tbuckley/cabot-search huggingface dataset:
Psychosocial burden and the impact of illness perceptions and stigma on quality of life, anxiety and depression in alopecia areata: results from the Alopecia+Me study
Authors: Evangelos Christou, Nikolina Lalagianni, Sheila M McSweeney, Chantal Cotter, Chuin Ying Ung, Jessica Walburn, Paul McCrone, Mark A Turner, John A McGrath, John Weinman, Christos Tziotzios
Journal: British Journal of Dermatology (2025)

Alopecia areata (AA) can significantly impact patients' quality of life (QoL) and mental health, with increased levels of anxiety and depression. It is unclear whether this impact is more strongly associated with disease severity or patients' disease perception, and which patients are more likely to have a greater psychological burden. Examine AA's psychosocial impact, whilst focusing on illness perceptions and stigma, aiming to identify high-risk subgroups and key perceptions linked to worse QoL, anxiety and depression. This was a UK cross-sectional online study. It comprised 596 patients with AA who self-reported disease severity and completed the Dermatology Life Quality Index (DLQI), EuroQol 5-dimensional 5-level (EQ-5D-5L), Hospital Anxiety and Depression Scale (HADS), Stigma Scale for Chronic Illnesses 8-Item (SSCI-8), and Brief Illness Perception Questionnaire (BIPQ). Patients with AA perceived their condition as chronic and life-impacting, with limited personal or treatment control, significant emotional effects, and high concern. Many reported high levels of anxiety, depression, stigma and impaired QoL, all strongly associated with illness perceptions. Hierarchical regression analyses showed that illness perceptions and stigma explained a higher proportion of variance in QoL, anxiety and depression than disease severity. Cluster analysis identified two distinct patient groups based on illness perceptions, with different levels of QoL, anxiety, depression, and stigma. AA has a severe psychosocial impact, more strongly linked to patients' illness perceptions and stigma than disease severity. The identification of two distinct patient profiles based on illness perceptions reveals differences in psychosocial burden, highlighting those at risk of worse outcomes and underscoring the value of evaluating illness perceptions along with stigma in clinical practice to improve patient outcomes.
Lipopeptide-mediated delivery of CRISPR/Cas9 ribonucleoprotein complexes for gene editing and correction
Authors: Mert Öktem, Thai Hoang Nguyen, Esmeralda D C Bosman, Marcel H A M Fens, Massimiliano Caiazzo, Enrico Mastrobattista, Zhiyong Lei, Olivier G de Jong
Journal: Journal of Controlled Release (2025)
Multi-view hybrid graph convolutional network for volume-to-mesh reconstruction in cardiovascular MRI
Authors: Nicolás Gaggion, Benjamin A. Matheson, Yan Xia, Rodrigo Bonazzola, Nishant Ravikumar, Zeike A. Taylor, Diego H. Milone, Alejandro F. Frangi, Enzo Ferrante
Journal: Medical Image Analysis (2025)
Xanthones as Neuroprotective Agents: A Comprehensive Review of Their Role in the Prevention and Treatment of Neurodegenerative Diseases
Authors: Dibyajyoti Das, Aparoop Das, Kunal Bhattacharya, Kinku Pritam Koch, Dhirak Jyoti Deuri, Dipankar Saikia, Nongmaithem Randhoni Chanu, Satyendra Deka
Journal: Ageing Research Reviews (2025)
Development and prospective implementation of a large language model based system for early sepsis prediction
Authors: Supreeth P Shashikumar, Sina Mohammadi, Rishivardhan Krishnamoorthy, Avi Patel, Gabriel Wardi, Joseph C Ahn, Karandeep Singh, Eliah Aronoff-Spencer, Shamim Nemati
Journal: npj Digital Medicine (2025)

