tbuckley/cabot-search huggingface dataset:
Statins, Mortality, and Major Adverse Cardiovascular Events Among US Veterans With Chronic Kidney Disease
Authors: Odeya Barayev, Chelsea E. Hawley, Helen Wellman, Hanna Gerlovin, Whitney Hsu, Julie M. Paik, Ernest I. Mandel, Christine K. Liu, Luc Djoussé, J. Michael Gaziano, David R. Gagnon, Ariela R. Orkaby
Journal: JAMA Network Open (2023)

Importance There are limited data for the utility of statins for primary prevention of atherosclerotic cardiovascular disease (ASCVD) and death in adults with chronic kidney disease (CKD). Objective To evaluate the association of statin use with all-cause mortality and major adverse cardiovascular events (MACE) among US veterans older than 65 years with CKD stages 3 to 4. Design, Setting, and Participants This cohort study used a target trial emulation design for statin initiation among veterans with moderate CKD (stages 3 or 4) using nested trials with a propensity weighting approach. Linked Veterans Affairs (VA) Healthcare System, Medicare, and Medicaid data were used. This study considered veterans newly diagnosed with moderate CKD between 2005 and 2015 in the VA, with follow-up through December 31, 2017. Veterans were older than 65 years, within 5 years of CKD diagnosis, had no prior ASCVD or statin use, and had at least 1 clinical visit in the year prior to trial baseline. Eligibility criteria were assessed for each nested trial, and Cox proportional hazards models with bootstrapping were run. Analysis was conducted from July 2021 to October 2023. Exposure Statin initiation vs none. Main Outcomes and Measures Primary outcome was all-cause mortality; secondary outcome was time to first MACE (myocardial infarction, transient ischemic attack, stroke, revascularization, or mortality). Results Included in the analysis were 14 828 veterans. Mean (SD) age at CKD diagnosis was 76.9 (8.2) years, 14 616 (99%) were men, 10 539 (72%) White, and 2568 (17%) Black. After expanding to person-trials and assessing eligibility at each baseline, there were 151 243 person-trials (14 685 individuals) of nonstatin initiators and 2924 person-trials (2924 individuals) of statin initiators included. Propensity score adjustment via overlap weighting with nonparametric bootstrapping resulted in covariate balance, with mean (SD) follow-up of 3.6 (2.7) years. The hazard ratio for all-cause mortality was 0.91 (95% CI, 0.85-0.97) comparing statin initiators to noninitiators. The hazard ratio for MACE was 0.96 (95% CI, 0.91-1.02). Results remained consistent in prespecified subgroup analyses. Conclusions and Relevance In this target trial emulation of statin initiation in US veterans older than 65 years with CKD stages 3 to 4 and no prior ASCVD, statin initiation was significantly associated with a lower risk of all-cause mortality but not MACE. Results should be confirmed in a randomized clinical trial.
Psychophysics may be the game-changer for deep neural networks (DNNs) to imitate the human vision
Authors: Keerthi S. Chandran, Amrita Mukherjee Paul, Avijit Paul, Kuntal Ghosh
Journal: Behavioral and Brain Sciences (2023)

Abstract Psychologically faithful deep neural networks (DNNs) could be constructed by training with psychophysics data. Moreover, conventional DNNs are mostly monocular vision based, whereas the human brain relies mainly on binocular vision. DNNs developed as smaller vision agent networks associated with fundamental and less intelligent visual activities, can be combined to simulate more intelligent visual activities done by the biological brain.
Risk Prediction for Atherosclerotic Cardiovascular Disease With and Without Race Stratification
Authors: Arnab K. Ghosh, Sara Venkatraman, Michael G. Nanna, Monika M. Safford, Lisandro D. Colantonio, Todd M. Brown, Laura C. Pinheiro, Eric D. Peterson, Ann Marie Navar, Madeline R. Sterling, Orysya Soroka, Musarrat Nahid, Samprit Banerjee, Parag Goyal
Journal: JAMA Cardiology (2023)

