tbuckley/cabot-search huggingface dataset:
Impact of body mass index on development of nontuberculous mycobacterial pulmonary disease
Authors: Jin Hwa Song, Bong Seong Kim, Nakwon Kwak, Kyungdo Han, Jae-Joon Yim
Journal: European Respiratory Journal (2020)

The incidence and prevalence of nontuberculous mycobacterial pulmonary disease (NTM-PD) have been increasing worldwide. The risk of NTM-PD may be higher in undernourished populations. In this study, we tried to elucidate the impact of body mass index (BMI) and its change on development of NTM-PD. We performed a retrospective cohort study including South Koreans aged &gt;40 years who underwent biennial National Health Insurance System (NHIS) health check-ups in both 2005 and 2009 or 2006 and 2010. We monitored eligible individuals from the study initiation date (NHIS health check-up date in 2009 or 2010) until the diagnosis of NTM-PD or until December 31, 2017. Enroled individuals were classified based on BMI at initiation date. By calculating hazard ratios, we compared NTM-PD incidence per 100 000 person-years by BMI group and by BMI change. A total of 5 670 229 individuals were included in the final analysis. Compared with the BMI &lt;18.5 kg·m −2 group, the incidence of NTM-PD gradually decreased with increased BMI (adjusted hazard ratio 0.38, 95% confidence interval (CI) 0.35–0.42 for BMI 18.5–22.9; 0.17, 95% CI 0.15–0.19 for BMI 23–24.9; 0.1, 95% CI 0.09–0.11 for BMI 25–29.9; and 0.1, 95% CI 0.07–0.13 for BMI ≥30). A BMI decrease of ≥1 kg·m −2 over 4 years increased the incidence of NTM-PD (adjusted hazard ratio 1.08, 95% CI 1.01–1.16) whereas a BMI increase of ≥1 kg·m −2 decreased the incidence of NTM-PD (adjusted hazard ratio 0.77, 95% CI 0.71–0.83). In conclusion, BMI was inversely related to development of NTM-PD and weight loss increased the risk of NTM-PD.
Abstract 14937: Proteinuria as a Predictor of Contrast Induced Acute Kidney Injury Following Coronary Angiography
Authors: Jayakumar Sreenivasan, Heyi Li, Mohammad Shahzeb Khan, Tauseef Akhtar, Juan Del Cid Fratti, Kifah Hussain, Min Zhuo, Neha Yadav
Journal: Circulation (2019)

Background: Contrast-induced acute kidney injury (CI-AKI) is an independent predictor of mortality after angiography and percutaneous interventions. Proteinuria is an indicator of glomerular or pro...
THU0240 Epidemiology of osteoarthritis in northern ethnic groups of russia
Authors: S Erdesz, R Protopopova, V Krivoshapkin
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> Till present there are practically no information on the prevalence and risk factors of osteoarthritis in populations residing in severe climatic zones of Russia and subject to the influence of a number of unfavourable environmental factors. <h3>Objectives</h3> To study the epidemiology of osteoarthritis among native population of rural areas of Siberian North – in Yakutia. <h3>Methods</h3> Cross-sectional study of residents of four Yakutian settlements (North/North-Eastern part of Siberia) was performed. At the moment of the study 1282 persons aged 18 and more resided lived there. Among them 1216 persons (94.8%) were examined. 1002 persons were Yakutians (Saha) and 214 – Evenks. <h3>Results</h3> Osteoarthritis was diagnosed in 218 settlement residents. Correspondingly the prevalence of OA in the population under study was 18.00.8%. Among women the OA prevalence was 22.51.4% and among men 12.61.4% (p &lt; 0.05). There was no reliable difference in prevalence between Yakuts and Evenks (correspondingly 17.3% and 21.0%, p &lt; 0.05). We found linear correlation (r = 0.96) between frequency of OA and age. <h3>Conclusion</h3> Thus, epidemiological study of osteoarthritis among rural population of Russian North demonstrated that the prevalence of the disease is 18.0% and women prevail and there is direct age relation between age and frequency of the disease.
COVID-19 and endoscopic management of superficial gastrointestinal neoplastic lesions: a multinational cross-sectional survey
Authors: Marta Rodríguez-Carrasco, Eduardo Albéniz, Pradeep Bhandari, Torsten Beyna, Michael J. Bourke, Ahyeon Min, Philip W. Y. Chiu, Simon Chu, Hon Chi Yip, Pierre H. Deprez, Fabian Emura, Alessandro Repici, Noriko Suzuki, Naohisa Yahagi, Yoko Kubosawa, Cesare Hassan, Mário Dinis-Ribeiro
Journal: Endoscopy (2020)

