tbuckley/cabot-search huggingface dataset:
Sepsis Alert Systems, Mortality, and Adherence in Emergency Departments
Authors: Hyung-Jun Kim, Ryoung-Eun Ko, Sung Yoon Lim, Sunghoon Park, Gee Young Suh, Yeon Joo Lee
Journal: JAMA Network Open (2024)

Importance Early detection and management of sepsis are crucial for patient survival. Emergency departments (EDs) play a key role in sepsis management but face challenges in timely response due to high patient volumes. Sepsis alert systems are proposed to expedite diagnosis and treatment initiation per the Surviving Sepsis Campaign guidelines. Objective To review and analyze the association of sepsis alert systems in EDs with patient outcomes. Data Sources A thorough search was conducted in PubMed, EMBASE, Web of Science, and the Cochrane Library from January 1, 2004, to November 19, 2023. Study Selection Studies that evaluated sepsis alert systems specifically designed for adult ED patients were evaluated. Inclusion criteria focused on peer-reviewed, full-text articles in English that reported on mortality, ICU admissions, hospital stay duration, and sepsis management adherence. Exclusion criteria included studies that lacked a control group or quantitative reports. Data Extraction and Synthesis The review followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline. Two independent reviewers conducted the data extraction using a standardized form. Any disagreements were resolved through discussion. The data were synthesized using a random-effects model due to the expected heterogeneity among the included studies. Main Outcomes and Measures Key outcomes included mortality, intensive care unit admissions, hospital stay duration, and adherence to the sepsis bundle. Results Of 3281 initially identified studies, 22 (0.67%) met inclusion criteria, encompassing 19 580 patients. Sepsis alert systems were associated with reduced mortality risk (risk ratio [RR], 0.81; 95% CI, 0.71 to 0.91) and length of hospital stay (standardized mean difference [SMD], −0.15; 95% CI, −0.20 to −0.11). These systems were also associated with better adherence to sepsis bundle elements, notably in terms of shorter time to fluid administration (SMD, −0.42; 95% CI, −0.52 to −0.32), blood culture (SMD, −0.31; 95% CI, −0.40 to −0.21), antibiotic administration (SMD, −0.34; 95% CI, −0.39 to −0.29), and lactate measurement (SMD, −0.15; 95% CI, −0.22 to −0.08). Electronic alerts were particularly associated with reduced mortality (RR, 0.78; 95% CI, 0.67 to 0.92) and adherence with blood culture guidelines (RR, 1.14; 95% CI, 1.03 to 1.27). Conclusions and Relevance These findings suggest that sepsis alert systems in EDs were associated with better patient outcomes along with better adherence to sepsis management protocols. These systems hold promise for enhancing ED responses to sepsis, potentially leading to better patient outcomes.
Health Care Needs and Costs for Children Exposed to Prenatal Substance Use to Adulthood
Authors: Evelyn Lee, Deborah Schofield, Mithilesh Dronavalli, Kate Lawler, Hannah Uebel, Lucinda Burns, Barbara Bajuk, Andrew Page, Yuanyuan Gu, John Eastwood, Michelle Dickson, Charles Green, Lauren Dicair, Ju Lee Oei
Journal: JAMA Pediatrics (2024)

Children exposed to substance use during pregnancy have increased health needs but whether these are influenced by engagement in out-of-home care is uncertain.
Improving Cardiac Rehabilitation Adherence in Patients With Lower Socioeconomic Status
Authors: Diann E. Gaalema, Sherrie Khadanga, Patrick D. Savage, Blair Yant, Brian R. Katz, Michael DeSarno, Philip A. Ades
Journal: JAMA Internal Medicine (2024)

Participation in cardiac rehabilitation is associated with significant decreases in morbidity and mortality. Despite the proven benefits, cardiac rehabilitation is severely underutilized in certain populations, specifically those with lower socioeconomic status (SES).
Accelerated Chest Pain Treatment With Artificial Intelligence–Informed, Risk-Driven Triage
Authors: Jeremiah S. Hinson, R. Andrew Taylor, Arjun Venkatesh, Benjamin D. Steinhart, Christopher Chmura, Rohit B. Sangal, Scott R. Levin
Journal: JAMA Internal Medicine (2024)