Use of race-specific risk prediction in clinical medicine is being questioned. Yet, the most commonly used prediction tool for atherosclerotic cardiovascular disease (ASCVD)-pooled cohort risk equations (PCEs)-uses race stratification.
For human-like models, train on human-like tasks
Authors: Katherine Hermann, Aran Nayebi, Sjoerd van Steenkiste, Matt Jones
Journal: Behavioral and Brain Sciences (2023)

Abstract Bowers et al. express skepticism about deep neural networks (DNNs) as models of human vision due to DNNs' failures to account for results from psychological research. We argue that to fairly assess DNNs, we must first train them on more human-like tasks which we hypothesize will induce more human-like behaviors and representations.
Development and Validation of a Model for Postpancreatectomy Hemorrhage Risk
Authors: Emrullah Birgin, Sebastian Hempel, Alina Reeg, Florian Oehme, Annika Schnizer, Johann S. Rink, Matthias F. Froelich, Svetlana Hetjens, Verena Plodeck, Heiner Nebelung, Schaima Abdelhadi, Mohammad Rahbari, Patrick Téoule, Erik Rasbach, Christoph Reissfelder, Jürgen Weitz, Stefan O. Schoenberg, Marius Distler, Nuh N. Rahbari
Journal: JAMA Network Open (2023)

Importance Postpancreatectomy hemorrhage (PPH) due to postoperative pancreatic fistula (POPF) is a life-threatening complication after pancreatoduodenectomy. However, there is no prediction tool for early identification of patients at high risk of late PPH. Objective To develop and validate a prediction model for PPH. Design, Setting, and Participants This retrospective prognostic study included consecutive patients with clinically relevant POPF who underwent pancreatoduodenectomy from January 1, 2009, to May 20, 2023, at the University Hospital Mannheim (derivation cohort), and from January 1, 2012, to May 31, 2022, at the University Hospital Dresden (validation cohort). Data analysis was performed from May 30 to July 29, 2023. Exposure Clinical and radiologic features of PPH. Main Outcomes and Measures Accuracy of a predictive risk score of PPH. A multivariate prediction model—the hemorrhage risk score (HRS)—was established in the derivation cohort (n = 139) and validated in the validation cohort (n = 154). Results A total of 293 patients (187 [64%] men; median age, 69 [IQR, 60-76] years) were included. The HRS comprised 4 variables with associations: sentinel bleeding (odds ratio [OR], 35.10; 95% CI, 5.58-221.00; P &amp;amp;lt; .001), drain fluid culture positive for Candida species (OR, 14.40; 95% CI, 2.24-92.20; P &amp;amp;lt; .001), and radiologic proof of rim enhancement of (OR, 12.00; 95% CI, 2.08-69.50; P = .006) or gas within (OR, 12.10; 95% CI, 2.22-65.50; P = .004) a peripancreatic fluid collection. Two risk categories were identified with patients at low risk (0-1 points) and high risk (≥2 points) to develop PPH. Patients with PPH were predicted accurately in the derivation cohort (C index, 0.97) and validation cohort (C index 0.83). The need for more invasive PPH management (74% vs 34%; P &amp;amp;lt; .001) and severe complications (49% vs 23%; P &amp;amp;lt; .001) were more frequent in high-risk patients compared with low-risk patients. Conclusions and Relevance In this retrospective prognostic study, a robust prediction model for PPH was developed and validated. This tool may facilitate early identification of patients at high risk for PPH.
Race, Racism, and Risk—Implications of Social Determinants of Health in Cardiovascular Disease Prediction
Authors: Sadiya S. Khan, Clyde W. Yancy
Journal: JAMA Cardiology (2023)

