tbuckley/cabot-search huggingface dataset:
Using patient-reported outcomes and health-related quality of life data in regulatory decisions on cancer treatment: highlights from an EMA-EORTC workshop
Authors: Madeline Pe, Caroline Voltz-Girolt, Jill Bell, Vishal Bhatnagar, Jan Bogaerts, Christopher Booth, Juan Garcia Burgos, Joseph C Cappelleri, Corneel Coens, Pierre Demolis, Harald Enzmann, Johannes M Giesinger, Alexandra Gilbert, Mogens Groenvold, Paul Kluetz, Claire Piccinin, Douwe Postmus, Chantal Quinten, Bettina Ryll, Maxime Sasseville, Michael Schlichting, Hans Schuerer, Anja Schiel, James W Shaw, Ashley Wilder Smith, Shun Tezuka, Carla Torre, Winette T A van der Graaf, Beate Wieseler, Friedrich Wittenbecher, Jaap C Reijneveld, Peter Mol
Journal: The Lancet Oncology (2025)
CONSORT 2025 statement: updated guideline for reporting randomised trials
Authors: Sally Hopewell, An-Wen Chan, Gary S Collins, Asbjørn Hróbjartsson, David Moher, Kenneth F Schulz, Ruth Tunn, Rakesh Aggarwal, Michael Berkwits, Jesse A Berlin, Nita Bhandari, Nancy J Butcher, Marion K Campbell, Runcie C W Chidebe, Diana Elbourne, Andrew Farmer, Dean A Fergusson, Robert M Golub, Steven N Goodman, Tammy C Hoffmann, John P A Ioannidis, Brennan C Kahan, Rachel L Knowles, Sarah E Lamb, Steff Lewis, Elizabeth Loder, Martin Offringa, Philippe Ravaud, Dawn P Richards, Frank W Rockhold, David L Schriger, Nandi L Siegfried, Sophie Staniszewska, Rod S Taylor, Lehana Thabane, David Torgerson, Sunita Vohra, Ian R White, Isabelle Boutron
Journal: The Lancet (2025)
CONSORT 2025 Statement
Authors: Sally Hopewell, An-Wen Chan, Gary S. Collins, Asbjørn Hróbjartsson, David Moher, Kenneth F. Schulz, Ruth Tunn, Rakesh Aggarwal, Michael Berkwits, Jesse A. Berlin, Nita Bhandari, Nancy J. Butcher, Marion K. Campbell, Runcie C. W. Chidebe, Diana Elbourne, Andrew Farmer, Dean A. Fergusson, Robert M. Golub, Steven N. Goodman, Tammy C. Hoffmann, John P. A. Ioannidis, Brennan C. Kahan, Rachel L. Knowles, Sarah E. Lamb, Steff Lewis, Elizabeth Loder, Martin Offringa, Philippe Ravaud, Dawn P. Richards, Frank W. Rockhold, David L. Schriger, Nandi L. Siegfried, Sophie Staniszewska, Rod S. Taylor, Lehana Thabane, David Torgerson, Sunita Vohra, Ian R. White, Isabelle Boutron
Journal: JAMA (2025)

Importance Well-designed and properly executed randomized trials are considered the most reliable evidence on the benefits of health care interventions. However, there is overwhelming evidence that the quality of reporting is not optimal. The CONSORT (Consolidated Standards of Reporting Trials) statement was designed to improve the quality of reporting and provides a minimum set of items to be included in a report of a randomized trial. CONSORT was first published in 1996, then updated in 2001 and 2010. Herein, we present the updated CONSORT 2025 statement, which aims to account for recent methodological advancements and feedback from end users. Observations We conducted a scoping review of the literature and developed a project-specific database of empirical and theoretical evidence related to CONSORT to generate a list of potential changes to the checklist. The list was enriched with recommendations provided by the lead authors of existing CONSORT extensions (harms, outcomes, nonpharmacological treatment), other related reporting guidelines (Template for Intervention Description and Replication [TIDieR]), and recommendations from other sources (eg, personal communications). The list of potential changes to the checklist was assessed in a large, international, online, 3-round Delphi survey involving 317 participants and discussed at a 2-day online expert consensus meeting of 30 invited international experts. We have made substantive changes to the CONSORT checklist. We added 7 new checklist items, revised 3 items, deleted 1 item, and integrated several items from key CONSORT extensions. We also restructured the CONSORT checklist, with a new section on open science. The CONSORT 2025 statement consists of a 30-item checklist of essential items that should be included when reporting the results of a randomized trial and a diagram for documenting the flow of participants through the trial. To facilitate implementation of CONSORT 2025, we have also developed an expanded version of the CONSORT 2025 checklist, with bullet points eliciting critical elements of each item. Conclusions and Relevance Authors, editors, reviewers, and other potential users should use CONSORT 2025 when writing and evaluating manuscripts of randomized trials to ensure that trial reports are clear and transparent.
