tbuckley/cabot-search huggingface dataset:
Evaluation of stenoses using AI video models applied to coronary angiography
Authors: Élodie Labrecque Langlais, Denis Corbin, Olivier Tastet, Ahmad Hayek, Gemina Doolub, Sebastián Mrad, Jean-Claude Tardif, Jean-François Tanguay, Guillaume Marquis-Gravel, Geoffrey H. Tison, Samuel Kadoury, William Le, Richard Gallo, Frederic Lesage, Robert Avram
Journal: npj Digital Medicine (2024)

Abstract The coronary angiogram is the gold standard for evaluating the severity of coronary artery disease stenoses. Presently, the assessment is conducted visually by cardiologists, a method that lacks standardization. This study introduces DeepCoro, a ground-breaking AI-driven pipeline that integrates advanced vessel tracking and a video-based Swin3D model that was trained and validated on a dataset comprised of 182,418 coronary angiography videos spanning 5 years. DeepCoro achieved a notable precision of 71.89% in identifying coronary artery segments and demonstrated a mean absolute error of 20.15% (95% CI: 19.88–20.40) and a classification AUROC of 0.8294 (95% CI: 0.8215–0.8373) in stenosis percentage prediction compared to traditional cardiologist assessments. When compared to two expert interventional cardiologists, DeepCoro achieved lower variability than the clinical reports (19.09%; 95% CI: 18.55–19.58 vs 21.00%; 95% CI: 20.20–21.76, respectively). In addition, DeepCoro can be fine-tuned to a different modality type. When fine-tuned on quantitative coronary angiography assessments, DeepCoro attained an even lower mean absolute error of 7.75% (95% CI: 7.37–8.07), underscoring the reduced variability inherent to this method. This study establishes DeepCoro as an innovative video-based, adaptable tool in coronary artery disease analysis, significantly enhancing the precision and reliability of stenosis assessment.
Association of physical activity pattern and risk of Parkinson’s disease
Authors: Fabin Lin, Yixiang Lin, Lina Chen, Tingting Huang, Tianxin Lin, Jiarui He, Xiaoyang Lu, Xiaochun Chen, Yingqing Wang, Qinyong Ye, Guoen Cai
Journal: npj Digital Medicine (2024)

Abstract Increasing evidence suggests an association between exercise duration and Parkinson’s disease. However, no high-quality prospective evidence exists confirming whether differences exist between the two modes of exercise, weekend warrior and equal distribution of exercise duration, and Parkinson’s risk. Hence, this study aimed to explore the association between different exercise patterns and Parkinson’s risk using exercise data from the UK Biobank. The study analyzed data from 89,400 UK Biobank participants without Parkinson’s disease. Exercise data were collected using the Axivity AX3 wrist-worn triaxial accelerometer. Participants were categorized into three groups: inactive, regularly active, and engaged in the weekend warrior (WW) pattern. The relationship between these exercise patterns and Parkinson’s risk was assessed using a multifactorial Cox model. During a mean follow-up of 12.32 years, 329 individuals developed Parkinson’s disease. In a multifactorial Cox model, using the World Health Organization–recommended threshold of 150 min of moderate-to-vigorous physical activity per week, both the active WW group [hazard ratio (HR) = 0.58; 95% confidence interval (CI) = 0.43–0.78; P &lt; 0.001] and the active regular group (HR = 0.44; 95% CI = 0.34–0.57; P &lt; 0.001) exhibited a lower risk of developing Parkinson’s disease compared with the inactive group. Further, no statistically significant difference was observed between the active WW and the active regular groups (HR = 0.77; 95% CI = 0.56–1.05; P = 0.099). In conclusion, in this cohort study, both the WW exercise pattern and an equal distribution of exercise hours were equally effective in reducing Parkinson’s risk.
Accelerating clinical trials in the EU (ACT EU): transforming the EU clinical trials landscape
Authors: Giacomo Capone, Björn Eriksson, Monique Al, Stan van Belkum, Karl Broich, Maria Lamas, Marianne Lunzer, Lorraine Nolan, Catriona Ester, Juan Garcia Burgos, Laura Pioppo, Ana Zanoletty, Peter Arlett
Journal: Nature Reviews Drug Discovery (2024)
Non-arterial line cardiac output calculation misclassifies exercise pulmonary hypertension and increases risk of data loss particularly in black, scleroderma and Raynaud's patients during invasive exercise testing
Authors: Luiz Campedelli, S. Mehdi Nouraie, Michael G. Risbano
Journal: European Respiratory Journal (2024)

