tbuckley/cabot-search huggingface dataset:
Pharmacologic Interventions for Breathlessness in Patients With Advanced Cancer
Authors: Josephine L. Feliciano, Julie M. Waldfogel, Ritu Sharma, Allen Zhang, Arjun Gupta, Ramy Sedhom, Jeff Day, Eric B. Bass, Sydney M. Dy
Journal: JAMA Network Open (2021)

Improved survival in patients with advanced cancer has increased the need for better understanding of how to manage common symptoms that they may experience, such as breathlessness.To assess the benefits and harms associated with pharmacologic interventions for breathlessness in adults with advanced cancer.PubMed, Embase, CINAHL, Web of Science, and the Cochrane Central Register of Controlled Trials were searched for studies published from database inception through May 31, 2020, using predefined eligibility criteria within a PICOTS (population, intervention, comparator, outcome, timing, setting) format.Randomized clinical trials (RCTs), non-RCTs, and observational studies with a comparison group that evaluated benefits and/or harms and cohort studies that reported harms were selected.Two reviewers independently screened studies for eligibility, serially abstracted data, independently assessed risk of bias, and graded strength of evidence (SOE).Benefits and harms of pharmacologic interventions were compared, focusing on breathlessness, anxiety, exercise capacity, and health-related quality of life. When possible, meta-analyses were conducted and standardized mean differences (SMDs) calculated.In this systematic review and meta-analysis, a total of 7729 unique citations were identified, of which 19 studies (17 RCTs and 2 retrospective studies) that included a total of 1424 patients assessed the benefits of medications for management of breathlessness in advanced cancer or reported harms. The most commonly reported type of cancer was lung cancer. Opioids were not associated with more effectiveness than placebo for improving breathlessness (SMD, -0.14; 95% CI, -0.47 to 0.18) or exercise capacity ( SMD, 0.06; 95% CI, -0.43 to 0.55) (SOE, moderate); most studies examined exertional breathlessness. Specific dose and/or route of administration of opioids did not differ in effectiveness for breathlessness (SMD, 0.15; 95% CI, -0.22 to 0.52) (SOE, low). Anxiolytics were not associated with more effectiveness than placebo for breathlessness or anxiety (reported mean between-group difference, -0.52; 95% CI, -1.045 to 0.005) (SOE, low). Evidence for other pharmacologic interventions was limited. Pharmacologic interventions demonstrated some harms compared with usual care, but dropout attributable to adverse events was minimal in these short-term studies (range 3.2%-16%).Evidence did not support the association of opioids or other pharmacologic interventions with improved breathlessness. Given that studies had many limitations, pharmacologic interventions should be considered in selected patients but need to be considered in the context of potential harms and evidence of an association of nonpharmacologic interventions with improved breathlessness.
Visualizing a joint future of neuroscience and neuromorphic engineering
Authors: Friedemann Zenke, Sander M. Bohté, Claudia Clopath, Iulia M. Comşa, Julian Göltz, Wolfgang Maass, Timothée Masquelier, Richard Naud, Emre O. Neftci, Mihai A. Petrovici, Franz Scherr, Dan F.M. Goodman
Journal: Neuron (2021)
CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues
Authors: Pawel F. Przytycki, Katherine S. Pollard
Journal: Genome biology (2021)

Abstract Single-cell and bulk genomics assays have complementary strengths and weaknesses, and alone neither strategy can fully capture regulatory elements across the diversity of cells in complex tissues. We present CellWalker, a method that integrates single-cell open chromatin (scATAC-seq) data with gene expression (RNA-seq) and other data types using a network model that simultaneously improves cell labeling in noisy scATAC-seq and annotates cell type-specific regulatory elements in bulk data. We demonstrate CellWalker’s robustness to sparse annotations and noise using simulations and combined RNA-seq and ATAC-seq in individual cells. We then apply CellWalker to the developing brain. We identify cells transitioning between transcriptional states, resolve regulatory elements to cell types, and observe that autism and other neurological traits can be mapped to specific cell types through their regulatory elements.
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Authors: Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Journal: Genome biology (2021)

