tbuckley/cabot-search huggingface dataset:
Industry Payments and Sentiments Toward Robotic Surgery Among US Physicians
Authors: Wei San Loh, Andrew M. Ibrahim, Sarah Sheskey, Colleen M. Stone, Kyle H. Sheetz
Journal: JAMA Network Open (2025)

Importance Given the rapid adoption of robotic surgery and its association with substantial industry payments, objective documentation of physicians’ perceptions toward robotic surgery is important. Objective To assess US-based physicians’ sentiments toward robotic surgery and whether industry payments are associated with their perceptions. Design, Setting, and Participants This cohort study analyzed publicly available posts made from March 19, 2009, to April 1, 2024, by 268 US-based physicians who followed the Society of American Gastrointestinal and Endoscopic Surgeons on X (formerly Twitter). Trainees and individuals without validated clinical practices were excluded. Physicians’ specialties were confirmed using the National Provider Identifier Registry. Exposure Payments from Intuitive Surgical Inc, a biotechnology company that manufactures robotic products for use in surgery, were identified via the Open Payments website. Among the physicians, 177 (66.0%) received payments and 91 (34.0%) did not. Main Outcomes and Measures Polarity and subjectivity scores of social media posts shared by physicians. Polarity was scored from −1 to 1, with higher scores reflecting more positive sentiment, lower scores reflecting more negative sentiment, and 0 indicating neutrality. Subjectivity was scored from 0 to 1, with higher scores reflecting more subjective opinions and lower scores reflecting objective facts. Results This study comprised 268 physicians (154 men [57.5%], 68 women [25.4%], and 46 physicians [17.2%] with sex not reported; 113 general surgeons [42.2%] and 155 physicians in surgical subspecialties [57.8%]). The overall sentiment scores ranged from −0.25 to 0.5 (mean [SD] score, 0.1 [0.2]; 95% CI, 0.09-0.13) and subjectivity scores ranged from 0 to 0.9 (mean [SD] score, 0.4 [0.2]; 95% CI, 0.38-0.41), suggesting that posts were relatively objective with occasional personal insights. No significant difference was seen in mean polarity scores between the 177 physicians who received payments and the 91 physicians who did not (mean [SD] score, 0.12 [0.2]; 95% CI, 0.09-0.14 vs 0.1 [0.2]; 95% CI, 0.07-0.14). Physicians posting before and after receiving industry payments showed consistent positive sentiments (median polarity, 0.1 [IQR, 0.03-0.21]) and decreased subjectivity after receiving payment. Physicians in the top 25% of payment distribution had more positive sentiments and increased subjectivity after receiving payments, whereas those in the bottom 75% showed little change. Conclusions and Relevance In this cohort study of US-based physicians, publicly available social media data were used to quantify perceptions of robotic surgery. These findings demonstrate the potential of such data to inform health care practices, guide balanced information dissemination, and uphold the integrity of health information shared by physicians.
Standardized Management of Direct Oral Anticoagulants for Elective Procedures
Authors: Alex C. Spyropoulos, James D. Douketis
Journal: JAMA Network Open (2025)

So-Ryoung Lee, MD, PhD; Kyung-Yeon Lee, MD; Jong-Sung Park, MD; Young Soo Lee, MD, PhD; Yong Seog Oh, MD, PhD; Sang-Jin Han, MD; June Namgung, MD, PhD; Ji Hyun Lee, MD, PhD; Woo-Hyun Lim, MD; Min Soo Ahn, MD, PhD; Soonil Kwon, MD; Hyo-Jeong Ahn, MD; Seil Oh, MD, PhD; Gregory Y. H. Lip, MD, PhD; Eue-Keun Choi, MD, PhD; PERIXa Investigators; Sung-Won Jang; Jong-Il Choi; Jung Ho Heo; Junbeom Park; Moo-Nyun Jin; Ki-Woon Kang; Sun Hwa Kim; Namsik Yoon; Yong-Soo Baek; Sung Ho Lee; Tae-Hoon Kim; Hee Tae Yu; Seung-Young Roh; Kwang Jin Chun; Ki-Byung Nam; Seongwook Han; Kwang-No Lee; Je-Wook Park; Jae-Sun Uhm; Jung Hoon Sung; Young Keun On; Sung-Soo Lee
European Myeloma Network Group Review and Consensus Statement on Primary Plasma Cell Leukemia
Authors: P Musto, M Engelhardt, N W C J van de Donk, F Gay, E Terpos, H Einsele, C Fernández de Larrea, N Sgherza, N Bolli, E Katodritou, M Gentile, B Royer, D Derudas, T Jelinek, E Zamagni, L Rosiñol, B Paiva, J Caers, M Kaiser, M Beksac, R Hájek, A Spencer, H Ludwig, M Cavo, J Bladé, P Moreau, M-V Mateos, J F San-Miguel, M A Dimopoulos, M Boccadoro, P Sonneveld