We aimed to report the impact of the pandemic lockdown period on the treatment and prognosis of superficial gastrointestinal neoplastic lesions.A survey was completed by 11 centers from four continents regarding postponements during the early lockdown period of the pandemic, and the same period in 2019.In 2020, 55 % of the scheduled procedures were deferred, which was 11 times higher than in 2019; the main reasons were directly related to COVID-19. In countries that were highly affected, this proportion rose to 76 % vs. 26 % in those where there was less impact. Despite the absolute reduction, the relative distribution in 2019 vs. 2020 was similar, the only exception being duodenal lesions (affected by a 92 % reduction in mucosectomies). Although it is expected that the majority of postponements will not affect the stage (based on the results from biopsies and/or endoscopic appearance), 3 % of delayed procedures will probably require surgery.The lockdown period caused by the SARS-CoV-2 pandemic led to a substantial reduction in the number of endoscopic resections for neoplastic lesions. Nevertheless, based on clinical judgment, the planned median delay will not worsen the prognosis of the affected patients.
Recommended physical activity and mortality: a round of golf a day keeps the doctor away
Authors: Conor O’Brien
Journal: BMJ (2020)

Mark Twain reputedly stated that golf was “a good walk spoilt.” Zhao and colleagues’ paper on the value of physical activity questions these words. It concludes that survival rates are best in populations that engage in both aerobic and muscle strengthening activities.1 Golf, therefore, is better described as a good walk enhanced: resistance activity and episodes of anaerobic activity …
Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study
Authors: Ankur Gupta-Wright, Katherine Fielding, Joep J van Oosterhout, Melanie Alufandika, Daniel J Grint, Elizabeth Chimbayo, Judith Heaney, Matthew Byott, Eleni Nastouli, Henry C Mwandumba, Elizabeth L Corbett, Ravindra K Gupta
Journal: The Lancet HIV (2020)

BackgroundAntiretroviral therapy (ART) scale-up in sub-Saharan Africa combined with weak routine virological monitoring has driven increasing HIV drug resistance. We investigated ART failure, drug resistance, and early mortality among patients with HIV admitted to hospital in Malawi.MethodsThis observational cohort study was nested within the rapid urine-based screening for tuberculosis to reduce AIDS-related mortality in hospitalised patients in Africa (STAMP) trial, which recruited unselected (ie, irrespective of clinical presentation) adult (aged ≥18 years) patients with HIV-1 at admission to medical wards. Patients were included in our observational cohort study if they were enrolled at the Malawi site (Zomba Central Hospital) and were taking ART for at least 6 months at admission. Patients who met inclusion criteria had frozen plasma samples tested for HIV-1 viral load. Those with HIV-1 RNA of at least 1000 copies per mL had drug resistance testing by ultra-deep sequencing, with drug resistance defined as intermediate or high-level resistance using the Stanford HIVDR program. Mortality risk was calculated 56 days from enrolment. Patients were censored at death, at 56 days, or at last contact if lost to follow-up. The modelling strategy addressed the causal association between HIV multidrug resistance and mortality, excluding factors on the causal pathway (most notably, CD4 cell count, clinical signs of advanced HIV, and poor functional and nutritional status).FindingsOf 1316 patients with HIV enrolled in the STAMP trial at the Malawi site between Oct 26, 2015, and Sept 19, 2017, 786 had taken ART for at least 6 months. 252 (32%) of 786 patients had virological failure (viral load ≥1000 copies per mL). Mean age was 41·5 years (SD 11·4) and 528 (67%) of 786 were women. Of 237 patients with HIV drug resistance results available, 195 (82%) had resistance to lamivudine, 128 (54%) to tenofovir, and 219 (92%) to efavirenz. Resistance to at least two drugs was common (196, 83%), and this was associated with increased mortality (adjusted hazard ratio 1·7, 95% CI 1·2–2·4; p=0·0042).InterpretationInterventions are urgently needed and should target ART clinic, hospital, and post-hospital care, including differentiated care focusing on patients with advanced HIV, rapid viral load testing, and routine access to drug resistance testing. Prompt diagnosis and switching to alternative ART could reduce early mortality among inpatients with HIV.FundingJoint Global Health Trials Scheme of the Medical Research Council, UK Department for International Development, and Wellcome Trust.
Human tool cognition relies on teleology
Authors: Mikołaj Hernik
Journal: Behavioral and Brain Sciences (2020)

