tbuckley/cabot-search huggingface dataset:
Circular RNA circDCUN1D4 suppresses hepatocellular carcinoma development via targeting the miR-590-5p/ TIMP3 axis
Authors: Hongyu Li, Bing Su, Yan Jiang, Boyang Zhang, Rulong Du, Can Song, Bin Hou, Kun Xu, Lida Wu, Yuchun Gu
Journal: Molecular Cancer (2025)

Hepatocellular carcinoma (HCC) is a major global health concern, necessitating innovative therapeutic strategies. In this study, we investigated the functional role of circular RNA circDCUN1D4 in HCC progression and its potential therapeutic implications. It was found that HCC patients exhibiting higher levels of circDCUN1D4 demonstrated a more favorable survival rate. Furthermore, we revealed that circDCUN1D4 suppressed HCC cell proliferation, migration, and invasion. Mechanistically, circDCUN1D4 was identified as a sponge for miR-590-5p, leading to the downregulation of its downstream target, Tissue Inhibitor of Metalloproteinase 3 (TIMP3). Importantly, circDCUN1D4 administration through In vivo jet-PEI exhibited a robust inhibitory effect on tumor progression without causing notable toxicity in mice. Overall, our findings highlight circDCUN1D4 as a promising therapeutic candidate for HCC, unraveling its intricate regulatory role through the miR-590-5p/TIMP3 axis. This study contributes valuable insights into the potential clinical applications of circRNA-based therapies for HCC.
Letter to the Editor: targeted enteral feeding for malnutrition in liver transplant candidates
Authors: Qingyu Chen
Journal: Hepatology (2025)

The Second School of Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China Correspondence Qingyu Chen, The Second School of Medicine, Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China. Email: [email protected]
Platelet‐rich plasma (<scp>PRP</scp>) versus injectable platelet‐rich fibrin (i‐<scp>PRF</scp>): A systematic review across all fields of medicine
Authors: Nima Farshidfar, Mohammad Amin Amiri, Nathan E. Estrin, Paras Ahmad, Anton Sculean, Yufeng Zhang, Richard J. Miron
Journal: Periodontology 2000 (2025)

Abstract This systematic review aimed to evaluate all available evidence across all fields of medicine regarding the comparative effectiveness of platelet‐rich plasma (PRP) versus injectable platelet‐rich fibrin (i‐PRF). A comprehensive search was conducted in PubMed, Scopus, and Web of Science up to September 30, 2024. Following a thorough screening process, studies were divided into in vitro, in vivo, and clinical studies based on their tissue/clinical indications. The initial search generated 2192 articles, of which 23 met the inclusion criteria. The findings demonstrated that i‐PRF yielded higher platelet concentrations and offered a more sustained, long‐term release of growth factors over time when compared to PRP. Overall, it was determined from in vitro studies that i‐PRF significantly improved the activity of many cell types, including for skin, cartilage, periodontal, bone, soft tissue around dental implants, and pulp cells. In vivo outcomes also generally indicated that i‐PRF outperformed PRP in cartilage and testicular regeneration. However, in orthodontic tooth movement, PRP was found to lead to superior short‐term effects, while i‐PRF showed more beneficial long‐term effects. Clinical studies also found superior outcomes of i‐PRF in skin regeneration, cartilage, and pulp regeneration. Outcomes regarding orthodontic tooth movement utilizing i‐PRF or PRP remain controversial. In 72% of studies, i‐PRF was found to lead to better outcomes across the various fields of medicine when compared to PRP, whereas 24% found no differences between the groups. Reasons and inconsistencies across the studies may be attributed to protocol differences and tissue types. Overall, additional clinical studies are needed with well‐designed research and centrifugation protocols to better understand the regenerative potential of platelet concentrates in medicine. i‐PRF offers a more sustained and prolonged release of growth factors and was favored in the majority of studies over PRP and should, therefore, be favored for the majority of medical and dental applications.
Daratumumab‐based regimens versus CyBorD in newly diagnosed patients with AL amyloidosis and IIIb cardiac stage: A matched case‐control study
Authors: Claudia Bellofiore, Marco Basset, Giuseppe Damiano Sanna, Andrea Foli, Roberta Mussinelli, Martina Nanci, Alessandro Fogliani, Martina Ciardo, Mario Nuvolone, Giampaolo Merlini, Giovanni Palladini, Paolo Milani
Journal: HemaSphere (2025)
Update on the genetics of allergic diseases
Authors: Lucinda P Lawson, Sreeja Parameswaran, Ronald A Panganiban, Gregory M Constantine, Matthew T Weirauch, Leah C Kottyan
Journal: Journal of Allergy and Clinical Immunology (2025)

