tbuckley/cabot-search huggingface dataset:
A systematic review of clinicians’ acceptance and use of clinical decision support systems over time
Authors: Nicki Newton, Adeola Bamgboje-Ayodele, Rowena Forsyth, Amina Tariq, Melissa T Baysari
Journal: npj Digital Medicine (2025)

Abstract Existing reviews have identified factors influencing Clinical Decision Support (CDS) adoption by clinicians in practice but overlook the dynamic and evolving nature of technology and users’ needs over time. This review aimed to identify factors that influence early, mid-term, and sustained acceptance and use of CDS in hospital settings. Five databases were searched from 2007 to January 2024 and 67 papers were included. Factors were extracted and synthesised according to the time that data were collected following CDS implementation. Factors relating to the CDS intervention (e.g. utility) and inner setting (e.g. fit with workflows) were reported across all time periods. Perceived outcomes were more often identified in the first year of use, and individual factors after the first 6 months of use. Strategies to work around CDS limitations were reported 5 years after implementation. Our review provides guidance for developing, implementing, and supporting ongoing use of CDS systems.
Dual targeted ferritin-based delivery system blocks the crosstalk between cancer cells and cancer-associated fibroblasts to potentiate immunotherapy of colorectal cancer
Authors: Zhian Chen, Jinmei Cheng, Zhenhao Li, Huilin Huang, Yingxin Ren, Yang Zhou, Jinhui Li, Qianbing Zhang, Xiaopin Duan, Yanfeng Hu
Journal: Journal of Controlled Release (2025)
Synergistic blockade of SHP-2 and A2AR signal pathways with targeted nanoparticles restores anti-tumor immunity of CD8+ T cells
Authors: Mingshui Chen, Lingyu Zhang, Wansong Lin, Zhifeng Zhou, Yang Wang, Ling Wang, Hexi Gu, Jieyu Li, Zhi Ping Xu
Journal: Journal of Controlled Release (2025)
Evolutionary Genomics Unravels the Responses and Adaptation to Climate Change in a Key Alpine Forest Tree Species
Authors: Zhiqin Long, Yupeng Sang, Jiajun Feng, Xinxin Zhang, Tingting Shi, Lushui Zhang, Kangshan Mao, Loren H Rieseberg, Jianquan Liu, Jing Wang
Journal: Molecular Biology and Evolution (2025)

Abstract Despite widespread biodiversity loss, our understanding of how species and populations will respond to accelerated climate change remains limited. In this study, we integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa, a key alpine forest tree species primarily distributed in the mountainous regions of a global biodiversity hotspot. Over historical timescales, our findings demonstrate that demographic dynamics, divergent selection, and long-term balancing selection have shaped and maintained genetic variation within and between populations. In examining genomic signatures of contemporary climate adaptation, we found that haplotype blocks, potentially caused by inversion polymorphisms that suppress recombination, are linked to enriched combinations of locally adaptive environmental variations. We further assessed the relative contributions of environmentally induced plastic responses, constitutive expression divergence between genetic clusters, and their interactions in driving gene expression variation and divergence. Notably, we observed a strong correlation between sequence divergence and constitutive differential expression among genetic clusters. Finally, by incorporating genetic adaptation, migration, and genetic load into our predictions of population-level climate change risks, we identified western populations-primarily distributed in the Hengduan Mountains, a region known for its environmental heterogeneity and significant biodiversity—as the most vulnerable to climate change. These populations should be prioritized for conservation and management. Overall, our study advances the understanding of the relative roles of long-term natural selection, local environmental adaptation, and immediate plastic expression changes in shaping the responses of natural populations of keystone species to climate change.
New insights in amino sugar metabolism by the gut microbiome
Authors: Wenqiang Shen, Jan Freark de Boer, Folkert Kuipers, Jingyuan Fu
Journal: Gut Microbes (2025)

Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of energy for intestinal bacteria are glycans, of which amino sugars are important components. Amino sugars are a class of carbohydrates in which one or more hydroxyl groups are substituted with amino groups. However, bacterial utilization of amino sugars and their impact on the gut microbiome and host health have not been thoroughly assessed. In this review, we summarize the latest discoveries about amino sugar metabolism by gut microbes, paying particular attention to the metabolism of N-acetyl-galactosamine (GalNAc), one of the most abundant amino sugars in the intestine, and its potential implications for microbial functionality and host health.
Transient mRNA CAR T cells targeting GD2 provide dose-adjusted efficacy against diffuse midline glioma and high grade glioma models
Authors: Jessica B Foster, Peter J Madsen, Kyra Harvey, Crystal Griffin, Allison Stern, Luke Patterson, Nikhil Joshi, Conor Dickson, Olivia McManus, Ezra Beaubien, Cullen Wilson, David R Beale, Valerie Baubet, Payush N Goel P, Nicholas A Vitanza, Javad Nazarian, Mateusz Koptyra, Phillip B Storm, Adam C Resnick
Journal: Neuro-Oncology (2025)

