tbuckley/cabot-search huggingface dataset:
TCT CONNECT-269 A First-in-Human Study of the Second-Generation, Thin-Strut, Everolimus-Eluting Bioresorbable Scaffold: Final IVUS and OCT Results From the FAST Clinical Trial
Authors: Takeshi Nishi, Ryo Kameda, Kozo Okada, Masayasu Ikutomi, M. Brooke Hollak, Paul Yock, Jeffrey Popma, Sujith Seneviratne, Darren Walters, Robert Whitbourn, Jim Stewart, Seif El-Jack, Dominic Allocco, Ian Meredith, Peter J. Fitzgerald, Yasuhiro Honda
Journal: Journal of the American College of Cardiology (2020)
Nutritional modulation of heart failure in mitochondrial pyruvate carrier–deficient mice
Authors: Kyle S. McCommis, Attila Kovacs, Carla J. Weinheimer, Trevor M. Shew, Timothy R. Koves, Olga R. Ilkayeva, Dakota R. Kamm, Kelly D. Pyles, M. Todd King, Richard L. Veech, Brian J. DeBosch, Deborah M. Muoio, Richard W. Gross, Brian N. Finck
Journal: Nature Metabolism (2020)
TCT CONNECT-126 Outcomes of Patients With Severe Aortic Stenosis and Left Ventricular Obstruction Undergoing Transcatheter Aortic Valve Replacement
Authors: Danon Kaewkes, Tomoki Ochiai, Nir Flint, Vivek Patel, Sahar Mahani, Matthias Raschpichler, Sung-Han Yoon, Sabah Skaf, Siddharth Singh, Tarun Chakravarty, Mamoo Nakamura, Wen Cheng, Raj Makkar
Journal: Journal of the American College of Cardiology (2020)
Abstract S03-01: Pan-HLA prediction of SARS-CoV-2 epitopes
Authors: Katie M. Campbell, Gabriela Steiner, Daniel K. Wells, Antoni Ribas, Anusha Kalbasi
Journal: Clinical Cancer Research (2020)

Abstract Introduction: Delineating antiviral T-cell responses to SARS-CoV-2 may shed light on the heterogeneity of clinical outcomes and inform vaccine or therapeutic approaches. Viral antigens can be predicted using computational tools that calculate the binding affinity between viral peptides and antigen presentation machinery. However, in order to account for the role of host genetics in the diversity of responses, this analysis must be performed with consideration of the global diversity of the human leukocyte antigen (HLA) proteins responsible for antigen presentation. Methods: We deployed binding predictions across the SARS-CoV-2 peptidome for 9,360 Class I HLA alleles (2,987 HLA-A; 3,707 HLA-B; 2,666 HLA-C; 9-mers) using a consensus approach of 7 algorithms and 3,486 Class II HLA alleles (15-mers) using a consensus approach of 4 algorithms. All pMHC predictions were filtered to include only those with consensus binding less than 500 nM. Results: There were 368,145 unique combinations of peptides and HLA alleles (pMHCs) with a predicted binding affinity of less than 500nM, including 1,103 unique 9-mer and 2,547 15-mer peptides and 1,022 MHC Class I and 8,075 MHC Class II HLA proteins. Of these pMHCs, 82% of 9-mers overlapped with 15-mers, suggesting cross-presentation to both CD4 and CD8 T cells in a subset of individuals. We evaluated this filtered dataset with respect to the population frequency of HLA haplotypes. While the predicted susceptibility of SARS-CoV-2 antigen presentation differed greatly across countries, there was a subset of 21 Class I antigens shared by common HLA types across 30 or more countries (out of 79 countries with reported population frequency data). Our database has been made publicly available, and we have developed a user interface to explore the results based upon viral proteins, HLA alleles, or country populations of interest. Conclusions: With the ongoing SARS-CoV-2 pandemic, there are worldwide efforts to generate a successful vaccine and to evaluate clinical samples to understand the viral pathogenesis and diverse outcomes in patients. This application can serve as a guide to identify responses of putative SARS-CoV-2-specific T cells across patients with a broad range of HLA haplotypes internationally. Citation Format: Katie M. Campbell, Gabriela Steiner, Daniel K. Wells, Antoni Ribas, Anusha Kalbasi. Pan-HLA prediction of SARS-CoV-2 epitopes [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr S03-01.
