tbuckley/cabot-search huggingface dataset:
Injury risk factors and their priority for mitigation in women’s netball: a systematic review and Delphi consensus
Authors: Sarah Whitehead, Lois Mackay, Ben Jones, Omar Heyward, Aaron S Fox, Lucy Jane Chesson, Sean Scantlebury, Dina Christina (Christa) Janse van Rensburg
Journal: British Journal of Sports Medicine (2025)

This study aimed to establish consensus on injury risk factors in netball via a combined systematic review and Delphi method approach. A systematic search of databases (PubMed, Scopus, MEDLINE, SPORTDiscus and CINAHL) was conducted from inception until June 2023. Twenty-four risk factors were extracted from 17 studies and combined with a three-round Delphi approach to achieve consensus. In round one, experts listed perceived risk factors for injury in netball which were combined with the risk factors identified via the systematic review. In round two and round three, experts rated their level of agreement with each risk factor on a 5-point Likert scale (1, strongly disagree to 5, strongly agree). Consensus was defined as ≥80% agreement (with&lt;10% in disagreement). In round three, experts also rated the priority for mitigating the risk factor (1, very low to 5, very high). Nineteen experts participated in round one and round two, and 16 participated in round three (response rate 84%). One-hundred and nine risk factors for injury were identified by the systematic review and experts combined. Sixty-one risk factors reached consensus, categorised into five groups: ‘individual characteristics’ (n=22), ‘lifestyle’ (n=11), ‘training and competition’ (n=14), ‘sport science and medical provision’ (n=6) and ‘facilities and equipment’ (n=8). ‘Poor landing technique/mechanics’ had a median (IQR) mitigation priority rating of 5 (1), while all others had median ratings of 3–4.5. This study identifies a range of risk factors for injury, provides focus areas for injury prevention and highlights the importance of a multidisciplinary approach to injury mitigation in netball.
Evidence-Based Anticoagulation Choice for Acute Pulmonary Embolism
Authors: Brandon C. Maughan, Christopher Kabrhel, Angela F. Jarman
Journal: JAMA Network Open (2025)

William B. Stubblefield, MD, MPH; Ron Helderman, MD; Natalie Strokes, DO, MPH, MS; Colin F. Greineder, MD, PhD; Geoffrey D. Barnes, MD, MsC; David R. Vinson, MD; Lauren M. Westafer, DO, MPH, MS
Construction of exosome non-coding RNA feature for non-invasive, early detection of gastric cancer patients by machine learning: a multi-cohort study
Authors: Ze-Rong Cai, Yong-Qiang Zheng, Yan Hu, Meng-Yao Ma, Yi-Jin Wu, Jia Liu, Lu-Ping Yang, Jia-Bo Zheng, Tian Tian, Pei-Shan Hu, Ze-Xian Liu, Lin Zhang, Rui-Hua Xu, Huai-Qiang Ju
Journal: Gut (2025)

Background and objective Gastric cancer (GC) remains a prevalent and preventable disease, yet accurate early diagnostic methods are lacking. Exosome non-coding RNAs (ncRNAs), a type of liquid biopsy, have emerged as promising diagnostic biomarkers for various tumours. This study aimed to identify a serum exosome ncRNA feature for enhancing GC diagnosis. Designs Serum exosomes from patients with GC (n=37) and healthy donors (n=20) were characterised using RNA sequencing, and potential biomarkers for GC were validated through quantitative reverse transcription PCR (qRT-PCR) in both serum exosomes and tissues. A combined diagnostic model was developed using LASSO-logistic regression based on a cohort of 518 GC patients and 460 healthy donors, and its diagnostic performance was evaluated via receiver operating characteristic curves. Results RNA sequencing identified 182 candidate biomarkers for GC, of which 31 were validated as potential biomarkers by qRT-PCR. The combined diagnostic score (cd-score), derived from the expression levels of four long ncRNAs (RP11.443C10.1, CTD-2339L15.3, LINC00567 and DiGeorge syndrome critical region gene (DGCR9)), was found to surpass commonly used biomarkers, such as carcinoembryonic antigen, carbohydrate antigen 19-9 (CA19-9) and CA72-4, in distinguishing GC patients from healthy donors across training, testing and external validation cohorts, with AUC values of 0.959, 0.942 and 0.949, respectively. Additionally, the cd-score could effectively identify GC patients with negative gastrointestinal tumour biomarkers and those in early-stage. Furthermore, molecular biological assays revealed that knockdown of DGCR9 inhibited GC tumour growth. Conclusions Our proposed serum exosome ncRNA feature provides a promising liquid biopsy approach for enhancing the early diagnosis of GC.
Factors in Initial Anticoagulation Choice in Hospitalized Patients With Pulmonary Embolism
Authors: William B. Stubblefield, Ron Helderman, Natalie Strokes, Colin F. Greineder, Geoffrey D. Barnes, David R. Vinson, Lauren M. Westafer
Journal: JAMA Network Open (2025)