Background The direct Fick principle is the standard for calculating cardiac output (CO) to detect CO-dependent conditions like exercise pulmonary hypertension (ePH). Fick CO arterial incorporates arterial haemoglobin (Hb a ) and oxygen saturation ( S aO 2 ) with oxygen consumption from exercise testing, while Fick CO non-arterial substitutes mixed venous haemoglobin (Hb mv ) and peripheral oxygen saturation ( S pO 2 ) in the absence of an arterial line. The decision to employ an arterial catheter for exercise testing varies, and discrepancies in oxygen saturation and haemoglobin between arterial and non-arterial methods may lead to differences in Fick CO, potentially affecting ePH classification. Methods We performed a retrospective analysis of 296 consecutive invasive cardiopulmonary exercise testing (iCPET) studies comparing oxygen saturation from pulse oximetry ( S pO 2 ) and radial arterial ( S aO 2 ), Hb a and Hb mv , and CO calculated with arterial (CO arterial ) and non-arterial (CO non-arterial ) values. We assessed the risk of misclassification of pre- and post-capillary ePH and data loss due to inaccurate S pO 2 . Results When considering all stages from rest to peak exercise, Hb a and Hb mv demonstrated high correlation, while S pO 2 and S aO 2 as well as CO arterial and CO non-arterial demonstrated low correlation. Data loss was significantly higher across all stages of exercise for S pO 2 (n=346/1926 (18%)) compared to S aO 2 (n=17/1923 (0.88%)). We found that pre- and post-capillary ePH were misclassified as CO non-arterial data (n=7/41 (17.1%) and n=2/23 (8.7%), respectively). Patients with scleroderma and/or Raynaud's (n=11/33 (33.3%)) and black patients (n=6/19 (31.6%)) had more S pO 2 data loss. Conclusion Reliance upon S pO 2 during invasive exercise testing results in the misclassification of pre- and post-capillary ePH, and unmeasurable S pO 2 for black, scleroderma and Raynaud's patients can preclude accurate exercise calculations, thus limiting the diagnostic and prognostic value of invasive exercise testing without an arterial line.
Prevalence of Stroke — Behavioral Risk Factor Surveillance System, United States, 2011–2022
Authors: Omoye E. Imoisili, Alina Chung, Xin Tong, Donald K. Hayes, Fleetwood Loustalot
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Stroke was the fifth leading cause of death in the United States in 2021, and cost U.S. residents approximately $56.2 billion during 2019-2020.During 2006-2010, selfreported stroke prevalence among noninstitutionalized adults had a relative decrease of 3.7%.Data from the Behavioral Risk Factor Surveillance System were used to analyze agestandardized stroke prevalence during 2011-2022 among adults aged ≥18 years.From 2011-2013 to 2020-2022, overall self-reported stroke prevalence increased by 7.8% nationwide.Increases occurred among adults aged 18-64 years; females and males; non-Hispanic Black or African American (Black), non-Hispanic White (White), and Hispanic or Latino (Hispanic) persons; and adults with less than a college degree.Stroke prevalence was higher among adults aged ≥65 years than among younger adults; among non-Hispanic American Indian or Alaska Native, non-Hispanic Native Hawaiian or Pacific Islander, and Black adults than among White adults; and among adults with less than a high school education than among those with higher levels of education.Stroke prevalence decreased in the District of Columbia and increased in 10 states.Initiatives to promote knowledge of the signs and symptoms of stroke, and the identification of disparities in stroke prevalence, might help to focus clinical and programmatic interventions, such as the Million Hearts 2027 initiative or the Paul Coverdell National Acute Stroke Program, to improve prevention and treatment of stroke.* https://www.cdc.gov/nchs/products/databriefs/db456.htm$56.2 billion during 2019-2020 (1).A report on stroke prevalence using Behavioral Risk Factor Surveillance System (BRFSS) data indicated that overall self-reported stroke prevalence among noninstitutionalized adults aged ≥18 years in all 50 states and the District of Columbia (DC) had a relative decrease of 3.7% during 2006-2010 (2).The current report used BRFSS data to assess stroke prevalence trends during 2011-2022 by sociodemographic characteristics and place of residence. Methods Data Source and Study ParticipantsBRFSS is a state-based surveillance system of noninstitutionalized U.S. civilian adults aged ≥18 years, administered in U.S. states and territories in coordination with CDC.Each year, health departments conduct a cross-sectional, randomdigit-dialed landline and cellular telephone survey assessing Morbidity and Mortality Weekly Report
Monkeypox Virus Infections After 2 Preexposure Doses of JYNNEOS Vaccine — United States, May 2022–May 2024
Authors: Sarah Anne J. Guagliardo, Ian Kracalik, Rosalind J. Carter, Christopher Braden, Rebecca Free, Mukesh Hamal, Alexandra Tuttle, Andrea M. McCollum, Agam K. Rao
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Two doses of JYNNEOS vaccine are effective in preventing many mpox cases and can reduce the severity of symptoms in infected persons.However, infections among fully vaccinated persons can occur.During May 2022-May 2024, a total of 271 mpox cases among fully vaccinated persons were reported to CDC from 27 U.S. jurisdictions.These reported infections are estimated to have occurred in <1% of fully vaccinated persons.Compared with cases among unvaccinated persons, infections among fully vaccinated persons were more likely to occur among non-Hispanic White men aged 30-39 years, were associated with increased numbers of sexual partners, and resulted in less severe disease (p<0.001).Among infections in fully vaccinated persons with complete data, infections after vaccination were reported more commonly after receipt of heterologous (subcutaneous and intradermal) (46%) or homologous subcutaneous (32%) JYNNEOS vaccination than after homologous intradermal (22%) vaccination.Disparate time intervals from vaccination to infection among fully vaccinated persons suggest that immunity is not waning.The median interval between the second vaccine dose and illness onset was longer for cases among persons who had received 2 intradermal doses (median = 363 days; IQR = 221-444 days) compared with cases in persons who had received 2 subcutaneous doses (median = 263 days; IQR = 47-334 days) (p<0.001).The implications of this finding are not known; however, these data should increase confidence in the effectiveness of vaccine doses that were administered intradermally, the preferred method of administration during the peak of the outbreak when vaccine supply was limited.Persons recommended to receive the JYNNEOS vaccine should receive 2 doses, irrespective of the route of administration, and at this time, additional doses are not recommended for the affected population.
<i>Notes from the Field:</i> Clade II Mpox Surveillance Update — United States, October 2023–April 2024
Authors: Alexandra Tuttle, Christine M. Hughes, Mitchell Dvorak, Leah Aeschleman, Whitni Davidson, Kimberly Wilkins, Crystal Gigante, Panayampalli S. Satheshkumar, Agam K. Rao, Faisal S. Minhaj, Bryan E. Christensen, Jennifer H. McQuiston, Christina L. Hutson, Andrea M. McCollum
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Two clades of monkeypox virus (MPXV) are known to cause human illness: clade I, which is endemic in Central Africa and is currently increasing in the Democratic Republic of the Congo, and clade II, which caused a global outbreak starting in 2022.Clade IIassociated disease is considered less severe than that of clade I and is typically self-limiting; however, immunocompromised persons, especially those with advanced HIV (i.e., CD4 T lymphocyte cell count <200 cells/mm 3 ), have experienced more severe infections (1,2).Clade II MPXV continues to circulate at low levels in the United States, but no cases of clade I MPXV have been reported.National mpox case counts peaked at approximately 3,000 per week during late July-August 2022 (Figure ), then sharply declined and remain substantially lower than case counts during the peak (59 cases per week during October 1, 2023 -April 30, 2024)).This report summarizes mpox surveillance data reported to CDC during October 1, 2023-April 30, 2024.This activity was reviewed by CDC, deemed not research, and was conducted consistent with federal law and CDC policy.*
Outbreak of Human Trichinellosis — Arizona, Minnesota, and South Dakota, 2022
Authors: Shama Cash-Goldwasser, Dustin Ortbahn, Muthu Narayan, Conor Fitzgerald, Keila Maldonado, James Currie, Anne Straily, Sarah Sapp, Henry S. Bishop, Billy Watson, Margaret Neja, Yvonne Qvarnstrom, David M. Berman, Sarah Y. Park, Kirk Smith, Stacy Holzbauer
Journal: MMWR Morbidity and Mortality Weekly Report (2024)