Abstract Osiurak and Reynaud's account of human tool cognition misses key element: human capacity for functional representations and teleological inferences. I argue that the teleofunctional approach accounts better for some features of human tool cognition and points to a viable candidate for the cognitive “difference-maker” behind human technological success.
Top Food Category Contributors to Sodium and Potassium Intake — United States, 2015–2016
Authors: Rebecca C. Woodruff, Lixia Zhao, Jaspreet K.C. Ahuja, Cathleen Gillespie, Joseph Goldman, Diane M. Harris, Sandra L. Jackson, Alanna Moshfegh, Donna Rhodes, Rhonda S. Sebastian, Ana Terry, Mary E. Cogswell
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

Most U.S. adults consume too much sodium and not enough potassium (1,2). For apparently healthy U.S. adults aged ≥19 years, guidelines recommend reducing sodium intake that exceeds 2,300 mg/day and consuming at least 3,400 mg/day of potassium for males and at least 2,600 mg/day for females* (1). Reducing population-level sodium intake can reduce blood pressure and prevent cardiovascular diseases, the leading causes of death in the United States (1,3). Adequate potassium intake might offset the hypertensive effects of excessive sodium intake (1). Data from the 2015-2016 What We Eat in America (WWEIA) dietary interview component of the National Health and Nutrition Examination Survey (NHANES)† were analyzed to identify top food categories contributing to sodium and potassium intake for U.S. residents aged ≥1 year. During 2015-2016, 40% of sodium consumed came from the top 10 food categories, which included prepared foods with sodium added (e.g., deli meat sandwiches and pizza). Approximately 43% of potassium consumed was from 10 food categories, which included foods naturally low in sodium (e.g., unflavored milk, fruit, vegetables) and prepared foods. These results can inform efforts to encourage consumption of foods naturally low in sodium, which might have the dual benefit of reducing sodium intake and increasing potassium intake, contributing to cardiovascular disease prevention.
Infections in baricitinib clinical trials for patients with active rheumatoid arthritis
Authors: Kevin L Winthrop, Masayoshi Harigai, Mark C Genovese, Stephen Lindsey, Tsutomu Takeuchi, Roy Fleischmann, John D Bradley, Nicole L Byers, David L Hyslop, Maher Issa, Atsushi Nishikawa, Terence P Rooney, Sarah Witt, Christina L Dickson, Josef S Smolen, Maxime Dougados
Journal: Annals of the Rheumatic Diseases (2020)