Abstract Background Diffuse midline glioma (DMG) and high grade glioma are devastating pediatric central nervous system tumors that remain incurable. Recent chimeric antigen receptor (CAR) T cell studies have shown proof of concept and early signs of efficacy against DMG targeting GD2. Prior work and ongoing clinical trials have focused on using viral vectors to create permanent CAR T cells. However, virally transduced GD2-directed CAR T cells have shown significant neurotoxicity in both pre-clinical models and human trials. Methods We evaluated transient CAR T cells targeting GD2 created with mRNA, assessing for efficacy and safety in cell line, organoid, and in vivo xenograft models with repetitive intratumoral dosing. Results We show that mRNA GD2-directed CAR T cells are active against both cell lines and organoid models of DMG and high grade glioma in vitro. Cytotoxicity consistently abates over 9 days, highlighting the potential to avoid toxicity from persistent T cell activity. In both pontine and thalamic DMG xenograft models, repeated doses of mRNA GD2-directed CAR T cells were titrated down to maintain therapeutic effect without causing neurologic toxicity. Conclusions Our results demonstrate the utility of transient mRNA CAR T cells delivered intratumorally to provide effective tumor killing with a defined half-life, allowing for modulation of the dose and potential side effects. We anticipate this study will expand the use of CAR T cell therapy for DMG and other central nervous system tumors and non-malignant disorders, where concern for toxicity from permanently expressing CAR T cells may hinder development.
Relaxed purifying selection is associated with an accumulation of transposable elements in flies
Authors: Vincent Mérel, Théo Tricou, Nelly Burlet, Annabelle Haudry
Journal: Molecular Biology and Evolution (2025)

Abstract Although the mechanisms driving genome size evolution are not yet fully understood, one potentially important factor is the dynamics of the accumulation of transposable elements (TEs). Since most TEs are neutral or slightly deleterious, a negative correlation between genome size and the efficacy of selection is expected. However, previous empirical studies on closely related species with distinct life history traits (thought to undergo different selective regimes) have yielded inconsistent results. Here, we perform the first large-scale analysis of the effect of genetic drift on genome size evolution, without any prior assumption on the amount of genetic drift. We reconstructed a phylogeny based on whole-genome data (2,242 genes) for 77 Drosophilid species to examine correlations between genome size, TE content, and the efficacy of selection (using dN/dS ratios of non-synonymous to synonymous divergence). Using an integrative approach that controls for shared evolutionary history, we reveal that genome-wide dN/dS are strongly positively correlated with genome size and TE content, particularly in GC-poor genes. This study suggests the critical importance of controlling for heterogeneity in base composition when estimating dN/dS. Furthermore, we emphasize that the lack of evidence for TE accumulation due to increased genetic drift in several previous studies may be due to a secondary effect of changes in life history traits (i.e. asexuality) on TE dynamics. In conclusion, this work provides evidence for TE proliferation in fly genomes when purifying selection is reduced, shedding new light on the role of TEs and genetic drift in the evolution of genome architecture.
DNA repair and the contribution to chemotherapy resistance
Authors: Ksenija Nesic, Phoebe Parker, Elizabeth M Swisher, John J Krais
Journal: Genome Medicine (2025)

The DNA damage response comprises a set of imperfect pathways that maintain cell survival following exposure to DNA damaging agents. Cancers frequently exhibit DNA repair pathway alterations that contribute to their intrinsic genome instability. This, in part, facilitates a therapeutic window for many chemotherapeutic agents whose mechanisms of action often converge at the generation of a double-strand DNA break. The development of therapy resistance occurs through countless molecular mechanisms that promote tolerance to DNA damage, often by preventing break formation or increasing repair capacity. This review broadly discusses the DNA damaging mechanisms of action for different classes of chemotherapeutics, how avoidance and repair of double-strand breaks can promote resistance, and strategic directions for counteracting therapy resistance.
Accounting for chimerism in demographic inference: reconstructing the history of common marmosets (<i>Callithrix jacchus</i>) from high-quality, whole-genome, population-level data
Authors: Vivak Soni, Cyril J Versoza, Eric J Vallender, Jeffrey D Jensen, Susanne P Pfeifer
Journal: Molecular Biology and Evolution (2025)