Time‐dependent effect of prophylactic trimethoprim‐sulfamethoxazole on the incidence of serious infections in <scp>ANCA</scp>‐associated vasculitis: A target trial emulation study
Authors: Yun Kyu Kim, Jeffrey R Curtis, Se Rim Choi, Jina Yeo, Min Jung Kim, Yun Jong Lee, Eun Bong Lee, Jun Won Park
Journal: Arthritis & Rheumatology (2025)

Objectives To investigate the effect of prophylactic trimethoprim‐sulfamethoxazole (TMP‐SMX) on the incidence of serious infections in patients with anti‐neutrophil cytoplasmic antibody‐associated vasculitis (AAV). Methods This multicenter cohort study designed to emulate a target trial studied 296 patients with AAV treated with rituximab or cyclophosphamide as induction therapy. Patients were grouped based on the administration of TMP‐SMX within 14 days following induction therapy (n=240 and 56 patients in prophylaxis and control groups, respectively) (intention‐to‐treat) and also as a time‐dependent exposure (time‐varying). Inverse probability weighting was applied to minimize the baseline imbalance between the two groups. Primary outcome was 1‐year incidence of serious infection. Results During the 252.1 person‐years of observation, 77 cases of serious infections were recorded in 65 patients, with a fatality rate of 18.5%. Most serious infections (n=66, 85.7%) occurred within the first 180 days of observation. The prophylaxis group showed a significantly lower incidence of serious infections than the control group (HR 0.48 [0.32–0.72]). However, this beneficial effect of TMP‐SMX was only significant during the first 180 days (HR 0.41 [0.22–0.76]) and not thereafter (HR 3.76 [0.46–29.43]) (interaction p=0.044). This result was also consistent with the time‐varying analysis result. Based on one case of severe adverse drug reaction related to TMP‐SMX, the number needed to harm was 127.4 whereas the number needed to treat to prevent one serious infection was 8.0. Conclusion Prophylactic TMP‐SMX significantly reduced the risk of serious infections in patients with AAV, particularly during the first 6 months of induction therapy with rituximab or cyclophosphamide.
Metagenomic source tracking after microbiota transplant therapy
Authors: Susan L. Hoops, Daphne Moutsoglou, Byron P. Vaughn, Alexander Khoruts, Dan Knights
Journal: Gut Microbes (2025)

Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.
Isotretinoin and peanut allergy: evidence of safety is staring us in the face
Authors: Davina Henderson, Paul J Turner, Jonathan O’B Hourihane
Journal: British Journal of Dermatology (2025)

There is no need for any precautions in using isotretinoin in peanut allergies. The existing advice was based on flawed risk assessments and has been overtaken by human studies that show safety.
