tbuckley/cabot-search huggingface dataset:
Assessment of Primary Care Clinician Concordance With Guidelines for Use of Magnetic Resonance Imaging in Patients With Nonspecific Low Back Pain in the Veterans Affairs Health System
Authors: Paul G. Barnett, Josephine C. Jacobs, Jeffrey G. Jarvik, Roger Chou, Derek Boothroyd, Jeanie Lo, Andrea Nevedal
Journal: JAMA Network Open (2020)

<h3>Importance</h3> Magnetic responance imaging (MRI) of the lumbar spine that is not concordant with treatment guidelines for low back pain represents an unnecessary cost for US health plans and may be associated with adverse effects. Use of MRI in the US Department of Veterans Affairs (VA) primary care clinics remains unknown. <h3>Objective</h3> To assess the use of MRI scans during the first 6 weeks (early MRI scans) of episodes of nonspecific low back pain in VA primary care sites and to determine if historical concordance can identify clinicians and sites that are the least concordant with guidelines. <h3>Design, Setting, and Participants</h3> Retrospective cohort study of electronic health records from 944 VA primary care sites from the 3 years ending in 2016. Data were analyzed between January 2017 and August 2019. Participants were patients with new episodes of nonspecific low back pain and the primary care clinicians responsible for their care. <h3>Exposures</h3> MRI scans. <h3>Main Outcomes and Measures</h3> The proportion of early MRI scans at VA primary care clinics was assessed. Clinician concordance with published guidelines over 2 years was used to select clinicians expected to have low concordance in a third year. <h3>Results</h3> A total of 1 285 405 new episodes of nonspecific low back pain from 920 547 patients (mean [SD] age, 56.7 [15.8] years; 93.6% men) were attributed to 9098 clinicians (mean [SD] age, 52.1 [10.1] years; 55.7% women). An early MRI scan of the lumbar spine was performed in 31 132 of the episodes (2.42%; 95% CI, 2.40%-2.45%). Historical concordance was better than a random draw in selecting the 10% of clinicians who were subsequently the least concordant with published guidelines. For primary care clinicians, the area under the receiver operating characteristic curve was 0.683 (95% CI, 0.658-0.701). For primary care sites, the area was under this curve was 0.8035 (95% CI, 0.754-0.855). The 10% of clinicians with the least historical concordance were responsible for just 19.2% of the early MRI scans performed in the follow-up year. <h3>Conclusions and Relevance</h3> VA primary care clinics had low rates of use of early MRI scans. A history of low concordance with imaging guidelines was associated with subsequent low concordance but with limited potential to select clinicians most in need of interventions to implement guidelines.
P-251 Diversity of Helicobacter pylori genotypes in tumoral, antral and normal tissue of Colombian patients with gastric cancer
Authors: A. Guevara-Tique, J. Suarez Olaya, F. Castro-Valencia, R. Torres, G. Parra Gil, J. Torres, L. Carvajal Carmona, M. Echeverry de Polanco, M. Bohorquez Lozano
Journal: Annals of Oncology (2020)
Development and Initial Validation Analyses of the Living with Idiopathic Pulmonary Fibrosis Questionnaire
Authors: Jeffrey J. Swigris, David A. Andrae, Tara Churney, Nathan Johnson, Mary Beth Scholand, Eric S. White, Alison Matsui, Karina Raimundo, Christopher J. Evans
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