Trichinellosis is a parasitic zoonotic disease transmitted through the consumption of meat from animals infected with Trichinella spp.nematodes.In North America, human trichinellosis is rare and is most commonly acquired through consumption of wild game meat.In July 2022, a hospitalized patient with suspected trichinellosis was reported to the Minnesota Department of Health.One week before symptom onset, the patient and eight other persons shared a meal that included bear meat that had been frozen for 45 days before being grilled and served rare with vegetables that had been cooked with the meat.Investigation identified six trichinellosis cases, including two in persons who consumed only the vegetables.Motile Trichinella larvae were found in remaining bear meat that had been frozen for >15 weeks.Molecular testing identified larvae from the bear meat as Trichinella nativa, a freeze-resistant species.Persons who consume meat from wild game animals should be aware that that adequate cooking is the only reliable way to kill Trichinella parasites and that infected meat can cross-contaminate other foods.TABLE.Demographic characteristics, clinical data, and laboratory test results from persons who consumed a meal that included bear meat infected with Trichinella nativa -Arizona, Minnesota, and South Dakota, 2022 Case status Age, yrs, sex
Breadth of Fc-mediated effector function correlates with clinical immunity following human malaria challenge
Authors: Irene N. Nkumama, Rodney Ogwang, Dennis Odera, Fauzia Musasia, Kennedy Mwai, Lydia Nyamako, Linda Murungi, James Tuju, Kristin Fürle, Micha Rosenkranz, Rinter Kimathi, Patricia Njuguna, Mainga Hamaluba, Melissa C. Kapulu, Roland Frank, Faith H.A. Osier
Journal: Immunity (2024)