Abstract As a species of considerable biomedical importance, characterizing the evolutionary genomics of the common marmoset (Callithrix jacchus) is of significance across multiple fields of research. However, at least two peculiarities of this species potentially preclude commonly utilized population genetic modeling and inference approaches: a high frequency of twin births and hematopoietic chimerism. We here investigate these effects within the context of demographic inference, demonstrating via simulation that neglecting these biological features results in significant mis-inference of the underlying population history. Based upon this result, we develop a novel approximate Bayesian inference approach accounting for both common twin-births as well as chimeric sampling. In addition, we newly present population genomic data from 15 individuals sequenced to high-coverage, and utilize gene-level annotations to identify neutrally evolving intergenic regions appropriate for demographic inference. Applying our developed methodology, we estimate a well-fitting population history for this species, which suggests robust ancestral and current population sizes, as well as a size reduction roughly 7,000 years ago likely associated with a shift from arboreal to savanna vegetation in north-eastern Brazil during this period.
<i>ShiNyP</i>: Unlocking SNP-Based Population Genetics—An AI-Assisted Platform for Rapid and Interactive Visual Exploration
Authors: Yen-Hsiang Huang, Ling-Yu Chen, Endang M Septiningsih, Pei-Hsiu Kao, Chung-Feng Kao
Journal: Molecular Biology and Evolution (2025)

Abstract Efficient and accessible analysis of genome-wide single nucleotide polymorphism (SNP) data is vital for advancing molecular biology, evolutionary genetics, and breeding research. However, current analytical pipelines are often fragmented and require command-line expertise, limiting accessibility for many researchers. Here, we present ShiNyP, an interactive R/Shiny platform that integrates all popular SNP analysis modules within a single and intuitive user interface, supporting the entire workflow from data import and quality control to population structure inference, diversity analysis, selective scan, and core collection. ShiNyP accommodates datasets from haploid, diploid, and polyploid species and automates the generation of over 70 publication-ready visualizations and summary tables. A distinctive feature is its automated report module, which employs generative AI to deliver structured, interpretable narratives of complex statistical results. Performance benchmarks demonstrate that ShiNyP efficiently processes large-scale datasets on standard hardware. The ShiNyP platform is freely available at https://github.com/TeddYenn/ShiNyP, providing an efficient, reproducible, and user-friendly solution for population genomics research.
Artificial-intelligence derived coronary plaque features predict incident acute ischemic stroke independent of cardioembolic risk factors
Authors: Robert Luceri, Francesca Calicchio, Fatima Amin, Livia De Sousa Domingues Da Silva, Eric Hu, Najah Khan, Gavin Cobb, Elizabeth Epstein, Melody Hermel, Shawn Newlander, Mary Kalafut, Austin Robinson, Jorge Gonzalez, George Wesbey III
Journal:  (2025)
Sustained oxygen-releasing hydrogel implants enhance flap regeneration by promoting mitochondrial biogenesis under mild hypoxia
Authors: Sungmi Jeon, Seol-Ha Jeong, Mi Hyun Lee, Jeong Wook Seo, Da-Seul Kim, Nicole Joy Bassous, Javier Alejandro Lozano Soto, Cholong Choi, Montserrat Legorreta Gonzalez, Elaine Belén Nolasco Díaz, Hyunho Kim, Su Ryon Shin, Ji-Ung Park
Journal: Bioactive Materials (2025)
Associations Between Unconditional Cash Transfers and Postpartum Outcomes in the United States
Authors: Sahar A. Choudhry, G. Saradjha Brédy, Cyerra Cruise, Qai Hinds, Margaret A. McConnell, Sumit Agarwal, David B. Flynn, Mara E. Murray Horwitz
Journal: Annals of Internal Medicine (2025)