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The association of age at psoriasis onset and HLA-C*06:02 with biologic survival in patients with moderate-to-severe psoriasis: a cohort study from the British Association of Dermatologists Biologics and Immunomodulators Register (BADBIR)
Authors: Oras A Alabas, Kayleigh J Mason, Zenas Z N Yiu, Richard B Warren, Nick Dand, Jonathan N Barker, Catherine H Smith, Christopher E M Grifﬁths, Jonathan Barker, Simon Morrison, Anthony Bewley, Ian Evans, Christopher Griffiths, Shehnaz Ahmed, Brian Kirby, Elise Kleyn, Philip Laws, Philip Hampton, Oras Alabas, Kathleen McElhone, Zenas Yiu, Teena Mackenzie, Tess McPherson, Ruth Murphy, Anthony Ormerod, Shernaz Walton, Nick Reynolds, Catherine Smith, Alexa Shipman, Christina Ye, Olivia Hughes, Richard Warren, Anja Strangfeld, Richard Weller, Girish Gupta, Vera Zietemann, Jonathan Barker, Michael R Barnes, A David Burden, Paola di Meglio, Richard Emsley, Anea Evans, Christopher E M Griffiths, Katherine Payne, Nick J Reynolds, Catherine Smith, Deborah Stocken, Richard B Warren
Journal: British Journal of Dermatology (2023)

Few studies have used real-world data to investigate the association between biologic therapy survival and age at psoriasis onset or HLA-C*06:02 status in patients with moderate-to-severe psoriasis. The robustness of these studies is limited by small sample size, short follow-up and diverse safety and effectiveness measures.
Successful Treatment of Recalcitrant Mpox Lesions With Intralesional Cidofovir in a Patient With HIV/AIDS
Authors: Connor R. Buechler, Zachary J. Anderson, Sara A. Kullberg, Daniel D. Miller, Aileen Ahiskali, Ronald Schut, Sara A. Hylwa
Journal: JAMA Dermatology (2023)

This case report describes a man in his 50s with HIV/AIDS who presented with widely scattered recalcitrant mpox lesions.
Precision Medicine for Sepsis Management in Low- and Middle-Income Countries—Melioidosis as a Model?
Authors: Yeo Tsin Wen, Allen C. Cheng, Yuwana Podin
Journal: American Journal of Respiratory and Critical Care Medicine (2023)

"Precision Medicine for Sepsis Management in Low- and Middle-Income Countries – Melioidosis as a Model?." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp.
Allogeneic NK cells induce monocyte-to-dendritic cell conversion, control tumor growth, and trigger a pro-inflammatory shift in patient-derived cultures of primary and metastatic colorectal cancer
Authors: Elisa C Toffoli, Amanda A van Vliet, Henk W M Verheul, Hans J van der Vliet, Jurriaan Tuynman, Jan Spanholtz, Tanja D de Gruijl
Journal: Journal for ImmunoTherapy of Cancer (2023)