This quality improvement study evaluates the use of artificial intelligence to accelerate triage of patients presenting to the emergency department with chest pain.
Prenatal Cannabis Use and Maternal Pregnancy Outcomes
Authors: Kelly C. Young-Wolff, Sara R. Adams, Stacey E. Alexeeff, Yeyi Zhu, Edwin Chojolan, Natalie E. Slama, Monique B. Does, Lynn D. Silver, Deborah Ansley, Carley L. Castellanos, Lyndsay A. Avalos
Journal: JAMA Internal Medicine (2024)

Many studies have evaluated whether in utero cannabis exposure is associated with fetal and neonatal outcomes, yet little is known about whether prenatal cannabis use is associated with maternal health outcomes during pregnancy.
Monoclonal Antibody Risankizumab for Ulcerative Colitis
Authors: Gilaad G. Kaplan
Journal: JAMA (2024)

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Medications for Obesity
Authors: Kimberly A. Gudzune, Robert F. Kushner
Journal: JAMA (2024)

Obesity affects approximately 19% of women and 14% of men worldwide and is associated with increased morbidity. Antiobesity medications (AOMs) modify biological processes that affect appetite and significantly improve outcomes, such as type 2 diabetes, hypertension, and dyslipidemia.
Ultraprocessed Foods at Home and Children's Attentional Bias Toward Those Foods
Authors: Katherine McNeel, Grace E. Shearrer, Afroditi Papantoni, Tonja R. Nansel, Leah M. Lipsky, Kyle S. Burger
Journal: JAMA Pediatrics (2024)

This study examines the association between exposure to ultraprocessed foods at home and children’s attentional bias for those foods.
Incidence of Nonsynostotic Plagiocephaly and Developmental Disorders
Authors: Mary E. Lynch, Melanie J. White, Amy E. Rabatin, Joline E. Brandenburg, Amanda B. Theuer, Katrina M. Viet, John H. Hollman, Sherilyn W. Driscoll
Journal: JAMA Pediatrics (2024)

Importance This is the first population-based study quantifying the incidence of nonsynostotic positional plagiocephaly and/or brachycephaly (PPB) in infancy and its association with developmental disorders. Objective To report the incidence of PPB before age 1 year, the incidence of craniosynostosis, and the percentage of children with PPB diagnosed with a developmental disorder by age 7 years. Design, Setting, and Participants This was a retrospective, population-based cohort study of children in the Rochester Epidemiology Project (REP) born in Olmsted County, Minnesota, from January 1, 2008, through December 31, 2012, with follow-up through age 7 years. Data were analyzed from March 2021 to April 2024. Exposure Physical examination detecting cranial deformity. Main Outcomes and Measures The primary outcome was the incidence of PPB. Secondary outcomes were the incidence of craniosynostosis and the percentage of children with PPB diagnosed with a developmental disorder by age 7 years. Results Of 9909 infants (5084 [51.3%] male; 9205 [92.9%] born at term and 704 [7.1%] born preterm) included in the study, 575 had PPB, for a PPB incidence of 5.8% (95% CI, 5.3%-6.3%). The incidence of PPB was 5.3% (95% CI, 4.8%-5.8%) in term infants vs 11.8% (95% CI, 9.4%-14.6%) in preterm infants. The incidence of craniosynostosis was 0.16% (95% CI, 0.09%-0.26%). A developmental disorder was known or suspected in 4.2% (95% CI, 2.7%-6.2%) of infants at the time of PPB diagnosis; among 402 infants with PPB and follow-up through age 7 years, 30 (7.5%; 95% CI, 5.0%-10.7%) had a confirmed developmental disorder by 7 years of age. The prevalence of autism spectrum disorder (ASD) in children with a history of PPB who were followed up to age 7 years was 2.2% (9 of 402 children). Conclusions and Relevance This study found that only a small percentage of the infants had positional head deformity significant enough to be documented and/or referred for subspecialty evaluation, and only a small subset of these children went on to have a developmental disorder in childhood. This information is helpful for counseling families about their child’s developmental risk at time of PPB diagnosis.
A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery
Authors: Yingjia Chen, Snehal N Chaudhari, David A Harris, Cullen F Roberts, Andrei Moscalu, Vasundhara Mathur, Lei Zhao, Ali Tavakkoli, A Sloan Devlin, Eric G Sheu
Journal: Cell Host & Microbe (2024)
Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation
Authors: Frank A Buquicchio, Raissa Fonseca, Patrick K Yan, Fangyi Wang, Maximilien Evrard, Andreas Obers, Jacob C Gutierrez, Colin J Raposo, Julia A Belk, Bence Daniel, Pirooz Zareie, Kathryn E Yost, Yanyan Qi, Yajie Yin, Katherine F Nico, Flora M Tierney, Michael R Howitt, Caleb A Lareau, Ansuman T Satpathy, Laura K Mackay
Journal: Immunity (2024)
Improving Collection and Analysis of Overall Survival Data
Authors: Lisa R. Rodriguez, Nicole J. Gormley, Ruixiao Lu, Anup K. Amatya, George D. Demetri, Keith T. Flaherty, Ruben A. Mesa, Richard Pazdur, Mikkael A. Sekeres, Minghua Shan, Steven Snapinn, Marc R. Theoret, Rukiya Umoja, Jonathon Vallejo, Nicholas J.H. Warren, Qing Xu, Kenneth C. Anderson
Journal: Clinical Cancer Research (2024)