Roles of follicular helper and regulatory T cells in allergic diseases and allergen immunotherapy
Authors: Yin Yao, Cai‐Ling Chen, Di Yu, Zheng Liu
Journal: Allergy (2020)

Abstract Allergic diseases are characterized by overactive type 2 immune responses to allergens and immunoglobulin E (IgE)‐mediated hypersensitivity. Emerging evidence suggests that follicular helper T (T FH ) cells, rather than type 2 T‐helper (T H 2) cells, play a crucial role in controlling IgE production. However, follicular regulatory T (T FR ) cells, a specialized subset of regulatory T (T REG ) cells resident in B‐cell follicles, restricts T FH cell‐mediated help in extrafollicular antibody production, germinal center (GC) formation, immunoglobulin affinity maturation, and long‐lived, high‐affinity plasma and memory B‐cell differentiation. In mouse models of allergic asthma and food allergy, CXCR5 + T FH cells, not CXCR5 − conventional T H 2 cells, are needed to support IgE production, otherwise exacerbated by CXCR5 + T FR cell deletion. Upregulation of T FH cell activities, including a skewing toward type 2 T FH (T FH 2) and IL‐13 producing T FH (T FH 13) phenotypes, and defects in T FR cells have been identified in patients with allergic diseases. Allergen immunotherapy (AIT) reinstates the balance between T FH and T FR cells in patients with allergic diseases, resulting in clinical benefits. Collectively, further understanding of T FH and T FR cells and their role in the immunopathogenesis of allergic diseases creates opportunities to develop novel therapeutic approaches.
TCT CONNECT-193 Radiation Exposure, Safety and Clinical Outcomes Following Interventional Coronary Diagnostic Procedures When Performed Without Planned Coronary Stenting
Authors: Amreen Kaur, Harish Sharma, John Townend, Peter Ludman, Sagar Doshi, Sohail Khan, Alexander Zaphiriou, Sudhakar George, M. Adnan Nadir
Journal: Journal of the American College of Cardiology (2020)
A Potential Role for Stress-Induced Microbial Alterations in IgA-Associated Irritable Bowel Syndrome with Diarrhea
Authors: Sunaina Rengarajan, Kathryn A. Knoop, Arvind Rengarajan, Jiani N. Chai, Jose G. Grajales-Reyes, Vijay K. Samineni, Emilie V. Russler-Germain, Prabha Ranganathan, Alessio Fasano, Gregory S. Sayuk, Robert W. Gereau, Andrew L. Kau, Dan Knights, Purna C. Kashyap, Matthew A. Ciorba, Rodney D. Newberry, Chyi-Song Hsieh
Journal: Cell Reports Medicine (2020)

Stress is a known trigger for flares of inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS); however, this process is not well understood. Here, we find that restraint stress in mice leads to signs of diarrhea, fecal dysbiosis, and a barrier defect via the opening of goblet-cell associated passages. Notably, stress increases host immunity to gut bacteria as assessed by immunoglobulin A (IgA)-bound gut bacteria. Stress-induced microbial changes are necessary and sufficient to elicit these effects. Moreover, similar to mice, many diarrhea-predominant IBS (IBS-D) patients from two cohorts display increased antibacterial immunity as assessed by IgA-bound fecal bacteria. This antibacterial IgA response in IBS-D correlates with somatic symptom severity and was distinct from healthy controls or IBD patients. These findings suggest that stress may play an important role in patients with IgA-associated IBS-D by disrupting the intestinal microbial community that alters gastrointestinal function and host immunity to commensal bacteria.