Despite guideline recommendations to use low-molecular-weight heparins (LMWHs) or direct oral anticoagulants in the treatment of most patients with acute pulmonary embolism (PE), US-based studies have found increasing use of unfractionated heparin (UFH) in hospitalized patients.
Long-term effect and safety of mesenchymal stromal cell therapy for radiation-induced hyposalivation in head and neck cancer survivors: A randomised, phase-2, trial
Authors: Amanda-Louise Fenger Carlander, Kathrine Kronberg. Jakobsen, Tobias Todsen, Natasja Paaske, Anne Kathrine. Østergaard Madsen, Simone Kloch. Bendtsen, Jens Kastrup, Jeppe Friborg, Charlotte Duch Lynggaard, Anne Werner. Hauge, Robin Christensen, Christian Grønhøj, Christian von Buchwald
Journal: Clinical Cancer Research (2025)

Abstract Background: The long-term effect of adipose-derived mesenchymal stromal cells (ASCs) to restore radiation-induced salivary gland hypofunction in previous head and neck cancer patients have not been validated in larger settings. Methods: The study was the 12-months follow-up of a randomised trial, including patients with hyposalivation. Patients were randomised to receive allogeneic ASCs or placebo in the submandibular glands. Primary endpoint was unstimulated whole saliva (UWS) followed by stimulated whole saliva, patient-reported outcomes (European Organization for Research and Treatment of Cancer Quality of Life Questionnaire, Head and Neck Module and the Xerostomia Questionnaire) and safety. Results: Of the 120 enrolled patients, 117 (97.5%) were assessed at 12 months. Treatment with ASCs did not increase UWS compared to placebo: increase in UWS was 0.02 mL/min (95% CI 0.01 to 0.04) in the ASC group and 0.02 mL/min (95% CI 0 to 0.03) in the placebo group, p=0.56. ASCs reduced the symptom burden for dry mouth with -10.07 units (95% CI -13.39 to -6.75) compared to -4.15 units (95% CI -7.46 to -0.84) in the placebo group, p=0.01. Compared to placebo, ASCs did not improve sticky saliva (-9.27 vs. -4.55 units, p=0.13), swallowing (-4.50 vs. 3.49 units, p=0.5) or xerostomia -3.12 vs. -2.74 units, p=0.82). Treatment was safe and associated with a transient immune response. Conclusion: Intraglandular ACS therapy in the submandibular glands significantly relieved subjective dry mouth symptoms. Both ASCs and placebo increased UWS, but ASCs did not prove superior to placebo in restoring salivary gland function, based on salivary flow rate.
Mortality Risk Prediction Models for People With Kidney Failure
Authors: Faisal Jarrar, Meghann Pasternak, Tyrone G. Harrison, Matthew T. James, Robert R. Quinn, Ngan N. Lam, Maoliosa Donald, Meghan Elliott, Diane L. Lorenzetti, Giovanni Strippoli, Ping Liu, Simon Sawhney, Thomas Alexander Gerds, Pietro Ravani
Journal: JAMA Network Open (2025)