Rationale: Several new drugs for idiopathic pulmonary fibrosis (IPF) are in development. Tools are needed to assess whether these drugs benefit patients on outcomes that matter most to them. Health-related quality of life (HRQL) is one such outcome. It is influenced by many factors, but symptoms and their impacts are two strong drivers.Objectives: To develop a questionnaire to assess symptoms, disease impacts, and HRQL specifically for patients with IPF.Methods: Working with the U.S. Food and Drug Administration through the Drug Development Tool Qualification process, focus groups, concept elicitation, and cognitive debriefing interviews were conducted to inform the development of a 44-item pilot questionnaire. The pilot paper-and-pen questionnaire was migrated to an equivalent electronic version and field-tested in a 14-day study. Response data were subjected to psychometric testing, including exploratory factor analysis, item calibration using item response theory models, test-retest reliability, and validity testing.Measurements and Main Results: A total of 125 patients with IPF (62.4% men) completed the longitudinal study. The mean ± SD age of the cohort was 69 ± 7.60 years, and the mean FVC% predicted was 71 ± 20.0. After factor and item analyses, 35 items were retained, and these comprise the two modules (symptoms and impacts) of the Living with IPF (L-IPF) questionnaire. The L-IPF yields five scales demonstrating good psychometric properties, including correlation with concurrently collected FVC% predicted and the ability to discriminate between patients with differing levels of IPF severity.Conclusions: The L-IPF is a new questionnaire that assesses symptoms, disease impacts, and HRQL in patients with IPF.
P-315 Impact of tumor location (right vs left) as a prognostic and predictive factor in colon cancer in a Moroccan population: A single-center study
Authors: M. Elfadli, N. Benhima, H. Jouihri, S. El Ouarzazi, M. Kaakoua, J. Bagorane, G. Adjade, S. Lalaoui Rachidi, K. Cisse, G. Negamiyimana, I. Essadi, R. Belbaraka
Journal: Annals of Oncology (2020)
PRMT5 control of cGAS/STING and NLRC5 pathways defines melanoma response to antitumor immunity
Authors: Hyungsoo Kim, Heejung Kim, Yongmei Feng, Yan Li, Hironari Tamiya, Stefania Tocci, Ze’ev A. Ronai
Journal: Science Translational Medicine (2020)

PRMT5 expression in melanoma suppresses inflammation and antigen presentation, suggesting that its inhibition could potentiate immunotherapy.
Evolving viral and serological stages of Zika virus RNA-positive blood donors and estimation of incidence of infection during the 2016 Puerto Rican Zika epidemic: an observational cohort study
Authors: Phillip C Williamson, Brad J Biggerstaff, Graham Simmons, Mars Stone, Val Winkelman, Gerardo Latoni, Jose Alsina, Sonia Bakkour, Christina Newman, Lisa L Pate, Susan A Galel, Steven Kleinman, Michael P Busch
Journal: The Lancet Infectious Diseases (2020)
Abstract 13175: Efficacy and Safety of Direct Oral Anticoagulants in Patients With Atrial Fibrillation and Chronic Kidney Disease
Authors: Harpreet S Bhatia, Joseph Bailey, Ozan Unlu, Robert J Kim
Journal: Circulation (2018)

Introduction: Direct Oral Anticoagulants (DOACs) are effective alternatives to warfarin for stroke prevention, including for CKD III patients. However, data on patient outcomes with DOACs for more ...
P-51 Immunoscore in rectal cancer patients receiving radiation followed by mFOLFOX with avelumab
Authors: I. Khalifeh, Z. El Husseini, Y. Zeidan, R. Turfa, J. Kattan, D. Mukherji, S. Temraz, S. Deeba, F. Jamali, I. Mohamad, F. Daoud, M. Al Darazi, M. Charafeddine, F. Geara, A. Shamseddine
Journal: Annals of Oncology (2020)
‘Halo Score’: missing large-vessel giant cell arteritis— do we need a ‘modified Halo Score’?
Authors: Arghya Chattopadhyay, Alakendu Ghosh
Journal: Annals of the Rheumatic Diseases (2020)

Figure 1 Proposed vascular territories for the assessment of modified Halo Score.Suggestions for inclusion of three vascular territories, instead of two, that is, bilateral temporal, subclavian (new addition) and axillary arteries.The final score will be based on the sum of the two higher scores.
P-112 HGCSG1801: A phase II trial of 2nd-line FOLFIRI plus aflibercept in patients with metastatic colorectal cancer refractory to anti-EGFR antibody
Authors: Y. Shindo, H. Nakatsumi, S. Yuki, Y. Kawamoto, O. Muto, M. Dazai, K. Harada, Y. Kobayashi, S. Sogabe, M. Katagiri, M. Kotaka, M. Nakamura, K. Hatanaka, A. Ishiguro, Y. Tsuji, T. Kobayashi, M. Tateyama, Y. Sasaki, T. Sasaki, R. Takagi, Y. Sakata, Y. Komatsu
Journal: Annals of Oncology (2020)
Efficacy and safety of nivolumab in asian patients with advanced hepatocellular carcinoma (HCC): Subanalysis of the CheckMate 040 Study
Authors: S.P. Choo, T. Yau, C. Hsu, Y-K Kang, M-M Hou, W. Yeo, K. Numata, A. Chopra, A. Baakili, C. Dela Cruz, H. Zhao, M. Kudo
Journal: Annals of Oncology (2017)
Recent Demographic History Inferred by High-Resolution Analysis of Linkage Disequilibrium
Authors: Enrique Santiago, Irene Novo, Antonio F Pardiñas, María Saura, Jinliang Wang, Armando Caballero
Journal: Molecular Biology and Evolution (2020)