Relocation of an Extrasynaptic GABAA Receptor to Inhibitory Synapses Freezes Excitatory Synaptic Strength and Preserves Memory
Authors: Christopher M. Davenport, Rajit Rajappa, Ljudmila Katchan, Charlotte R. Taylor, Ming-Chi Tsai, Caleb M. Smith, Johannes W. de Jong, Don B. Arnold, Stephan Lammel, Richard H. Kramer
Journal: Neuron (2020)
A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020
Authors: Nicola Murphy, Máirín Boland, Niamh Bambury, Margaret Fitzgerald, Liz Comerford, Niamh Dever, Margaret B O’Sullivan, Naomi Petty-Saphon, Regina Kiernan, Mette Jensen, Lois O’Connor
Journal: Eurosurveillance (2020)

An outbreak of 59 cases of coronavirus disease (COVID-19) originated with 13 cases linked by a 7 h, 17% occupancy flight into Ireland, summer 2020. The flight-associated attack rate was 9.8-17.8%. Spread to 46 non-flight cases occurred country-wide. Asymptomatic/pre-symptomatic transmission in-flight from a point source is implicated by 99% homology across the virus genome in five cases travelling from three different continents. Restriction of movement on arrival and robust contact tracing can limit propagation post-flight.
THE EFFECT OF NEOADJUVANT THERAPY ON ANASTOMOTIC LEAKAGE AND POSTOPERATIVE MORTALITY IN RECTAL CANCER
Authors: H.A.M. Swellengrebel, E. Peters, H.G.T. Blaauwgeers, O. Visser, C.A.M. Marijnen, A. Cats
Journal: Annals of Oncology (2010)
Temporal Trends in Heart Failure Incidence Among Medicare Beneficiaries Across Risk Factor Strata, 2011 to 2016
Authors: Rohan Khera, Nitin Kondamudi, Lin Zhong, Muthiah Vaduganathan, Joshua Parker, Sandeep R. Das, Justin L. Grodin, Ethan A. Halm, Jarett D. Berry, Ambarish Pandey
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Heart failure (HF) incidence is declining among Medicare beneficiaries. However, the epidemiological mechanisms underlying this decline are not well understood. <h3>Objective</h3> To evaluate trends in HF incidence across risk factor strata. <h3>Design, Setting, and Participants</h3> Retrospective, national cohort study of 5% of all fee-for-service Medicare beneficiaries with no prior HF followed up from 2011 to 2016. The study examined annual trends in HF incidence among groups with and without primary HF risk factors (hypertension, diabetes, and obesity) and predisposing cardiovascular conditions (acute myocardial infarction [MI] and atrial fibrillation [AF]). <h3>Exposures</h3> The presence of comorbid HF risk factors including hypertension, diabetes, obesity, acute MI, and AF identified by<i>International Classification of Diseases</i>,<i>Ninth Revision</i>,<i>Clinical Modification</i>codes and<i>International Statistical Classification of Diseases</i>,<i>Tenth Revision</i>,<i>Clinical Modification</i>codes. <h3>Main Outcomes and Measures</h3> Incident HF, defined using at least 1 inpatient HF claim or at least 2 outpatient HF claims among those without a previous diagnosis of HF. <h3>Results</h3> Of 1 799 027 unique Medicare beneficiaries at risk for HF (median age, 73 years [interquartile range, 68-79 years]; 56% female [805 060-796 253 participants during the study period]), 249 832 had a new diagnosis of HF. The prevalence of all 5 risk factors increased over time (0.8% mean increase in hypertension per year, 1.9% increase in diabetes, 2.9% increase in obesity, 0.2% increase in acute MI, and 0.4% increase in AF). Heart failure incidence declined from 35.7 cases per 1000 beneficiaries in 2011 to 26.5 cases per 1000 beneficiaries in 2016, consistent across subgroups based on sex and race/ethnicity. A greater decline in HF incidence was observed among patients with prevalent hypertension (relative excess decline, 12%), diabetes (relative excess decline, 3%), and obesity (relative excess decline, 16%) compared with those without corresponding risk factors. In contrast, there was a relative increase in HF incidence among individuals with acute MI (26% vs no acute MI) and AF (22% vs no AF). <h3>Conclusions and Relevance</h3> Findings of this study suggest that the temporal decline in HF incidence among Medicare beneficiaries reflects a decrease in HF incidence among those with primary HF risk factors. The increase in HF incidence among those with acute MI and those with AF highlights potential targets for future HF prevention strategies.