Introduction Natural killer (NK) cells are innate lymphocytes with a key role in the defense against tumors. Recently, allogeneic NK cell-based therapies have gained interest because of their ability to directly lyse tumor cells without inducing graft-versus-host disease. As NK cells are also able to influence the function of other immune cells (most notably dendritic cells (DC)), a better understanding of the effects of allogeneic NK cell products on the host immune system is required. In this study, we analyzed the effects of an allogeneic off-the-shelf NK cell product, on the tumor microenvironment (TME) of primary and metastatic colorectal cancer (pCRC and mCRC, respectively). Moreover, we explored if the combination of NK cells with R848, a toll-like receptors 7/8 ligand, could further enhance any pro-inflammatory effects. Methods Ex vivo expanded umbilical cord blood stem cell derived NK cells were co-cultured with pCRC or mCRC single-cell suspensions in the presence or absence of R848 for 5 days, during and after which flow cytometry and cytokine release profiling were performed. Results NK cells efficiently induced lysis of tumor cells in both pCRC and mCRC single-cell suspensions and thereby controlled growth rates during culture. They also induced differentiation of infiltrating monocytic cells to an activated DC phenotype. Importantly, this NK-mediated myeloid conversion was also apparent in cultures after tumor cell depletion and was further enhanced by combining NK cells with R848. Moreover, NK cells, and to a greater extent, the combination of NK cells and R848, triggered CD8 + and CD4 + T-cell activation as well as a reduction in activated regulatory T cell rates. Finally, the combination of NK cells and R848 induced a pro-inflammatory shift in the cytokine release profile resulting in higher levels of interferon (IFN)-γ, interleukin (IL)-2, IL-12p70, and IFN-α as well as a reduction in IL-6, in both pCRC and mCRC cultures. Conclusion Allogeneic NK cells engaged in favorable myeloid crosstalk, displayed effective antitumor activity and, when combined with R848, induced a pro-inflammatory shift of the CRC TME. These findings prompt the investigation of NK cells and R848 as a combination therapy for solid tumors.
Fibrinogen-like protein 2 promotes tumor immune suppression by regulating cholesterol metabolism in myeloid-derived suppressor cells
Authors: Lei Wu, Xudong Liu, Juan Lei, Nan Zhang, Huakan Zhao, Jiangang Zhang, Huan Deng, Yongsheng Li
Journal: Journal for ImmunoTherapy of Cancer (2023)

Background Myeloid-derived suppressor cells (MDSCs) are crucial mediators of tumor-associated immune suppression. Targeting the accumulation and activation of MDSCs has been recognized as a promising approach to enhance the effectiveness of immunotherapies for different types of cancer. Methods The MC38 and B16 tumor-bearing mouse models were established to investigate the role of Fgl2 during tumor progression. Fgl2 and FcγRIIB-deficient mice, adoptive cell transfer, RNA-sequencing and flow cytometry analysis were used to assess the role of Fgl2 on immunosuppressive activity and differentiation of MDSCs. Results Here, we show that fibrinogen-like protein 2 (Fgl2) regulates the differentiation and immunosuppressive functions of MDSCs. The absence of Fgl2 leads to an increase in antitumor CD8 + T-cell responses and a decrease in granulocytic MDSC accumulation. The regulation mechanism involves Fgl2 modulating cholesterol metabolism, which promotes the accumulation of MDSCs and immunosuppression through the production of reactive oxygen species and activation of XBP1 signaling. Inhibition of Fgl2 or cholesterol metabolism in MDSCs reduces their immunosuppressive activity and enhances differentiation. Targeting Fgl2 could potentially enhance the therapeutic efficacy of anti-PD-1 antibody in immunotherapy. Conclusion These results suggest that Fgl2 plays a role in promoting immune suppression by modulating cholesterol metabolism and targeting Fgl2 combined with PD-1 checkpoint blockade provides a promising therapeutic strategy for antitumor therapy.
Standardized Definitions for Evaluation of Acute Decompensated Heart Failure Therapies
Authors: Anuradha Lala, Carine E. Hamo, Biykem Bozkurt, Mona Fiuzat, Vanessa Blumer, Daniel Bukhoff, Javed Butler, Maria Rosa Costanzo, G. Michael Felker, Gerasimos Filippatos, Marvin A. Konstam, John J.V. McMurray, Robert J. Mentz, Marco Metra, Mitchell A. Psotka, Scott D. Solomon, John Teerlink, William T. Abraham, Christopher M. O’Connor
Journal: JACC Heart Failure (2023)