Abstract Background To investigate the mechanisms driving regulatory evolution across tissues, we experimentally mapped promoters, enhancers, and gene expression in the liver, brain, muscle, and testis from ten diverse mammals. Results The regulatory landscape around genes included both tissue-shared and tissue-specific regulatory regions, where tissue-specific promoters and enhancers evolved most rapidly. Genomic regions switching between promoters and enhancers were more common across species, and less common across tissues within a single species. Long Interspersed Nuclear Elements (LINEs) played recurrent evolutionary roles: LINE L1s were associated with tissue-specific regulatory regions, whereas more ancient LINE L2s were associated with tissue-shared regulatory regions and with those switching between promoter and enhancer signatures across species. Conclusions Our analyses of the tissue-specificity and evolutionary stability among promoters and enhancers reveal how specific LINE families have helped shape the dynamic mammalian regulome.
Hidradenitis Suppurativa in the Pediatric Population
Authors: Carmen Liy-Wong, Mary Kim, A. Yasmine Kirkorian, Lawrence F. Eichenfield, Lucia Z. Diaz, Amir Horev, Megha Tollefson, Teresa Oranges, Roderic Philips, Yvonne E. Chiu, Ghazal Ghafari, Justin D. Arnold, Jessica Sprague, Henry Nguyen, Stephanie Wan, Eshetu G. Atenafu, Elena Pope, Jill Hamilton, Haley B. Naik, Irene Lara-Corrales
Journal: JAMA Dermatology (2021)

<h3>Importance</h3> Hidradenitis suppurativa (HS) in pediatric patients has been understudied. Increased awareness and recognition of HS prevalence in children demand efforts to better understand this condition. <h3>Objective</h3> To describe the demographics, clinical features, treatment, associated comorbidities, and outcomes in a large cohort of pediatric patients with HS. <h3>Design, Setting, and Participants</h3> International, multicenter, retrospective medical record review of pediatric patients (aged 1-18 years) with a clinical diagnosis of HS carried out in 10 dermatology clinics across the US, Canada, Israel, Australia, and Italy from January 1996 to January 2017. <h3>Main Outcomes and Measures</h3> Patient demographics, clinical features, severity, associated comorbidities, and treatments in pediatric patients with HS. <h3>Results</h3> This cross-sectional study included 481 patients diagnosed with HS. Overall, 386 (80%) were girls. The mean (SD) age of disease onset was 12.5 (2.9) years, and the mean (SD) age at diagnosis was 14.4 (3.5) years. Family history of HS was present in 111 of 271 (41%) patients. First signs/symptoms reported at disease onset were cyst/abscess in 229 of 481 (48%), pain/tenderness in 118 of 481 (25%), and papules/pustules in 117 of 481 (24%). At initial dermatologic assessment, 233 of 481 (48%) patients already had evidence of skin scarring. Disease severity (Hurley staging) was documented in 288 of 481 (60%) patients (47% stage 1, 45% stage 2 and 8% stage 3). Comorbid conditions were reported in 406 of 481 (85%) patients, the most common being obesity (263/406 [65%]) and acne vulgaris (118/406 [29%]). Complications occurred in 378 of 481 (79%) patients, the most common of which were scars or contractures (301/378 [80%]). <h3>Conclusions and Relevance</h3> The findings of this study indicate that there is a gap in recognizing and diagnosing pediatric HS. Pediatric patients with HS are likely to present with other comorbidities. Prospective observational and interventional studies are needed to better understand clinical course and optimal treatments for pediatric HS.
Humoral signatures of protective and pathological SARS-CoV-2 infection in children
Authors: Yannic C. Bartsch, Chuangqi Wang, Tomer Zohar, Stephanie Fischinger, Caroline Atyeo, John S. Burke, Jaewon Kang, Andrea G. Edlow, Alessio Fasano, Lindsey R. Baden, Eric J. Nilles, Ann E. Woolley, Elizabeth W. Karlson, Alex R. Hopke, Daniel Irimia, Eric S. Fischer, Edward T. Ryan, Richelle C. Charles, Boris D. Julg, Douglas A. Lauffenburger, Lael M. Yonker, Galit Alter
Journal: Nature Medicine (2021)
Reply to Michael Froehner, Rainer Koch, and Markus Graefen’s Letter to the Editor re: Nicolas Mottet, Roderick C.N. van den Bergh, Erik Briers, et al. EAU-EANM-ESTRO-ESUR-SIOG Guidelines on Prostate Cancer—2020 Update. Part 1: Screening, Diagnosis, and Local Treatment with Curative Intent. Eur Urol 2021;79:243–62. Comorbidity Measurement in Patients with Prostate Cancer
Authors: Roderick C.N. van den Bergh, Shane O’Hanlon, Philip Cornford, Nicolas Mottet
Journal: European Urology (2021)
Maternal asthma is associated with reduced lung function in male infants in a combined analysis of the BLT and BILD cohorts
Authors: Patricia de Gouveia Belinelo, Adam M Collison, Vanessa E Murphy, Paul D Robinson, Kathryn Jesson, Kate Hardaker, Ediane de Queiroz Andrade, Christopher Oldmeadow, Gabriela Martins Costa Gomes, Peter D Sly, Jakob Usemann, Rhea Appenzeller, Olga Gorlanova, Oliver Fuchs, Philipp Latzin, Peter G Gibson, Urs Frey, Joerg Mattes
Journal: Thorax (2021)

