tbuckley/cabot-search huggingface dataset:
Stevens-johnson syndrome and toxic epidermal necrolysis standard reporting and evaluation guidelines
Authors: Emanual Maverakis, Elizabeth A Wang, Kanade Shinkai, Surakameth Mahasirimongkol, David J Margolis, Mark Avigan, Wen-Hung Chung, Jennifer Goldman, Lois La Grenade, Munir Pirmohamed, Neil H Shear, Wichittra Tassaneeyakul, Wolfram Hoetzenecker, Jettanong Klaewsongkram, Ticha Rerkpattanapipat, Wiparat Manuyakorn, Sally Usdin Yasuda, Victoria R Sharon, Andrea Sukhov, Robert Micheletti, Jeff Struewing, Lars E French, Michelle Y Cheng
Journal: JAMA Dermatology (2017)

Importance: Toxic epidermal necrolysis (TEN) and Stevens-Johnson Syndrome (SJS) are rare, acute, life-threatening dermatologic disorders involving the skin and mucous membranes. Research into these conditions is hampered by a lack of standardization of case reporting and data collection.
Objective: To establish a standardized case report form to facilitate comparisons and maintain data quality based on an international panel of SJS/TEN experts who performed a Delphi consensus-building exercise.
Evidence Review: The elements presented for committee scrutiny were adapted from previous case report forms and from PubMed literature searches of highly cited manuscripts pertaining to SJS/TEN. The expert opinions and experience of the members of the consensus group were included in the discussion.
Findings: Overall, 21 out of 29 experts who were invited to participate in the online Delphi exercise agreed to participate. Surveys at each stage were administered via an online survery software tool. For the first 2 Delphi rounds, results were analyzed using the Interpercentile Range Adjusted for Symmetry method and statements that passed consensus formulated a new case report form. For the third Delphi round, the case report form was presented to the committee, who agreed that it was appropriate and useful for documenting cases of SJS/TEN, making it more reliable and valuable for future research endeavors.
Conclusions and Relevance: With the consensus of international experts, a case report form for SJS/TEN has been created to help standardize the collection of patient information in future studies and the documentation of individual cases.
Endovascular Reconstruction From Aortic Valve to Aortic Arch Using 1-Piece Valved Fenestrated Bifurcated Endografting
Authors: Jiaxuan Feng, Xianhao Bao, Tao Li, Yuxi Zhao, Mingwei Wu, Junjun Liu, Aikebaierjiang Ainiwaer, Rui Feng, Jian Zhou, Zaiping Jing
Journal: Journal of the American College of Cardiology (2020)
<i>Bifidobacterium longum</i> alleviates irritable bowel syndrome-related visceral hypersensitivity and microbiota dysbiosis via Paneth cell regulation
Authors: Chunhua Zhou, Xue Fang, Jiajia Xu, Jun Gao, Ling Zhang, Jiulong Zhao, Yuting Meng, Wei Zhou, Xu Han, Yu Bai, Zhaoshen Li, Duowu Zou
Journal: Gut Microbes (2020)

Although the oral administration of Bifidobacterium longum (B. longum) relieves the signs of irritable bowel syndrome (IBS) in clinical settings, the mechanisms underlying its effects are unclear. In this study, we evaluated the precise effects of B. longum on IBS via regulation of Paneth cell function. We confirmed the beneficial effects of B. longum on defecation habits and visceral hypersensitivity in WAS rats. Further analysis revealed that B. longum enhanced mucosal repair, promoted lysozyme production, and ameliorated dysbiosis of the microbiota in WAS rats. These processes are closely correlated with Paneth cell functions. In vitro, we incubated primary cultured enteroids with B. longum and found that B. longum promoted the proliferation of these organoids; this may be attributed to the upregulation of the stem niche factors WNT3A and TGF-β, which are secreted by Paneth cells. Based on our findings, we propose that B. longum relieves IBS by restoring the antimicrobial activity and stem niche maintenance function of Paneth cells.
Early-Life Environmental Exposures and Childhood Obesity: An Exposome-Wide Approach
Authors: Martine Vrijheid, Serena Fossati, Léa Maitre, Sandra Márquez, Theano Roumeliotaki, Lydiane Agier, Sandra Andrusaityte, Solène Cadiou, Maribel Casas, Montserrat de Castro, Audrius Dedele, David Donaire-Gonzalez, Regina Grazuleviciene, Line S. Haug, Rosemary McEachan, Helle Margrete Meltzer, Eleni Papadopouplou, Oliver Robinson, Amrit K. Sakhi, Valerie Siroux, Jordi Sunyer, Per E. Schwarze, Ibon Tamayo-Uria, Jose Urquiza, Marina Vafeiadi, Antonia Valentin, Charline Warembourg, John Wright, Mark J. Nieuwenhuijsen, Cathrine Thomsen, Xavier Basagaña, Rémy Slama, Leda Chatzi
Journal: Environmental Health Perspectives (2020)