Advances in anticancer therapies have provided crucial benefits for millions of patients who are living long and fulfilling lives. Although these successes should be celebrated, there is certainly room to continue improving cancer care. Increased long-term survival presents additional challenges for determining whether new therapies further extend patients' lives through clinical trials, commonly known as the gold standard endpoint of overall survival (OS). As a result, an increasing reliance is observed on earlier efficacy endpoints, which may or may not correlate with OS, to continue the timely pace of translating innovation into novel therapies available for patients. Even when not powered as an efficacy endpoint, OS remains a critical indication of safety for regulatory decisions and is a key aspect of the FDA's Project Endpoint. Unfortunately, in the pursuit of earlier endpoints, many registrational clinical trials lack adequate planning, collection, and analysis of OS data, which complicates interpretation of a net clinical benefit or harm. This article shares best practices, proposes novel statistical methodologies, and provides detailed recommendations to improve the rigor of using OS data to inform benefit-risk assessments, including incorporating the following in clinical trials intending to demonstrate the safety and effectiveness of cancer therapy: prospective collection of OS data, establishment of fit-for-purpose definitions of OS detriment, and prespecification of analysis plans for using OS data to evaluate for potential harm. These improvements hold promise to help regulators, patients, and providers better understand the benefits and risks of novel therapies.
Single‐cell RNA sequencing reveals reduced intercellular adhesion molecule crosstalk between activated hepatic stellate cells and neutrophils alleviating liver fibrosis in hepatitis B virus transgenic mice post menstrual blood‐derived mesenchymal stem cell transplantation
Authors: Lijun Chen, Yuqi Huang, Ning Zhang, Jingjing Qu, Yangxin Fang, Jiamin Fu, Yin Yuan, Qi Zhang, Hang Li, Zuoshi Wen, Li Yuan, Lu Chen, Zhenyu Xu, Yifei Li, Huadong Yan, Hiromi Izawa, Lanjuan Li, Charlie Xiang
Journal: MedComm (2024)

Abstract Liver fibrosis can cause hepatitis B virus (HBV)‐associated hepatocellular carcinoma. Menstrual blood‐derived mesenchymal stem cells (MenSCs) can ameliorate liver fibrosis through paracrine. Single‐cell RNA sequencing (scRNA‐seq) may be used to explore the roadmap of activated hepatic stellate cell (aHSC) inactivation to target liver fibrosis. This study established HBV transgenic (HBV‐Tg) mouse model of carbon tetrachloride (CCl 4 )‐induced liver fibrosis and demonstrated that MenSCs migrated to the injured liver to improve serological indices and reduce fibrotic accumulation. RNA‐bulk analysis revealed that MenSCs mediated extracellular matrix accumulation and cell adhesion. Liver parenchymal cells and nonparenchymal cells were identified by scRNA‐seq in the control, CCl 4 , and MenSC groups, revealing the heterogeneity of fibroblasts/HSCs. A CellChat analysis revealed that diminished intercellular adhesion molecule (ICAM) signaling is vital for MenSC therapy. Specifically, Icam1 in aHSCs acted on Itgal / Itgb2 and Itgam / Itgb2 in neutrophils, causing decreased adhesion. The expression of Itgal , Itgam , and Itgb2 was higher in CCl 4 group than in the control group and decreased after MenSC therapy in neutrophil clusters. The Lcn2 , Pglyrp1 , Wfdc21 , and Mmp8 had high expression and may be potential targets in neutrophils. This study highlights interacting cells, corresponding molecules, and underlying targets for MenSCs in treating HBV‐associated liver fibrosis.
Endothelial dysfunction: molecular mechanisms and clinical implications
Authors: Xia Wang, Ben He
Journal: MedComm (2024)