The field of genetic etiology of allergic diseases has advanced significantly in recent years. Shared risk loci reflect the contribution of genetic factors to the sequential development of allergic conditions across the atopic march, while unique risk loci provide opportunities to understand tissue specific manifestations of allergic disease. Most identified risk variants are non-coding, indicating that they likely influence gene expression through gene regulatory mechanisms. Despite recent advances, challenges persist, particularly regarding the need for increased ancestral diversity in research populations. Further, while polygenic risk scores show promise for identifying individuals at higher genetic risk for allergic diseases, their predictive accuracy varies across different ancestries and can be difficult to translate to an individual's absolute risk of developing a disease. Methodologies, including "nearest gene", 3D chromatin interaction analysis, expression quantitative trait locus analysis, experimental screens, and integrative bioinformatic models have established connection between genetic variants and their regulatory targets, enhancing our understanding of disease risk and phenotypic variability. In this review, we focus on the state of knowledge of allergic sensitization and five allergic diseases: asthma, atopic dermatitis, allergic rhinitis, food allergy, and eosinophilic esophagitis. We summarize recent progress and highlight opportunities for advancing our understanding of their genetic etiology.
Update in GVHD Prophylaxis: Novel Pharmacologic and Graft Manipulation Strategies
Authors: Elizabeth O. Hexner, Zachariah DeFilipp
Journal: American Journal of Hematology (2025)

ABSTRACT Prevention of graft‐versus‐host disease (GVHD) is critical to successful allogeneic hematopoietic cell transplantation (HCT), but for many years was difficult to achieve. Advances in the understanding of allogeneic HCT biology and immunology have paved the way for novel clinical approaches to GVHD prophylaxis, highlighted by the broad adoption of posttransplant cyclophosphamide and the approval of abatacept by the US Food and Drug Administration to prevent acute GVHD. Patients undergoing allogeneic HCT are now experiencing severe acute GVHD at historically low rates, and significant improvements in preventing chronic GVHD are also being achieved. This review highlights key pharmacological approaches and graft manipulation strategies being used or investigated for GVHD prophylaxis. Furthermore, we discuss the ongoing unmet needs in GVHD prevention and the challenges in addressing these areas in future clinical trials.
Optimal dietary patterns for healthy aging
Authors: Anne-Julie Tessier, Fenglei Wang, Andres Ardisson Korat, A. Heather Eliassen, Jorge Chavarro, Francine Grodstein, Jun Li, Liming Liang, Walter C. Willett, Qi Sun, Meir J. Stampfer, Frank B. Hu, Marta Guasch-Ferré
Journal: Nature Medicine (2025)

