tbuckley/cabot-search huggingface dataset:
Patterns of outpatient antibiotic prescribing in older adults by social determinants of healthcare access: a population-based retrospective cohort study
Authors: Mia E Sapin, Colleen J Maxwell, Anna E Clarke, Curtis Cooper, Miranda So, Kevin L Schwartz, Nick Daneman, Sharmistha Mishra, Derek MacFadden
Journal: Clinical Microbiology and Infection (2025)

Strategies to improve antibiotic use may exacerbate health inequities if they do not consider existing barriers to healthcare access. We examined associations between social determinants of healthcare access (SDOH) and antibiotic prescribing and variations in these associations pre- and post-COVID-19 emergence. We conducted a retrospective cohort study of community-dwelling adults ≥66 years of age in Ontario, Canada between March 2018 to March 2020 (pre-pandemic period) and March 2020 to March 2022 (pandemic period). Multivariable Fine-Gray subdistribution hazard models were used to examine associations between three SDOH variables (neighbourhood-level income and proportion racialized, and individual-level recent immigration) and incident antibiotic prescriptions, accounting for mortality as a competing risk. We assessed for potential effect modification by the pandemic period. The pre-pandemic (n=2,567,382) and pandemic (n=2,744,337) cohorts were similar in average age (75 years). Antibiotic prescribing was slightly higher among residents in the highest income neighbourhoods in pre-pandemic (subdistribution hazard ratio [sHR] 1.03 [95% confidence interval 1.02-1.04], compared with lowest income) and pandemic (sHR 1.02 [1.01-1.03]) periods. Prescribing was higher among recent immigrants (vs. long-term residents) in both periods, with a more pronounced difference observed during the pandemic (sHR 1.21 [1.18-1.25]) than pre-pandemic (sHR 1.12 [1.09-1.16]) period. Prescribing was lower among residents living in the most diverse neighbourhoods (vs. least diverse) in both periods, with a more pronounced difference during the pandemic (sHR 0.81 [0.80-0.82]) than pre-pandemic (sHR 0.92 [0.91-0.93]) period. SDOH variables are associated with antibiotic prescribing patterns over time among older outpatients, and the COVID-19 pandemic further modified some of these associations.
Using a Difficult-to-treat Resistance Index to Gauge Imbalance between Countries’ Antibiotic Resistance Prevalence and Access to Antibiotics: A Scoping Review and Concept Proposal
Authors: Morgan K Walker, Emad A Chishti, Christina Yek, Sadia Sarzynski, Sahil Angelo, Jennifer Cohn, Alicia A Livinski, Sameer S Kadri
Journal: Clinical Microbiology and Infection (2025)
Immune-modulated adhesive hydrogel for enhancing osteochondral graft adhesion and cartilage repair
Authors: Jiaqi Zhou, Xiongfa Ji, Yu Xue, Wenjie Yang, Guoqing Zhong, Zhiyang Zhou, Xingmei Chen, Zehua Lei, Teliang Lu, Yu Zhang, Ji Liu, Limin Ma
Journal: Bioactive Materials (2025)
BCMA-targeted therapies for multiple myeloma: latest updates from 2024 ASH annual meeting
Authors: Huijian Zheng, Huajian Xian, Wenjie Zhang, Chaoqun Lu, Renyao Pan, Han Liu, Zhenshu Xu
Journal: Journal of Hematology & Oncology (2025)

B-cell maturation antigen (BCMA) is currently the most extensively explored target for multiple myeloma (MM). BCMA-targeted therapies such as antibody-drug conjugate (ADC), bispecific antibodies (BsAbs), chimeric antigen receptor T(CAR-T) cell have shown promising therapeutic prospects in MM. We have summarized the latest reports on the three types of drugs for MM at the 2024 ASH Annual Meeting.
CAR-NK cell therapy: latest updates from the 2024 ASH annual meeting
Authors: Ran Kong, Bingyu Liu, Hua Wang, Tiange Lu, Xiangxiang Zhou
Journal: Journal of Hematology & Oncology (2025)