Asthma in pregnancy is associated with respiratory diseases in the offspring.To investigate if maternal asthma is associated with lung function in early life.Data on lung function measured at 5-6 weeks of age were combined from two large birth cohorts: the Bern Infant Lung Development (BILD) and the Australian Breathing for Life Trial (BLT) birth cohorts conducted at three study sites (Bern, Switzerland; Newcastle and Sydney, Australia). The main outcome variable was time to reach peak tidal expiratory flow as a percentage of total expiratory time(tPTEF:tE%). Bayesian linear hierarchical regression analyses controlling for study site as random effect were performed to estimate the effect of maternal asthma on the main outcome, adjusting for sex, birth order, breast feeding, weight gain and gestational age. In separate adjusted Bayesian models an interaction between maternal asthma and sex was investigated by including an interaction term.All 406 BLT infants were born to mothers with asthma in pregnancy, while 193 of the 213 (91%) BILD infants were born to mothers without asthma. A significant interaction between maternal asthma and male sex was negatively associated with tPTEF:tE% (intercept 37.5; estimate: -3.5; 95% credible interval -6.8 to -0.1). Comparing the model posterior probabilities provided decisive evidence in favour of an interaction between maternal asthma and male sex (Bayes factor 33.5).Maternal asthma is associated with lower lung function in male babies, which may have lifelong implications on their lung function trajectories and future risk of wheezing and asthma.
Artificial intelligence in EUS for autoimmune pancreatitis: bias and real life
Authors: Matteo Tacelli, Piera Zaccari, Gabriele Capurso, Paolo Giorgio Arcidiacono
Journal: Gut (2021)

The diagnosis of autoimmune pancreatitis (AIP) is often challenging and distinguishing it from chronic pancreatitis or pancreatic cancer (PC) could be very difficult. In particular, AIP can present at CT scan, MRI or endoscopic ultrasound (EUS) as a focal mass, sometimes with no other specific peculiarities. Furthermore, current international guidelines1 2 consider EUS only as a way to obtain cyto-histological specimens to exclude malignancy, regardless to its diagnostic capacity based on morphologic aspects.

For these reasons, we read with great interest the paper by Marya et al 3 about the possible role of a new EUS-convolutional neural network (EUS-CNN) model for the diagnosis of AIP. In this model, videos and pictures of EUS, accurately preselected by the endosonographers, were evaluated …
Paracardial fat remodeling affects systemic metabolism through alcohol dehydrogenase 1
Authors: Jennifer M. Petrosino, Jacob Z. Longenecker, Srinivasagan Ramkumar, Xianyao Xu, Lisa E. Dorn, Anna Bratasz, Lianbo Yu, Santosh Maurya, Vladimir Tolstikov, Valerie Bussberg, Paul M.L. Janssen, Muthu Periasamy, Michael A. Kiebish, Gregg Duester, Johannes von Lintig, Ouliana Ziouzenkova, Federica Accornero
Journal: Journal of Clinical Investigation (2021)