BACKGROUND: Chemical and nonchemical environmental exposures are increasingly suspected to influence the development of obesity, especially during early life, but studies mostly consider single exposure groups.OBJECTIVES: Our study aimed to systematically assess the association between a wide array of early-life environmental exposures and childhood obesity, using an exposome-wide approach.METHODS: The HELIX (Human Early Life Exposome) study measured child body mass index (BMI), waist circumference, skinfold thickness, and body fat mass in 1,301 children from six European birth cohorts age 6-11 y.We estimated 77 prenatal exposures and 96 childhood exposures (crosssectionally), including indoor and outdoor air pollutants, built environment, green spaces, tobacco smoking, and biomarkers of chemical pollutants (persistent organic pollutants, metals, phthalates, phenols, and pesticides).We used an exposure-wide association study (ExWAS) to screen all exposure-outcome associations independently and used the deletion-substitution-addition (DSA) variable selection algorithm to build a final multiexposure model. RESULTS:The prevalence of overweight and obesity combined was 28.8%.Maternal smoking was the only prenatal exposure variable associated with higher child BMI (z-score increase of 0.28, 95% confidence interval: 0.09, 0.48, for active vs. no smoking).For childhood exposures, the multiexposure model identified particulate and nitrogen dioxide air pollution inside the home, urine cotinine levels indicative of secondhand smoke exposure, and residence in more densely populated areas and in areas with fewer facilities to be associated with increased child BMI.Child blood levels of copper and cesium were associated with higher BMI, and levels of organochlorine pollutants, cobalt, and molybdenum were associated with lower BMI.Similar results were found for the other adiposity outcomes.DISCUSSION: This first comprehensive and systematic analysis of many suspected environmental obesogens strengthens evidence for an association of smoking, air pollution exposure, and characteristics of the built environment with childhood obesity risk.Cross-sectional biomarker results may suffer from reverse causality bias, whereby obesity status influenced the biomarker concentration.
The autoimmune susceptibility gene, <i>PTPN2</i>, restricts expansion of a novel mouse adherent-invasive <i>E. coli</i>
Authors: Ali Shawki, Rocio Ramirez, Marianne R. Spalinger, Paul M. Ruegger, Anica Sayoc-Becerra, Alina N. Santos, Pritha Chatterjee, Vinicius Canale, Jonathan D. Mitchell, John C. Macbeth, Casey M. Gries, Michel L. Tremblay, Ansel Hsiao, James Borneman, Declan F. McCole
Journal: Gut Microbes (2020)

Inflammatory bowel disease (IBD) pathogenesis involves significant contributions from genetic and environmental factors. Loss-of-function single-nucleotide polymorphisms (SNPs) in the protein tyrosine phosphatase non-receptor type 2 (PTPN2) gene increase IBD risk and are associated with altered microbiome population dynamics in IBD. Expansion of intestinal pathobionts, such as adherent-invasive E. coli (AIEC), is strongly implicated in IBD pathogenesis as AIEC increases pro-inflammatory cytokine production and alters tight junction protein regulation – suggesting a potential mechanism of pathogen-induced barrier dysfunction and inflammation. We aimed to determine if PTPN2 deficiency alters intestinal microbiome composition to promote expansion of specific bacteria with pathogenic properties. In mice constitutively lacking Ptpn2, we identified increased abundance of a novel mouse AIEC (mAIEC) that showed similar adherence and invasion of intestinal epithelial cells, but greater survival in macrophages, to the IBD-associated AIEC, LF82. Furthermore, mAIEC caused disease when administered to mice lacking segmented-filamentous bacteria (SFB), and in germ-free mice but only when reconstituted with a microbiome, thus supporting its classification as a pathobiont, not a pathogen. Moreover, mAIEC infection increased the severity of, and prevented recovery from, induced colitis. Although mAIEC genome sequence analysis showed >90% similarity to LF82, mAIEC contained putative virulence genes with >50% difference in gene/protein identities from LF82 indicating potentially distinct genetic features of mAIEC. We show for the first time that an IBD susceptibility gene, PTPN2, modulates the gut microbiome to protect against a novel pathobiont. This study generates new insights into gene-environment-microbiome interactions in IBD and identifies a new model to study AIEC-host interactions.
High-Risk Patients and Utilization of Primary Care in the US Veterans Affairs Health System
Authors: Said A. Ibrahim
Journal: JAMA Network Open (2020)