Genetics of osteonecrosis in pediatric acute lymphoblastic leukemia and general populations
Authors: Wenjian Yang, Meenakshi Devidas, Yiwei Liu, Colton Smith, Yunfeng Dai, Naomi Winick, Stephen P. Hunger, Mignon L. Loh, Elizabeth A. Raetz, Eric C. Larsen, William L. Carroll, Stuart S. Winter, Kimberly P. Dunsmore, Leonard A. Mattano, Mary V. Relling, Seth E. Karol
Journal: Blood (2020)
TCT CONNECT-145 Wearable Activity Monitoring and the Impact of Frailty on Physical Activity After Transcatheter Aortic Valve Replacement
Authors: Katherine McGee, Laura Davidson, Alexander Meyer, S. Chris Malaisrie, Ranya Sweis, Duc Thinh Pham, Andrei Churyla, Adin-Cristian Andrei, James Flaherty, Charles Davidson
Journal: Journal of the American College of Cardiology (2020)
TCT CONNECT-297 Percutaneous Access Versus Surgical Cutdown in TAVI: A 2-Center Analysis
Authors: Konstantinos Stathogiannis, George Latsios, Maria Drakopoulou, Pantelis Toskas, Maria Xanthopoulou, Stergios Soulaidopoulos, Andreas Synetos, Dimitris Tousoulis, Konstantinos Toutouzas
Journal: Journal of the American College of Cardiology (2020)
QT Interval in Patients With COVID-19
Authors: Ingrid Berling, Robert S. Hoffman, Sophie Gosselin
Journal: JAMA Cardiology (2020)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Cardiology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Cardiology journal
Best practices for variant calling in clinical sequencing
Authors: Daniel C. Koboldt
Journal: Genome Medicine (2020)

Abstract Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer. Accurate variant calling in NGS data is a critical step upon which virtually all downstream analysis and interpretation processes rely. Just as NGS technologies have evolved considerably over the past 10 years, so too have the software tools and approaches for detecting sequence variants in clinical samples. In this review, I discuss the current best practices for variant calling in clinical sequencing studies, with a particular emphasis on trio sequencing for inherited disorders and somatic mutation detection in cancer patients. I describe the relative strengths and weaknesses of panel, exome, and whole-genome sequencing for variant detection. Recommended tools and strategies for calling variants of different classes are also provided, along with guidance on variant review, validation, and benchmarking to ensure optimal performance. Although NGS technologies are continually evolving, and new capabilities (such as long-read single-molecule sequencing) are emerging, the “best practice” principles in this review should be relevant to clinical variant calling in the long term.