Natural killer cells, integral to the innate immune response, exhibit the inherent capacity to identify and eliminate cancer cells without prior exposure, positioning them as prime candidates for immunotherapeutic strategies. Chimeric antigen receptor-engineered natural killer (CAR-NK) cells obviate the requirement for human leukocyte antigen compatibility, simplifying personalized schedules and facilitating the manufacture of off-the-shelf products. In addition, CAR-NK cell therapy possesses lower risk of cytokine release syndrome and neurotoxicity, benefitting patients with higher security. Nevertheless, CAR-NK cell therapy is also confronted with challenges, including but not limited to short lifespan and restrictions from tumor microenvironment. Here, we summarized the latest advancements in the preclinical investigations and clinical trials of CAR-NK cell therapy from the 2024 ASH Annual Meeting.
Pancreas-targeted lipid nanoparticles for relatively non-invasive interleukin-12 mRNA therapy in orthotopic pancreatic ductal adenocarcinoma
Authors: Qian Shen, Jia Liu, Ling Zeng, Yupeng Ren, Jing Liao, Sijie Chen, Yingsen Tang, Zixi Zhang, Meng Jiang, Hangping Liao, Lingyun Wang, Xiaoding Xu, Jinjin Chen
Journal: Journal of Controlled Release (2025)
Nose-to-brain delivery of targeted lipid nanoparticles as two-pronged β-amyloid nanoscavenger for Alzheimer’s disease therapy
Authors: Yanyan Xu, Xiangtong Ye, Yanfeng Du, Wenqin Yang, Fan Tong, Wei Li, Qianqian Huang, Yongke Chen, Hanmei Li, Huile Gao, Weiwei Zhang
Journal: Acta Pharmaceutica Sinica B (2025)
Four months daily rifampicin versus three months daily rifampicin/isoniazid for the treatment of tuberculosis infection in asylum seekers: a randomized controlled trial
Authors: Alberto Matteelli, Giulia Russo, Luca Rossi, Carlo Cerini, Claudia Cimaglia, Beatrice Formenti, Mirella Dall'Asta, Irene Cristini, Natalia Gregori, Carlotta Ghilardi, Andrea Ciccarone, Letizia Previtali, Gianluca Di Rosario, Daniela Maria Cirillo, Enrico Girardi
Journal: Clinical Microbiology and Infection (2025)
Nanozyme-Functionalized Microalgal Biohybrid Microrobots in Inflammatory Bowel Disease Treatment
Authors: Jinmei Yang, Jiamin Ye, Runtan Li, Ruiyan Li, Xinting Liu, Jingwen Han, Yiwen Yang, Nana Ran, Mengyu Yuan, Zhuhong Zhang, Wei Chong, Xiaoyuan Ji
Journal: Biomaterials (2025)
The global stress response regulator <i>oxyS</i> in an adherent-invasive <i>Escherichia coli</i> strain attenuates experimental colitis
Authors: Diana Arsene, Sandrine Y. Tchaptchet, Jonathan J. Hansen
Journal: Gut Microbes (2025)

Crohn's disease and ulcerative colitis in humans and experimental immune-mediated colitis in mice are likely due in part to overactive immune responses to resident intestinal bacteria, including certain strains of adherent-invasive Escherichia coli (E. coli) such as E. coli NC101. We have previously shown that specific E. coli NC101 stress responses are upregulated during experimental colitis and attenuate inflammation. However, the roles of broader stress response pathways in E. coli NC101 during experimental colitis are unknown. We hypothesize that the global stress response regulator in E. coli, oxyS, also reduces experimental colitis. We show that intestinal E. coli NC101 upregulate oxyS expression during colitis in monocolonized interleukin-10 deficient mice. Furthermore, we demonstrate that oxyS-sufficient E. coli NC101 have decreased motility and biofilm formation in vitro and attenuated intestinal translocation and colitogenic potential in vivo compared with oxyS-deficient E. coli. These data suggest that activation of a generalized E. coli stress response, oxyS, reduces experimental colitis and may be a potential therapeutic target.
Mitral Regurgitation from Ischemic Papillary-Muscle Rupture
Authors: Priyanka Bhugra, Nadia Fida
Journal: New England Journal of Medicine (2025)