Journal: Annals of Oncology (2025)
Second order kinematic surface fitting in anatomical structures
Authors: Wilhelm Wimmer, Hervé Delingette
Journal: Medical Image Analysis (2025)

Symmetry detection and morphological classification of anatomical structures play pivotal roles in medical image analysis. The application of kinematic surface fitting, a method for characterizing shapes through parametric stationary velocity fields, has shown promising results in computer vision and computer-aided design. However, existing research has predominantly focused on first order rotational velocity fields, which may not adequately capture the intricate curved and twisted nature of anatomical structures. To address this limitation, we propose an innovative approach utilizing a second order velocity field for kinematic surface fitting. This advancement accommodates higher rotational shape complexity and improves the accuracy of symmetry detection in anatomical structures. We introduce a robust fitting technique and validate its performance through testing on synthetic shapes and real anatomical structures. Our method not only enables the detection of curved rotational symmetries (core lines) but also facilitates morphological classification by deriving intrinsic shape parameters related to curvature and torsion. We illustrate the usefulness of our technique by categorizing the shape of human cochleae in terms of the intrinsic velocity field parameters. The results showcase the potential of our method as a valuable tool for medical image analysis, contributing to the assessment of complex anatomical shapes.
Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice
Authors: Ali Yousefian-Jazi, Suhyun Kim, Jiyeon Chu, Seung-Hye Choi, Phuong Thi Thanh Nguyen, Uiyeol Park, Min-gyeong Kim, Hongik Hwang, Kyungeun Lee, Yeyun Kim, Seung Jae Hyeon, Hyewhon Rhim, Hannah L. Ryu, Grewo Lim, Thor D. Stein, Kayeong Lim, Hoon Ryu, Junghee Lee
Journal: Molecular Neurodegeneration (2025)

Abstract Background Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the loss of both upper and lower motor neurons, leading to progressive paralysis. Both genetic alterations and epigenetic modifications contribute to neuronal dysfunction in the pathogenesis of ALS. However, the mechanism behind genetic mutations in the non-coding region of genes that affect epigenetic modifications remains unclear. Methods Convolutional neural network was used to identify an ALS-associated SNP located in the intronic region of MEF2C (rs304152), residing in a putative enhancer element. To examine the alteration of MEF2C transcription by the SNP, we generated HEK293T cells carrying the major or minor allele by CRISPR-Cas9. To verify the role of MEF2C -knockdown ( MEF2C -KD) in mice, we developed AAV expressing shRNA for MEF2C based on AAV-U6 promoter vector. Neuropathological alterations of MEF2C -KD mice with mitochondrial dysfunction and motor neuronal damage were observed by confocal microscopy and transmission electron microscope (TEM). Behavioral changes of mice were examined through longitudinal study by tail suspension, inverted grid test and automated gait analysis. Results Here, we show that enhancer mutation of MEF2C reduces own gene expression and consequently impairs mitochondrial function in motor neurons. MEF2C localizes and binds to the mitochondria DNA, and directly modulates mitochondria-encoded gene expression. CRISPR/Cas-9-induced mutation of the MEF2C enhancer decreases expression of mitochondria-encoded genes. Moreover, MEF2C mutant cells show reduction of mitochondrial membrane potential, ATP level but elevation of oxidative stress. MEF2C deficiency in the upper and lower motor neurons of mice impairs mitochondria-encoded genes, and leads to mitochondrial metabolic disruption and progressive motor behavioral deficits. Conclusions Together, MEF2C dysregulation by the enhancer mutation leads to mitochondrial dysfunction and oxidative stress, which are prevalent features in motor neuronal damage and ALS pathogenesis. This genetic and epigenetic crosstalk mechanism provides insights for advancing our understanding of motor neuron disease and developing effective treatments.
Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance
Authors: Irena Josephina Johanna Muffels, Hans R. Waterham, Giuseppina D’Alessandro, Guido Zagnoli-Vieira, Michael Sacher, Dirk J. Lefeber, Celine Van der Vinne, Chaim M. Roifman, Koen L. I. Gassen, Holger Rehmann, Desiree Y. Van Haaften-Visser, Edward S. S. Nieuwenhuis, Stephen P. Jackson, Sabine A. Fuchs, Femke Wijk, Peter van Hasselt
Journal: Genome Medicine (2025)

Deciphering variants of uncertain significance (VUS) represents a major diagnostic challenge, partially due to the lack of easy-to-use and versatile cellular readouts that aid the interpretation of pathogenicity and pathophysiology. To address this challenge, we propose a high-throughput screening of cellular functionality through an imaging flow cytometry (IFC)-based platform. Six assays to evaluate autophagic-, lysosomal-, Golgi- health, mitochondrial function, ER stress, and NF-κβ activity were developed in fibroblasts. Assay sensitivity was verified with compounds (N = 5) and positive control patients (N = 6). Eight healthy controls and 20 individuals with VUS were screened. All molecular compounds and positive controls showed significant changes on their cognate assays, confirming assay sensitivity. Simultaneous screening of positive control patients on all six assays revealed distinct phenotypic profiles. In addition, individuals with VUS(es) in well-known disease genes showed distinct - but similar-phenotypic profiles compared to patients with pathogenic variants in the same gene.. For all individuals with VUSes in Genes of Uncertain Significance (GUS), we found one or more of six assays were significantly altered. Broadening the screening to an untargeted approach led to the identification of two clusters that allowed for the recognition of altered cell cycle dynamics and DNA damage repair defects. Experimental follow-up of the 'DNA damage repair defect cluster' led to the discovery of highly specific defects in top2cc release from double-strand DNA breaks in one of these individuals, harboring a VUS in the RAD54L2 gene. Our high-throughput IFC-based platform simplifies the process of identifying VUS pathogenicity through six assays and allows for the recognition of useful pathophysiological markers that structure follow-up experiments, thereby representing a novel valuable tool for precise functional diagnostics in genomics.
Long and Accurate: How HiFi Sequencing is Transforming Genomics
Authors: Bo Wang, Peng Jia, Shenghan Gao, Huanhuan Zhao, Gaoyang Zheng, Linfeng Xu, Kai Ye
Journal: Genomics Proteomics & Bioinformatics (2025)

Abstract Recent developments in PacBio high-fidelity (HiFi) sequencing technologies have transformed genomic research, with circular consensus sequencing now achieving 99.9% accuracy for long (up to 25 kb) single-molecule reads. This method circumvents biases intrinsic to amplification-based approaches, enabling thorough analysis of complex genomic regions [including tandem repeats, segmental duplications, ribosomal DNA (rDNA) arrays, and centromeres] as well as direct detection of base modifications, furnishing both sequence and epigenetic data concurrently. This has streamlined a number of tasks including genome assembly, variant detection, and full-length transcript analysis. This review provides a comprehensive overview of the applications and challenges of HiFi sequencing across various fields, including genomics, transcriptomics, and epigenetics. By delineating the evolving landscape of HiFi sequencing in multi-omics research, we highlight its potential to deepen our understanding of genetic mechanisms and to advance precision medicine.