As the global population ages, it is critical to identify diets that, beyond preventing noncommunicable diseases, optimally promote healthy aging. Here, using longitudinal questionnaire data from the Nurses' Health Study (1986–2016) and the Health Professionals Follow-Up Study (1986–2016), we examined the association of long-term adherence to eight dietary patterns and ultraprocessed food consumption with healthy aging, as assessed according to measures of cognitive, physical and mental health, as well as living to 70 years of age free of chronic diseases. After up to 30 years of follow-up, 9,771 (9.3%) of 105,015 participants (66% women, mean age = 53 years (s.d. = 8)) achieved healthy aging. For each dietary pattern, higher adherence was associated with greater odds of healthy aging and its domains. The odds ratios for the highest quintile versus the lowest ranged from 1.45 (95% confidence interval (CI) = 1.35–1.57; healthful plant-based diet) to 1.86 (95% CI = 1.71–2.01; Alternative Healthy Eating Index). When the age threshold for healthy aging was shifted to 75 years, the Alternative Healthy Eating Index diet showed the strongest association with healthy aging, with an odds ratio of 2.24 (95% CI = 2.01–2.50). Higher intakes of fruits, vegetables, whole grains, unsaturated fats, nuts, legumes and low-fat dairy products were linked to greater odds of healthy aging, whereas higher intakes of trans fats, sodium, sugary beverages and red or processed meats (or both) were inversely associated. Our findings suggest that dietary patterns rich in plant-based foods, with moderate inclusion of healthy animal-based foods, may enhance overall healthy aging, guiding future dietary guidelines. In two longitudinal cohorts followed for 30 years, the associations of eight different dietary patterns with healthy aging—encompassing cognitive, physical and mental health—were studied, identifying food constituents linked to greater or lesser odds of healthy aging.
A pontine center in descending pain control
Authors: Tianming Li, Wenjie Zhou, Jin Ke, Matthew Chen, Zhen Wang, Lauren Hayashi, Xiaojing Su, Wenbin Jia, Wenxi Huang, Chien-Sheng Wang, Kapsa Bengyella, Yang Yang, Rafael Hernandez, Yan Zhang, Xinglei Song, Tianle Xu, Tianwen Huang, Yuanyuan Liu
Journal: Neuron (2025)
Improving Methodologies for Cumulative Risk Assessment: A Case Study of Noncarcinogenic Health Risks from Volatile Organic Compounds in Fenceline Communities in Southeastern Pennsylvania
Authors: Andrea A. Chiger, Carolyn Gigot, Ellis S. Robinson, Mina W. Tehrani, Megan Claflin, Edward Fortner, Harald Stark, Jordan Krechmer, Manjula R. Canagaratna, Scott Herndon, Tara I. Yacovitch, Kirsten Koehler, Ana M. Rule, Thomas A. Burke, Mary A. Fox, Peter F. DeCarlo, Keeve E. Nachman
Journal: Environmental Health Perspectives (2025)

Cumulative risk assessment (CRA) is key to characterizing health risks in fenceline and disadvantaged communities, which face environmental pollution and challenging socioeconomic conditions. Traditional approaches for inclusion of mixtures in CRA are limited and only assess the most sensitive target organ system for each chemical.
Ensemble Deep Learning Algorithm for Structural Heart Disease Screening Using Electrocardiographic Images
Authors: Lovedeep S Dhingra, Arya Aminorroaya, Veer Sangha, Aline F Pedroso, Sumukh Vasisht Shankar, Andreas Coppi, Murilo Foppa, Luisa C C Brant, Sandhi M Barreto, Antonio Luiz P Ribeiro, Harlan M Krumholz, Evangelos K Oikonomou, Rohan Khera
Journal: Journal of the American College of Cardiology (2025)
Guideline-Directed Medical Therapy and Outcomes in the ISCHEMIA Trial
Authors: David J Maron, Jonathan D Newman, Rebecca Anthopolos, Ying Lu, Susanna Stevens, William E Boden, Kreton Mavromatis, Jason Linefsky, Rajesh G Nair, Olga Bockeria, Gilbert Gosselin, Gian P Perna, Elena Demchenko, David Foo, Michael D Shapiro, Mary Ann Champagne, Christie Ballantyne, Peter McCullough, Jose Luis Lopez-Sendon, Frank Rockhold, Frank Harrell, Yves Rosenberg, Gregg W Stone, Sripal Bangalore, Harmony R Reynolds, John A Spertus, Judith S Hochman
Journal: Journal of the American College of Cardiology (2025)
Invasive vs Conservative Management of Patients With Chronic Total Occlusion
Authors: Sripal Bangalore, G B John Mancini, Jonathan Leipsic, Mathew J Budoff, Yifan Xu, Rebecca Anthopolos, Emmanouil S Brilakis, Aeshita Dwivedi, John A Spertus, Phil G Jones, Yoon Joo Cho, Daniel B Mark, Cameron J Hague, James K Min, Harmony R Reynolds, Ahmed Elghamaz, Rajesh Goplan Nair, Kreton Mavromatis, Gilbert Gosselin, Subhash Banerjee, Hristo Pejkov, Steven Lindsay, J Aaron Grantham, David O Williams, Gregg W Stone, Sean M O'Brien, Judith S Hochman, David J Maron
Journal: Journal of the American College of Cardiology (2025)
Supply, Demand, and a Growing US Kidney Transplant Waiting List
Authors: David C. Cron, Rachel E. Patzer, Joel T. Adler
Journal: JAMA Network Open (2025)

Jillian S. Caldwell, DO, MS; Xingxing S. Cheng, MD, MS; Glenn M. Chertow, MD, MPH; Jeremy D. Goldhaber-Fiebert, PhD
Appropriate Deprescribing and Payment in Hospice Dementia Care
Authors: Nathan M. Stall, Sharon K. Inouye, Lona Mody
Journal: JAMA Internal Medicine (2025)