Abstract Cardiovascular disease (CVD) and its complications are a leading cause of death worldwide. Endothelial dysfunction plays a crucial role in the initiation and progression of CVD, serving as a pivotal factor in the pathogenesis of cardiovascular, metabolic, and other related diseases. The regulation of endothelial dysfunction is influenced by various risk factors and intricate signaling pathways, which vary depending on the specific disease context. Despite numerous research efforts aimed at elucidating the mechanisms underlying endothelial dysfunction, the precise molecular pathways involved remain incompletely understood. This review elucidates recent research findings on the pathophysiological mechanisms involved in endothelial dysfunction, including nitric oxide availability, oxidative stress, and inflammation‐mediated pathways. We also discuss the impact of endothelial dysfunction on various pathological conditions, including atherosclerosis, heart failure, diabetes, hypertension, chronic kidney disease, and neurodegenerative diseases. Furthermore, we summarize the traditional and novel potential biomarkers of endothelial dysfunction as well as pharmacological and nonpharmacological therapeutic strategies for endothelial protection and treatment for CVD and related complications. Consequently, this review is to improve understanding of emerging biomarkers and therapeutic approaches aimed at reducing the risk of developing CVD and associated complications, as well as mitigating endothelial dysfunction.
Multiple hERG channel blocking pathways: implications for macromolecules
Authors: Bernd J. Zünkler
Journal: Trends in Pharmacological Sciences (2024)

Numerous non-cardiovascular drugs have a potential to induce life-threatening torsades de pointes (TdP) ventricular cardiac arrhythmias by blocking human ether-à-go-go-related gene (hERG) currents via binding to the channel's inner cavity. Identification of the hERG current-inhibiting properties of candidate drugs is performed focusing on binding sites in the channel pore. It has been suggested that biologicals have a low likelihood of hERG current inhibition, since their poor diffusion across the plasma membrane prevents them from reaching the binding site in the channel pore. However, biologicals could influence hERG channel function by binding to 'unconventional' noncanonical binding sites. This Opinion gives an overview on noncanonical blockers of hERG channels that might be of relevance for the assessment of the possible torsadogenic potential of macromolecular therapeutics.
Disease burden, management strategies, and unmet needs in α‐thalassemia due to hemoglobin <scp>H</scp> disease
Authors: Ashutosh Lal, Vip Viprakasit, Elliott Vichinsky, Yongrong Lai, Meng‐Yao Lu, Antonis Kattamis
Journal: American Journal of Hematology (2024)

Abstract Alpha‐thalassemia is an inherited blood disorder caused by impaired α‐globin chain production, leading to anemia and other complications. Hemoglobin H (HbH) disease is caused by a combination of mutations generally affecting the expression of three of four α‐globin alleles; disease severity is highly heterogeneous, largely driven by genotype. Notably, non‐deletional mutations cause a greater degree of ineffective erythropoiesis and hemolysis, higher transfusion burden, and increased complication risks versus deletional mutations. There are limited treatment options for HbH disease, and effective therapies are needed. This review discusses the pathophysiology of HbH disease, current management strategies, unmet needs, and emerging treatment options.
Indexing left ventricular end‐systolic dimension to body size: Association with mortality in patients with degenerative mitral regurgitation
Authors: Christophe Tribouilloy, Dan Rusinaru, Francesco Grigioni, Jean‐François Avierinos, Jean‐Louis Vanoverschelde, Giovanni Benfari, Francesca Bursi, Andrea Barbieri, Yohann Bohbot, Benjamin Essayagh, Hector Michelena, Maurice Enriquez‐Sarano
Journal: European Journal of Heart Failure (2024)
A foundation model for clinical-grade computational pathology and rare cancers detection
Authors: Eugene Vorontsov, Alican Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, Nicolo Fusi, Ellen Yang, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, Eric Robert, Yi Kan Wang, Jeremy D. Kunz, Matthew C. H. Lee, Jan H. Bernhard, Ran A. Godrich, Gerard Oakley, Ewan Millar, Matthew Hanna, Hannah Wen, Juan A. Retamero, William A. Moye, Razik Yousfi, Christopher Kanan, David S. Klimstra, Brandon Rothrock, Siqi Liu, Thomas J. Fuchs
Journal: Nature Medicine (2024)