Incidence and mortality of melanoma <i>in situ</i> and malignant melanoma in England between 2001 and 2020
Authors: Dimitrios Karponis, Birgitta van Bodegraven, Khaylen Mistry, Vasiliki Nikolaou, Alexander J Stratigos, Nick J Levell, Zoe C Venables
Journal: British Journal of Dermatology (2025)

Abstract Background Rising incidence of melanoma has been reported globally since the 20th century, while melanoma mortality is no longer increasing in England and other countries. Improved therapeutics have reduced mortality. However, this phenomenon implicates “overdiagnosis”, where thinner melanomas of unclear malignant potential are being diagnosed possibly due to ‘diagnostic drift’. Objectives To assess the incidence and mortality trends for melanoma in situ (MIS) and malignant melanoma (MM) in England between 2001-2020 by age and gender. Methods Routinely collected data were analysed from the National Disease Registration Service for MIS and MM in England between 2001-2020. Joinpoint regression analysis calculated the trends and average annual percentage change (APC) in mortality, age-specific and age-standardised incidence by age and gender per 100,000 person years (PYs). Results Between 2001-2020, 86,792 MIS and 220,286 MM were recorded in England. Incidence (per 100,000 PYs) for MM increased most rapidly during 2001-06 from 14.6 to 19.6 (APC 6.29%), then to 26.7 during 2006-14 (APC 4.06%) and decelerated to 28.4 during 2014-19 (APC 1.35%). Incidence rates for MIS (per 100,000 PYs) decelerated over time from 4.5 to 12.5 in 2001-15 (APC 7.51%) and to 13.3 during 2015-19 (APC 1.90%). In those 0-24 years old, incidence of MM and MIS has been decreasing since the late 2000s, whereas MM incidence in those over 50 is mostly rising, with the greatest increases seen in those over 70. Mortality from MM remained higher in males, reduced in people under 60, and in adults 60-74 years old since the early 2010s. Mortality rates continued to increase in those over 75. Conclusion The deceleration of MM and MIS incidence rates may be due to stabilisation of any diagnostic drift, diversifying ethnicity and reduced sun seeking behaviours, particularly in younger generations. Mortality rates from MM have decreased since therapeutic developments in the early 2010s, and in younger generations before this. MM incidence and mortality are increasing most rapidly in males over 75 years old, the age-group with the highest incidence and expected growth in the future. These results support the importance of early melanoma detection, public health sun awareness campaigns, and better melanoma diagnostics.
Smooth Muscle Extracellular Matrix Modified Small Intestinal Submucosa Conduits Promote Peripheral Nerve Repair
Authors: Ya-Xing Li, Long-Mei Zhao, Xiu-Zhen Zhang, Xi-Kun Ma, Jing-Qi Liang, Ting-Jiang Gan, Heng Gong, Yan-Lin Jiang, Ye Wu, Yu-Ting Song, Yi Zhang, Yue Li, Xiao-Ting Chen, Cong-Hui Xu, Xiang-Yu Ouyang, Jesse Li-Ling, Hui Zhang, Hui-Qi Xie
Journal: Biomaterials (2025)
Proton pump inhibitors and the risk of Clostridioides difficile infection: A systematic review and dose-response meta-analysis
Authors: Matilda Finke, Annelies Boven, Erika Vlieghe, Lars Engstrand, Nicola Orsini, Nele Brusselaers
Journal: Journal of Infection (2025)

Clostridioides difficile is a leading cause of healthcare-associated infections globally with proton pump inhibitor (PPI) use as important modifiable risk factor. This study aimed to systematically synthesise global evidence on the dose-response relationship of PPI usage and the Clostridioides difficile infection (CDI) risk and to identify potential safe thresholds of PPI usage regarding CDI. PubMed, Embase, Web of Science, and Cochrane Library were searched for longitudinal studies regarding PPIs and CDI. Aggregated data were included in two separate two-stage random-effects dose-response meta-analyses regarding Defined Daily Dose (DDD) and PPI therapy duration. Pooled adjusted relative risks (RRs) with 95% confidence intervals compared to non-users of PPIs were estimated. Overall, 15 observational cohort and case-control studies were included with 7 studies (n=483,821) in the meta-analysis per DDD and 7 studies (n=516,441) per PPI therapy duration. Risk of bias was modest. Pooled dose-response estimates suggest linear trends with a RR of 1.05 (95% CI 0.89,1.23) per 10mg DDD, and of 1.02 (95% CI 1.00,1.05) per day of PPI therapy. Substantial residual heterogeneity was detected in both analyses (I2=91.4% per DDD and I2=99.4% per therapy duration), but inferring potential sources was limited. Our results indicate a possible increase in the risk of CDI with increasing dose and duration of PPI therapy. Underlying mechanisms and dosage thresholds for a clinically relevant risk increase remain unclear. There was no funding source for this study.