The relationship between adiposity and metabolic health is well established. However, very little is known about the fat depot, known as paracardial fat (pCF), located superior to and surrounding the heart. Here, we show that pCF remodels with aging and a high-fat diet and that the size and function of this depot are controlled by alcohol dehydrogenase 1 (ADH1), an enzyme that oxidizes retinol into retinaldehyde. Elderly individuals and individuals with obesity have low ADH1 expression in pCF, and in mice, genetic ablation of Adh1 is sufficient to drive pCF accumulation, dysfunction, and global impairments in metabolic flexibility. Metabolomics analysis revealed that pCF controlled the levels of circulating metabolites affecting fatty acid biosynthesis. Also, surgical removal of the pCF depot was sufficient to rescue the impairments in cardiometabolic flexibility and fitness observed in Adh1-deficient mice. Furthermore, treatment with retinaldehyde prevented pCF remodeling in these animals. Mechanistically, we found that the ADH1/retinaldehyde pathway works by driving PGC-1α nuclear translocation and promoting mitochondrial fusion and biogenesis in the pCF depot. Together, these data demonstrate that pCF is a critical regulator of cardiometabolic fitness and that retinaldehyde and its generating enzyme ADH1 act as critical regulators of adipocyte remodeling in the pCF depot.
The Importance of Body Mass Index Assessment and Surveillance in Schools
Authors: Anisha I. Patel, Emma V. Sanchez-Vaznaugh, Gail Woodward-Lopez
Journal: JAMA Pediatrics (2021)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Pediatrics HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Pediatrics journal
Day-to-day variability in sleep parameters and depression risk: a prospective cohort study of training physicians
Authors: Yu Fang, Daniel B. Forger, Elena Frank, Srijan Sen, Cathy Goldstein
Journal: npj Digital Medicine (2021)

Abstract While 24-h total sleep time (TST) is established as a critical driver of major depression, the relationships between sleep timing and regularity and mental health remain poorly characterized because most studies have relied on either self-report assessments or traditional objective sleep measurements restricted to cross-sectional time frames and small cohorts. To address this gap, we assessed sleep with a wearable device, daily mood with a smartphone application and depression through the 9-item Patient Health Questionnaire (PHQ-9) over the demanding first year of physician training (internship). In 2115 interns, reduced TST ( b = −0.11, p &lt; 0.001), later bedtime ( b = 0.068, p = 0.015), along with increased variability in TST ( b = 0.4, p = 0.0012) and in wake time ( b = 0.081, p = 0.005) were associated with more depressive symptoms. Overall, the aggregated impact of sleep variability parameters and of mean sleep parameters on PHQ-9 were similar in magnitude (both r 2 = 0.01). Within individuals, increased TST ( b = 0.06, p &lt; 0.001), later wake time ( b = 0.09, p &lt; 0.001), earlier bedtime ( b = − 0.07, p &lt; 0.001), as well as lower day-to-day shifts in TST ( b = −0.011, p &lt; 0.001) and in wake time ( b = −0.004, p &lt; 0.001) were associated with improved next-day mood. Variability in sleep parameters substantially impacted mood and depression, similar in magnitude to the mean levels of sleep parameters. Interventions that target sleep consistency, along with sleep duration, hold promise to improve mental health.
Follow-up Survey of US Adult Reports of Mental Health, Substance Use, and Suicidal Ideation During the COVID-19 Pandemic, September 2020
Authors: Mark É. Czeisler, Rashon I. Lane, Joshua F. Wiley, Charles A. Czeisler, Mark E. Howard, Shantha M. W. Rajaratnam
Journal: JAMA Network Open (2021)

This survey study compared patterns of mental health concerns, substance use, and suicidal ideation during June and September 2020 of the COVID-19 pandemic and examined at-risk demographic groups.
Abstract SP112: Spatial variance signatures/Intra-tumor zonation in TNBC
Authors: M Park, C Martínez Ramirez, Y Yang, A Blanchet-Cohen, H Kuasne, A Fortier, J Ragoussis, P Savage, A Omeroglou, S Meterissian, S Costantino, C Kleinman
Journal: Cancer Research (2021)

Abstract It is increasingly clear that triple negative breast cancer (TNBC) is a heterogeneous disease with variable clinical presentation, histological features and response to therapy. While these differences have been partially explained by inter- and intra-tumoral heterogeneity, spatial heterogeneity represented by the tumor architecture plays a critical role in clonal evolution and displays a landscape for different compartment-specific processes and cell-to-cell specific interactions. To better understand the impact of spatial heterogeneity on gene-expression-defined cell populations, we have coupled single-cell RNA sequencing with multiplex immunofluorescence (IF). Multiplex immunofluorescence using specific markers for each cell cluster, integrated with computational image analyses and neighborhood maps, has revealed spatial zonation of single cell subpopulations. Zonation of single cell populations was coupled to hypoxia and overlayed distinct metabolic tumor zones and defined areas of differential stress and cell plasticity that give rise to tumor cells with enhanced fitness and aggressivity. Citation Format: M Park, C Martínez Ramirez, Y Yang, A Blanchet-Cohen, H Kuasne, A Fortier, J Ragoussis, P Savage, A Omeroglou, S Meterissian, S Costantino, C Kleinman. Spatial variance signatures/Intra-tumor zonation in TNBC [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP112.
Covid-19 vaccine hesitancy among ethnic minority groups
Authors: Mohammad S Razai, Tasnime Osama, Douglas G J McKechnie, Azeem Majeed
Journal: BMJ (2021)

