tbuckley/cabot-search huggingface dataset:
Incidence and prevalence of tuberculosis in incarcerated populations: a systematic review and meta-analysis
Authors: Olivia Cords, Leonardo Martinez, Joshua L Warren, Jamieson Michael O'Marr, Katharine S Walter, Ted Cohen, Jimmy Zheng, Albert I Ko, Julio Croda, Jason R Andrews
Journal: The Lancet Public Health (2021)

Prisons are recognised as high-risk environments for tuberculosis, but there has been little systematic investigation of the global and regional incidence and prevalence of tuberculosis, and its determinants, in prisons. We did a systematic review and meta-analysis to assess the incidence and prevalence of tuberculosis in incarcerated populations by geographical region.In this systematic review and meta-analysis, we searched MEDLINE, Embase, Web of Knowledge, and the LILACS electronic database from Jan 1, 1980, to Nov 15, 2020, for cross-sectional and cohort studies reporting the incidence of Mycobacterium tuberculosis infection, incidence of tuberculosis, or prevalence of tuberculosis among incarcerated individuals in all geographical regions. We extracted data from individual studies, and calculated pooled estimates of incidence and prevalence through hierarchical Bayesian meta-regression modelling. We also did subgroup analyses by region. Incidence rate ratios between prisons and the general population were calculated by dividing the incidence of tuberculosis in prisons by WHO estimates of the national population-level incidence.We identified 159 relevant studies; 11 investigated the incidence of M tuberculosis infection (n=16 318), 51 investigated the incidence of tuberculosis (n=1 858 323), and 106 investigated the prevalence of tuberculosis (n=6 727 513) in incarcerated populations. The overall pooled incidence of M tuberculosis infection among prisoners was 15·0 (95% credible interval [CrI] 3·8-41·6) per 100 person-years. The incidence of tuberculosis (per 100 000 person-years) among prisoners was highest in studies from the WHO African (2190 [95% CrI 810-4840] cases) and South-East Asia (1550 [240-5300] cases) regions and in South America (970 [460-1860] cases), and lowest in North America (30 [20-50] cases) and the WHO Eastern Mediterranean region (270 [50-880] cases). The prevalence of tuberculosis was greater than 1000 per 100 000 prisoners in all global regions except for North America and the Western Pacific, and highest in the WHO South-East Asia region (1810 [95% CrI 670-4000] cases per 100 000 prisoners). The incidence rate ratio between prisons and the general population was much higher in South America (26·9; 95% CrI 17·1-40·1) than in other regions, but was nevertheless higher than ten in the WHO African (12·6; 6·2-22·3), Eastern Mediterranean (15·6; 6·5-32·5), and South-East Asia (11·7; 4·1-27·1) regions.Globally, people in prison are at high risk of contracting M tuberculosis infection and developing tuberculosis, with consistent disparities between prisons and the general population across regions. Tuberculosis control programmes should prioritise preventive interventions among incarcerated populations.US National Institutes of Health.
COVID-19 in patients with lung cancers inNew York City
Authors: J. Luo, H. Rizvi, I. R. Preeshagul, J. V. Egger, D. Hoyos, C. Bandlamudi, M. T. A. Donoghue, M. Luksza, B. D. Greenbaum, J. D. Wolchok, M. G. Kris, M. D. Hellmann
Journal: Clinical Cancer Research (2020)

Background: Patients with lung cancers may have distinct vulnerability to severe COVID-19  Understanding thepatient-specific and cancer-specific features that impact severity of COVID-19 may inform optimal cancer careduring this pandemic  A key question is whether PD-1 blockade therapy impacts COVID-19 severity  Methods: We identified consecutive patients with lung cancer and a positive SARS-CoV-2 RT-PCR test seen at asingle cancer center in New York City  We performed detailed manual review of the disease course, medical andoncologic history  COVID-19 severity outcomes were predefined, including need for hospitalization, ICU/intubation/transition to DNI-status, or death  We examined clinical features associated with severity using singleand multivariable analyses  Regarding the impact of PD-1 blockade, we prespecified several bio-plausiblecomparisons of PD-1 exposure  HLA alleles were inferred from NGS and compared to controls with lung cancer andno known COVID-19  Results: We identified 102 patients with lung cancers and a SARS-CoV-2 positive swab between March 12, 2020and May 6, 2020  Patients were followed until May 11, 2020  COVID-19 was severe in patients with lung cancers(62% hospitalized, 25% died), but accounted for only 11% of deaths among patients with lung cancer during thepandemic  Determinants of COVID-19 severity were largely patient specific, including smoking status and chronicobstructivesystemic therapies, did not impact severity  Likelihood of severe COVID-19 was generally similar across HLA class Isupertypes  We found no significant differences in the impact of PD-1 blockade on COVID-19 severity  Modestnumerical increases in severity of COVID-19 associated with prior PD-1 blockade were diminished (Odds ratio 0 86-1 01) after adjusting for expected imbalances in prior smoking history  Most patients recovered from COVID-19, including 25% of patients initially requiring intubation  Conclusion: COVID-19 is associated with a high burden of severity in patients with lung cancers  Patient-specificfeatures, rather than cancer-specific features or treatments, were the greatest determinants of severity  In particular, PD-1 blockade did not appear to impact severity of COVID-19 in patients with lung cancers
Combination immunotherapy using G-CSF and oncolytic virotherapy reduces tumor growth in osteosarcoma
Authors: Alvaro Morales-Molina, Stefano Gambera, Angela Leo, Javier García-Castro
Journal: Journal for ImmunoTherapy of Cancer (2021)