Sepsis is a dysregulated host response to infection with high mortality and morbidity. Early detection and intervention have been shown to improve patient outcomes, but existing computational models relying on structured electronic health record data often miss contextual information from unstructured clinical notes. This study introduces COMPOSER-LLM, an open-source large language model (LLM) integrated with the COMPOSER model to enhance early sepsis prediction. For high-uncertainty predictions, the LLM extracts additional context to assess sepsis-mimics, improving accuracy. Evaluated on 2500 patient encounters, COMPOSER-LLM achieved a sensitivity of 72.1%, positive predictive value of 52.9%, F-1 score of 61.0%, and 0.0087 false alarms per patient hour, outperforming the standalone COMPOSER model. Prospective validation yielded similar results. Manual chart review found 62% of false positives had bacterial infections, demonstrating potential clinical utility. Our findings suggest that integrating LLMs with traditional models can enhance predictive performance by leveraging unstructured data, representing a significant advance in healthcare analytics.
Social determinants of health extraction from clinical notes across institutions using large language models
Authors: Vipina K Keloth, Salih Selek, Qingyu Chen, Christopher Gilman, Sunyang Fu, Yifang Dang, Xinghan Chen, Xinyue Hu, Yujia Zhou, Huan He, Jungwei W Fan, Karen Wang, Cynthia Brandt, Cui Tao, Hongfang Liu, Hua Xu
Journal: npj Digital Medicine (2025)

Detailed social determinants of health (SDoH) is often buried within clinical text in EHRs. Most current NLP efforts for SDoH have limitations, investigating limited factors, deriving data from a single institution, using specific patient cohorts/note types, with reduced focus on generalizability. We aim to address these issues by creating cross-institutional corpora and developing and evaluating the generalizability of classification models, including large language models (LLMs), for detecting SDoH factors using data from four institutions. Clinical notes were annotated with 21 SDoH factors at two levels: level 1 (SDoH factors only) and level 2 (SDoH factors and associated values). Compared to other models, instruction tuned LLM achieved top performance with micro-averaged F1 over 0.9 on level 1 corpora and over 0.84 on level 2 corpora. While models performed well when trained and tested on individual datasets, cross-dataset generalization highlighted remaining obstacles. Access to trained models will be made available at https://github.com/BIDS-Xu-Lab/LLMs4SDoH .
Vutrisiran Improves Survival and Reduces Cardiovascular Events in ATTR Amyloid Cardiomyopathy
Authors: Ronald M Witteles, Pablo Garcia-Pavia, Thibaud Damy, Martha Grogan, Farooq H Sheikh, Caroline Morbach, Shaun Bender, Jason Exter, Satish A Eraly, Marianna Fontana
Journal: Journal of the American College of Cardiology (2025)