Objectives To evaluate the incidence of infection in patients with active rheumatoid arthritis (RA) treated with baricitinib, an oral selective Janus kinase (JAK)1 and JAK2 inhibitor. Methods Infections are summarised from an integrated database (8 phase 3/2/1b clinical trials and 1 long-term extension (LTE)) with data to 1 April 2017. The ‘all-bari-RA’ analysis set included patients who received any baricitinib dose. Placebo comparison was based on six studies with 4 mg and placebo to week 24, including four trials with 2 mg (placebo-controlled set). Dose–response assessment was based on four studies with 2 mg and 4 mg, including LTE data (2–4 mg extended set). Results There were 3492 patients who received baricitinib for 7860 patient-years (PY) of exposure (median 2.6 years, maximum 6.1 years). Treatment-emergent infections were higher for baricitinib versus placebo (exposure-adjusted incidence rate (IR)/100 PY: placebo 75.9, 2 mg 84.0 (p not significant), 4 mg 88.4 (p≤0.001)). The IR of serious infection was similar for baricitinib versus placebo and stable over time (all-bari-RA IR 3.0/100 PY). There were 11 cases of tuberculosis (all-bari-RA IR 0.1/100 PY); all occurred with 4 mg in endemic regions. Herpes zoster (HZ) IR/100 PY was higher for baricitinib versus placebo (placebo 1.0, 2 mg 3.1 (p not significant), 4 mg 4.3 (p≤0.01)); rates remained elevated and stable over time (all-bari-RA 3.3). Opportunistic infections, including multidermatomal HZ, were infrequent in the baricitinib programme (all-bari-RA IR 0.5/100 PY). Conclusions Increased rates of treatment-emergent infections including HZ were observed in patients with RA treated with baricitinib, consistent with baricitinib’s immunomodulatory mode of action.
Needles in a haystack: Extremely rare invasive fungal infections reported in FungiScopeⓇ—Global Registry for Emerging Fungal Infections
Authors: Jon Salmanton-García, Philipp Koehler, Anupma Kindo, Iker Falces-Romero, Julio García-Rodríguez, Zdeněk Ráčil, Sharon C.-A. Chen, Nikolai Klimko, Guillaume Desoubeaux, George R. Thompson, Miguel-Ángel Benítez-Peñuela, José-Yesid Rodríguez, Donald C. Sheppard, Martin Hoenigl, Yohann Le Govic, Hamid Badali, John W. Baddley, Jagdish Chander, Paul R. Ingram, Diana L. Pakstis, Sibylle C. Mellinghoff, Serkan Atıcı, Simone Cesaro, Arunaloke Chakrabarti, Damien Dupont, Gloria M. González, Lóránt Hatvani, Raoul Herbrecht, Galina Klyasova, Cornelia Lass-Flörl, Mihai Mareș, Kathleen Mullane, Donald C. Vinh, Hilmar Wisplinghoff, Michaela Lackner, Oliver A. Cornely, Danila Seidel, Barbara D. Alexander, María Almagro-Molto, Eduardo Álvarez-Duarte, Martha Avilés-Robles, Aleksandra Barać, Vanda Chrenková, Patricia Cornejo-Juárez, Nicole Desbois-Nogard, Mario Fernández-Ruiz, Luis Figueira, Jesús García-Martínez, Sandra Gräber, Barbara Graf, Georg Haerter, Shariq Haider, Pamela Hartman, Melina Heinemann, Aamer Ikram, Frédéric Janvier, Jeffrey D. Jenks, Carol Kauffman, Robert Krause, Me-Linh Luong, Shruti Malik, Vincent Marconi, Rodrigo Martino, Sanjay R. Mehta, Lisa Meintker, Andrea Mocná, Michele I. Morris, Alessandro C. Pasqualotto, Atul Patel, Olaf Penack, Nicolas Pichon, Mathias W. Pletz, Carlos Seas, Uluhan Sili, Monica Slavin, Kenji Uno, Jose A. Vazquez, Thomas Weber, Barbora Weinbergerova, Deniz Yilmaz-Karapinar, Seda Yilmaz-Semerci, Jin Yu
Journal: Journal of Infection (2020)
Survival on the Heart Transplant Waiting List
Authors: Syed Shahyan Bakhtiyar, Elizabeth L. Godfrey, Shayan Ahmed, Harveen Lamba, Jeffrey Morgan, Gabriel Loor, Andrew Civitello, Faisal H. Cheema, Whitson B. Etheridge, John Goss, Abbas Rana
Journal: JAMA Cardiology (2020)