Abstract Inferring changes in effective population size (Ne) in the recent past is of special interest for conservation of endangered species and for human history research. Current methods for estimating the very recent historical Ne are unable to detect complex demographic trajectories involving multiple episodes of bottlenecks, drops, and expansions. We develop a theoretical and computational framework to infer the demographic history of a population within the past 100 generations from the observed spectrum of linkage disequilibrium (LD) of pairs of loci over a wide range of recombination rates in a sample of contemporary individuals. The cumulative contributions of all of the previous generations to the observed LD are included in our model, and a genetic algorithm is used to search for the sequence of historical Ne values that best explains the observed LD spectrum. The method can be applied from large samples to samples of fewer than ten individuals using a variety of genotyping and DNA sequencing data: haploid, diploid with phased or unphased genotypes and pseudohaploid data from low-coverage sequencing. The method was tested by computer simulation for sensitivity to genotyping errors, temporal heterogeneity of samples, population admixture, and structural division into subpopulations, showing high tolerance to deviations from the assumptions of the model. Computer simulations also show that the proposed method outperforms other leading approaches when the inference concerns recent timeframes. Analysis of data from a variety of human and animal populations gave results in agreement with previous estimations by other methods or with records of historical events.
Withdrawal of inhaled corticosteroids in COPD
Authors: James D. Chalmers, Marc Miravitlles
Journal: European Respiratory Journal (2020)

We thank A. Agusti for his interest in the European Respiratory Society (ERS) guideline on withdrawal of inhaled corticosteroids (ICS) in COPD [1]. He raises an important concern, that we might be recommending discontinuing a potentially effective treatment. This was carefully considered by the panel and there are important reasons to be sure that this is not the case. ICS can be withdrawn in COPD patients without history of exacerbations <https://bit.ly/2TorQZd>
Assessment of Clinical Conditions Associated With Splenic Infarction in Adult Patients
Authors: Allan S. Brett, Neda Azizzadeh, Emily M. Miller, Robert J. Collins, Mary B. Seegars, Matthew A. Marcus
Journal: JAMA Internal Medicine (2020)