Background Osteosarcoma is the most common malignant solid tumor that affects bones, however, survival rates of patients with relapsed osteosarcoma have not improved in the last 30 years. Oncolytic virotherapy, which uses viruses designed to selectively replicate in cancer cells, has emerged as a promising treatment for solid tumors. Our group uses mesenchymal stem cells (MSCs) to transport oncolytic adenoviruses (OAds) to the tumor site, a therapeutic strategy called Celyvir. This treatment has been already applied in human patients, canine patients and different mouse models. In parallel, previous results have probed that administration of granulocyte-colony stimulating factor (G-CSF) increased immune infiltration in tumors. We then hypothesized that the mobilization of immune cells by G-CSF may increase the antitumor efficacy of Celyvir treatment by increasing the immune infiltration into the tumors. Methods In this study, we use a murine version of Celyvir consisting in murine MSCs carrying the murine OAd dlE102—here called OAd-MSCs—in an immunocompetent model of osteosarcoma. We tested the antitumoral efficacy of the combination of OAd-MSCs plus G-CSF. Results Our results show that treatment with OAd-MSCs or the union of OAd-MSCs with G-CSF (Combination) significantly reduced tumor growth of osteosarcoma in vivo. Moreover, treated tumors presented higher tumor infiltration of immune cells—especially tumor-infiltrating lymphocytes—and reduced T cell exhaustion, which seems to be enhanced in tumors treated with the Combination. The comparison of our results to those obtained from a cohort of pediatric osteosarcoma patients showed that the virotherapy induces immunological changes similar to those observed in patients with good prognosis. Conclusions The results open the possibility of using cellular virotherapy for the treatment of bone cancers. Indeed, its combination with G-CSF may be considered for the improvement of the therapy.
Development of a Histopathology Informatics Pipeline for Classification and Prediction of Clinical Outcomes in Subtypes of Renal Cell Carcinoma
Authors: Eliana Marostica, Rebecca Barber, Thomas Denize, Isaac S. Kohane, Sabina Signoretti, Jeffrey A. Golden, Kun-Hsing Yu
Journal: Clinical Cancer Research (2021)

Abstract Purpose: Histopathology evaluation is the gold standard for diagnosing clear cell (ccRCC), papillary, and chromophobe renal cell carcinoma (RCC). However, interrater variability has been reported, and the whole-slide histopathology images likely contain underutilized biological signals predictive of genomic profiles. Experimental Design: To address this knowledge gap, we obtained whole-slide histopathology images and demographic, genomic, and clinical data from The Cancer Genome Atlas, the Clinical Proteomic Tumor Analysis Consortium, and Brigham and Women's Hospital (Boston, MA) to develop computational methods for integrating data analyses. Leveraging these large and diverse datasets, we developed fully automated convolutional neural networks to diagnose renal cancers and connect quantitative pathology patterns with patients' genomic profiles and prognoses. Results: Our deep convolutional neural networks successfully detected malignancy (AUC in the independent validation cohort: 0.964–0.985), diagnosed RCC histologic subtypes (independent validation AUCs of the best models: 0.953–0.993), and predicted stage I ccRCC patients' survival outcomes (log-rank test P = 0.02). Our machine learning approaches further identified histopathology image features indicative of copy-number alterations (AUC &amp;gt; 0.7 in multiple genes in patients with ccRCC) and tumor mutation burden. Conclusions: Our results suggest that convolutional neural networks can extract histologic signals predictive of patients' diagnoses, prognoses, and genomic variations of clinical importance. Our approaches can systematically identify previously unknown relations among diverse data modalities.
A Comprehensive, Multisystemic Early Childhood Program and Obesity at Age 37 Years
Authors: Arthur J. Reynolds, Lauren Eales, Suh-Ruu Ou, Christina F. Mondi, Alison Giovanelli
Journal: JAMA Pediatrics (2021)