With continuing improvements in medical devices and more than a decade since the 2006 United Network for Organ Sharing (UNOS) allocation policy, it is pertinent to assess survival among patients on the heart transplantation waiting list, especially given the recently approved 2018 UNOS allocation policy.To assess survival outcomes among patients on the heart transplant waiting list during the past 3 decades and to examine the association of ventricular assist devices (VADs) and the 2006 UNOS allocation policy with survival.A retrospective cross-sectional used the UNOS database to perform an analysis of 95 323 candidates wait-listed for heart transplantation between January 1, 1987, and December 29, 2017. Candidates for all types of combined transplants were excluded (n = 2087). Patients were followed up from the time of listing to death, transplantation, or removal from the list due to clinical improvement. Competing-risk, Kaplan-Meier, and multivariable Cox proportional hazards regression analyses were used.The analysis involved an unadjusted and adjusted survival analysis in which the primary outcome was death on the waiting list. Because of changing waiting list preferences and policies during the study period, the intrinsic risk of death for wait-listed candidates was assessed by individually analyzing, comparing, and adjusting for several candidate risk factors.In total, 95 323 candidates (72 915 men [76.5%]; mean [SD] age, 51.9 [12.0] years) were studied. In the setting of changes in listing preferences, 1-year survival on the waiting list increased from 34.1% in 1987-1990 to 67.8% in 2011-2017 (difference in proportions, 0.34%; 95% CI, 0.32%-0.36%; P < .001). The 1-year waiting list survival for candidates with VADs increased from 10.2% in 1996-2000 to 70.0% in 2011-2017 (difference in proportions, 0.60%; 95% CI, 0.58%-0.62%; P < .001). Similarly, in the setting of changing mechanical circulatory support indications, the 1-year waiting list survival for patients without VADs increased from 53.9% in 1996-2000 to 66.5% in 2011-2017 (difference in proportions, 0.13%; 95% CI, 0.12%-0.14%; P < .001). In the decade prior to the 2006 UNOS allocation policy, the 1-year waiting list survival was 51.1%, while in the decade after it was 63.9% (difference in proportions, 0.13%; 95% CI, 0.12%-0.14%; P < .001). In adjusted analysis, each time period after 1987-1990 had a marked decrease in waiting list mortality.This study found temporally associated increases in heart transplant waiting list survival for all patient groups (with or without VADs, UNOS status 1 and status 2 candidates, and candidates with poor functional status).
Survival analysis in treated plasmablastic lymphoma patients: a population‐based study
Authors: Jorge A. Florindez, Juan P. Alderuccio, Isildinha M. Reis, Izidore S. Lossos
Journal: American Journal of Hematology (2020)

Abstract Herein we analyzed survival outcomes in chemotherapy‐treated patients with plasmablastic lymphoma (PBL) diagnosed between 2010 to 2016 (n = 248). Data was acquired from the Surveillance, Epidemiology, and End Results (SEER) 18 registries database (April 2019 release based on November 2018 submission). The majority of patients were male (81.9%) and younger than 60 years (71.0%). Oral and gastrointestinal (GI) sites were the most frequent primary extranodal locations (23% and 19.4%, respectively). Oral primary location was inversely associated with presence of B symptoms and advanced Ann‐Arbor stage. The 3‐year and 5‐year overall survival (OS) rates of treated PBL patients were 54% (95% CI: 46.5%‐60.8%) and 52.8% (95% CI: 45.2%‐59.8%). Three‐year conditional survival for 2‐year and 3‐year survivors were 90.3% and 97.8%, overlapping the survival of a general population matched by age, sex and calendar year. In a multivariable analysis, oral primary location was associated with not only better OS (HR 0.43; 95% CI: 0.21‐0.88, P = .021) but also better lymphoma‐specific survival (LSS) (SHR 0.36; 95% CI: 0.15‐0.86, P = .022); age ≥60 years was associated with shorter LSS (SHR 1.73; 95% CI: 1.02‐2.96, P = .043). Seven registries granted access to HIV status (n = 93) where HIV infection was detected in 52.7% of cases. The HIV status did not affect survival outcomes in unadjusted and adjusted analyses. We identified clinical characteristics associated with survival and showed that treated PBL patients may achieve long‐term survival.
Ibrutinib Therapy in Patients with Relapsed/Refractory Marginal Zone Lymphoma: Analysis By Prior Rituximab Treatment and Baseline Mutations
Authors: Robert Chen, Sven de Vos, Catherine Thieblemont, Peter Martin, Christopher Flowers, Franck Morschhauser, Graham Collins, Shuo Ma, Morton Coleman, Shachar Peles, Stephen D. Smith, Jacqueline C. Barrientos, Alina Smith, Brian Munneke, Shiquan Wu, Leo Cheung, Kevin Kwei, Selda Samakoglu, Israel Arango-Hisijara, Isaiah Dimery, Ariela Noy
Journal: Blood (2017)
Abstract 07: Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma
Authors: Lola Rahib, Mark Shapiro, Jeff Shrager, Bryan Federowics, Conan Kinsey
Journal: Clinical Cancer Research (2020)