Yet little is known regarding determinants of nonforensic autopsy rates.In this issue of JAMA Internal Medicine, Gupta et al 4 provide contemporary, nationwide data on the association of race with the use of clinical autopsy.Using a national Centers for Disease Control and Prevention death database, the investigators found an overall 7.9% autopsy rate among more than 20 million total decedents between 2008 and 2017, which is less than half the autopsy rate in the 1970s.Moreover, rates continued to decrease during the decade of study for all causes of death except those associated with diabetes.The overall autopsy rate was significantly higher in black (12.7%) than white (7.3%) decedents and higher in black individuals for all causes of death.Given the current state of health care policy and financial incentives, autopsy is likely to become an even scarcer resource; therefore, it is critical that we understand and monitor the determinants of autopsy.Gupta et al 4 hypothesize that the higher rate of autopsies in black decedents may reflect health care disparities, a mistrust in the health care system, and less-extensive premortem diagnostics in minority populations.However, it is easy to envision a near future where autopsy availability, restricted to academic hospitals or affluent populations, reflects health care privilege.Overall, further study, education, and advocacy are needed to preserve access to the invaluable clinical autopsy.
LBA-1 First-line liposomal irinotecan + 5 fluorouracil/leucovorin + oxaliplatin in patients with pancreatic ductal adenocarcinoma: Long-term follow-up results from a phase 1/2 study
Authors: Z. Wainberg, T. Bekaii-Saab, P. Boland, F. Dayyani, T. Macarulla, K. Mody, B. Belanger, F. Maxwell, Y. Moore, A. Thiagalingam, T. Wang, B. Zhang, A. Dean
Journal: Annals of Oncology (2020)
PD-6 Gemcitabine + nab-paclitaxel or gemcitabine alone after FOLFIRINOX failure in patients with metastatic pancreatic adenocarcinoma: A population-based, multicenter AGEO study
Authors: S. Zaibet, V. Hautefeuille, E. Auclin, A. Lièvre, D. Tougeron, M. Sarabi, M. Gilabert, J. Wasselin, J. Edeline, P. Artru, D. Bechade, C. Morin, J. Taieb, S. Pernot
Journal: Annals of Oncology (2020)
P-125 Radiomic prediction model for pathological responses of neoadjuvant chemotherapy with S-1 plus oxaliplatin (G-SOX) in clinical stage III gastric cancer
Authors: D. Manaka, S. Konishi, K. Kawaguchi, R. Kudo, Y. Ikeda, T. Ota, H. An, N. Sasaki, S. Hamasu, R. Nishitai, N. Inamoto, K. Shibamoto, A. Ogata, Y. Mori, T. Yamaoka, Y. Himoto
Journal: Annals of Oncology (2020)
A risk-stratified therapy for infants with acute lymphoblastic leukemia: a report from the JPLSG MLL-10 trial
Authors: Daisuke Tomizawa, Takako Miyamura, Toshihiko Imamura, Tomoyuki Watanabe, Akiko Moriya Saito, Atsushi Ogawa, Yoshihiro Takahashi, Masahiro Hirayama, Tomohiko Taki, Takao Deguchi, Toshinori Hori, Masashi Sanada, Shigeru Ohmori, Masami Haba, Akihiro Iguchi, Yuki Arakawa, Yuhki Koga, Atsushi Manabe, Keizo Horibe, Eiichi Ishii, Katsuyoshi Koh
Journal: Blood (2020)
Intestinal Virome in Patients With Alcoholic Hepatitis
Authors: Lu Jiang, Sonja Lang, Yi Duan, Xinlian Zhang, Bei Gao, Jessica Chopyk, Leila K. Schwanemann, Meritxell Ventura‐Cots, Ramon Bataller, Francisco Bosques‐Padilla, Elizabeth C. Verna, Juan G. Abraldes, Robert S. Brown, Victor Vargas, Jose Altamirano, Juan Caballería, Debbie L. Shawcross, Samuel B. Ho, Alexandre Louvet, Michael R. Lucey, Philippe Mathurin, Guadalupe Garcia‐Tsao, Tatiana Kisseleva, David A. Brenner, Xin M. Tu, Peter Stärkel, David Pride, Derrick E. Fouts, Bernd Schnabl
Journal: Hepatology (2020)