Identification of Small Open Reading Frame Encoded Proteins from the Human Genome
Authors: Hitesh Kore, Satomi Okano, Keshava K Datta, Jackson Thorp, Parthiban Periasamy, Mayur Divate, Upekha Liyanage, Gunter Hartel, Shivashankar H Nagaraj, Harsha Gowda
Journal: Genomics Proteomics & Bioinformatics (2025)

Abstract One of the main goals of human genome project was to identify all the protein-coding genes. There are ∼ 20,500 protein-coding genes annotated in human reference databases. However, in the last few years, proteogenomics studies have predicted thousands of novel protein-coding regions including low molecular weight proteins encoded by small open reading frames (ORFs) in untranslated regions of messenger RNAs and non-coding RNAs. Most of these predictions are based on bioinformatics analysis and ribosome footprints. The validity of some of these small ORF (sORF) encoded proteins (SEPs) has been established following functional characterization. With the growing number of predicted novel proteins, a strategy to identify reliable candidates that warrant further studies is needed. We developed an integrated proteogenomics workflow to identify reliable set of novel protein-coding regions in the human genome based on their recurrent observations across multiple samples. Publicly available ribosome profiling and global proteomics datasets were used to establish protein-coding evidence. We predicted protein translation from 4008 ORFs based on recurrent ribosome occupancy signals across samples. In addition, we identified 825 SEPs based on proteomics data. Some of the novel protein-coding regions identified were in genome-wide association studies (GWAS) loci associated with various traits and disease phenotypes. Peptides from SEPs are also presented by major histocompatibility complex class I (MHC-I) complex similar to canonical proteins. Novel protein-coding regions reported in this study expand the current catalog of protein-coding genes and warrant experimental studies to elucidate cellular functions regulated by these proteins and their role in human diseases.
Molecular determinants of cross-strain influenza A virus recognition by αβ T cell receptors
Authors: Sergio M. Quiñones-Parra, Stephanie Gras, Thi H. O. Nguyen, Carine Farenc, Christopher Szeto, Louise C. Rowntree, Priyanka Chaurasia, Sneha Sant, Adrianus C. M. Boon, Dhilshan Jayasinghe, Guus F. Rimmelzwaan, Jan Petersen, Peter C. Doherty, Adam P. Uldrich, Dene R. Littler, Jamie Rossjohn, Katherine Kedzierska
Journal: Science Immunology (2025)

Cross-reactive αβ T cell receptors (TCRs) recognizing multiple peptide variants can provide effective control of rapidly evolving viruses yet remain understudied. By screening 12 naturally occurring influenza-derived HLA-B*35:01–restricted nucleoprotein (NP) 418–426 epitopes (B*35:01-NP 418 ) that emerged since 1918 within influenza A viruses, including 2024 A/H5N1 viruses, we identified functional broadly cross-reactive T cells universally recognizing NP 418 variants. Binding studies demonstrated that TCR cross-reactivity was concomitant with diminished antigen sensitivity. Primary human B*35:01/NP 418 + CD8 + T cell lines displayed reduced cross-reactivity in the absence of CD8 coreceptor binding, validating the low avidity of cross-reactive B*35:01-NP 418 + CD8 + T cell responses. Six TCR–HLA-B*35:01/NP 418 crystal structures showed how cross-reactive TCRs recognized multiple B*35:01/NP 418 epitope variants. Specific TCR interactions were formed with invariant and conserved peptide-HLA features, thus remaining distal from highly varied positions of the NP 418 epitope. Our study defines molecular mechanisms associated with extensive TCR cross-reactivity toward naturally occurring viral variants highly relevant to universal protective immunity against influenza.