Patients with transthyretin amyloidosis with cardiomyopathy (ATTR-CM) have high mortality and morbidity. Vutrisiran, a subcutaneous RNA interference therapeutic, reduced the composite of all-cause mortality (ACM) and cardiovascular (CV) events (CV hospitalizations and urgent heart failure [HF] visits) in HELIOS-B (A Study to Evaluate Vutrisiran in Patients With Transthyretin Amyloidosis With Cardiomyopathy) in patients with ATTR-CM. Here we present data from HELIOS-B evaluating the impact of vutrisiran on ACM and CV mortality with additional patient follow-up through 42 months, and CV events such as CV hospitalizations, HF hospitalizations, and urgent HF visits. The HELIOS-B trial randomized 655 patients to vutrisiran 25 mg or placebo once every 3 months for up to 33 to 36 months in the double-blind (DB) period, followed by an open-label extension. Prespecified mortality and CV mortality analyses used data through 39 to 42 months of follow-up (DB period and up to 6 months of the open-label extension). CV hospitalizations and HF events were evaluated over the DB period of 33 to 36 months. Differences between vutrisiran and placebo were evaluated in the overall population, and in those stratified by baseline tafamidis use. In the overall population, vutrisiran reduced the risk of ACM (HR: 0.64; 95% CI: 0.46-0.88) and CV mortality (HR: 0.67; 95% CI: 0.47-0.96) vs placebo. Vutrisiran also reduced the risk of a composite of CV mortality and CV events (HR: 0.72; 95% CI: 0.55-0.94), and lowered rates of CV hospitalizations (rate ratio [RR]: 0.75; 95% CI: 0.62-0.91), urgent HF visits (RR: 0.54; 95% CI: 0.30-0.98), and HF hospitalizations (RR: 0.67; 95% CI: 0.52-0.86) vs placebo. Consistent trends were seen regardless of baseline tafamidis use. Consistent with the primary trial results, vutrisiran reliably reduced the risk of ACM, CV mortality, CV hospitalizations, HF hospitalizations, and urgent HF visits vs placebo in patients with ATTR-CM. (HELIOS-B: A Study to Evaluate Vutrisiran in Patients With Transthyretin Amyloidosis With Cardiomyopathy; NCT04153149).
Prostatic diseases in transgender women: a systematic review of diagnosis, risk, and management
Authors: Alice Bourillon, Cyrille Guillot-Tantay, Lucas Freton, Lee Zhao, Benoit Mesnard, Nicolas Morel-Journel, Romain Mathieu, Paul Neuville, Aurélie Schirmann, Benoit Peyronnet, François-Xavier Madec
Journal: International Journal of Transgender Health (2025)
Metal-Polyphenol Nanocomposite Hybrid Hydrogel: A Multifunctional Platform for Treating Diabetic Foot Ulcers through Metabolic Microenvironment Reprogramming
Authors: Heng Gong, Li Yang, Yaxing Li, Xinyi Zhang, Cheng Zheng, Tingjiang Gan, Shijiu Yin, Hui Zhang, Cheng Hu, Yunbing Wang
Journal: Biomaterials (2025)
Rurality, travel distance, and effectiveness of remote patient management in patients with heart failure in the TIM-HF2 trial in Germany: a pre-specified analysis of an open-label, randomised controlled trial
Authors: Fabian Kerwagen, Stefan Störk, Kerstin Koehler, Eik Vettorazzi, Maximilian Bauser, Jasmin Zernikow, Gina Barzen, Meike Hiddemann, Jan Gröschel, Michael Gross, Christoph Melzer, Karl Stangl, Gerhard Hindricks, Friedrich Koehler, Sebastian Winkler, Sebastian Spethmann
Journal: The Lancet Regional Health - Europe (2025)
Engaging an advisory board in discussions about the ethical relevance of algorithmic bias and fairness
Authors: Laura Brandt, Larry Au, Clinton Castro, Gabriel J Odom
Journal: npj Digital Medicine (2025)

We are an interdisciplinary team of researchers that are working to advance algorithmic fairness in the research of opioid use disorders. We discuss challenges that our research team faced when engaging with our Advisory Board, as well as several strategies that we came up with to help us find a common language to ensure semantic transparency and to ensure the thick alignment with values of affected parties.
The intestinal mucosa-associated microbiota in IBD-associated arthritis displays lower relative abundance of <i>Roseburia intestinalis</i>
Authors: Madeline Alizadeh, Uni Wong, Bernadette C. Siaton, Michael T. France, Seema A. Patil, Lauren George, Dania Hudhud, Kiran Motwani, William H. Scott, Jean-Pierre Raufman, Erik C. von Rosenvinge, Raymond K. Cross, Jacques Ravel
Journal: Gut Microbes (2025)