Unconditional cash transfers (UCTs) through social programs or direct cash transfers (DCTs) may address drivers of pregnancy-related morbidity and mortality. To summarize evidence on UCTs and postpartum outcomes in the United States. PubMed, Embase, Web of Science, Social Science Research Network, and structured internet searches through 28 January 2025. Primary research reporting associations between UCTs and postpartum outcomes (0 to 2 years after delivery) in the United States. Dual data extraction with predefined outcomes: infant or child care, reproductive health, substance use, other mental health outcomes, and other outcomes. Study quality was assessed using the Cochrane Risk of Bias 2 and ROBINS-I (Risk Of Bias In Non-randomised Studies - of Interventions) tools. Strength of evidence (SOE) was assessed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach. Eleven reports from 6 studies were identified. Four quasi-experimental (QE) studies examined 3 different social programs, 2 of which targeted populations with low incomes. Seven reports from 2 randomized controlled trials (RCTs) examined DCTs to postpartum persons with low incomes. The evidence on UCTs showed an increase in breastfeeding (high SOE [2 RCTs, 2 QE studies]), little or no difference in postpartum mood (high SOE [1 RCT, 2 QE studies]), and low SOE or insufficient evidence for all other associations. Unpublished studies and those not published in English may have been missed. Nonrandomized studies were subject to reporting or recall bias, reducing SOE. Study heterogeneity prevented meta-analysis. Unconditional cash transfers increase breastfeeding in diverse settings and populations and result in little or no difference in postpartum mood specifically in persons with low incomes. No studies examined DCTs given during pregnancy. More evidence is needed on associations between UCTs and key clinical outcomes, such as postpartum maternal morbidity and mortality. None. (Registered on Open Science Framework [https://osf.io/4c3nx]).
Statin Therapy as Primary Prevention for Persons With HIV: A Synopsis of Recommendations From the U.S. Department of Health and Human Services Antiretroviral Treatment Guidelines Panel
Authors: Craig Beavers, Alice K. Pau, David Glidden, Emily Hyle, Safia Kuriakose, Seth S. Martin, Grace McComsey, Melanie Thompson, Salim Virani, Jason V. Baker
Journal: Annals of Internal Medicine (2025)

REPRIEVE (Randomized Trial to Prevent Vascular Events in HIV) showed benefits of pitavastatin as preventive therapy for atherosclerotic cardiovascular disease (ASCVD) in people with HIV (PWH). In February 2024, the U.S. Department of Health and Human Services Panel for the Use of Antiretroviral Agents in Adults and Adolescents with HIV (ARV Guidelines Panel) developed statin therapy recommendations for PWH. These recommendations were issued in collaboration with representatives from the American College of Cardiology (ACC), the American Heart Association (AHA), and the HIV Medicine Association (HIVMA). This synopsis summarizes the development process, the recommendations, and how they supplement the AHA/ACC/multisociety cholesterol guidelines and outlines gaps in primary prevention of ASCVD for PWH. The ARV Guidelines Panel convened a writing group of 10 members (6 members of the Panel with expertise in HIV-related comorbid conditions, biostatistics, and pharmacology and 4 consultants representing ACC, AHA, and HIVMA with cardiometabolic and HIV management expertise). The writing group reviewed REPRIEVE trial data, other studies evaluating the use of statins in PWH, and the AHA/ACC/multisociety cholesterol guidelines to devise recommendations. Recommendations were based on scientific evidence with a rating scheme developed since the 1998 inception of the ARV guidelines. Proposed recommendations were presented to the full ARV Guidelines Panel, rated via vote, and approved by the Panel's voting members. These recommendations were then endorsed by ACC, AHA, and HIVMA. The ARV Guidelines Panel issued a strong recommendation for initiating statin therapy among PWH with a 10-year ASCVD risk score of 5% or higher, whose absolute benefit from statins in REPRIEVE was greatest. For patients with a 10-year ASCVD risk score below 5%, the Panel favored statins but recommended patient-clinician risk discussions considering additional HIV-related factors that can increase ASCVD risk.
All-cause mortality and infection-related outcomes of hospital-initiated kangaroo care versus conventional neonatal care for low-birthweight infants: a systematic review and meta-analysis
Authors: Chiara Minotti, Kerstin Jost, Soheila Aghlmandi, Chloé Schlaeppi, Elske Sieswerda, C Henri van Werkhoven, Sven M Schulzke, Julia A Bielicki
Journal: The Lancet Child & Adolescent Health (2025)
Cost-effective pricing of long-acting injectable HIV pre-exposure prophylaxis for adolescent girls and young women in South Africa: a model-based analysis
Authors: Elena Y Jin, Ali R Ahmed, Linda-Gail Bekker, Elzette Rousseau, Caitlin M Dugdale, Clare F Flanagan, Melissa Wallace, Kenneth A Freedberg, Catherine Orrell, Krishna P Reddy, A David Paltiel, Andrea L Ciaranello, Anne M Neilan
Journal: The Lancet Global Health (2025)
Health-related quality of life, pain, and symptomatic skeletal events with [177Lu]Lu-PSMA-617 in patients with progressive metastatic castration-resistant prostate cancer (PSMAfore): an open-label, randomised, phase 3 trial
Authors: Karim Fizazi, Michael J Morris, Neal D Shore, Kim N Chi, Michael Crosby, Johann S de Bono, Ken Herrmann, Guilhem Roubaud, James Nagarajah, Mark Fleming, Brian Lewis, Luke Nordquist, Natalie Carnahan, Samson Ghebremariam, Marianna Hertelendi, Daniel Castellano, Oliver Sartor
Journal: The Lancet Oncology (2025)
Mast cells activated in vitro can modulate macrophage polarization and antibacterial responses
Authors: Dorothea B. Holter, Sophie Zahalka, Jessica Brösamlen, Mariem Radhouani, Martin L. Watzenboeck, Tyler J. Artner, Asma Farhat, Riem Gawish, Karin Lakovits, Anastasiya Hladik, Federica Quattrone, Wolfgang Weninger, Thomas Krausgruber, Shane J.F. Cronin, Shweta Tikoo, Rohit Jain, Sylvia Knapp, Nikolaus Fortelny, Philipp Starkl
Journal: Journal of Allergy and Clinical Immunology (2025)
The chemokine CCL20 promotes hepatocyte cholesterol deposition during metabolic dysfunction-associated steatohepatitis by regulating OLR1 expression
Authors: Min Yin, Yan Zhang, Suosi Liu, Qianrong Wang, Yu Zhang, Jiali Min, Jiahui Yang, Yuyan Zhao, Zhiguang Zhou, Xia Li, Shanshan Liu
Journal: Metabolism (2025)
Humans as a potential reservoir for the emerging ST301 Shiga toxin-producing Escherichia coli clones of serotype O80:H2 ?
Authors: Frédéric Auvray, Federica Gigliucci, Valeria Michelacci, Gaia Scavia, Laurent Cavalié, Aurélie Cointe, Florence Crombé, Flemming Scheutz, Claire Jenkins, Stefano Morabito, Stéphane Bonacorsi, Eric Oswald
Journal: Clinical Microbiology and Infection (2025)
Body-site specific associations between human skin microbiome composition and psychological wellbeing
Authors: John Tyson-Carr, Joy Leng, Margaret Scott, Suzi Adams, Michael Hoptroff, Barry Murphy, Nick Fallon, Steve Paterson, Anna Thomas, Timo Giesbrecht, Carl Roberts
Journal: British Journal of Dermatology (2025)