Comparative Effectiveness of Infliximab vs Ustekinumab for Endoscopic and Transmural Remission in Biologic Naïve Crohn’s Disease
Authors: Zicheng Huang, Na Diao, Qin Guo, Miao Li, Wenjie Cheng, Qingfan Yang, Hongsheng Yang, Zhaopeng Huang, Lishuo Shi, Jian Tang, Xiang Gao, Kang Chao
Journal: Clinical Gastroenterology and Hepatology (2025)
Continuous versus intermittent bolus dosing of beta-lactam antibiotics in a South African multi-disciplinary intensive care unit: a randomized controlled trial
Authors: Ayesha Bibi Khan, Mohd Hafiz Abdul-Aziz, Lucy Hindle, Jeffrey Lipman, Fetolang Simelela, Shahed Omar
Journal: Journal of Infection (2025)

Beta-lactams exhibit time-dependent bactericidal effects with continuous infusion (CI) suggested to provide superior antibiotic concentrations compared to intermittent bolus (IB). To determine whether beta-lactam CI improves day 14 clinical cure compared to IB in a South African, multi-disciplinary intensive care unit (ICU). Adult patients with sepsis receiving amoxicillin-clavulanate, piperacillin-tazobactam, imipenem-cilastatin and meropenem were randomized to 24-hour CI or IB. On screening, patients who received study antibiotics for more than 24hours, pregnant patients or patients on renal replacement therapy were excluded. The primary outcome, clinical cure, was defined as completion of antibiotics by day 14 without recommencement within 48hours. Secondary outcomes included ICU length of stay (LOS), ICU, day 28 and day 90 mortality. We enrolled 122 patients. The groups were balanced for baseline age, weight, sex, severity of illness, organ support, HIV status, diagnostic category and site of infection. Median antibiotic duration, CI group, 7 days (IQR 5-8.5) vs. IB group, 6 days (IQR 4-8), p=0.191, and median ICU LOS, CI, 9.5 days (IQR 6-15.5) vs. IB, 9 days (IQR 5-16), p= 0.575, were similar. Clinical cure in the CI group was 81% (52/64) vs. 74.1% (43/58) in the IB group), p=0.345. Day 90 relative risk of death was 0,57, 95% Confidence Interval 0.32 - 1.01) for the CI group compared to IB. Among critically ill patients meeting the sepsis-3 definition, this study could not demonstrate superiority of continuous infusion of beta-lactam antibiotics compared to intermittent bolus in achieving clinical cure.