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Physician Perspectives on Ambient AI Scribes
Authors: Shreya J. Shah, Trevor Crowell, Yejin Jeong, Anna Devon-Sand, Margaret Smith, Betsy Yang, Stephen P. Ma, April S. Liang, Clarissa Delahaie, Caroline Hsia, Tait Shanafelt, Michael A. Pfeffer, Christopher Sharp, Steven Lin, Patricia Garcia
Journal: JAMA Network Open (2025)

Importance Limited qualitative studies exist evaluating ambient artificial intelligence (AI) scribe tools. Such studies can provide deeper insights into ambient AI implementations by capturing lived experiences. Objective To evaluate physician perspectives on ambient AI scribes. Design, Setting, and Participants A qualitative study using semistructured interviews guided by the Reach, Efficacy, Adoption, Implementation, Maintenance/Practical, Robust Implementation, and Sustainability Model (RE-AIM/PRISM) framework, with thematic analysis using both inductive and deductive approaches. Physicians participating in an AI scribe pilot that included community and faculty practices, across primary care and ambulatory specialties, were invited to participate in interviews. This ambient AI scribe pilot at a health care organization in California was conducted from November 2023 to January 2024. Main Outcome and Measures Facilitators and barriers to adoption, practical effectiveness, and suggestions for improvement to enhance sustainability. Results Twenty-two semistructured interviews were conducted with AI pilot physicians from primary care (13 [59%]) and ambulatory specialties (9 [41%]), including physicians from community practices (12 [55%]) and faculty practices (10 [45%]). Facilitators to adoption included ease of use, ease of editing, and generally positive perspectives of tool quality. Physicians expressed positive sentiments about the impact of the ambient AI scribe tool on cognitive demand (16 of 16 comments [100%]), temporal demand (28 comments [62%]), work-life integration (10 of 11 comments [91%]), and overall workload (8 of 9 comments [89%]). Physician perspectives of the impact of the ambient AI scribe tool on their engagement with patients were mostly positive (38 of 56 comments [68%]). Barriers to adoption included limited functionality with non-English speaking patients and lack of access for physicians without a specific device. Physician perspectives on accuracy and style were largely negative, particularly regarding note length and editing requirements. Several specific suggestions for tool improvement were identified, and physicians were optimistic regarding the potential for long-term use of ambient AI scribes. Conclusion and Relevance In this qualitative study, ambient AI scribes were found to positively impact physician workload, work-life integration, and patient engagement. Key facilitators and barriers to adoption were identified, along with specific suggestions for tool improvement. These findings suggest the potential for ambient AI scribes to reduce clinician burden, with user-centered recommendations offering practical guidance on ways to improve future iterations and improve adoption.
Reaching for Individualized Medicine in Diabetic Kidney Disease
Authors: Mallory Mandel, Sylvia E. Rosas
Journal: JAMA Network Open (2025)

Jelle M. Beernink, MD; Niels Jongs, PhD; Cees J. A. Doelman, PhD; Gozewijn D. Laverman, MD, PhD; Hiddo J. L. Heerspink, PhD
Differences in Arterial Blood Gas Testing by Race and Sex Across 161 US Hospitals in 4 EHR Databases
Authors: João Matos, Mahmoud Alwakeel, Sicheng Hao, Dana Naamani, Tristan Struja, Judy Wawira Gichoya, Leo Anthony Celi, Timothy McMahon, Heather King, Christopher E Cox, Warren A. Kibbe, Chuan Hong, A. Ian Wong
Journal: American Journal of Respiratory and Critical Care Medicine (2025)