Acute decompensated heart failure (ADHF) is one of the most common reasons for hospitalizations or urgent care and is associated with poor outcomes. Therapies shown to improve outcomes are limited, however, and innovation in pharmacologic and device-based therapeutics are therefore actively being sought. Standardizing definitions for ADHF and its trajectory is complex, limiting the generalizability and translation of clinical trials to effect clinical care and policy change. The Heart Failure Collaboratory is a multistakeholder organization comprising clinical investigators, clinicians, patients, government representatives (including U.S. Food and Drug Administration and National Institutes of Health participants), payors, and industry collaborators. The following expert consensus document is the product of the Heart Failure Collaboratory convening with the Academic Research Consortium, including members from academia, the U.S. Food and Drug Administration, and industry, for the purposes of proposing standardized definitions for ADHF and highlighting important endpoint considerations to inform the design and conduct of clinical trials for drugs and devices in this clinical arena.
ACOX1-mediated peroxisomal fatty acid oxidation contributes to metabolic reprogramming and survival in chronic lymphocytic leukemia
Authors: Mariana Tannoury, Marianne Ayoub, Léa Dehgane, Ivan Nemazanyy, Kenza Dubois, Charlotte Izabelle, Aurélie Brousse, Damien Roos-Weil, Karim Maloum, Hélène Merle-Béral, Brigitte Bauvois, Bruno Saubamea, Elise Chapiro, Florence Nguyen-Khac, Delphine Garnier, Santos A. Susin
Journal: Leukemia (2023)
Genetic Characterization of Primary Mediastinal B-Cell Lymphoma: Pathogenesis and Patient Outcomes
Authors: Daniel Noerenberg, Franziska Briest, Cornelius Hennch, Kenichi Yoshida, Raphael Hablesreiter, Yasuhide Takeuchi, Hiroo Ueno, Annette M. Staiger, Marita Ziepert, Fazila Asmar, Benjamin N. Locher, Erika Toth, Thomas Weber, Rose-Marie Amini, Wolfram Klapper, Maria Bouzani, Viola Poeschel, Andreas Rosenwald, Gerhard Held, Elías Campo, Naveed Ishaque, Kostas Stamatopoulos, George Kanellis, Ioannis Anagnostopoulos, Lars Bullinger, Neta Goldschmidt, Pier Luigi Zinzani, Csaba Bödör, Richard Rosenquist, Theodoros P. Vassilakopoulos, German Ott, Seishi Ogawa, Frederik Damm
Journal: Journal of Clinical Oncology (2023)

Primary mediastinal large B-cell lymphoma (PMBCL) is a rare aggressive lymphoma predominantly affecting young female patients. Large-scale genomic investigations and genetic markers for risk stratification are lacking.
High Mannose Correlates With Surrogate Indexes of Insulin Resistance and Is Associated With an Increased Risk of Cardiovascular Events Independently of Glycemic Status and Traditional Risk Factors
Authors: Elena Fortin, Beatrice Campi, Ele Ferrannini, Andrea Mari, Linda G. Mellbin, Anna Norhammar, Per Näsman, Lars Rydén, Alessandro Saba, Giulia Ferrannini
Journal: Diabetes Care (2023)

OBJECTIVE To explore the associations among mannose, indexes of insulin resistance (IR) and secretion, and long-term cardiovascular outcomes. RESEARCH DESIGN AND METHODS Fasting mannose was assayed in 1,403 participants, one-half of which had a first myocardial infarction (MI) with either normal glucose tolerance (n = 1,045) or newly detected dysglycemia (i.e., impaired glucose tolerance or type 2 diabetes; n = 358). Regression models were used to explore mannose associations with surrogate indexes of IR/insulin secretion. Multivariate Cox models were used to investigate the independent association between high (higher quartile) versus low (lower three quartiles) mannose and major adverse cardiac events (MACE) (n = 163) during the 10-year follow-up. RESULTS Mannose was independently associated with IR indexes (all P ≤ 0.001). High versus low mannose was independently associated with MACE (hazard ratio 1.54, 95% CI 1.07–2.20) in the overall population. CONCLUSIONS Mannose might represent a new biomarker able to track early, potentially detrimental glucometabolic alterations independently of glycemic state.
Modbed track: Visualization of modified bases in single-molecule sequencing
Authors: Daofeng Li, Xiaoyu Zhuo, Jessica K. Harrison, Shane Liu, Ting Wang
Journal: Cell Genomics (2023)