People with kidney failure have a high risk of death and poor quality of life. Mortality risk prediction models may help them decide which form of treatment they prefer.
Exposure to School Racial Segregation and Late-Life Cognitive Outcomes
Authors: Zhuoer Lin, Yi Wang, Thomas M. Gill, Xi Chen
Journal: JAMA Network Open (2025)

Disparities in cognition, including dementia occurrence, persist between non-Hispanic Black (hereinafter, Black) and non-Hispanic White (hereinafter, White) older adults, and are possibly influenced by early educational differences stemming from structural racism. However, the association between school racial segregation and later-life cognition remains underexplored.
Nearly 1 in 3 US Pharmacies Have Closed Since 2010, Widening Access Gaps
Authors: Samantha Anderer
Journal: JAMA (2025)

Kelly E. Anderson, PhD, MPP; Maitreyi Sahu, MSPH; Michael J. DiStefano, PhD, MBE; Carl V. Asche, MBA, MSc, PhD; T. Joseph Mattingly II, PharmD, MBA, PhD
Quantifying the evolutionary dynamics of structure and content in closely-related E. coli genomes
Authors: Marco Molari, Liam P Shaw, Richard A Neher
Journal: Molecular Biology and Evolution (2025)

Abstract Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of E. coli ST131, which likely shared a common ancestor around one hundred years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2000 structural changes within the accessory genome, i.e. one structural change for every 3 core genome substitutions. 63% of loci with structural diversity could be resolved into individual gain and loss events with ten-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.
Clustering patients with COVID-19 according to respiratory support requirements, and its impact on short- and long-term outcome (RECOVID study)
Authors: Rosario Menéndez, Raúl Méndez, Ana Latorre, Paula González-Jiménez, Germán Peces-Barba, María Molina-Molina, Pedro Pablo España, Estela García, Angélica Consuegra-Vanegas, Marta María García-Clemente, Carolina Panadero, Juan Marco Figueira-Gonçalves, David De la Rosa-Carrillo, Oriol Sibila, María Dolores Martínez-Pitarch, Nuria Toledo-Pons, Cecilia López-Ramírez, Wanda Almonte-Batista, Abigail Macías-Paredes, Mercedes Villamon, Marisol Domínguez-Álvarez, Eli Nancy Pérez-Rodas, Javier Lázaro, Sarai Quirós, Rosa Cordovilla, Irene Cano-Pumarega, Antoni Torres
Journal: Pulmonology (2025)

Introduction The Spanish Society of Pulmonology and Thoracic Surgery created a registry for hospitalised patients with COVID-19 and the different types of respiratory support used (RECOVID). Objectives. To describe the profile of hospitalised patients with COVID-19, comorbidities, respiratory support treatments and setting. In addition, we aimed to identify varying profiles of patients according to outcomes and the complexity of respiratory support needed.
Tissue-resident NK cells do their own glandscaping
Authors: Jacob A. Myers, Shanelle P. Reilly, Laurent Brossay
Journal: The Journal of Experimental Medicine (2025)

In this issue of JEM, Sparano et al. (https://doi.org/10.1084/jem.20240930) present compelling evidence that salivary gland trNK cells originate from cNK cells and are developmentally distinct from ILC1 cells. Mechanistically, they demonstrate that continuous autocrine TGF-β signaling drives salivary gland tissue residency and works in synergy with IL-15 to enhance Hobit-dependent cytotoxicity.
Proteomic changes upon treatment with semaglutide in individuals with obesity
Authors: Lasse Maretty, Dipender Gill, Lotte Simonsen, Keng Soh, Loukas Zagkos, Michael Galanakis, Jonas Sibbesen, Miquel Triana Iglesias, Anna Secher, Dirk Valkenborg, Jonathan Q. Purnell, Lotte Bjerre Knudsen, Abd A. Tahrani, Milan Geybels
Journal: Nature Medicine (2025)