Abstract The analysis of histopathology images with artificial intelligence aims to enable clinical decision support systems and precision medicine. The success of such applications depends on the ability to model the diverse patterns observed in pathology images. To this end, we present Virchow, the largest foundation model for computational pathology to date. In addition to the evaluation of biomarker prediction and cell identification, we demonstrate that a large foundation model enables pan-cancer detection, achieving 0.95 specimen-level area under the (receiver operating characteristic) curve across nine common and seven rare cancers. Furthermore, we show that with less training data, the pan-cancer detector built on Virchow can achieve similar performance to tissue-specific clinical-grade models in production and outperform them on some rare variants of cancer. Virchow’s performance gains highlight the value of a foundation model and open possibilities for many high-impact applications with limited amounts of labeled training data.
Condensin I folds the Caenorhabditis elegans genome
Authors: Moushumi Das, Jennifer I Semple, Anja Haemmerli, Valeriia Volodkina, Janik Scotton, Todor Gitchev, Ahrmad Annan, Julie Campos, Cyril Statzer, Alexander Dakhovnik, Collin Y Ewald, Julien Mozziconacci, Peter Meister
Journal: Nature Genetics (2024)
Co-mutation landscape and its prognostic impact on newly diagnosed adult patients with NPM1-mutated de novo acute myeloid leukemia
Authors: Yiyi Yao, Yile Zhou, Nanfang Zhuo, Wanzhuo Xie, Haitao Meng, Yinjun Lou, Liping Mao, Hongyan Tong, Jiejing Qian, Min Yang, Wenjuan Yu, De Zhou, Jie Jin, Huafeng Wang
Journal: Blood Cancer Journal (2024)
Risk factors in DUX4-positive childhood and adolescent B-cell acute lymphoblastic leukemia
Authors: Dagmar Schinnerl, Marion Riebler, Angela Schumich, Sabrina Haslinger, Alice Bramböck, Andrea Inthal, Marek Nykiel, Margarita Maurer-Granofszky, Oskar A. Haas, Ulrike Pötschger, Stefan Köhrer, Karin Nebral, Michael N. Dworzak, Andishe Attarbaschi, Sabine Strehl
Journal: Blood Cancer Journal (2024)
A functional analysis of a resorbable citrate-based composite tendon anchor
Authors: Arun Thirumaran, Meletios-Nikolaos Doulgkeroglou, Magesh Sankar, Jeremiah T Easley, Ben Gadomski, Anup Poudel, Manus Biggs
Journal: Bioactive Materials (2024)

Rapid and efficient tendon fixation to a bone following trauma or in response to degenerative processes can be facilitated using a tendon anchoring device. Osteomimetic biomaterials, and in particular, bio-resorbable polymer composites designed to match the mineral phase content of native bone, have been shown to exhibit osteoinductive and osteoconductive properties
Granulocytes and mast cells in AllergoOncology—Bridging allergy to cancer: An <scp>EAACI</scp> position paper
Authors: Mariona Pascal, Heather J. Bax, Christoph Bergmann, Rodolfo Bianchini, Mariana Castells, Jitesh Chauhan, Leticia De las Vecillas, Karin Hartmann, Elena Izquierdo Álvarez, Uta Jappe, Teodorikez‐Wilfox Jimenez‐Rodriguez, Edward Knol, Francesca Levi‐Schaffer, Cristobalina Mayorga, Aurélie Poli, Frank Redegeld, Alexandra F. Santos, Erika Jensen‐Jarolim, Sophia N. Karagiannis
Journal: Allergy (2024)

Derived from the myeloid lineage, granulocytes, including basophils, eosinophils, and neutrophils, along with mast cells, play important, often disparate, roles across the allergic disease spectrum. While these cells and their mediators are commonly associated with allergic inflammation, they also exhibit several functions either promoting or restricting tumor growth. In this Position Paper we discuss common granulocyte and mast cell features relating to immunomodulatory functions in allergy and in cancer. We highlight key mechanisms which may inform cancer treatment and propose pertinent areas for future research. We suggest areas where understanding the communication between granulocytes, mast cells, and the tumor microenvironment, will be crucial for identifying immune mechanisms that may be harnessed to counteract tumor development. For example, a comprehensive understanding of allergic and immune factors driving distinct neutrophil states and those mechanisms that link mast cells with immunotherapy resistance, might enable targeted manipulation of specific subpopulations, leading to precision immunotherapy in cancer. We recommend specific areas of investigation in AllergoOncology and knowledge exchange across disease contexts to uncover pertinent reciprocal functions in allergy and cancer and allow therapeutic manipulation of these powerful cell populations. These will help address the unmet needs in stratifying and managing patients with allergic diseases and cancer.