Evelyn T. Chang, MD, MSHS; Donna M. Zulman, MD, MS; Karin M. Nelson, MD, MSHS; Ann-Marie Rosland, MD, MS; David A. Ganz, MD, PhD; Stephan D. Fihn, MD, MPH; Rebecca Piegari, MS; Lisa V. Rubenstein, MD, MSPH
Asymptomatic SARS-CoV-2 infection: the tip or the iceberg?
Authors: Alexander J Keeley, Cariad M Evans, Thushan I de Silva
Journal: Thorax (2020)

A case of-Behçet9s syndrome is described in which, in addition to the usual features of the condition, there was evidence of renal, gastric and cardiac involvement. Neurological involvement presented as hemisphere, transient ischaemic episodes. Immune complexes were detected and the patient responded promptly to prednisolone.
The efficacy of adding short-term psychodynamic psychotherapy to antidepressants in the treatment of depression: A systematic review and meta-analysis of individual participant data
Authors: Ellen Driessen, Jack J.M. Dekker, Jaap Peen, Henricus L. Van, Giuseppe Maina, Gianluca Rosso, Sylvia Rigardetto, Francesco Cuniberti, Veronica G. Vitriol, Ramon U. Florenzano, Antonio Andreoli, Yvonne Burnand, Jaime López-Rodríguez, Valerio Villamil-Salcedo, Jos W.R. Twisk, Pim Cuijpers
Journal: Clinical Psychology Review (2020)
Triple Inhaled Therapy at Two Glucocorticoid Doses in Moderate-to-Very-Severe COPD
Authors: Klaus F. Rabe, Fernando J. Martinez, Gary T. Ferguson, Chen Wang, Dave Singh, Jadwiga A. Wedzicha, Roopa Trivedi, Earl St. Rose, Shaila Ballal, Julie McLaren, Patrick Darken, Magnus Aurivillius, Colin Reisner, Paul Dorinsky
Journal: New England Journal of Medicine (2020)

Triple fixed-dose regimens of an inhaled glucocorticoid, a long-acting muscarinic antagonist (LAMA), and a long-acting β2-agonist (LABA) for chronic obstructive pulmonary disease (COPD) have been studied at single dose levels of inhaled glucocorticoid, but studies at two dose levels are lacking.
The effect of catch-up growth in the first year of life on later wheezing phenotypes
Authors: Sarah J. Kotecha, John Lowe, Raquel Granell, W. John Watkins, A. John Henderson, Sailesh Kotecha
Journal: European Respiratory Journal (2020)

<b>This study shows that catch-up growth in infancy is associated with increased early wheeze in childhood, so care is needed to not to excessively feed in early infancy</b>https://bit.ly/2YPxtBw
Immunology of COVID‐19: Mechanisms, clinical outcome, diagnostics, and perspectives—A report of the European Academy of Allergy and Clinical Immunology (EAACI)
Authors: Milena Sokolowska, Zuzanna M. Lukasik, Ioana Agache, Cezmi A. Akdis, Deniz Akdis, Mübeccel Akdis, Weronika Barcik, Helen A. Brough, Thomas Eiwegger, Andrzej Eljaszewicz, Stefanie Eyerich, Wojciech Feleszko, Cristina Gomez‐Casado, Karin Hoffmann‐Sommergruber, Jozef Janda, Rodrigo Jiménez‐Saiz, Marek Jutel, Edward F. Knol, Inge Kortekaas Krohn, Akash Kothari, Joanna Makowska, Marcin Moniuszko, Hideaki Morita, Liam O'Mahony, Kari Nadeau, Cevdet Ozdemir, Isabella Pali‐Schöll, Oscar Palomares, Francesco Papaleo, Mary Prunicki, Carsten B. Schmidt‐Weber, Anna Sediva, Jürgen Schwarze, Mohamed H. Shamji, Gerdien A. Tramper‐Stranders, Willem van de Veen, Eva Untersmayr
Journal: Allergy (2020)