With mass covid-19 vaccination efforts under way in many countries, including the UK, we need to understand and redress the disparities in its uptake.Data to 14 February 2021 show that over 90% of adults in Britain have received or would be likely to accept the covid-19 vaccine if offered. 1 However, surveys have indicated much greater vaccine hesitancy among people from some ethnic minorities. 2 -4 In a UK survey in December 2020, vaccine hesitancy was highest among black (odds ratio 12.96, 95% confidence interval 7.34 to 22.89), Bangladeshi, and Pakistani (both 2.31, 1.55 to 3.44) populations compared with people from a white ethnic background. 5en more worryingly, data up to 15 January 2021 show substantially lower rates of covid-19 vaccinations among over 80s in ethnic minority (white people 42.5%, black people 20.5%) and deprived communities (least deprived 44.7%, most deprived 37.9%) in England. 6Similarly, data from an NHS trust show lower covid-19 vaccination rates among ethnic minority healthcare workers (70.9% in white workers v 58.5% in South Asian and 36.8% in black workers; P<0.001 for both).
Defective CD95-induced apoptosis in children with autoimmune lymphoproliferative syndrome (ALPS)/Canale-Smith-Syndrome (CSS) in the absence of CD95 mutations.
Authors: T Bohler, C Posovszky, S Fulda, C Scheuerpflug, G Holzl-Wenig, E Meyer, C Beltinger, Jutte van der Werff ten Bosch, I Herr, KM Debatin
Journal: Blood (1999)
Association between lung function of school age children and short-term exposure to air pollution and pollen: the PARIS cohort
Authors: Hélène Amazouz, Nicolas Bougas, Michel Thibaudon, Guillaume Lezmi, Nicole Beydon, Mélisande Bourgoin-Heck, Jocelyne Just, Isabelle Momas, Fanny Rancière
Journal: Thorax (2021)

Background Daily levels of ambient air pollution and pollen may affect lung function but have rarely been studied together. We investigated short-term exposure to pollen and air pollution in relation to lung function in school-age children from a French population-based birth cohort. Methods This study included 1063 children from the PARIS (Pollution and Asthma Risk: an Infant Study) cohort whose lung function and FeNO measurements were performed at age 8 years old. Exposure data were collected up to 4 days before testing. We estimated daily total pollen concentration, daily allergenic risk indices for nine pollen taxa, as well as daily concentrations of three air pollutants (particulate matter less than 10 µm (PM 10 ), nitrogen dioxide (NO 2 ), ozone (O 3 )). Children with similar pollen and air pollution exposure were grouped using multidimensional longitudinal cluster analysis. Associations between clusters of pollen and air pollution exposure and respiratory indices (FEV 1 , FVC, FeNO) were studied using multivariable linear and logistic regression models adjusted for potential confounders. Results Four clusters of exposure were identified: no pollen and low air pollution (Cluster 1), grass pollen (Cluster 2), PM 10 (Cluster 3) and birch/plane-tree pollen with high total pollen count (Cluster 4). Compared with children in Cluster 1, children in Cluster 2 had significantly lower FEV 1 and FVC levels, and children from Cluster 3 had higher FeNO levels. For FEV 1 and FVC, the associations appeared stronger in children with current asthma. Additional analysis suggested a joint effect of grass pollen and air pollution on lung function. Conclusion Daily ambient chemical and biological air quality could adversely influence lung function in children.
Echocardiographic Characteristics and Their Association With Outcome in Hospitalized Covid-19 Patients With Cardiovascular Disease
Authors: Y. M. Li, L. Y. Fang, S. S. Zhu, Y. J. Xie, B. Wang, H. Lin, D. Q. Zhang, Y. X. Zhang, H. L. Yuan, C. Wu, W. Sun, Y. T. Zhang, M. Li, Y. Cai, L. Cui, J. Wang, Y. L. Yang, L. Qing, L. Zhang, M. X. Xie
Journal: Circulation (2020)