Abstract XCELSIOR is an IRB-approved, patient-centric, real-world data and outcomes registry for developing operational and analytic methods in precision oncology. Earlier this year, Kinsey et al. reported on an exceptional response in a heavily pretreated pancreatic adenocarcinoma patient using combined MEK inhibition with autophagy inhibition (Nature Medicine 2019). We sought to understand the utilization of this regimen in clinical practice and analyze safety and outcomes information from patients in XCELSIOR identified as being treated with this combination. Searching the XCELSIOR database, we identified eleven patients for whom this regimen had been considered, four patients at different centers who received this regimen as part of their clinical care for pancreatic adenocarcinoma, and two more patients expected to start treatment soon. As part of their participation in XCELSIOR, these patients shared access to their full medical records, which were collected, processed, and abstracted into a 21 CFR 11 compliant database for analysis. We intend to present demographics, safety, biomarkers, and survival data on these patients and five additional patients treated with this combination at the Huntsman Cancer Center. For late-stage cancer patients, a patient-centric outcomes registry can provide continuous high-quality, real-world data to rapidly identify safety and outcomes information for cancer patients treated in clinical practice with novel and potentially efficacious off-label combinations, and to aggregate that data into a high-quality dataset for further Bayesian analysis. Citation Format: Lola Rahib, Mark Shapiro, Jeff Shrager, Bryan Federowics, Conan Kinsey. Use of a real-world data registry to rapidly generate outcomes data following a case study of a novel treatment combination in pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 07.
Characterization of Cooperating Mutations in Murine Acute Leukemias: Towards Establishing Leukemia Models with Genetic Lesions in Defined Cellular Pathways
Authors: Sarvenaz Taghavi, Rhea Desai, Jenny Chien, Heidi Super, Peter Browett, Purvi M Kakadia, Stefan K. Bohlander
Journal: Blood (2017)
Early and Profound Exhausted Phenotype of Central Memory and Memory Stem T Cells in the Bone Marrow of AML Patients Characterizes and Predicts Relapse after Allo-HSCT
Authors: Maddalena Noviello, Francesco Manfredi, Tommaso Perini, Oliveira Giacomo, Filippo Cortesi, Pantaleo De Simone, Cristina Toffalori, Valentina Gambacorta, Attilio Bondanza, Raffaella Greco, Jacopo Peccatori, Giulia Casorati, Paolo Dellabona, Nicoletta Cieri, Luca Vago, Fabio Ciceri, Chiara Bonini
Journal: Blood (2017)
Author Correction: Novel Hexb-based tools for studying microglia in the CNS
Authors: Takahiro Masuda, Lukas Amann, Roman Sankowski, Ori Staszewski, Maximilian Lenz, Paolo d´Errico, Nicolas Snaidero, Marta Joana Costa Jordão, Chotima Böttcher, Katrin Kierdorf, Steffen Jung, Josef Priller, Thomas Misgeld, Andreas Vlachos, Melanie Meyer-Luehmann, Klaus-Peter Knobeloch, Marco Prinz
Journal: Nature Immunology (2020)