Alcoholic hepatitis (AH) is a severe manifestation of alcohol-associated liver disease (ALD) with high mortality. Although gut bacteria and fungi modulate disease severity, little is known about the effects of the viral microbiome (virome) in patients with ALD.We extracted virus-like particles from 89 patients with AH who were enrolled in a multicenter observational study, 36 with alcohol use disorder (AUD), and 17 persons without AUD (controls). Virus-like particles from fecal samples were fractionated using differential filtration techniques, and metagenomic sequencing was performed to characterize intestinal viromes. We observed an increased viral diversity in fecal samples from patients with ALD, with the most significant changes in samples from patients with AH. Escherichia-, Enterobacteria-, and Enterococcus phages were over-represented in fecal samples from patients with AH, along with significant increases in mammalian viruses such as Parvoviridae and Herpesviridae. Antibiotic treatment was associated with higher viral diversity. Specific viral taxa, such as Staphylococcus phages and Herpesviridae, were associated with increased disease severity, indicated by a higher median Model for End-Stage Liver Disease score, and associated with increased 90-day mortality.In conclusion, intestinal viral taxa are altered in fecal samples from patients with AH and associated with disease severity and mortality. Our study describes an intestinal virome signature associated with AH.
Once-daily mometasone plus indacaterol versus mometasone or twice-daily fluticasone plus salmeterol in patients with inadequately controlled asthma (PALLADIUM): a randomised, double-blind, triple-dummy, controlled phase 3 study
Authors: Richard N van Zyl-Smit, Matthias Krüll, Christian Gessner, Yasuhiro Gon, Oliver Noga, Alexia Richard, Amy de los Reyes, Xu Shu, Abhijit Pethe, Ana-Maria Tanase, Peter D'Andrea
Journal: The Lancet Respiratory Medicine (2020)
Margetuximab plus pembrolizumab in patients with previously treated, HER2-positive gastro-oesophageal adenocarcinoma (CP-MGAH22–05): a single-arm, phase 1b–2 trial
Authors: Daniel V T Catenacci, Yoon-Koo Kang, Haeseong Park, Hope E Uronis, Keun-Wook Lee, Matthew C H Ng, Peter C Enzinger, Se Hoon Park, Philip J Gold, Jill Lacy, Howard S Hochster, Sang Cheul Oh, Yeul Hong Kim, Kristen A Marrone, Ronan J Kelly, Rosalyn A Juergens, Jong Gwang Kim, Johanna C Bendell, Thierry Alcindor, Sun Jin Sym, Eun-Kee Song, Cheng Ean Chee, Yee Chao, Sunnie Kim, A Craig Lockhart, Keith L Knutson, Jennifer Yen, Aleksandra Franovic, Jeffrey L Nordstrom, Daner Li, Jon Wigginton, Jan K Davidson-Moncada, Minori Koshiji Rosales, Yung-Jue Bang
Journal: The Lancet Oncology (2020)
P-163 Systemic chemotherapy for previously treated metastatic small bowel adenocarcinoma
Authors: T. Nakazawa, Y. Narita, R. Kumanishi, T. Ogata, Y. Matsubara, K. Nozawa, K. Kato, K. Honda, T. Masuishi, H. Bando, S. Kadowaki, M. Ando, K. Hara, M. Tajika, K. Muro
Journal: Annals of Oncology (2020)
SO-33 Clonal selection of RAS mutant metastatic colorectal cancer into RAS wild-type during first-line therapy
Authors: S. Klein-Scory, I. Wahner, M. Maslova, Y. Al-Sewaidi, M. Pohl, T. Mika, S. Ladigan, R. Schroers, A. Baraniskin
Journal: Annals of Oncology (2020)
Quantitative planar array screen of 1000 proteins uncovers novel urinary protein biomarkers of lupus nephritis
Authors: Kamala Vanarsa, Sanam Soomro, Ting Zhang, Briony Strachan, Claudia Pedroza, Malavika Nidhi, Pietro Cicalese, Christopher Gidley, Shobha Dasari, Shree Mohan, Nathan Thai, Van Thi Thanh Truong, Nicole Jordan, Ramesh Saxena, Chaim Putterman, Michelle Petri, Chandra Mohan
Journal: Annals of the Rheumatic Diseases (2020)

The goal of these studies is to discover novel urinary biomarkers of lupus nephritis (LN).
No Evidence of Increased Hospitalization Rate for COVID-19 in Community-Dwelling Patients With Type 1 Diabetes
Authors: Roman Vangoitsenhoven, Pieter-Jan Martens, Falco van Nes, Carolien Moyson, Frank Nobels, Paul Van Crombrugge, Katrien Wierckx, Inge van Pottelbergh, Liesbeth Van Huffel, Pieter Gillard, Chantal Mathieu
Journal: Diabetes Care (2020)

Evidence on the association between diabetes and adverse outcomes for the novel coronavirus disease 2019 (COVID-19) is emerging, but most studies start from observations in hospitalized patients (1–3). Uncertainty remains as to whether the predisposing factor for COVID-19 severity is the multimorbid profile of these patients or dysglycemia itself. In particular, it is unclear whether people living with type 1 diabetes (T1D) are at high risk for adverse COVID-19 outcomes.