The ‘SELection End points in Communities of bacTeria’ (SELECT) Method: A Novel Experimental Assay to Facilitate Risk Assessment of Selection for Antimicrobial Resistance in the Environment
Authors: Aimee K. Murray, Isobel C. Stanton, Jessica Wright, Lihong Zhang, Jason Snape, William H. Gaze
Journal: Environmental Health Perspectives (2020)

Background: Antimicrobial resistance (AMR) is one of the most significant health threats to society. A growing body of research demonstrates selection for AMR likely occurs at environmental concentrations of antibiotics. However, no standardized experimental approaches for determining selective concentrations of antimicrobials currently exist, preventing appropriate environmental and human health risk assessment of AMR. Objectives: We aimed to design a rapid, simple, and cost-effective novel experimental assay to determine selective effect concentrations of antibiotics and to generate the largest experimental data set of selective effect concentrations of antibiotics to date. Methods: Previously published methods and data were used to validate the assay, which determines the effect concentration based on reduction of bacterial community (wastewater) growth. Risk quotients for test antibiotics were generated to quantify risk. Results: The assay (SELection End points in Communities of bacTeria, or the SELECT method) was used to rapidly determine selective effect concentrations of antibiotics. These were in good agreement with quantitative polymerase chain reaction effect concentrations determined within the same experimental system. The SELECT method predicted no effect concentrations were minimally affected by changes in the assay temperature, growth media, or microbial community used as the inoculum. The predicted no effect concentrations for antibiotics tested ranged from 0.05μg/L for ciprofloxacin to 1,250μg/L for erythromycin. Discussion: The lack of evidence demonstrating environmental selection for AMR, and of associated human health risks, is a primary reason for the lack of action in the mitigation of release of antibiotics into the aquatic environment. We present a novel method that can reliably and rapidly fill this data gap to enable regulation and subsequent mitigation (where required) to lower the risk of selection for, and human exposure to, AMR in aquatic environments. In particular, ciprofloxacin and, to a lesser extent, azithromycin, cefotaxime, and trimethoprim all pose a significant risk for selection of AMR in the environment. https://doi.org/10.1289/EHP6635
TCT CONNECT-22 Microvascular Obstruction and Prognosis in Women Compared With Men After Primary Percutaneous Coronary Intervention in ST-Segment Elevation Myocardial Infarction: Results From an Individual Patient-Level Pooled Analysis of 6 Randomized Trials
Authors: Bahira Shahim, Ioanna Kosmidou, Mahesh Madhavan, Manesh Patel, Akiko Maehara, Zixuan Zhang, Ingo Eitel, Holger Thiele, Gregg Stone
Journal: Journal of the American College of Cardiology (2020)
Macrophage markers do not add to the prediction of liver fibrosis by transient elastography in patients with non-alcoholic fatty liver disease
Authors: Konstantin Kazankov, Chiara Rosso, Ramy Younes, Hannes Hagström, Holger Jon Møller, Per Stal, Elisabetta Bugianesi, Henning Grønbæk
Journal: Journal of Hepatology (2020)
Graphene‐Based Biomaterials for Bone Regenerative Engineering: A Comprehensive Review of the Field and Considerations Regarding Biocompatibility and Biodegradation
Authors: Leila Daneshmandi, Mohammed Barajaa, Armin Tahmasbi Rad, Stefanie A. Sydlik, Cato T. Laurencin
Journal: Advanced Healthcare Materials (2020)

Abstract Graphene and its derivatives have continued to garner worldwide interest due to their unique characteristics. Having expanded into biomedical applications, there have been efforts to employ their exceptional properties for the regeneration of different tissues, particularly bone. This article presents a comprehensive review on the usage of graphene‐based materials for bone regenerative engineering. The graphene family of materials (GFMs) are used either alone or in combination with other biomaterials in the form of fillers in composites, coatings for both scaffolds and implants, or vehicles for the delivery of various signaling and therapeutic agents. The applications of the GFMs in each of these diverse areas are discussed and emphasis is placed on the characteristics of the GFMs that have implications in this regard. In tandem and of importance, this article evaluates the safety and biocompatibility of the GFMs and carefully elucidates how various factors influence the biocompatibility and biodegradability of this new class of nanomaterials. In conclusion, the challenges and opportunities regarding the use of the GFMs in regenerative engineering applications are discussed, and future perspectives for the developments in this field are proposed.