Abstract Obesity and type 2 diabetes are prevalent chronic diseases effectively managed by semaglutide. Here we studied the effects of semaglutide on the circulating proteome using baseline and end-of-treatment serum samples from two phase 3 trials in participants with overweight or obesity, with or without diabetes: STEP 1 ( n = 1,311) and STEP 2 ( n = 645). We identified evidence supporting broad effects of semaglutide, implicating processes related to body weight regulation, glycemic control, lipid metabolism and inflammatory pathways. Several proteins were regulated with semaglutide, after accounting for changes in body weight and HbA 1c at end of trial, suggesting effects of semaglutide on the proteome beyond weight loss and glucose lowering. A comparison of semaglutide with real-world proteomic profiles revealed potential benefits on disease-specific proteomic signatures including the downregulation of specific proteins associated with cardiovascular disease risk, supporting its reported effects of lowering cardiovascular disease risk and potential drug repurposing opportunities. This study showcases the potential of proteomics data gathered from randomized trials for providing insights into disease mechanisms and drug repurposing opportunities. These data also highlight the unmet need for, and importance of, examining proteomic changes in response to weight loss pharmacotherapy in future trials.
Single immunization with genetically attenuated Pf∆mei2 (GA2) parasites by mosquito bite in controlled human malaria infection: a placebo-controlled randomized trial
Authors: Geert V. T. Roozen, Roos van Schuijlenburg, Annefleur D. O. Hensen, Jan Pieter R. Koopman, Olivia A. C. Lamers, Fiona J. A. Geurten, Jeroen C. Sijtsma, Els Baalbergen, Jacqueline J. Janse, Séverine Chevalley-Maurel, Chanel M. Naar, Sascha Bezemer, Hans Kroeze, Huybert J. F. van de Stadt, Bram de Visser, Pauline Meij, Mara S. Tihaya, Emil Colstrup, Eva Iliopoulou, Helena M. de Bes-Roeleveld, Els Wessels, M. Y. Eileen C. van der Stoep, Chris J. Janse, Rajagopal Murugan, Blandine M. D. Franke-Fayard, Meta Roestenberg
Journal: Nature Medicine (2025)

Abstract Malaria vaccines consisting of metabolically active Plasmodium falciparum ( Pf ) sporozoites can offer improved protection compared with currently deployed subunit vaccines. In a previous study, we demonstrated the superior protective efficacy of a three-dose regimen of late-arresting genetically attenuated parasites administered by mosquito bite (GA2-MB) compared with early-arresting counterparts (GA1-MB) against a homologous controlled human malaria infection. Encouraged by these results, we explored the potency of a single GA2-MB immunization in a placebo-controlled randomized trial. Primary outcomes were safety and tolerability, time-to-parasitemia and protective efficacy. Humoral and cellular immunological results were considered secondary outcomes. Here we report the safe administration of GA2-MB with no breakthrough malaria and sterile protection in nine of ten participants at 6 weeks after a single immunization with 50 GA2-infected mosquitoes, compared with none of five mock-immunized participants, against a homologous controlled human malaria infection. Immunization increased circulating Pf -specific polyfunctional effector memory CD4 + T cells coexpressing tumor necrosis factor and interleukin-2. This unprecedented 90% protective efficacy after a single low-dose immunization holds great promise for the potency of GA2 immunization. Future studies should demonstrate whether GA2 is similarly efficacious in pre-exposed populations and whether the favorable safety profile reported here holds up in larger groups. ClinicalTrials.gov registration: NCT05468606 .
The Prognostic Role of HPV or p16INK4a Status in Penile Squamous Cell Carcinoma: A Meta-Analysis
Authors: Arfa Mustasam, Kevin Parza, Filip Ionescu, Keerthi Gullapalli, Mahati Paravathaneni, Youngchul Kim, Reagan E. Sandstrom, Majd Al Assaad, G. Daniel Grass, Peter Johnstone, Steven Eschrich, Houssein Safa, Juskaran Chadha, Gabriel Roman Souza, Jerel David, Adele Semaan, Niki M. Zacharias, Curtis Pettaway, Anna R. Giuliano, Philippe E. Spiess, Jad Chahoud
Journal: Journal of the National Comprehensive Cancer Network (2025)