With the worldwide spread of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) resulting in declaration of a pandemic by the World Health Organization (WHO) on March 11, 2020, the SARS-CoV-2-induced coronavirus disease-19 (COVID-19) has become one of the main challenges of our times. The high infection rate and the severe disease course led to major safety and social restriction measures worldwide. There is an urgent need of unbiased expert knowledge guiding the development of efficient treatment and prevention strategies. This report summarizes current immunological data on mechanisms associated with the SARS-CoV-2 infection and COVID-19 development and progression to the most severe forms. We characterize the differences between adequate innate and adaptive immune response in mild disease and the deep immune dysfunction in the severe multiorgan disease. The similarities of the human immune response to SARS-CoV-2 and the SARS-CoV and MERS-CoV are underlined. We also summarize known and potential SARS-CoV-2 receptors on epithelial barriers, immune cells, endothelium and clinically involved organs such as lung, gut, kidney, cardiovascular, and neuronal system. Finally, we discuss the known and potential mechanisms underlying the involvement of comorbidities, gender, and age in development of COVID-19. Consequently, we highlight the knowledge gaps and urgent research requirements to provide a quick roadmap for ongoing and needed COVID-19 studies.
Percentage of Children Who Developed Type 1 Diabetes After Rotavirus Vaccination
Authors: Mary A. M. Rogers
Journal: JAMA Pediatrics (2020)

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Assessment of Health Information Technology–Related Outpatient Diagnostic Delays in the US Veterans Affairs Health Care System
Authors: Lauren Powell, Dean F. Sittig, Kristin Chrouser, Hardeep Singh
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Diagnostic delay in the outpatient setting is an emerging safety priority that health information technology (HIT) should help address. However, diagnostic delays have persisted, and new safety concerns associated with the use of HIT have emerged. <h3>Objective</h3> To analyze HIT-related outpatient diagnostic delays within a large, integrated health care system. <h3>Design, Setting, and Participants</h3> This cohort study involved qualitative content analysis of safety concerns identified in aggregated root cause analysis (RCA) data related to HIT and outpatient diagnostic delays. The setting was the US Department of Veterans Affairs using all RCAs submitted to the Veterans Affairs (VA) National Center for Patient Safety from January 1, 2013, to July 31, 2018. <h3>Main Outcomes and Measures</h3> Common themes associated with the role of HIT-related safety concerns were identified and categorized according to the Health IT Safety framework for measuring, monitoring, and improving HIT safety. This framework includes 3 related domains (ie, safe HIT, safe use of HIT, and using HIT to improve safety) situated within an 8-dimensional sociotechnical model accounting for interacting technical and nontechnical variables associated with safety. Hence, themes identified enhanced understanding of the sociotechnical context and domain of HIT safety involved. <h3>Results</h3> Of 214 RCAs categorized by the terms<i>delay</i>and<i>outpatient</i>submitted during the study period, 88 were identified as involving diagnostic delays and HIT, from which 172 unique HIT-related safety concerns were extracted (mean [SD], 1.97 [1.53] per RCA). Most safety concerns (82.6% [142 of 172]) involved problems with safe use of HIT, predominantly sociotechnical factors associated with people, workflow and communication, and a poorly designed human-computer interface. Fewer safety concerns involved problems with safe HIT (14.5% [25 of 172]) or using HIT to improve safety (0.3% [5 of 172]). The following 5 key high-risk areas for diagnostic delays emerged: managing electronic health record inbox notifications and communication, clinicians gathering key diagnostic information, technical problems, data entry problems, and failure of a system to track test results. <h3>Conclusions and Relevance</h3> This qualitative study of a national RCA data set suggests that interventions to reduce outpatient diagnostic delays could aim to improve test result management, interoperability, data visualization, and order entry, as well as to decrease information overload.
Mutations in genes encoding desmosomal proteins: spectrum of cutaneous and extracutaneous abnormalities*
Authors: J.Y.W. Lee, J.A. McGrath
Journal: British Journal of Dermatology (2020)