Characterisation of patients with severe asthma in the UK Severe Asthma Registry in the biologic era
Authors: David J Jackson, John Busby, Paul E Pfeffer, Andrew Menzies-Gow, Thomas Brown, Robin Gore, Martin Doherty, Adel H Mansur, Simon Message, Robert Niven, Mitesh Patel, Liam G Heaney
Journal: Thorax (2020)

Background The UK Severe Asthma Registry (UKSAR) is the world’s largest national severe asthma registry collecting standardised data on referrals to UK specialist services. Novel biologic therapies have transformed the management of type 2(T2)-high severe asthma but have highlighted unmet need in patients with persisting symptoms despite suppression of T2-cytokine pathways with corticosteroids. Methods Demographic, clinical and treatments characteristics for patients meeting European Respiratory Society / American Thoracic Society severe asthma criteria were examined for 2225 patients attending 15 specialist severe asthma centres. We assessed differences in biomarker low patients (fractional exhaled nitric oxide (FeNO) &lt;25 ppb, blood eosinophils &lt;150/μL) compared with a biomarker high population (FeNO ≥25 ppb, blood eosinophils ≥150/µL). Results Age (mean 49.6 (14.3) y), age of asthma onset (24.2 (19.1) y) and female predominance (62.4%) were consistent with prior severe asthma cohorts. Poor symptom control (Asthma Control Questionnaire-6: 2.9 (1.4)) with high exacerbation rate (4 (IQR: 2, 7)) were common despite high-dose treatment (51.7% on maintenance oral corticosteroids (mOCS)). 68.9% were prescribed biologic therapies including mepolizumab (50.3%), benralizumab (26.1%) and omalizumab (22.6%). T2-low patients had higher body mass index (32.1 vs 30.2, p&lt;0.001), depression/anxiety prevalence (12.3% vs 7.6%, p=0.04) and mOCS use (57.9% vs 42.1%, p&lt;0.001). Many T2-low asthmatics had evidence of a historically elevated blood eosinophil count (0.35 (0.13, 0.60)). Conclusions The UKSAR describes the characteristics of a large cohort of asthmatics referred to UK specialist severe asthma services. It offers the prospect of providing novel insights across a range of research areas and highlights substantial unmet need with poor asthma control, impaired lung function and high exacerbation rates. T2-high phenotypes predominate with significant differences apparent from T2-low patients. However, T2-low patients frequently have prior blood eosinophilia consistent with possible excessive corticosteroid exposure.
TCT CONNECT-468 Postoperative Atrial Fibrillation or Flutter Following Transcatheter or Surgical Aortic Valve Replacement for Severe Aortic Stenosis in Patients at Low Surgical Risk: An Analysis From the PARTNER 3 Trial
Authors: Bahira Shahim, S. Chris Malaisrie, Isaac George, Vinod Thourani, Mark Russo, Angelo Biviano, Michael Mack, David L. Brown, Vasilis Babaliaros, Robert Guyton, Susheel Kodali, Tamim Nazif, Philippe Genereux, Raj Makkar, Mathew Williams, James McCabe, John Webb, Michael Lu, Xiao Yu, Martin Leon, Ioanna Kosmidou
Journal: Journal of the American College of Cardiology (2020)
TCT CONNECT-345 Transseptal Transcatheter Mitral Valve Annuloplasty With PolyCor Anchors (Micro Interventional Devices) in a Beating Human Cadaver Heart Biosimulator
Authors: Yanping Cheng, Gerard Conditt, Michael Whitman, Preston Morris, Willard Hennemann, Grzegorz Kaluza, Juan Granada, Genghua Yi
Journal: Journal of the American College of Cardiology (2020)
Lessons Learned From Acute Myocardial Infarction Care in China
Authors: Timothy D. Henry, James G. Jollis
Journal: JAMA Network Open (2020)

Qi Zhong, MD; Yan Gao, MA; Xin Zheng, MD, PhD; Jiyan Chen, MD, PhD; Frederick A. Masoudi, MD, MSPH; Yuan Lu, ScD; Yingqing Feng, MD, PhD; Shuang Hu, PhD; Qiuli Zhang, PhD; Cheng Huang, MD, PhD; Yun Wang, PhD; Harlan M. Krumholz, MD, SM; Xi Li, MD, PhD; Yingling Zhou, MD, PhD