A 59-year-old woman presented with progressive dyspnea. There was a pansystolic murmur at the cardiac apex. Echocardiography (shown in videos) showed rupture of the anterolateral papillary muscle and severe mitral regurgitation.
Value of clinical review for AI-guided deep vein thrombosis diagnosis with ultrasound imaging by non-expert operators
Authors: Giancarlo Speranza, Sven Mischkewitz, Fouad Al-Noor, Bernhard Kainz
Journal: npj Digital Medicine (2025)

Deep vein thrombosis (DVT) carries high morbidity, mortality, and costs globally. Point of care ultrasound (POCUS) image acquisition by non-ultrasound-trained providers, supported by an AI-based guidance and remote image review system, is believed to improve the timeliness and cost-effectiveness of diagnosis. We examine a database of 381 patients with suspected DVT who underwent an AI-guided ultrasound scan by a non-ultrasound-trained nurse and an expert sonographer-performed standard compression ultrasound scan. Each AI-guided scan was reviewed remotely by blinded radiologists or blinded independent POCUS-certified American Emergency Medicine (EM) physicians. Remote reviewer and standard scan diagnoses were compared. The primary endpoint is AI-guidance system sensitivity with clinician review; secondary endpoints include specificity, positive predictive value, negative predictive value, image quality, inter-observer image quality, and vein compressibility agreement. Data was analysed through the bootstrapping method, bootstrapping with a second reader for each scan, and a majority voting system. Eighty percent (n = 304) of scans were of sufficient diagnostic quality. Radiologist reviewer sensitivity ranged from 90%–95%, specificity from 74%–84%, NPV from 98%–99%, PPV from 30%–42%, and potential expert-led ultrasound scans avoided from 39%–50%. Inter-observer agreement for image quality was 0.15 and for compressibility 0.61. EM reviewer sensitivity ranged from 95%–98%, specificity from 97%–100%, NPV was 99%, PPV from 81%–100%, and potential expert-led ultrasound scans avoided from 29%–38%. Inter-observer agreement for image quality was 0.59 and for compressibility 0.67. Diagnosing lower extremity DVT through AI-guided image acquisition with clinician review is feasible. Performance is influenced by reviewer expertise. We find potential positive impacts on health economics, including safely avoiding expert-led ultrasound scans.
Myeloid neoplasms with PHF6 mutations: context-dependent genomic and prognostic characterization in 176 informative cases
Authors: Saubia Fathima, Ali Alsugair, Rong He, Abhishek A. Mangaonkar, Kebede H. Begna, Animesh Pardanani, Cinthya J. Zepeda Mendoza, Kaaren K. Reichard, Naseema Gangat, Ayalew Tefferi
Journal: Blood Cancer Journal (2025)
Natural language processing of electronic health records for early detection of cognitive decline: a systematic review
Authors: Ravi Shankar, Anjali Bundele, Amartya Mukhopadhyay
Journal: npj Digital Medicine (2025)

Abstract This systematic review evaluated natural language processing (NLP) approaches for detecting cognitive impairment in electronic health record clinical notes. Following PRISMA guidelines, we analyzed 18 studies ( n = 1,064,530) that employed rule-based algorithms (67%), traditional machine learning (28%), and deep learning (17%). NLP models demonstrated robust performance in identifying cognitive decline, with median sensitivity 0.88 (IQR 0.74–0.91) and specificity 0.96 (IQR 0.81–0.99). Deep learning architectures achieved superior results, with area under the receiver operating characteristic curves up to 0.997. Major implementation challenges included incomplete electronic health record data capture, inconsistent clinical documentation practices, and limited external validation. While NLP demonstrates promise, successful clinical translation requires establishing standardized approaches, improving access to annotated datasets, and developing equitable deployment frameworks.
Developing a named entity framework for thyroid cancer staging and risk level classification using large language models
Authors: Matrix M. H. Fung, Eric H. M. Tang, Tingting Wu, Yan Luk, Ivan C. H. Au, Xiaodong Liu, Victor H. F. Lee, Chun Ka Wong, Zhili Wei, Wing Yiu Cheng, Isaac C. Y. Tai, Joshua W. K. Ho, Jason W. H. Wong, Brian H. H. Lang, Kathy S. M. Leung, Zoie S. Y. Wong, Joseph T. Wu, Carlos K. H. Wong
Journal: npj Digital Medicine (2025)