Pulse oximetry accuracy varies across races, underscoring the importance of routine arterial blood gas (ABG) testing, the gold standard for assessing oxygen saturation. The study aimed to assess disparities in ABG testing among critically ill patients by race and sex. Records from 2001-2019 in 161 U.S. hospitals were analyzed, including Duke, MIMIC-III, MIMIC-IV, and eICU-CRD. The study evaluated ABG test incidence; time to first test; and frequency of subsequent tests, adjusting for confounders, including SOFA, hospital, and age. Subgroup analyses focused on patients with arterial lines and mechanical ventilation. The cohort included 184,178 ICU admissions (35.0% with ABG tests; 1.9% Asian, 16.5% Black, 3.5% Hispanic or Latino, 78.1% White; 45.7% female). Compared to White patients, Asian, Black, Hispanic or Latino patients were less likely to have an ABG [Odds Ratio (OR(95%CI)): 0.807 (0.741,0.879), 0.859 (0.830,0.888), 0.919 (0.865,0.976), respectively], experienced delays to initial ABG [Hazard Ratio (HR(95%CI)) Asian, 0.855(0.803,0.911); Black, 0.833(0.814,0.853), p<0.001], and were less likely to repeated ABGs [Adjusted Coefficient (95%CI): Asian 0.016 (-0.097,-0.064), Black -0.082 (-0.111-,-0.054)]. Compared to male patients, female patients received less ABG tests [OR(95%CI): 0.926(0.905-0.948)], had delays in initial testing [HR(95%CI): 0.958(0.942-0.974)], and fewer repeated ABGs [Adjusted Coefficient (95%CI): -0.051(-0.072 to -0.030)]. Findings were consistent among patients who were mechanically ventilated and had arterial lines. Asian, Black, and female patients demonstrated significantly reduced and delayed rates of ABG testing. Inequitable ABG testing may exacerbate the prevalence of hidden hypoxemia. Until skin-tone-corrected pulse oximeters are available, equitable ABG testing remains the best strategy to mitigate hidden hypoxemia.
Human Myobundle Platform for Studying the Role of Notch Signaling in Satellite Cell Phenotype and Function
Authors: Torie Broer, Nick Tsintolas, Stewart Hammond, Abbigail Helfer, Joonbum Lee, Karly Purkey, Sophia DeLuca, Alastair Khodabukus, Nenad Bursac
Journal: Advanced Healthcare Materials (2025)

Abstract Notch signaling plays a pivotal role in regulating satellite cell (SC) behavior during skeletal muscle development, homeostasis, and repair. While well‐characterized in mouse models, the impact of Notch signaling in human muscle tissues remains largely underexplored. Here, a 3D tissue‐engineered model of human skeletal muscle (“myobundles”) is utilized as an in vitro platform for temporal control and studies of Notch singaling. Myofiber‐specific overexpression of the Notch ligand, DLL1, early in myobundle differentiation increases the abundance of 3D SCs and shifts their phenotype to a more quiescent‐like state, along with decreasing muscle mass and function. In contrast, myofiber‐specific DLL1 overexpression after one week of myobundle differentiation does not affect 3D SC abundance or muscle function, but increases transcriptomic markers of SC quiescence, confirming the temporal dependence of SC activation and self‐renewal on Notch signaling activity. Finally, for the first time these studies show that even after a transient, myofiber‐specific upregulation of Notch signaling in myobundles, 3D SCs expanded from these tissues can re‐form functional “secondary” myobundles containing an amplified SC pool. Future studies in the described human myobundle platform are expected to aid the development of novel Notch‐targeted therapies for muscular dystrophies and aging.
Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape
Authors: Sven Liesenfelder, Mohamed H. Elsafi Mabrouk, Jessica Iliescu, Monica Varona Baranda, Athanasia Mizi, Juan-Felipe Perez-Correa, Martina Wessiepe, Argyris Papantonis, Wolfgang Wagner
Journal: Nature Aging (2025)

Abstract Aging is reflected by genome-wide DNA methylation changes, which form the basis of epigenetic clocks, but it is largely unclear how these epigenetic modifications are regulated and whether they directly affect the aging process. In this study, we performed epigenetic editing at age-associated CpG sites to explore the consequences of interfering with epigenetic clocks. CRISPR-guided editing targeted at individual age-related CpGs evoked genome-wide bystander effects, which were highly reproducible and enriched at other age-associated regions. 4C-sequencing at age-associated sites revealed increased interactions with bystander modifications and other age-related CpGs. Subsequently, we multiplexed epigenetic editing in human T cells and mesenchymal stromal cells at five genomic regions that become either hypermethylated or hypomethylated upon aging. While targeted methylation seemed more stable at age-hypermethylated sites, both approaches induced bystander modifications at CpGs with the highest correlations with chronological age. Notably, these effects were simultaneously observed at CpGs that gain and lose methylation with age. Our results demonstrate that epigenetic editing can extensively modulate the epigenetic aging network and interfere with epigenetic clocks.