Background: HPV infection is implicated in approximately half of global penile squamous cell carcinoma (PSCC) cases. Previous studies on HPV DNA and p16 INK4a status in PSCC have yielded inconclusive prognostic findings. This meta-analysis aims to elucidate the prognostic role of HPV in PSCC by pooling data on disease-free survival (DFS), disease-specific survival (DSS), and overall survival (OS). Methods: We systematically searched Medline and Embase up to January 2023 for relevant human studies. Data from eligible publications reporting HPV DNA or p16 INK4a status, along with and DFS, DSS, or OS outcomes, were extracted. A random-effects meta-analysis model was used to synthesize data, with study weights based on size and significance. The study protocol was registered with PROSPERO (CRD42019131355). Results: Out of 544 studies screened, 34 publications were included, comprising a pooled sample size of 3,944 patients. p16 INK4a -positive status was associated with improved OS (hazard ratio [HR], 0.54; 95% CI, 0.39–0.75; I 2 =31%), DFS (HR, 0.52; 95% CI, 0.29–0.94; I 2 =20%), and DSS (HR, 0.34; 95% CI, 0.23–0.50; I 2 =18%). HPV DNA positivity was significantly associated with improved DFS (HR, 0.63; 95% CI, 0.46–0.87; I 2 =13%) and DSS (HR, 0.46; 95% CI, 0.29–0.75; I 2 =47%) but not OS (HR, 0.92; 95% CI, 0.74–1.11; I 2 =0%). Conclusions: This meta-analysis, comprising the largest number of patients with PSCC to date, shows a notable correlation between p16 INK4a immunohistochemistry positivity and survival outcomes. These findings support the understanding that penile cancer cases not associated with HPV tend to behave more aggressively. We support p16 INK4a immunohistochemistry testing as part of the initial diagnostic evaluation of patients with PSCC.
Researchers Compared Hospital Early Warning Scores for Clinical Deterioration—Here’s What They Learned
Authors: Roy Perlis, Jennifer Abbasi
Journal: JAMA (2025)

This Medical News article is an interview with Dana P. Edelson, MD, MS, an expert in cardiac resuscitation at the University of Chicago and cofounder and chief medical officer of AgileMD, the company that makes the AI-driven early warning score software eCART.
Longer Ice Hockey Play Tied to Greater Risk of CTE
Authors: Samantha Anderer
Journal: JAMA (2025)

Jesse Mez, MD, MS; Daniel H. Daneshvar, MD, PhD; Patrick T. Kiernan, BA; Bobak Abdolmohammadi, BA; Victor E. Alvarez, MD; Bertrand R. Huber, MD, PhD; Michael L. Alosco, PhD; Todd M. Solomon, PhD; Christopher J. Nowinski, PhD; Lisa McHale, EdS; Kerry A. Cormier, BA; Caroline A. Kubilus; Brett M. Martin, MS; Lauren Murphy, MBA; Christine M. Baugh, MPH; Phillip H. Montenigro, BA; Christine E. Chaisson, MPH; Yorghos Tripodis, PhD; Neil W. Kowall, MD; Jennifer Weuve, MPH, ScD; Michael D. McClean, ScD; Robert C. Cantu, MD; Lee E. Goldstein, MD, PhD; Douglas I. Katz, MD; Robert A. Stern, PhD; Thor D. Stein, MD, PhD; Ann C. McKee, MD
Cancer Prevention, Screening Averted Several Million More Deaths Than Treatment Over 45 Years
Authors: Samantha Anderer
Journal: JAMA (2025)