Cumulative Excess Body Mass Index and MGUS Progression to Myeloma
Authors: Lawrence Liu, Nikhil Grandhi, Mei Wang, Ekaterina Proskuriakova, Theodore Thomas, Martin W. Schoen, Kristen M. Sanfilippo, Kenneth R. Carson, Alissa Visram, Celine Vachon, Graham Colditz, Murali Janakiram, Mengmeng Ji, Su-Hsin Chang
Journal: JAMA Network Open (2025)

Importance Obesity is a risk factor associated with multiple myeloma (MM) and its precursor, monoclonal gammopathy of unknown significance (MGUS). However, it is unclear how cumulative exposure to obesity affects the risk of MGUS progression to MM. Objective To determine the association of cumulative exposure to excess body mass index (EBMI), defined as BMI (calculated as weight in kilograms divided by height in meters squared) greater than 25, with risk of MGUS progression to MM. Design, Setting, and Participants This cohort study included patients with MGUS, including immunoglobin G, immunoglobin A, or light chain MGUS, from the nationwide US Veterans Health Administration database from October 1, 1999, to December 31, 2021. A published natural language processing–assisted model was used to confirm diagnoses of MGUS and progression to MM. Data were analyzed from February 12 to November 4, 2024. Exposures Cumulative EBMI was calculated by area under the curve of measured BMI subtracting the reference BMI at 25 during the first 3 years after MGUS diagnosis. Main Outcomes and Measures The main outcome was progression from MGUS to MM. Multivariable Fine-Gray time-to-competing-event analyses, with death as the competing event, were used to determine associations. Results The cohort included 22 429 patients with MGUS (median [IQR] age, 70.5 [63.5-77.9] years; 21 613 [96.4%] male), with 8329 Black patients (37.1%) and 14 100 White patients (62.9%). There were 4862 patients (21.7%) with reference range BMI (18.5 to &amp;amp;lt;25), 7619 patients (34.0%) with BMI 25 to less than 30, and 8513 patients (38.0%) with BMI 30 or greater at the time of MGUS diagnosis. Compared with reference range BMI at MGUS diagnosis, patients with BMI 25 to less than 30 (adjusted hazard ratio [aHR], 1.17; 95% CI, 1.03-1.34) or 30 or greater (aHR, 1.27; 95% CI, 1.09-1.47) at MGUS diagnosis had higher risk of progression to MM. In patients with reference range BMI at MGUS diagnosis, each 1-unit increase of EBMI per year was associated with a 21% increase in progression risk (aHR, 1.21; 95% CI, 1.04-1.40). However, for patients with BMI 25 or greater at MGUS diagnosis, the incremental risk associated with cumulative EBMI exposure was not statistically significant. Conclusions and Relevance This cohort study found that, for patients with BMI 18.5 to less than 25 at the time of MGUS diagnosis, cumulative exposure to BMI 25 or greater was associated with an increased risk of progression. These findings suggest that for these patients, maintaining a healthy and stable weight following MGUS diagnosis may prevent progression to MM.
Prevalence of poor sleep quality among stroke survivors: a meta-analysis and systematic review
Authors: Yue-Ying Wang, Jia-Xin Li, Yu-Fei Liu, Wei Bai, He-Li Sun, Tong Leong Si, Zhaohui Su, Teris Cheung, Gabor S Ungvari, Chee H Ng, Qinge Zhang, Yu-Tao Xiang
Journal: Sleep Medicine Reviews (2025)
Erratum: Fulvestrant Versus Anastrozole in Endocrine Therapy–Naïve Women With Hormone Receptor–Positive Advanced Breast Cancer: Final Overall Survival in the Phase III FALCON Trial
Authors: John F.R. Robertson, Zhimin Shao, Shinzaburo Noguchi, Igor Bondarenko, Lawrence Panasci, Sandeep Singh, Shankar Subramaniam, Matthew J. Ellis
Journal: Journal of Clinical Oncology (2025)
Long-term outcomes of pancreatic islet transplantation alone in type 1 diabetes: a 20-year single-centre study in Italy
Authors: Davide Catarinella, Raffaella Melzi, Alessia Mercalli, Paola Magistretti, Stefano Tentori, Chiara Gremizzi, Vera Paloschi, Francesco De Cobelli, Giuseppe Esposto, Sabrina Costa, Antonio Secchi, Rossana Caldara, Paola Maffi, Rita Nano, Lorenzo Piemonti