CONSORT 2025 statement: updated guideline for reporting randomized trials
Authors: Sally Hopewell, An-Wen Chan, Gary S Collins, Asbjørn Hróbjartsson, David Moher, Kenneth F Schulz, Ruth Tunn, Rakesh Aggarwal, Michael Berkwits, Jesse A Berlin, Nita Bhandari, Nancy J Butcher, Marion K Campbell, Runcie C W Chidebe, Diana Elbourne, Andrew Farmer, Dean A Fergusson, Robert M Golub, Steven N Goodman, Tammy C Hoffmann, John P A Ioannidis, Brennan C Kahan, Rachel L Knowles, Sarah E Lamb, Steff Lewis, Elizabeth Loder, Martin Offringa, Philippe Ravaud, Dawn P Richards, Frank W Rockhold, David L Schriger, Nandi L Siegfried, Sophie Staniszewska, Rod S Taylor, Lehana Thabane, David Torgerson, Sunita Vohra, Ian R White, Isabelle Boutron
Journal: Nature Medicine (2025)
Hydroxyapatite microspheres encapsulated within hybrid hydrogel promote skin regeneration through the activation of Calcium Signaling and Motor Protein pathway
Authors: Shuo Liu, Lu Song, Shuwen Huang, Zhanhong Liu, Yang Xu, Zhiyuan Wang, He Qiu, Jing Wang, Zhiru Chen, Yumei Xiao, Hang Wang, Xiangdong Zhu, Kai Zhang, Xingdong Zhang, Hai Lin
Journal: Bioactive Materials (2025)
CONSORT 2025 statement: Updated guideline for reporting randomised trials
Authors: Sally Hopewell, An-Wen Chan, Gary S Collins, Asbjørn Hróbjartsson, David Moher, Kenneth F Schulz, Ruth Tunn, Rakesh Aggarwal, Michael Berkwits, Jesse A Berlin, Nita Bhandari, Nancy J Butcher, Marion K Campbell, Runcie C W Chidebe, Diana Elbourne, Andrew Farmer, Dean A Fergusson, Robert M Golub, Steven N Goodman, Tammy C Hoffmann, John P A Ioannidis, Brennan C Kahan, Rachel L Knowles, Sarah E Lamb, Steff Lewis, Elizabeth Loder, Martin Offringa, Philippe Ravaud, Dawn P Richards, Frank W Rockhold, David L Schriger, Nandi L Siegried, Sophie Staniszewska, Rod S Taylor, Lehana Thabane, David Torgerson, Sunita Vohra, Ian R White, Isabelle Boutron
Journal: PLoS Medicine (2025)

Background Well designed and properly executed randomised trials are considered the most reliable evidence on the benefits of healthcare interventions. However, there is overwhelming evidence that the quality of reporting is not optimal. The CONSORT (Consolidated Standards of Reporting Trials) statement was designed to improve the quality of reporting and provides a minimum set of items to be included in a report of a randomised trial. CONSORT was first published in 1996, then updated in 2001 and 2010. Here, we present the updated CONSORT 2025 statement, which aims to account for recent methodological advancements and feedback from end users. Methods We conducted a scoping review of the literature and developed a project-specific database of empirical and theoretical evidence related to CONSORT, to generate a list of potential changes to the checklist. The list was enriched with recommendations provided by the lead authors of existing CONSORT extensions (Harms, Outcomes, Non-pharmacological Treatment), other related reporting guidelines (TIDieR) and recommendations from other sources (e.g., personal communications). The list of potential changes to the checklist was assessed in a large, international, online, three-round Delphi survey involving 317 participants and discussed at a two-day online expert consensus meeting of 30 invited international experts. Results We have made substantive changes to the CONSORT checklist. We added seven new checklist items, revised three items, deleted one item, and integrated several items from key CONSORT extensions. We also restructured the CONSORT checklist, with a new section on open science. The CONSORT 2025 statement consists of a 30-item checklist of essential items that should be included when reporting the results of a randomised trial and a diagram for documenting the flow of participants through the trial. To facilitate implementation of CONSORT 2025, we have also developed an expanded version of the CONSORT 2025 checklist, with bullet points eliciting critical elements of each item. Conclusions Authors, editors, reviewers, and other potential users should use CONSORT 2025 when writing and evaluating manuscripts of randomised trials to ensure that trial reports are clear and transparent.