The most common extra-intestinal manifestation (EIM) of inflammatory bowel disease (IBD), IBD-associated arthritis (IAA), occurs in 25-40% of patients and can be debilitating. In IBD, mucosal and stool microbiota richness is decreased, and compositional changes can precede or accompany disease onset. Likewise, spondyloarthritides are associated with altered gut microbiota, with overlapping bacterial signatures observed in IBD, suggesting key shared microbial factors are involved in both conditions. Much has been learned about the role of the intestinal microbiome in IBD, but less is known regarding its role in IAA. To address this knowledge gap, we analyzed the mucosa-associated intestinal microbiota of participants enrolled in the LOCATION-IBD cohort. Microbiota composition was established using 16S rRNA gene amplicon sequencing of intestinal biopsy samples taken from participants with IBD, with or without arthropathy. Microbiota samples clustered predominantly by participant, and similar taxa were present across the colon. The mucosal intestinal microbiota of females with IAA displayed a lower relative abundance of R. intestinalis, while males with IAA had a higher relative abundance of Corynebacterium, even when controlling for IBD-type, whether samples were taken from a site of inflammation and intestinal location. These findings indicate the mucosa-associated intestinal microbiota is associated with IAA in a sex-specific manner.
First-Line Treatment of Pulmonary Sarcoidosis with Prednisone or Methotrexate
Authors: Vivienne Kahlmann, Montse Janssen Bonás, Catharina C. Moor, Jan C. Grutters, Rémy L.M. Mostard, Henricus N.A.J. van Rijswijk, Jan van der Maten, Emiel R. Marges, Linda A.A. Moonen, Maria J. Overbeek, Bart Koopman, Daan W. Loth, Esther J. Nossent, Michiel Wagenaar, Henk Kramer, Pascal L.M.L. Wielders, Peter I. Bonta, Stefan Walen, Brigitte A.H.A. Bogaarts, Réne Kerstens, Mayka Overgaauw, Marcel Veltkamp, Marlies S. Wijsenbeek
Journal: New England Journal of Medicine (2025)

Prednisone is currently recommended as the first-line treatment for pulmonary sarcoidosis but is associated with many side effects. Methotrexate, which is recommended as a second-line treatment, appears to have fewer side effects than prednisone but a slower onset of action. Data are needed on the efficacy and side-effect profile of methotrexate as compared with prednisone as first-line treatment for pulmonary sarcoidosis. In this multicenter, open-label, noninferiority trial involving patients with pulmonary sarcoidosis who had not previously received treatment, we randomly assigned patients, in a 1:1 ratio, to receive prednisone or methotrexate according to a prespecified treatment schedule. The primary end point was the mean change from baseline to week 24 in the percentage of the predicted forced vital capacity (FVC), as estimated with the use of mixed models for repeated measures. The noninferiority margin for the primary end point was 5 percentage points. Of the 138 patients who underwent randomization, 70 were assigned to receive prednisone and 68 to receive methotrexate. The unadjusted mean change from baseline to week 24 in the percentage of the predicted FVC was 6.75 percentage points (95% confidence interval [CI], 4.50 to 8.99) in the prednisone group and 6.11 percentage points (95% CI, 3.72 to 8.50) in the methotrexate group. Methotrexate was noninferior to prednisone with regard to the primary end point, with an adjusted between-group difference of -1.17 percentage points (95% CI, -4.27 to 1.93). Adverse events occurred in a similar percentage of patients in the two trial groups. Weight gain, insomnia, and increased appetite were the most common adverse events with prednisone, and nausea, fatigue, and any abnormal liver-function test were among the most common adverse events with methotrexate. In patients with pulmonary sarcoidosis, initial treatment with methotrexate was noninferior to that with prednisone with regard to the change from baseline to week 24 in the percentage of the predicted FVC. Differences in the side-effect profile between methotrexate and prednisone may inform shared decision making by providers and patients about the appropriate treatment approach. (Funded by the Dutch Lung Foundation; PREDMETH ClinicalTrials.gov number, NCT04314193.).
Single particle charge detection mass spectrometry enables molecular characterization of lipid nanoparticles and mRNA packaging
Authors: Zachary M Miller, Lokesh Narsineni, Yue-Xuan Li, Matthew R Gardner, Justin W Torpey, Evan R Williams
Journal: Journal of Controlled Release (2025)