Journal: The Lancet Diabetes & Endocrinology (2025)
Efficacy and Safety of Mechanical Thrombectomy in Acute Ischemic Stroke Secondary to Infective Endocarditis
Authors: Pau Lapeña, Xabier Urra, Jaume Llopis, Marta Hernández-Meneses, Guillermo Cuervo, Olga Maisterra, Francesc Escrihuela-Vidal, Luis Prats-Sánchez, Carmen Sáez, Carmen Olmos, Francisco Hernández-Fernández, Mariano Werner, Natalia Pérez de la Ossa, Eduard Quintana, Asunción Moreno, Angel Chamorro, Jose M Miró, Jose M Miró, Marta Hernández-Meneses, Guillermo Cuervo, Adrian Téllez, Juan M Pericàs, Anders Dahl, Delia García, Asuncion Moreno, Juan Ambrosioni, Cristina García de la Mària, María Alexandra Cañas, Javier García-González, Francesc Marco, Climent Casals, Jordi Vila, Eduard Quintana, Elena Sandoval, Carlos Falces, Daniel Pereda, Marta Sitges, Barbara Vidal, Manuel Castella, José Ortiz, José M Tolosana, Irene Rovira, David Fuster, Andres Perissinotti, Jose Ramírez, Mercè Brunet, Dolors Soy, Pedro Castro, Jaume Llopis, Nuria Fernández-Hidalgo, Laura Escolà-Vergé, Olga Maisterra, Rubén Fernández, Maria Teresa Gonzàlez-Alujas, María Nazarena Pizzi, Pau Rello, Toni Soriano, Antònia Pijuan, Antonia Sambola, Remedios Ríos, Carlota Vigil, Albert Roque, Francesc Escrihuela-Vidal, Jordi Carratalà, Inmaculada Grau, Carmen Ardanuy, Dámaris Berbel, Jose Carlos Sánchez Salado, Oriol Alegre, Alejandro Ruiz Majoral, Fabrizio Sbraga, Arnau Blasco, Laura Gràcia Sánchez, Iván Sánchez-Rodríguez, María Luisa Pedro-Botet, Nieves Sopena, Luis Prats-Sánchez, Natividad de Benito, Juan Pablo Horcajada, Jaume Roquer, Carmen Sáez, Marta Sanz, Carmen Ramos, Álvaro Ximénez-Carrillo, Juan Vega, Isidre Vilacosta
Journal: Clinical Microbiology and Infection (2025)
HIV Impairs Immune Responses to Tumor Neoepitopes Without Altering Mutational Profiles in Non-Small Cell Lung Cancer
Authors: Baptiste Abbar, Karim Labreche, Jacques Cadranel, Marianne Veyri, Véronique Morin, Fatou Seck Thiam, Nathalie Desire, Marine Baron, Erell Guillerm, Alexandre Perrier, Vincent Fallet, Thomas Maitre, Anthony Canellas, Nadine Tarantino, Oulfata Mze, Assia Samri, Lisa Dejancourt, Cecilia Nakid-Cordero, Aurore Vozy, Alberto Picca, Mehdi Touat, Amélie Guihot, Christos Chouaid, Karima Mokhtari, Franck Bielle, Isabelle Brocheriou, Philippe Rouvier, Anita Rodenas Osorio, David Buob, Amira Bouzidi, Yannick Marie, Jalal Assouad, Pierre-Yves Boelle, Florence Coulet, Vincent Vieillard, Jean-Philippe Spano, Brigitte Autran
Journal: Journal of Thoracic Oncology (2025)
LINE-1 ORF1p Mimics Viral Innate Immune Evasion Mechanisms in Pancreatic Ductal Adenocarcinoma
Authors: Eunae You, Bidish K. Patel, Alexandra S. Rojas, Siyu Sun, Patrick Danaher, Natalie I. Ho, Ildiko E. Phillips, Michael J. Raabe, Yuhui Song, Katherine H. Xu, Joshua R. Kocher, Peter M. Richieri, Phoebe Shin, Martin S. Taylor, Linda T. Nieman, Benjamin D. Greenbaum, David T. Ting
Journal: Cancer Discovery (2025)

Abstract Repeat element viral mimicry is a common feature in pancreatic ductal adenocarcinoma (PDAC) that require mechanisms to manage this repeat “viral” load and attenuate innate immune responses. Here, we show that the LINE-1 ORF1 protein (ORF1p) in PDAC cells plays a role in shielding repeat RNAs from activating a pathogen recognition receptor (PRR)-mediated antiviral response that is independent of retrotransposition. Suppression of ORF1p using short hairpin RNA induces innate immune responses through the dsRNA sensors RIG-I and MAVS. Low ORF1p PDAC cell lines have suppressed expression of PRRs demonstrating convergent mechanisms to suppress innate immune signaling. Localization of ORF1p in processing bodies (PBs) with the dsRNA helicase MOV10 were found important for these antiviral responses. Loss of ORF1p resulted in significant growth reduction in tumorspheres and mouse xenografts with an enriched epithelial cell state, and high ORF1p expression was associated with worsened survival in a cohort of human PDAC patients.