Katrina A. B. Goddard, PhD; Eric J. Feuer, PhD; Jeanne S. Mandelblatt, MD, MPH; Rafael Meza, PhD; Theodore R. Holford, PhD; Jihyoun Jeon, PhD; Iris Lansdorp-Vogelaar, PhD; Roman Gulati, MS; Natasha K. Stout, PhD; Nadia Howlader, PhD; Amy B. Knudsen, PhD; Daniel Miller, BA; Jennifer L. Caswell-Jin, MD; Clyde B. Schechter, MD; Ruth Etzioni, PhD; Amy Trentham-Dietz, PhD; Allison W. Kurian, MD, MSc; Sylvia K. Plevritis, PhD; John M. Hampton, MS; Sarah Stein, PhD; Liyang P. Sun, MS; Asad Umar, DVM, PhD; Philip E. Castle, PhD
Validating a Case Definition for Transgender Adults Using Administrative Data
Authors: Chantal L. Rytz, James A. King, Nathalie Saad, Paul E. Ronksley, Ranjani Somayaji, Satish R. Raj, Sandra M. Dumanski, Amelia M. Newbert, Lindsay D. Peace, Sofia B. Ahmed
Journal: JAMA Network Open (2025)

Importance Administrative health data serve as promising data sources to study transgender health at a population level in the absence of self-reported gender identity. Objective To develop and validate case definitions identifying transgender adults in administrative data compared with the reference standard of self-reported gender identity in a universal health care setting. Design, Setting, and Participants In this cohort study conducted in Alberta, Canada, data from provincial administrative health data sources including inpatient hospitalizations, emergency department encounters, primary care visits, prescription drug dispensations, and the provincial health insurance registry were linked and used to develop 15 case definitions (9 for transgender women and 6 for transgender men). Participants aged 18 years or older with a provincial health care number between April 1, 1994, and March 31, 2021, were included and stratified by sex marker (eg, female or male) at study entry. Data analysis was from December 2023 to March 2024. Main Outcomes and Measures For each case definition, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated against the reference standard of self-reported gender identity. Results In this cohort study of 5 375 735 individuals, the reference standard consisted of 141 self-identified transgender women, 174 self-identified transgender men, 111 self-identified cisgender women, and 65 self-identified cisgender men. The final cohort representing transgender women participants who met at least 1 case definition and/or were part of the standard reference totaled 63 977. Combining a case definition employing male sex registry identification and 2 or more dispensations of estrogen or a case definition employing male sex registry identification and at least 1 gender-related diagnostic code demonstrated a sensitivity of 86.6% (95% CI, 79.9%-91.7%), specificity of 62.5% (95% CI, 51.5%-72.6%), PPV of 78.8% (95% CI, 71.6%-85.0%), and NPV of 74.3% (95% CI, 62.8%-83.8%). The final cohort representing transgender men participants who met at least 1 case definition and/or were part of the standard reference totaled 26 852. Combining a case definition employing female sex registry identification and 2 or more dispensations of testosterone or a case definition employing female sex registry identification and at least 1 gender-related diagnostic code demonstrated a sensitivity of 78.2% (95% CI, 71.3%-84.1%), specificity of 89.2% (95% CI, 82.2%-94.1%), PPV of 91.3% (95% CI, 85.5%-95.3%), and NPV of 73.8% (95% CI, 65.8%-80.7%). Conclusion and Relevance These findings suggest that case definitions using transgender-related diagnostic codes and gender-affirming hormone prescriptions can be used to study the epidemiology, disease burden, and health care utilization of transgender populations.
Development of KRAS Inhibitors and Their Role for Metastatic Colorectal Cancer
Authors: Dustin A. Deming
Journal: Journal of the National Comprehensive Cancer Network (2025)

Colorectal cancer (CRC) is a heterogeneous group of diseases comprising several molecular subtypes. Comprehensive DNA sequencing is now standard practice to identify these subtype. Until recently, KRAS mutation status in metastatic CRC was primarily used as a biomarker to predict resistance to EGFR inhibition. However, with up to 40% of CRC cases harboring KRAS mutations, therapeutic targeting of RAS has been an area of great need. The development of KRAS G12C inhibitors has led to the FDA approval of drugs for treating non–small cell lung cancer. Recently, these and other newly developed inhibitors have been investigated as monotherapies and in combination for metastatic KRAS G12C -mutant CRC. This review examines the development of these inhibitors and highlights data supporting the inclusion of sotorasib and adagrasib, in combination with either panitumumab or cetuximab, in the NCCN Guidelines for CRC for the treatment of refractory metastatic disease.