A Comprehensive, Multisystemic Early Childhood Program and Obesity at Age 37 YearsGiven the scarcity of effective obesity prevention programs, there is a pressing need for innovative and scalable models that begin early in life and break risk cycles.Promising evidence exists that multisystemic preschool programs can promote healthy body mass and positive behaviors, 1,2 but to our knowledge, no existing or large-scale programs have assessed long-term links between such programs and health outcomes in midlife.We assessed the association of participation in an evidence-based, multicomponent Child-Parent Center (CPC) preschool program in Chicago, Illinois, 3 with body mass and obesity at age 37 years for a sample of predominately Black individuals who grew up in poverty.
EUS-guided percutaneous endoscopic jejunostomy in cases not suitable for conventional gastrostomy: after bariatric (SADI-S) and cancer surgery
Authors: Sandra Maisterra, Julio G. Velásquez-Rodríguez, Sandra Llauradó-Paco, Ana Casajoana-Badia, Humberto Aranda, Nuria Vilarrasa-García, Joan B. Gornals
Journal: Endoscopy (2021)

In a few cases, endoscopic ultrasound (EUS)-guided percutaneous endoscopic gastrostomy (PEG) has been reported as a safe alternative in cases that are not suitable for conventional PEG [1] [2] [3]. In the present case series, EUS-guided percutaneous endoscopic jejunostomy (PEJ) is offered as another option in scenarios with excessive distance from the stomach.
Differences in Total and After-hours Electronic Health Record Time Across Ambulatory Specialties
Authors: Lisa S. Rotenstein, A. Jay Holmgren, N. Lance Downing, David W. Bates
Journal: JAMA Internal Medicine (2021)

psychotropic drugs at the onset of the COVID-19 pandemic that persisted through September 2020.Although absolute increases in prescribing were small, they were disproportionate to expected secular prescribing trends from April 2018 to February 2020, and they were distinct from observed prescribing changes for other drugs during the pandemic.This study examined the prescribing patterns of multiple classes of psychotropic drugs as well as drugs for which prescribing patterns were not expected to change during the pandemic.The results thus expand on those of a study in the United Kingdom, which reported increased prescribing of antipsychotic medications among patients with dementia during the pandemic. 3Our study is limited by a lack of data on prescribing indications.Although psychotropic medications may have been prescribed for residents who were dying of COVID-19, drugs such as antidepressants and trazodone are not typically used for acute palliative management.Therefore, it is likely that prescribing increases were also associated with the consequences of prolonged social isolation produced by infection prevention and control measures. 4,5Furthermore, clinicians may have been less likely to prioritize favorable nonpharmacological management for common issues, such as responsive behaviors, because of diminished resources, including lack of staffing.Overall, the study's findings highlight the importance of balancing infection prevention and control measures in nursing homes with the well-being of residents during the COVID-19 pandemic.Further studies are warranted to characterize additional factors that may be associated with drug prescribing during the pandemic, including prescriber and nursing home characteristics.
P88.03 Asymptomatic COVID-19 in a ROS1 positive Non Small Cell Lung Cancer.
Authors: A. Datta, P. Mohapatra, B. Mishra, S. Mitra, S. Padmaja, M. Panigrahi, S. Bhuniya, S. Bal, S. Goud, S. Ghosh, S. Panigrahi, G. Durgeshwar, V.R. Acharyulu
Journal: Journal of Thoracic Oncology (2021)
P84.01 The ARIA Study: Activity of Next-Generation ALK TKIs Based on ALK Resistance Mutations Detected by Liquid Biopsy in ALK Positive NSCLC Patients.
Authors: L. Mezquita, A. Swalduz, E. Auclin, M. Carter, C. Steendam, M. Aldea, M. Scheffler, J. Corral, S. Viteri, E. Segui, A. Barba, E. Dubbink, D. Planchard, D. Vasseur, R. Reyes, C. Caramella, G. Recondo, P. Saintigny, F. Blackhall, A. Dingemans, B. Besse
Journal: Journal of Thoracic Oncology (2021)
Adherence to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist in articles published in EAACI Journals: A bibliographic study
Authors: Elena Wiehn, Cristian Ricci, Alberto Alvarez‐Perea, Michael R. Perkin, Christina J. Jones, Cezmi Akdis, Jean Bousquet, Philippe Eigenmann, Clive Grattan, Christian J. Apfelbacher, Jon Genuneit
Journal: Allergy (2021)