We developed a named entity (NE) framework for information extraction from semi-structured clinical notes retrieved from The Cancer Genome Atlas-Thyroid Cancer (TCGA-THCA) database and examined Large Language Models (LLMs) strategies to classify the 8th edition of American Joint Committee on Cancer (AJCC) staging and American Thyroid Association (ATA) risk category for patients with well-differentiated thyroid cancer. The NE framework consisted of annotation guidelines development, ground truth labelling, prompting approaches, and evaluation codes. Four LLMs (Mistral-7B-Instruct, Llama-3.1-8B-Instruct, Gemma-2-9B-Instruct, and Qwen2.5-7B-Instruct) were offline utilised for information extraction, comparing with expert-curated ground truth. Our framework was developed using 50 TCGA-THCA pathology notes. 289 TCGA-THCA notes and 35 pseudo-clinical cases were used for validation. Taking an ensemble-like majority-vote strategy achieved satisfactory performance for AJCC and ATA in both development and validation sets. Our framework and ensemble classifier optimised efficiency and accuracy of classifying stage and risk category in thyroid cancer patients.
Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart
Authors: Guanying Zhang, Ping Huang, Hongyu Yuan, Entao Li, Xiangyang Chi, Hancong Sun, Jin Han, Ting Fang, Yunzhu Dong, Jie Li, Yaoxing Wang, Jianmin Li, Sandra Chiu, Changming Yu
Journal: Molecular Therapy (2025)
Efficacy and Safety of Finerenone in Type 2 Diabetes: A Pooled Analysis of Trials of Heart Failure and Chronic Kidney Disease
Authors: John W. Ostrominski, Brian L. Claggett, Zi Michael Miao, Gerasimos Filippatos, Akshay S. Desai, Pardeep S. Jhund, Alasdair Henderson, Meike Brinker, Patrick Schloemer, Prabhakar Viswanathan, Andrea Lage, Katja Rohwedder, Carolyn S.P. Lam, Michele Senni, Sanjiv J. Shah, Adriaan A. Voors, Faiez Zannad, Peter Rossing, Luis M. Ruilope, Stefan D. Anker, Bertram Pitt, Rajiv Agarwal, John J.V. McMurray, Scott D. Solomon, Muthiah Vaduganathan
Journal: Diabetes Care (2025)

To evaluate the efficacy and safety of finerenone, a nonsteroidal mineralocorticoid receptor antagonist, in individuals with type 2 diabetes (T2D) and either chronic kidney disease (CKD) or heart failure (HF) with mildly reduced ejection fraction (HFmrEF) or preserved ejection fraction (HFpEF). In this prespecified participant-level pooled analysis of all phase III clinical trials evaluating finerenone versus placebo conducted to date (FINE-HEART), the safety and efficacy of finerenone was evaluated among participants with a history of T2D. Treatment effects on the primary outcome of cardiovascular death and other secondary outcomes were evaluated according to baseline glycated hemoglobin (HbA1c) and glucose-lowering therapy (GLT) regimen using stratified Cox proportional hazards models. Of 18,991 FINE-HEART participants, 15,365 (80.9%) had T2D and available HbA1c at baseline (mean age, 66 ± 10 years; 32% women; mean HbA1c, 7.6 ± 1.4%). The most common GLT regimens were insulin alone (n = 2,652), insulin and metformin (n = 2,005), metformin alone (n = 1,616), metformin and sulfonylurea (n = 1,039), and "other" (n = 8,117), including sodium-glucose cotransporter 2 inhibitor (SGLT2i) and glucagon-like peptide 1 receptor agonist (GLP-1RA). Over a median follow-up of 2.9 years, treatment effects of finerenone versus placebo on cardiovascular death were consistent across baseline HbA1c (Pinteraction = 0.75) and GLT regimen (Pinteraction = 0.46). Finerenone consistently reduced the kidney composite outcome, HF hospitalization, major adverse cardiovascular events, and all-cause mortality, irrespective of baseline HbA1c and GLT regimen. Treatment effects of finerenone were also consistent across number of background GLTs and irrespective of concomitant treatment with a SGLT2i or GLP-1RA. Finerenone consistently reduced morbidity and mortality in individuals with T2D across a broad range of glycemia and glucose-lowering regimens.
BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia
Authors: Stephen Jun Fei Chong, Junyan Lu, Rebecca Valentin, Timothy Z. Lehmberg, Jie Qing Eu, Jing Wang, Fen Zhu, Li Ren Kong, Stacey M. Fernandes, Jeremy Zhang, Charles Herbaux, Boon Cher Goh, Jennifer R. Brown, Carsten U. Niemann, Wolfgang Huber, Thorsten Zenz, Matthew S. Davids
Journal: Molecular Cancer (2025)