Lipid nanoparticles (LNPs) are effective delivery systems for RNA therapeutics, yet their intrinsic heterogeneity in size and composition make them challenging to characterize. Charge detection mass spectrometry (CDMS) was used to rapidly weigh thousands of individual LNPs. Diameter distributions of empty LNPs from CDMS and cryo-TEM measurements are in excellent agreement demonstrating that these particles are sufficiently stable in the high vacuum environment of the mass spectrometer for accurate mass analysis. A similarly prepared mRNA-packaged LNP sample has a peak mass at ~70 MDa, 31 MDa higher than that of the empty LNP sample. Four freeze-thaw (FT) cycles of the mRNA-LNPs results in a peak mass at ~26.5 MDa, indicating significantly degraded LNPs. The degraded LNPs are about 28 % of the population of the mRNA-LNP sample after the first FT cycle. A non-linear least squares fitting routine was developed to convolve the mass distribution of the LNP core with a function that describes the packaging distribution to fit the mRNA-LNP data. Two models of the lipid core mass distribution were used to obtain the distribution of mRNA in the packaged LNPs. These two models provide a lower and upper limit to the average mRNA packaging of 43 and 107 mRNA copies, consistent with a rough estimate of an average of 62 mRNA copies obtained from cryo-TEM images. These results demonstrate the potential for label-free, rapid characterization of mass, diameter, packaging, and stability of LNPs with CDMS.
Navigational Bronchoscopy or Transthoracic Needle Biopsy for Lung Nodules
Authors: Robert J. Lentz, Katherine Frederick-Dyer, Virginia B. Planz, Tatsuki Koyama, Matthew C. Aboudara, Sameer K. Avasarala, Jonathan D. Casey, George Z. Cheng, Pierre-François D’Haese, Jennifer D. Duke, Eric L. Grogan, Todd C. Hoopman, Joyce Johnson, James M. Katsis, Jonathan S. Kurman, See-Wei Low, Kamran Mahmood, Otis B. Rickman, Lance Roller, Cristina Salmon, Samira Shojaee, Briana Swanner, Momen M. Wahidi, Charla Walston, Gerard A. Silvestri, Lonny Yarmus, Najib M. Rahman, Fabien Maldonado
Journal: New England Journal of Medicine (2025)

Each year, millions of pulmonary nodules are identified incidentally or through lung cancer screening, and many involve biopsy to distinguish cancer from benign processes. Both navigational bronchoscopy and computed tomography-guided transthoracic needle biopsy are commonly used in patients undergoing biopsies of peripheral pulmonary nodules, but the relative diagnostic accuracy of these two approaches is unclear. In this multicenter, randomized, parallel-group, noninferiority trial, we assigned patients with an intermediate-risk or high-risk peripheral pulmonary nodule measuring 10 to 30 mm in diameter to undergo navigational bronchoscopy or transthoracic needle biopsy at seven centers across the United States. The primary outcome was diagnostic accuracy, which was defined as the percentage of patients with biopsies that showed a specific diagnosis (cancer or a specific benign condition) that was confirmed to be accurate through 12 months of clinical follow-up (nonferiority margin, 10 percentage points). Secondary outcomes included procedural complications such as the occurrence of pneumothorax. Among the 234 patients included in the primary-outcome analysis (5 of whom were lost to follow-up), biopsy resulted in a specific diagnosis that was confirmed to be accurate through month 12 in 94 of 119 patients (79.0%) in the navigational bronchoscopy group and in 81 of 110 patients (73.6%) in the transthoracic needle biopsy group (absolute difference, 5.4 percentage points; 95% confidence interval, -6.5 to 17.2; P = 0.003 for noninferiority; P = 0.17 for superiority). Pneumothorax occurred in 4 of 121 patients (3.3%) in the navigational bronchoscopy group and in 32 of 113 patients (28.3%) in the transthoracic needle biopsy group and led to the placement of a chest tube, hospital admission, or both in 1 patient (0.8%) and 13 patients (11.5%), respectively. The diagnostic accuracy of navigational bronchoscopy was noninferior to that of transthoracic needle biopsy among patients with peripheral pulmonary nodules measuring 10 to 30 mm. (Funded by Medtronic and others; VERITAS ClinicalTrials.gov number, NCT04250194.).
Nerandomilast in Patients with Idiopathic Pulmonary Fibrosis
Authors: Luca Richeldi, Arata Azuma, Vincent Cottin, Michael Kreuter, Toby M. Maher, Fernando J. Martinez, Justin M. Oldham, Claudia Valenzuela, Emmanuelle Clerisme-Beaty, Maud Gordat, Daniel Wachtlin, Yi Liu, Christina Schlecker, Susanne Stowasser, Donald F. Zoz, Marlies S. Wijsenbeek
Journal: New England Journal of Medicine (2025)