The desmosome is a type of intercellular junction found in epithelial cells, cardiomyocytes and other specialized cell types. Composed of a network of transmembranous cadherins and intracellular armadillo, plakin and other proteins, desmosomes contribute to cell-cell adhesion, signalling, development and differentiation. Mutations in genes encoding desmosomal proteins result in a spectrum of erosive skin and mucosal phenotypes that also may affect hair or heart. This review summarizes the molecular pathology and phenotypes associated with desmosomal dysfunction with a focus on inherited disorders that involve the skin/hair, as well as associated extracutaneous pathologies. We reviewed the relevant literature to collate studies of pathogenic human mutations in desmosomes that have been reported over the last 25 years. Mutations in 12 different desmosome genes have been documented, with mutations in nine genes affecting the skin/mucous membranes (DSG1, DSG3, DSC2, DSC3, JUP, PKP1, DSP, CDSN, PERP) and eight resulting in hair abnormalities (DSG4, DSC2, DSC3, JUP, PKP1, DSP, CDSN, PERP). Mutations in three genes can result in cardiocutaneous syndromes (DSC2, JUP, DSP), although mutations have been described in five genes in inherited heart disorders that may lack any dermatological manifestations (DSG2, DSC2, JUP, PKP2, DSP). Understanding the diverse nature of these clinical phenotypes, as well as the desmosome gene mutation(s), has clinical value in managing and counselling patients, as well as demonstrating the biological role and activity of specific components of desmosomes in skin and other tissues.
Evaluation of Chilblains as a Manifestation of the COVID-19 Pandemic
Authors: Anne Herman, Caroline Peeters, Alexia Verroken, Isabelle Tromme, Dominique Tennstedt, Liliane Marot, Claire Dachelet, Damien Gruson, Cedric Hermans, Marie Baeck
Journal: JAMA Dermatology (2020)

During the coronavirus disease 2019 (COVID-19) pandemic, several cases of chilblains have been reported.
The evolution of clinical trials in renal cell carcinoma: A status report for 2013-2016 from the clinicaltrials.gov website.
Authors: Pooja Ghatalia, David Pisarcik, Rebecca Koenigsberg, Elizabeth Handorf, Daniel M. Geynisman, Matthew R. Zibelman
Journal: Journal of Clinical Oncology (2017)

e16050 Background: The treatment paradigm for renal cell carcinoma (RCC) continues to rapidly evolve. We previously published a snapshot analysis of clinical trials in RCC using the publicly available ClinicalTrials.gov registry. Here we present a 3 year update in order to understand the current trends in RCC clinical research, to identify opportunities for improvement, and to compare this data to the landscape in 2013. Methods: The Website’s advanced search function was used to search for the terms “renal cell carcinoma”, “kidney cancer”, “kidney neoplasm” or “renal neoplasm”. The search was further refined to “open studies”, “interventional” and “age ≥18”. Basket trials with ≥7 tumors with non-RCC tumor histologies, terminated studies and pediatric studies were excluded. The phase, stage, treatment setting, type of intervention, study design, histologies, use of biomarkers, studied outcomes, sponsors and location of the trials were recorded. Results: We locked our search on May 26, 2016 and 165 trials were eligible, compared with 169 trials on Sep 25, 2013. There were more phase I and I/II trials in 2016 compared to 2013 (p = 0.05): phase I (25.6% vs 15.4%) and phase I/II (15.2% vs 9.5%). More clinical trials in 2016 compared to 2013 used immunotherapy (IT) alone or in combination with other drugs (24.2 % vs 10.7%, p = 0.001), and the use of targeted therapy alone (TT) declined (32.9% vs 47.9%, p = 0.005). IT alone was used in 15.2% of current trials, compared to 5.96% in 2013. TT+IT combination trials more than doubled (6.7% vs 2.3%, p = 0.07). The number of trials with treatment in neoadjuvant/adjuvant settings in 2016 and 2013 were similar (9.7% vs 10.6%, p = 0.77), respectively. Compared to 2013, the number of trials with non-clear cell histology remained low (n = 10). Many more trials were sponsored by pharmaceutical industry in 2016 vs 2013 (41.5% vs 16.0%, p = &lt; 0.001). Conclusions: More clinical trials included immunotherapy in 2016 compared to 2013, and there was a significant increase in industry sponsored trials. The increase in industry sponsored studies may reflect use of new expensive drugs. More studies in (neo)adjuvant settings and for non-clear cell histologies are needed.