Recent advances in long-read sequencing technologies have not only dramatically increased sequencing read length but also have improved the accuracy of detecting chemical modifications to the canonical nucleotide bases, thus opening exciting venues to investigate the epigenome. Currently, the ability to visualize modified bases from long-read sequencing data in genome browsers is still limited, preventing users from easily and fully exploring these type of data. To address this limitation, the WashU Epigenome Browser introduces the modbed track type, which provides visualization of modification details in each single read as well as aggregated modifications of individual or multiple molecules across a dynamic range of resolutions. The modbed file can be uploaded for visualization as a local track or viewed with an accessible URL freely on the WashU Epigenome Browser at https://epigenomegateway.wustl.edu/.
Using DNNs to understand the primate vision: A shortcut or a distraction?
Authors: Yaoda Xu, Maryam Vaziri-Pashkam
Journal: Behavioral and Brain Sciences (2023)

Abstract Bowers et al. bring forward critical issues in the current use of deep neural networks (DNNs) to model primate vision. Our own research further reveals fundamentally different algorithms utilized by DNNs for visual processing compared to the brain. It is time to reemphasize the value of basic vision research and put more resources and effort on understanding the primate brain itself.
Cold snare for your polyps &lt;10mm; cold snare for the planet
Authors: Enrique Rodriguez de Santiago
Journal: Endoscopy (2023)

In the world of modern medicine, where technological advancements often steal the spotlight, the beauty of simplicity sometimes goes unnoticed. Endoscopists and researchers tend to be fascinated by impossible endoscopic resections, navigating the peritoneum, testing new endoscopic devices, or study designs founded in advanced statistical methods that are hard to understand for most Earthlings. Yet, it is precisely in simplicity that we often find the most elegant solutions to complex challenges. The study by Rex et al., focusing on universal cold snaring of colorectal polyps ≤10mm, is a shining example of how a straightforward approach can deliver remarkable results [1]. This study not only simplifies procedures, but also offers a practical solution to the growing environmental concerns surrounding the environmental impact of gastrointestinal endoscopy [2].
Interpreting the Significance of Changes in Health-Related Quality-of-Life Scores
Authors: D Osoba, G Rodrigues, J Myles, B Zee, J Pater
Journal: Journal of Clinical Oncology (2023)

To determine the significance to patients of changes in health-related quality-of-life (HLQ) scores assessed by the European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire (QLQ-C30).
The Functional Assessment of Cancer Therapy Scale: Development and Validation of the General Measure
Authors: D F Cella, D S Tulsky, G Gray, B Sarafian, E Linn, A Bonomi, M Silberman, S B Yellen, P Winicour, J Brannon
Journal: Journal of Clinical Oncology (2023)

We developed and validated a brief, yet sensitive, 33-item general cancer quality-of-life (QL) measure for evaluating patients receiving cancer treatment, called the Functional Assessment of Cancer Therapy (FACT) scale.
Transitional community adherence support for people leaving incarceration in South Africa: a pragmatic, open-label, randomised controlled trial
Authors: Tonderai Mabuto, Daniel M Woznica, Pretty Ndini, Derrick Moyo, Munazza Abraham, Colleen Hanrahan, Salome Charalambous, Barry Zack, Stefan Baral, Jill Owczarzak, Christopher J Hoffmann
Journal: The Lancet HIV (2023)
Neutralisation activity of mucosal IgA against XBB sublineages and BA.2.86
Authors: Fanglei Zuo, Yunlong Cao, Rui Sun, Ayijiang Yisimayi, Likun Du, Federico Bertoglio, Maren Schubert, Concetta Guerra, Andrea Cavalli, Michael Hust, Davide F Robbiani, Hassan Abolhassani, Xiaoliang Sunney Xie, Lennart Hammarström, Harold Marcotte, Qiang Pan-Hammarström
Journal: The Lancet Infectious Diseases (2023)