Nerandomilast (BI 1015550) is an orally administered preferential inhibitor of phosphodiesterase 4B with antifibrotic and immunomodulatory effects. In a phase 2 trial involving patients with idiopathic pulmonary fibrosis, treatment with nerandomilast stabilized lung function over a period of 12 weeks. In this phase 3, double-blind trial, we randomly assigned patients with idiopathic pulmonary fibrosis in a 1:1:1 ratio to receive nerandomilast at a dose of 18 mg twice daily, nerandomilast at a dose of 9 mg twice daily, or placebo, with stratification according to background antifibrotic therapy (nintedanib or pirfenidone vs. none). The primary end point was the absolute change from baseline in forced vital capacity (FVC), measured in milliliters, at week 52. A total of 1177 patients underwent randomization, of whom 77.7% were taking nintedanib or pirfenidone at enrollment. Adjusted mean changes in FVC at week 52 were -114.7 ml (95% confidence interval [CI], -141.8 to -87.5) in the nerandomilast 18-mg group, -138.6 ml (95% CI, -165.6 to -111.6) in the nerandomilast 9-mg group, and -183.5 ml (95% CI, -210.9 to -156.1) in the placebo group. The adjusted difference between the nerandomilast 18-mg group and the placebo group was 68.8 ml (95% CI, 30.3 to 107.4; P<0.001), and the adjusted difference between the nerandomilast 9-mg group and the placebo group was 44.9 ml (95% CI, 6.4 to 83.3; P = 0.02). The most frequent adverse event in the nerandomilast groups was diarrhea, reported in 41.3% of the 18-mg group and 31.1% of the 9-mg group, as compared with 16.0% in the placebo group. Serious adverse events were balanced across trial groups. In patients with idiopathic pulmonary fibrosis, treatment with nerandomilast resulted in a smaller decline in the FVC than placebo over a period of 52 weeks. (Funded by Boehringer Ingelheim; FIBRONEER-IPF ClinicalTrials.gov number, NCT05321069.).
Maximizing therapeutic potential and safety: Exploring multi/dual-payload antibody conjugates as cancer theranostics
Authors: Meysam Khosravifarsani, Fabrice Ngoh Njotu, Dede Api Fon, Humphrey Fonge
Journal: Advanced Drug Delivery Reviews (2025)

Tumor heterogeneity greatly contributes to the failure of traditional cancer treatments. This leads to tumor relapse, recurrence, and ultimately metastasis, presenting serious clinical challenges. In recent decades, advances in antibody-based immunotherapy have emerged as promising new pillars to combat cancers. Although single payload antibody drug conjugates (ADCs) have resulted in drastic improvements in patient outcomes compared with unconjugated antibodies, multiple de novo and acquired resistance mechanisms inherent with cancer cells have left patients with less than desired outcomes. Newer studies are exploring the use of dual and multiple payload ADCs to enhance effectiveness. These payloads include chemotherapeutic and/or radiotherapeutic agents. The approaches leverage the synergistic effects of the different payloads alongside the immunotherapeutic properties of the antibody carriers. This review presents a comprehensive overview of dual-payload monoclonal antibody conjugates for cancer therapy and diagnosis (theranostics). Additionally, it explores the use of various imageable radiometals that are conjugated to the ADCs for imaging/diagnosis. It discusses the role of radioisotope decay schemes (such as alpha emission, beta emission, or Auger electron emission) along with factors such as linker type and chelator, as well as drug-to-antibody ratio (DAR), which are aimed at enhancing the synergistic effects between the therapeutic payloads while ensuring safety. Because none of these dual-payload ADCs have reached the clinic, this review employs a predictive method to estimate human equivalent dose (HED), maximum tolerable dose (MTD), and radiotoxicity in humans based on preclinical data. Additionally, it discusses the combinatorial behavior of two cytotoxic payloads linked to a monoclonal antibody.