Here, we report the hospitalization rate in community-dwelling people living with T1D during the first 3 months of the COVID-19 pandemic in Belgium. We retrospectively analyzed medical records of all adults with T1D that have their diabetes care contract in either of two diabetes specialist centers. All data were retrieved through data queries from the electronic patient record and were checked manually for validity. Hospitalization in other Belgian hospitals was checked using the national electronic patient record. Patients were selected on the basis of their clinical diagnosis. For the study period of 1 February to 30 April, we retrieved hospital admission date, location, and primary indication as well as BMI, glycemic control (HbA1c), blood pressure, history of macroangiopathy, nephropathy, and hypertension, and angiotensin-converting enzyme (ACE) inhibitor or angiotensin …
Severe refractory Kawasaki disease in seven infants in the COVID-19 era
Authors: Stefania Vergnano, Nele Alders, Catherine Armstrong, Andrew R Bamber, Srini Bandi, Jennifer A Evans, Nadia Hajiani, Julia Kenny, Filip Kucera, Andrew Tometzki, Orhan Uzun, Nick Wilkinson, Athimalaipet V Ramanan
Journal: The Lancet Rheumatology (2020)
Disabled Homolog 2 Controls Prometastatic Activity of Tumor-Associated Macrophages
Authors: Ilaria Marigo, Rosalinda Trovato, Francesca Hofer, Vincenzo Ingangi, Giacomo Desantis, Kevin Leone, Francesco De Sanctis, Stefano Ugel, Stefania Canè, Anna Simonelli, Alessia Lamolinara, Manuela Iezzi, Matteo Fassan, Massimo Rugge, Federico Boschi, Giulia Borile, Thomas Eisenhaure, Siranush Sarkizova, David Lieb, Nir Hacohen, Luca Azzolin, Stefano Piccolo, Rita Lawlor, Aldo Scarpa, Luisa Carbognin, Emilio Bria, Silvio Bicciato, Peter J. Murray, Vincenzo Bronte
Journal: Cancer Discovery (2020)

Tumor-associated macrophages (TAM) are regulators of extracellular matrix (ECM) remodeling and metastatic progression, the main cause of cancer-associated death. We found that disabled homolog 2 mitogen-responsive phosphoprotein (DAB2) is highly expressed in tumor-infiltrating TAMs and that its genetic ablation significantly impairs lung metastasis formation. DAB2-expressing TAMs, mainly localized along the tumor-invasive front, participate in integrin recycling, ECM remodeling, and directional migration in a tridimensional matrix. DAB2+ macrophages escort the invasive dissemination of cancer cells by a mechanosensing pathway requiring the transcription factor YAP. In human lobular breast and gastric carcinomas, DAB2+ TAMs correlated with a poor clinical outcome, identifying DAB2 as potential prognostic biomarker for stratification of patients with cancer. DAB2 is therefore central for the prometastatic activity of TAMs. SIGNIFICANCE: DAB2 expression in macrophages is essential for metastasis formation but not primary tumor growth. Mechanosensing cues, activating the complex YAP-TAZ, regulate DAB2 in macrophages, which in turn controls integrin recycling and ECM remodeling in 3-D tissue matrix. The presence of DAB2+ TAMs in patients with cancer correlates with worse prognosis.This article is highlighted in the In This Issue feature, p. 1611.
Stair-climbing test: beyond the height
Authors: Maria Rodriguez
Journal: Thorax (2020)

Patient selection has contributed significantly to improve the incidence of postoperative complications after anatomical lung resection. Stair-climbing test is one of the low technology alternatives available, sometimes underused, to improve this selection. In the current issue, Boujibar and colleagues1 present the first systematic review and meta-analysis assessing stair-climbing test as a tool to predict postoperative complications after lung resection and to determine which patients require further high-technology cardiopulmonary evaluation.

Boujibar and colleagues describe the first systematic review and meta-analysis, which addresses the role of the stair-climbing test in predicting the incidence of postoperative complications after major lung resection.1 The authors conclude that achieved height during the stair-climbing test is a useful screening tool to decide whether a patient, due for thoracic surgery, needs further high-technology cardiopulmonary evaluation or can proceed directly to the operation. Despite the great heterogeneity of the six studies included in the …