Research data derived from observational studies are accumulating quickly in the field of allergy and immunology and a large amount of observational studies are published every year. The aim of the present study was to evaluate the adherence to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) checklist by papers published in the three European Academy of Allergy and Clinical Immunology journals, during the period 2009-2018. To this end, we conducted a bibliographic study of up to eight randomly selected papers per year per Journal. Our literature search resulted in 223 papers. Amongst those, 80, 80 and 63 records were from Paediatric Allergy and Immunology, Allergy and Clinical and Translational Allergy, respectively; the latter was published only from 2011 on. Prospective, case control and cross-sectional designs were described in 88, 43 and 92 papers, respectively. Full reporting of all STROBE items was present in 47.4%, 45.6% and 41.2% for the cohort, cross-sectional and case-control studies, respectively. Generally, no time trend in adherence of reporting STROBE items was observed, apart from reporting funding, which increased from 60% in 2009/2010 to more than 90% in 2018. We identified a cluster of STROBE items with low proportions of full reporting constituted by the items on reporting study design in the title and methods, variables types along with their measurement/assessment, bias and confounding, study size, and grouping of variables. It appears that the STROBE checklist is a suitable tool in observational allergy epidemiology. However, adherence to the STROBE checklist appeared suboptimal.
P43.02 A Multiplex Plasma Protein Panel for Detection of Lung Cancer in Ever Smokers Not Currently Eligible for Screening
Authors: S. Lam, R. Myers, S. Atkar-Khattra, J. Yee, K. Grant, A. Mcguire, A. Lee, B. Melosky, C. Ho, A. Dybuncio, M. Tammemagi
Journal: Journal of Thoracic Oncology (2021)
Research Priorities for Patients with Heart Failure and Central Sleep Apnea. An Official American Thoracic Society Research Statement
Authors: Jeremy E. Orr, Indu Ayappa, Danny J. Eckert, Jack L. Feldman, Chandra L. Jackson, Shahrokh Javaheri, Rami N. Khayat, Jennifer L. Martin, Reena Mehra, Matthew T. Naughton, Winfried J. Randerath, Scott A. Sands, Virend K. Somers, M. Safwan Badr
Journal: American Journal of Respiratory and Critical Care Medicine (2021)

Background: Central sleep apnea (CSA) is common among patients with heart failure and has been strongly linked to adverse outcomes. However, progress toward improving outcomes for such patients has been limited. The purpose of this official statement from the American Thoracic Society is to identify key areas to prioritize for future research regarding CSA in heart failure.Methods: An international multidisciplinary group with expertise in sleep medicine, pulmonary medicine, heart failure, clinical research, and health outcomes was convened. The group met at the American Thoracic Society 2019 International Conference to determine research priority areas. A statement summarizing the findings of the group was subsequently authored using input from all members.Results: The workgroup identified 11 specific research priorities in several key areas: 1) control of breathing and pathophysiology leading to CSA, 2) variability across individuals and over time, 3) techniques to examine CSA pathogenesis and outcomes, 4) impact of device and pharmacological treatment, and 5) implementing CSA treatment for all individualsConclusions: Advancing care for patients with CSA in the context of heart failure will require progress in the arenas of translational (basic through clinical), epidemiological, and patient-centered outcome research. Given the increasing prevalence of heart failure and its associated substantial burden to individuals, society, and the healthcare system, targeted research to improve knowledge of CSA pathogenesis and treatment is a priority.
HSR21-064: The Effectiveness of Psychological Intervention on Reducing Distress in Patients With Prostate Cancer: A Literature Meta-Analysis
Authors: Rhea Mundle, Evans Afenya, Neeraj Agarwal
Journal: Journal of the National Comprehensive Cancer Network (2021)

"HSR21-064: The Effectiveness of Psychological Intervention on Reducing Distress in Patients With Prostate Cancer: A Literature Meta-Analysis" published on 17 Mar 2021 by National Comprehensive Cancer Network.
OA02.06 PSM Analysis Results from REFRACT: A Multi-Center Cohort Study Investigating the Treatment Patterns in EGFR-Mutant Unresectable LA- NSCLC
Authors: N. Bi, K. Xu, H. Ge, M. Chen, M. E, L. Zhang, J. Cao, X. Zhang, X. Ding, B. Xia, L. Zhao, L. Han, J. Li, C. Hu, L. Wang
Journal: Journal of Thoracic Oncology (2021)
GMC welcomes proposed reforms to simplify fitness to practise cases
Authors: Abi Rimmer
Journal: BMJ (2021)

The General Medical Council (GMC) has welcomed government recommendations that would allow it to deliver faster decisions about complaints against doctors and to better monitor medical education.