Abstract Background/Objectives There is increasing scientific interest in understanding the interplay between psychological wellbeing and the human microbiome, with a particular focus on the gut microbiome's impact on psychological health. However, the role of the skin microbiome remains underexplored. The current study addresses this gap by investigating the relationship between the human skin microbiome at various body sites (face, scalp, forearm, axilla) and psychological wellbeing. This unique multi body site investigation aims to provide an understanding of the skin microbiome’s role in psychological health. Methods Fifty-three participants underwent microbiome sampling via skin swabbing from four body regions (forearm, face, scalp, and axilla) and completed psychological measures of global/general wellbeing (Affect Grid, Sleep Quality, Stress NRS-11, PSS-10) and body site-related wellbeing (Hair &amp; ScalpCARE, SkinCARE, UnderarmCARE). All bacterial DNA extracts were analysed using quantitative polymerase chain reaction (qPCR) and Illumina sequencing of the V1 – V2 region of the 16S gene. Microbial diversity was computed as Shannon diversity and Faith’s Phylogenetic diversity. Correlations were determined between psychological measures, microbial diversity, and genera for each body site. Results The current study uncovered that specific bacterial genera were associated with aspects of wellbeing. Specifically, Cutibacterium showed consistent associations with psychological wellbeing across multiple body locations. Key findings showed increased Cutibacterium on the face and axilla was associated with reduced stress, increased Cutibacterium in the axilla was associated with increased mood pleasantness. Conclusions These findings highlight, for the first time, the nuanced relationship between skin microbiome and psychological wellbeing. Increased Cutibacterium across multiple body-sites was consistently associated with positive wellbeing outcomes. This underscores the need for further investigation into specific bacterial taxa that may be involved in a skin-brain axis, as well as the importance of specific microbial communities on the body and their potential influence on this connection.
Successful preoperative esophageal cleansing for achalasia with esophageal dilatation using the drainage method and gel immersion
Authors: Satoshi Abiko, Haruhiro Inoue, Kei Ushikubo, Kazuki Yamamoto, Yohei Nishikawa, Ippei Tanaka, Naoya Sakamoto
Journal: Endoscopy (2025)