Corrigendum to “Genomic and transcriptional heterogeneity of multifocal hepatocellular carcinoma”
Authors: L X Xu, M H He, Z H Dai, J Yu, J G Wang, X C Li, B B Jiang, Z F Ke, T H Su, Z W Peng, Y Guo, Z B Chen, S L Chen, S Peng, M Kuang
Journal: Annals of Oncology (2025)
Cis-regulatory Alterations in FOXP4 Modulate Esophageal Cancer Susceptibility Induced by Chronic Alcohol Exposure
Authors: Siyuan Niu, Jialing Ma, Shasha Liu, Yueping Li, Xinying Yue, Miaoxin Pan, Lina Song, Yutong Wu, Zifei Yang, Yuqian Tan, Linglong Gu, Chaolong Wang, Jiang Chang
Journal: Cancer Research (2025)

Abstract Chronic alcohol exposure is a risk factor for developing esophageal squamous cell carcinoma (ESCC). To identify alcohol-responsive genes involved in esophageal carcinogenesis, we employed mouse models to systematically investigate alterations in cis-regulatory elements (CREs) in the esophageal epithelium across different ethanol exposure durations. A key exposure duration, 16 weeks of exposure to 20% ethanol, corresponded with increased expression of 222 genes that correlated with ESCC progression and were enriched in pathways related to epithelial proliferation and oncogenesis. Construction of a comprehensive CRE-gene map in human ESCC enables further evaluation of the role of the alcohol-responsive genes in ESCC susceptibility, identifying promoter and enhancer variants. A three-stage case-control study involving 9,033 ESCC cases and 10,801 controls revealed an enhancer variant, rs10223516, in FOXP4 that was associated with ESCC susceptibility through gene-alcohol interaction. The rs10223516 variant modulated FOXP4 expression through a long-range interaction, with the T allele exhibiting higher enhancer activity. Alcohol drinkers with the TT genotype exhibited a 76% higher risk of developing ESCC than non-drinkers with CC or TC genotype. Functional assays confirmed that the variant enhanced FOXP4 transcriptional activity, and upregulated FOXP4 promoted ESCC development in vivo. ChIP-seq and RNA-seq analyses further demonstrated that FOXP4 enhanced ESCC susceptibility and tumor growth by transcriptionally activating CYP26B1 and MYC. These findings highlight the complex gene-environment interactions between alcohol consumption and epigenetic alterations in esophageal tumorigenesis, offering potential targets for ESCC detection and prevention.
Immunological Tolerance to Luciferase and Fluorescent Proteins using Tol Mice Enables Development of Improved Tumor Models for Investigating Immunity and Metastasis
Authors: Kabir A. Khan, Areeba A. Qureshi, Ping Xu, Hung-Yang Kuo, Ton N. Schumacher, Iacovos P. Michael, Robert S. Kerbel
Journal: Cancer Research (2025)

Abstract There is a continuing need for improved preclinical mouse models of cancer that more accurately predict therapy outcomes for future clinical translation. Luciferase and bioluminescence have long been utilized to generate models conducive to non-invasive imaging to monitor tumor growth, disease progression and response to therapy. However, luciferase, as well as fluorescent reporter proteins, are highly immunogenic, limiting their use in some syngeneic tumor models in immunocompetent mice. Here, we described the utility of transgenic mice engineered to have tolerance to luciferase and several other reporter proteins, known as Tol mice, in cancer immunology research. Tumor cell lines expressing both luciferase and GFP were completely rejected in wild-type mice but maintained robust growth in Tol mice. Additionally, Tol mice allowed the development of an experimental brain metastasis model and a post-surgical resection spontaneous metastasis model. Importantly, even when certain cell lines carrying reporter proteins successfully formed tumors in immunocompetent wild-type mice, underlying immunity existed that could be reinvigorated by immune checkpoint inhibitors. Therefore, caution is needed when using such models in wild-type mice as exaggerated effects may be induced by immunotherapy. Tol mice circumvent this problem and will likely widen the number of orthotopic and metastatic tumor models that can be used in immunotherapy studies in both C57Bl/6 and BALB/c mice.