Charlie Massey, GMC chief executive, said that the consultation provided a “once-in-a-generation opportunity to deliver real change,” since the legislation underpinning the GMC had not been changed for 40 years.

The consultation,1 Regulating Healthcare Professionals, Protecting the Public , was launched by the Department of Health and Social Care on 24 March and proposes a new legislative framework for regulating healthcare professionals.

Among the proposals set out in the 12 week consultation is the introduction of …
Evolution of outcomes for patients hospitalised during the first 9 months of the SARS-CoV-2 pandemic in France: A retrospective national surveillance data analysis
Authors: Noémie Lefrancq, Juliette Paireau, Nathanaël Hozé, Noémie Courtejoie, Yazdan Yazdanpanah, Lila Bouadma, Pierre-Yves Boëlle, Fanny Chereau, Henrik Salje, Simon Cauchemez
Journal: The Lancet Regional Health - Europe (2021)

As SARS-CoV-2 continues to spread, a thorough characterisation of healthcare needs and patient outcomes, and how they have changed over time, is essential to inform planning.We developed a probabilistic framework to analyse detailed patient trajectories from 198,846 hospitalisations in France during the first nine months of the pandemic. Our model accounts for the varying age- and sex- distribution of patients, and explore changes in outcome probabilities as well as length of stay.We found that there were marked changes in the age and sex of hospitalisations over the study period. In particular, the proportion of hospitalised individuals that were >80y varied between 27% and 48% over the course of the epidemic, and was lowest during the inter-peak period. The probability of hospitalised patients entering ICU dropped from 0·25 (0·24-0·26) to 0·13 (0·12-0·14) over the four first months as case numbers fell, before rising to 0·19 (0·19-0·20) during the second wave. The probability of death followed a similar trajectory, falling from 0·25 (0·24-0·26) to 0·10 (0·09-0·11) after the first wave before increasing again during the second wave to 0·19 (0·18-0·19). Overall, we find both the probability of death and the probability of entering ICU were significantly correlated with COVID-19 ICU occupancy.There are large scale trends in patients outcomes by age, sex and over time. These need to be considered in ongoing healthcare planning efforts.INCEPTION.
Circulating blood metabolite trajectories and risk of rheumatoid arthritis among military personnel in the Department of Defense Biorepository
Authors: Karen H Costenbader, Michael DiIorio, Su H Chu, Jing Cui, Jeffrey A Sparks, Bing Lu, LauraKay Moss, Lindsay Kelmenson, Marie Feser, Jess Edison, Clary Clish, Jessica Lasky-Su, Kevin D Deane, Elizabeth W Karlson
Journal: Annals of the Rheumatic Diseases (2021)

<h3>Objectives</h3> We sought to identify metabolic changes potentially related to rheumatoid arthritis (RA) pathogenesis occurring in the blood prior to its diagnosis. <h3>Methods</h3> In a US military biorepository, serum samples collected at two timepoints prior to a diagnosis of RA were identified. These were matched to controls who did not develop RA by subject age, race and time between sample collections and RA diagnosis time to stored serum samples. Relative abundances of 380 metabolites were measured using liquid chromatography–tandem mass spectrometry. We determined whether pre-RA case versus control status predicted metabolite concentration differences and differences over time (trajectories) using linear mixed models, assessing for interactions between time, pre-RA status and metabolite concentrations. We separately examined pre-RA and pre-seropositive RA cases versus matched controls and adjusted for smoking. Multiple comparison adjustment set the false discovery rate to 0.05. <h3>Results</h3> 291 pre-RA cases (80.8% pre seropositive RA) were matched to 292 controls, all with two serum samples (2.7±1.6 years; 1.0±0.9 years before RA/matched date). 52.0% were women; 52.8% were White, 26.8% Black and 20.4% other race. Mean age was 31.2 (±8.1) years at earliest blood draw. Fourteen metabolites had statistically significant trajectory differences among pre-RA subjects versus controls, including sex steroids, amino acid/lipid metabolism and xenobiotics. Results were similar when limited to pre seropositive RA and after adjusting for smoking. <h3>Conclusions</h3> In this military case–control study, metabolite concentration trajectory differences in pre-RA cases versus controls implicated steroidogenesis, lipid/amino acid metabolism and xenobiotics in RA pathogenesis. Metabolites may have potential as biomarkers and/or therapeutic targets preceding RA diagnosis.