Malaria is a life-threatening disease of global health importance, particularly in sub-Saharan Africa. The growth inhibition assay (GIA) is routinely used to evaluate, prioritize, and quantify the efficacy of malaria blood-stage vaccine candidates but does not reliably predict either naturally acquired or vaccine-induced protection. Controlled human malaria challenge studies in semi-immune volunteers provide an unparalleled opportunity to robustly identify mechanistic correlates of protection. We leveraged this platform to undertake a head-to-head comparison of seven functional antibody assays that are relevant to immunity against the erythrocytic merozoite stage of Plasmodium falciparum. Fc-mediated effector functions were strongly associated with protection from clinical symptoms of malaria and exponential parasite multiplication, while the gold standard GIA was not. The breadth of Fc-mediated effector function discriminated clinical immunity following the challenge. These findings present a shift in the understanding of the mechanisms that underpin immunity to malaria and have important implications for vaccine development.
Enterococcus-derived tyramine hijacks α2A-adrenergic receptor in intestinal stem cells to exacerbate colitis
Authors: Chaoliang Li, Panrui Zhang, Yadong Xie, Shishan Wang, Meng Guo, Xiaowei Wei, Kaiguang Zhang, Dan Cao, Rongbin Zhou, Sheng Wang, Xinyang Song, Shu Zhu, Wen Pan
Journal: Cell Host & Microbe (2024)
Molecular subtypes of neuroendocrine carcinomas: A cross-tissue classification framework based on five transcriptional regulators
Authors: Zhanyu Wang, Chengming Liu, Sufei Zheng, Yuxin Yao, Sihui Wang, Xinfeng Wang, Enzhi Yin, Qingpeng Zeng, Chaoqi Zhang, Guochao Zhang, Wei Tang, Bo Zheng, Liyan Xue, Zhen Wang, Xiaoli Feng, Yan Wang, Jianming Ying, Qi Xue, Nan Sun, Jie He
Journal: Cancer Cell (2024)
Meningioma transcriptomic landscape demonstrates novel subtypes with regional associated biology and patient outcome
Authors: H. Nayanga Thirimanne, Damian Almiron-Bonnin, Nicholas Nuechterlein, Sonali Arora, Matt Jensen, Carolina A. Parada, Chengxiang Qiu, Frank Szulzewsky, Collin W. English, William C. Chen, Philipp Sievers, Farshad Nassiri, Justin Z. Wang, Tiemo J. Klisch, Kenneth D. Aldape, Akash J. Patel, Patrick J. Cimino, Gelareh Zadeh, Felix Sahm, David R. Raleigh, Jay Shendure, Manuel Ferreira, Eric C. Holland
Journal: Cell Genomics (2024)