Established genetic biomarkers in chronic lymphocytic leukemia (CLL) have been useful in predicting response to chemoimmunotherapy but are less predictive of response to targeted therapies. With several such targeted therapies now approved for CLL, identifying novel, non-genetic predictive biomarkers of response may help to select the optimal therapy for individual patients. We coupled data from a functional precision medicine technique called BH3-profiling, which assesses cellular cytochrome c loss levels as indicators for survival dependence on anti-apoptotic proteins, with multi-omics data consisting of targeted and whole-exome sequencing, genome-wide DNA methylation profiles, RNA-sequencing, protein and functional analyses, to identify biomarkers for treatment response in CLL patients. We initially studied 73 CLL patients from a discovery cohort. We found that greater dependence on the anti-apoptotic BCL-2 protein was associated with prognostically favorable genetic biomarkers. Furthermore, BCL-2 dependence was strongly associated with gene expression patterns and signaling pathways that suggest a more targeted drug-sensitive milieu and was predictive of drug responses. We subsequently demonstrated that these associations were causal in cell lines and additional CLL patient samples. To validate the findings from our discovery cohort and in vitro studies, we utilized primary CLL cells from 54 additional patients treated on a prospective, phase-2 clinical trial of the BTK inhibitor ibrutinib given in combination with chemoimmunotherapy (fludarabine, cyclophosphamide, rituximab) and confirmed in this independent dataset that higher BCL-2 dependence predicted favorable clinical response, independent of the genetic background of the CLL cells. We comprehensively defined BCL-2 dependence as a potential functional and predictive biomarker of treatment response in CLL, underscoring the importance of characterizing apoptotic signaling in CLL to stratify patients beyond genetic markers and identifying novel combinations to exploit BCL-2 dependence therapeutically. Our approach has the potential to help optimize targeted therapy combinations for CLL patients.
Expert consensus on intentional tooth replantation
Authors: Zhengmei Lin, Dingming Huang, Shuheng Huang, Zhi Chen, Qing Yu, Benxiang Hou, Lihong Qiu, Wenxia Chen, Jiyao Li, Xiaoyan Wang, Zhengwei Huang, Jinhua Yu, Jin Zhao, Yihuai Pan, Shuang Pan, Deqin Yang, Weidong Niu, Qi Zhang, Shuli Deng, Jingzhi Ma, Xiuping Meng, Jian Yang, Jiayuan Wu, Lan Zhang, Jin Zhang, Xiaoli Xie, Jinpu Chu, Kehua Que, Xuejun Ge, Xiaojing Huang, Zhe Ma, Lin Yue, Xuedong Zhou, Junqi Ling
Journal: International Journal of Oral Science (2025)

