p&amp;lt;0.001). LAFVs were present in the following genes: TP53 (110;64.7%), NF1 (23;13.5%), CHEK2 (13;7.6%), ATM (12; 7.1%), and BRCA1 (4;2.4%). Ancillary testing performed on 62 cases with LAFVs confirmed 17.7% (11/62) as constitutional mosaicism. Conclusion: LAFVs were infrequently detected in MGPT, representing 0.8% of the total variants and 0.1% of total tested. Ancillary testing is needed to understand the origins and clinical implications of LAFVs in patients and families.
Visualizing the burden of brain tissue hypoxia and metabolic dysfunction assessed by multimodal neuromonitoring in subarachnoid hemorrhage patients: the TITAN study
Authors: Elisa Gouvêa Bogossian, Bavo Kempen, Michael Veldeman, Soojin Park, Verena Rass, Stephane Marinesco, Miriam Weiss, Gerrit Alexander Schubert, Nick Kastenholz, Jan Claassen, Philipp Kindl, Anna Berek, Marco Anderloni, Catharina Conzen-Dilger, Sophie Schuind, Baptiste Balança, Yannick Tholance, E Sander Connolly, Geert Meyfroidt, Raimund Helbok, Giorgia Carra, Fabio Silvio Taccone
Journal: Intensive Care Medicine (2025)
Identification and validation of robust hospital-acquired pneumonia subphenotypes associated with all-cause mortality: a multi-cohort derivation and validation
Authors: Florian Pierre Martin, Cécile Poulain, Jelle Haitsma Mulier, Ana Motos, Victor Gourain, Ismaël Ogan, Emmanuel Montassier, Yoann Launey, Sigismond Lasocki, Raphaël Cinotti, Claire Dahyot Fizelier, Otavio Ranzani, Luis Felipe Reyes, Ignacio Martin-Loeches, Lennie Derde, Antoni Torres, Olaf Cremer, Antoine Roquilly
Journal: Intensive Care Medicine (2025)
The use of left ventricular ejection fraction in the diagnosis and management of heart failure. A clinical consensus statement of the Heart Failure Association (HFA) of the ESC, the Heart Failure Society of America (HFSA), and the Japanese Heart Failure Society (JHFS)
Authors: Giuseppe M.C. Rosano, John R. Teerlink, Koichiro Kinugawa, Antoni Bayes‐Genis, Ovidiu Chioncel, James Fang, Barry Greenberg, Nasrien E. Ibrahim, Teruhiko Imamura, Takayuki Inomata, Koichiro Kuwahara, Brenda Moura, Anekwe Onwuanyi, Naoki Sato, Gianluigi Savarese, Yasuhiko Sakata, Nancy Sweitzer, Jane Wilcox, Kazuhiro Yamamoto, Marco Metra, Andrew J.S. Coats
Journal: European Journal of Heart Failure (2025)
B cells modulate lung antiviral inflammatory responses via the neurotransmitter acetylcholine
Authors: Antonio Cembellin-Prieto, Zheng Luo, Heather Kulaga, Nicole Baumgarth
Journal: Nature Immunology (2025)

Abstract The rapid onset of innate immune defenses is critical for early control of viral replication in an infected host and yet it can also lead to irreversible tissue damage, especially in the respiratory tract. Sensitive regulators must exist that modulate inflammation, while controlling the infection. In the present study, we identified acetylcholine (ACh)-producing B cells as such early regulators. B cells are the most prevalent ACh-producing leukocyte population in the respiratory tract demonstrated with choline acetyltransferase (ChAT)-green fluorescent protein (GFP) reporter mice, both before and after infection with influenza A virus. Mice lacking ChAT in B cells, disabling their ability to generate ACh (ChatBKO), but not those lacking ChAT in T cells, significantly, selectively and directly suppressed α7-nicotinic-ACh receptor-expressing interstitial, but not alveolar, macrophage activation and their ability to secrete tumor necrosis factor (TNF), while better controlling virus replication at 1 d postinfection. Conversely, TNF blockade via monoclonal antibody treatment increased viral loads at that time. By day 10 of infection, ChatBKO mice showed increased local and systemic inflammation and reduced signs of lung epithelial repair despite similar viral loads and viral clearance. Thus, B cells are key participants of an immediate early regulatory cascade that controls lung tissue damage after viral infection, shifting the balance toward reduced inflammation at the cost of enhanced early viral replication.