Meningiomas, although mostly benign, can be recurrent and fatal. World Health Organization (WHO) grading of the tumor does not always identify high-risk meningioma, and better characterizations of their aggressive biology are needed. To approach this problem, we combined 13 bulk RNA sequencing (RNA-seq) datasets to create a dimension-reduced reference landscape of 1,298 meningiomas. The clinical and genomic metadata effectively correlated with landscape regions, which led to the identification of meningioma subtypes with specific biological signatures. The time to recurrence also correlated with the map location. Further, we developed an algorithm that maps new patients onto this landscape, where the nearest neighbors predict outcome. This study highlights the utility of combining bulk transcriptomic datasets to visualize the complexity of tumor populations. Further, we provide an interactive tool for understanding the disease and predicting patient outcomes. This resource is accessible via the online tool Oncoscape, where the scientific community can explore the meningioma landscape.
Olfactory neuroblastoma mimics molecular heterogeneity and lineage trajectories of small-cell lung cancer
Authors: John B. Finlay, Abbie S. Ireland, Sarah B. Hawgood, Tony Reyes, Tiffany Ko, Rachelle R. Olsen, Ralph Abi Hachem, David W. Jang, Diana Bell, Joseph M. Chan, Bradley J. Goldstein, Trudy G. Oliver
Journal: Cancer Cell (2024)

The olfactory epithelium undergoes neuronal regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare tumor of unclear origins. Employing alterations in Rb1/Trp53/Myc (RPM), we establish a genetically engineered mouse model of high-grade metastatic ONB exhibiting a NEUROD1
A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death
Authors: Jonathan Mannion, Valentina Gifford, Benjamin Bellenie, Winnie Fernando, Laura Ramos Garcia, Rebecca Wilson, Sidonie Wicky John, Savita Udainiya, Emmanuel C. Patin, Crescens Tiu, Angel Smith, Maria Goicoechea, Andrew Craxton, Nathalia Moraes de Vasconcelos, Naomi Guppy, Kwai-Ming J. Cheung, Nicholas J. Cundy, Olivier Pierrat, Alfie Brennan, Theodoros I. Roumeliotis, Graeme Benstead-Hume, John Alexander, Gareth Muirhead, Scott Layzell, Wenxin Lyu, Victoria Roulstone, Mark Allen, Holly Baldock, Arnaud Legrand, Florian Gabel, Natalia Serrano-Aparicio, Chris Starling, Hongyan Guo, Jason Upton, Mads Gyrd-Hansen, Marion MacFarlane, Benedict Seddon, Florence Raynaud, Ioannis Roxanis, Kevin Harrington, Syed Haider, Jyoti S. Choudhary, Swen Hoelder, Tencho Tenev, Pascal Meier
Journal: Immunity (2024)