Abstract Intentional tooth replantation (ITR) is an advanced treatment modality and the procedure of last resort for preserving teeth with inaccessible endodontic or resorptive lesions. ITR is defined as the deliberate extraction of a tooth; evaluation of the root surface, endodontic manipulation, and repair; and placement of the tooth back into its original socket. Case reports, case series, cohort studies, and randomized controlled trials have demonstrated the efficacy of ITR in the retention of natural teeth that are untreatable or difficult to manage with root canal treatment or endodontic microsurgery. However, variations in clinical protocols for ITR exist due to the empirical nature of the original protocols and rapid advancements in the field of oral biology and dental materials. This heterogeneity in protocols may cause confusion among dental practitioners; therefore, guidelines and considerations for ITR should be explicated. This expert consensus discusses the biological foundation of ITR, the available clinical protocols and current status of ITR in treating teeth with refractory apical periodontitis or anatomical aberration, and the main complications of this treatment, aiming to refine the clinical management of ITR in accordance with the progress of basic research and clinical studies; the findings suggest that ITR may become a more consistent evidence-based option in dental treatment.
Identification of a JAK–STAT–miR155HG positive feedback loop in regulating natural killer (NK) cells proliferation and effector functions
Authors: Songyang Li, Yongjie Liu, Xiaofeng Yin, Yao Yang, Xinjia Liu, Jiaxing Qiu, Qinglan Yang, Yana Li, Zhiguo Tan, Hongyan Peng, Peiwen Xiong, Shuting Wu, Lanlan Huang, Xiangyu Wang, Sulai Liu, Yuxing Gong, Yuan Gao, Lingling Zhang, Junping Wang, Yafei Deng, Zhaoyang Zhong, Youcai Deng
Journal: Acta Pharmaceutica Sinica B (2025)
New effective and less painful high frequency electrochemotherapy protocols: From optimization on 3D models to pilot study on veterinary patients
Authors: Alexia de Caro, Jean-Baptiste Leroy, Loïck Royant, David Sayag, Ilaria Marano, Elodie Lallemand, Marion Toussaint, Jelena Kolosnjaj-Tabi, Marie-Pierre Rols, Muriel Golzio
Journal: Journal of Controlled Release (2025)
A multi-analyte blood test for acute spinal cord injury
Authors: Tej D Azad, Kathleen R Ran, Joshua D Materi, Divyaansh Raj, Timour Al-Khindi, Sameer Gabbita, Marvin Li, Elizabeth T Wang, A Karim Ahmed, Megan Parker, Anita L Kalluri, Daniel Lubelski, Christopher M Jackson, Daniel M Sciubba, Jon D Weingart, Ali Bydon, Timothy F Witham, David W Nauen, Srinivasan Yegnasubramanian, Nicholas Theodore, Chetan Bettegowda
Journal: Journal of Clinical Investigation (2025)

BACKGROUNDRapid diagnosis to facilitate urgent intervention is critical for treatment of acute spinal cord injury (SCI). We hypothesized that a multi-analyte blood biomarker would support point-of-care SCI diagnosis, correlate with injury severity, and predict long-term neurologic outcomes.METHODSDroplet digital PCR (ddPCR) assays were designed to amplify differentially hypomethylated genomic loci in spinal cord tissue. An optimized ddPCR assay was applied to cell-free DNA (cfDNA) from plasma samples collected from prospectively enrolled acute SCI patients. Targeted proteomic profiling was also performed. Spinal cord-derived cfDNA and plasma proteins were tested for their association with SCI and ability to predict conversion in American Spinal Injury Association (ASIA) score at 6 months.RESULTSA bespoke ddPCR assay detected spinal cord-derived cfDNA in plasma of 50 patients with acute SCI (AUC: 0.89, 95% CI 0.83-0.95, P < 0.0001). Levels of cfDNA were highest in patients with the most severe injury, i.e., ASIA A, compared with those with ASIA B (P = 0.04), ASIA C (P = 0.009), and ASIA D injuries (P < 0.001). Dimensionality reduction identified 4 candidate proteins (FABP3, REST, IL-6, NF-H) that were integrated with spinal cord-derived cfDNA to derive the Spinal Cord Injury Index (SCII), which has high sensitivity and specificity for SCI diagnosis (AUC: 0.91, 95% CI 0.82-0.99, P < 0.0001), correlates with injury severity (P < 0.0001), and predicts 6-month neurologic improvement (AUC: 0.77, 95% CI 0.61-0.93, P = 0.006).CONCLUSIONThe detection of spinal cord-derived cfDNA and plasma protein alterations as part of a multi-analyte blood test can inform SCI diagnosis and prognosis.FUNDINGNorth American Spine Society Young Investigator Award; Morton Cure Paralysis Fund.