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) functions as a critical stress sentinel that coordinates cell survival, inflammation, and immunogenic cell death (ICD). Although the catalytic function of RIPK1 is required to trigger cell death, its non-catalytic scaffold function mediates strong pro-survival signaling. Accordingly, cancer cells can hijack RIPK1 to block necroptosis and evade immune detection. We generated a small-molecule proteolysis-targeting chimera (PROTAC) that selectively degraded human and murine RIPK1. PROTAC-mediated depletion of RIPK1 deregulated TNFR1 and TLR3/4 signaling hubs, accentuating the output of NF-κB, MAPK, and IFN signaling. Additionally, RIPK1 degradation simultaneously promoted RIPK3 activation and necroptosis induction. We further demonstrated that RIPK1 degradation enhanced the immunostimulatory effects of radio- and immunotherapy by sensitizing cancer cells to treatment-induced TNF and interferons. This promoted ICD, antitumor immunity, and durable treatment responses. Consequently, targeting RIPK1 by PROTACs emerges as a promising approach to overcome radio- or immunotherapy resistance and enhance anticancer therapies.
Distinct roles of TREM2 in central nervous system cancers and peripheral cancers
Authors: Jian Zhong, Xudong Xing, Yixin Gao, Lei Pei, Chenfei Lu, Huixin Sun, Yanxing Lai, Kang Du, Feizhe Xiao, Ying Yang, Xiuxing Wang, Yu Shi, Fan Bai, Nu Zhang
Journal: Cancer Cell (2024)
Expanding the Overton Window in Deceased Kidney Donor Eligibility—Enough to Make a Difference?
Authors: Xingxing S. Cheng, Colin R. Lenihan
Journal: JAMA (2024)

Yumeng Wen, MD, PhD; Sherry G. Mansour, MD, MSc; Nityasree Srialluri, MD, MS, MHS; David Hu, MS; Heather Thiessen Philbrook, MMath; Isaac E. Hall, MD, MS; Mona D. Doshi, MD; Sumit Mohan, MD, MPH; Peter P. Reese, MD, PhD; Chirag R. Parikh, MD, PhD
Kidney Transplant Outcomes From Deceased Donors Who Received Dialysis
Authors: Yumeng Wen, Sherry G. Mansour, Nityasree Srialluri, David Hu, Heather Thiessen Philbrook, Isaac E. Hall, Mona D. Doshi, Sumit Mohan, Peter P. Reese, Chirag R. Parikh
Journal: JAMA (2024)

Recipient outcomes after kidney transplant from deceased donors who received dialysis prior to kidney donation are not well described.
Hypertension and Kidney Function After Living Kidney Donation
Authors: Amit X. Garg, Jennifer B. Arnold, Meaghan S. Cuerden, Christine Dipchand, Liane S. Feldman, John S. Gill, Martin Karpinski, Scott Klarenbach, Greg Knoll, Charmaine E. Lok, Matthew Miller, Mauricio Monroy-Cuadros, Christopher Nguan, G. V. Ramesh Prasad, Jessica M. Sontrop, Leroy Storsley, Neil Boudville
Journal: JAMA (2024)

Recent guidelines call for better evidence on health outcomes after living kidney donation.
Prospectively Examining Outcomes After Living Kidney Donation
Authors: Elizabeth C. Lorenz, Wolfgang C. Winkelmayer
Journal: JAMA (2024)

Amit X. Garg, MD, PhD; Jennifer B. Arnold, BSc; Meaghan S. Cuerden, PhD; Christine Dipchand, MD; Liane S. Feldman, MD; John S. Gill, MD; Martin Karpinski, MD; Scott Klarenbach, MD; Greg Knoll, MD; Charmaine E. Lok, MD; Matthew Miller, MD; Mauricio Monroy-Cuadros, MD; Christopher Nguan, MD; G. V. Ramesh Prasad, MD; Jessica M. Sontrop, PhD; Leroy Storsley, MD; Neil Boudville, MD