tbuckley/cabot-search huggingface dataset:
The BET inhibitor GS-5829 targets chronic lymphocytic leukemia cells and their supportive microenvironment
Authors: Ekaterina Kim, Elisa ten Hacken, Mariela Sivina, Astrid Clarke, Philip A. Thompson, Nitin Jain, Alessandra Ferrajoli, Zeev Estrov, Michael J. Keating, William G. Wierda, Kapil N. Bhalla, Jan A. Burger
Journal: Leukemia (2019)
Uncrewed aircraft systems versus motorcycles to deliver laboratory samples in west Africa: a comparative economic study
Authors: Walter O Ochieng, Tun Ye, Christina Scheel, Aun Lor, John Saindon, Sue Lin Yee, Martin I Meltzer, Vikas Kapil, Kevin Karem
Journal: The Lancet Global Health (2019)

BackgroundTransportation of laboratory samples in low-income and middle-income countries is often constrained by poor road conditions, difficult geographical terrain, and insecurity. These constraints can lead to long turnaround times for laboratory diagnostic tests and hamper epidemic control or patient treatment efforts. Although uncrewed aircraft systems (UAS)—ie, drones—can mitigate some of these transportation constraints, their cost-effectiveness compared with land-based transportation systems is unclear.MethodsWe did a comparative economic study of the costs and cost-effectiveness of UAS versus motorcycles in Liberia (west Africa) for transportation of laboratory samples under simulated routine conditions and public health emergency conditions (based on the 2013–16 west African Ebola virus disease epidemic). We modelled three UAS with operational ranges of 30 km, 65 km, and 100 km (UAS30, UAS65, and UAS100) and lifespans of 1000 to 10 000 h, and compared the costs and number of samples transported with an established motorcycle transportation programme (most commonly used by the Liberian Ministry of Health and the charity Riders for Health). Data for UAS were obtained from Skyfire (a UAS consultancy), Vayu (a UAS manufacturer), and Sandia National Laboratories (a private company with UAS research experience). Motorcycle operational data were obtained from Riders for Health. In our model, we included costs for personnel, equipment, maintenance, and training, and did univariate and probabilistic sensitivity analyses for UAS lifespans, range, and accident or failures.FindingsUnder the routine scenario, the per sample transport costs were US$0·65 (95% CI 0·01–2·85) and $0·82 (0·56–5·05) for motorcycles and UAS65, respectively. Per-sample transport costs under the emergency scenario were $24·06 (95% CI 21·14–28·20) for motorcycles, $27·42 (95% CI 19·25–136·75) for an unadjusted UAS model with insufficient geographical coverage, and $34·09 (95% CI 26·70–127·40) for an adjusted UAS model with complementary motorcycles. Motorcycles were more cost-effective than short-range UAS (ie, UAS30). However, with increasing range and operational lifespans, UAS became increasingly more cost-effective.InterpretationGiven the current level of technology, purchase prices, equipment lifespans, and operational flying ranges, UAS are not a viable option for routine transport of laboratory samples in west Africa. Field studies are required to generate evidence about UAS lifespan, failure rates, and performance under different weather conditions and payloads.FundingNone.
Annals Graphic Medicine - Progress Notes: 2 a.m., Hospital ER
Authors: Michael Natter
Journal: Annals of Internal Medicine (2019)

Web Exclusives17 December 2019Annals Graphic Medicine - Progress Notes: 2 a.m., Hospital ERFREEMichael Natter, MDMichael Natter, MDNYU School of Medicine, New York, New York (M.N.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/G19-0072 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Download figure Download PowerPoint Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAffiliations: NYU School of Medicine, New York, New York (M.N.)Disclosures: The author has disclosed no conflicts of interest. The form can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=G19-0002.Author/Illustrator Information: Michael Natter, MD, is a current internal medicine resident at NYU School of Medicine and a graduate of Sidney Kimmel Medical College of Thomas Jefferson University in Philadelphia. His artwork is inspired by his medical training, patient encounters, and the human condition. A type 1 diabetic, Dr. Natter views himself as a patient as well as a doctor and plans to pursue a fellowship in endocrinology to help others who also share his disease. You can find more of his illustrations, stories, and comics on Instagram (www.instagram.com/mike.natter) and Twitter (@mike_natter).About Progress Notes: Progress Notes explores the everyday emotional, clinical, humorous, and ethical challenges of the medical residency training process. As implied by the title of the series, these pieces act as a visual bildungsroman, graphically dissecting the subtext of what it means to be a young doctor in today's medical world. Progress Notes appears monthly in Annals Graphic Medicine at Annals.org. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 17 December 2019Volume 171, Issue 12Page: W79-W80KeywordsConflicts of interestDisclosureEmotionsEndocrinologyFellowshipsGraduate medical educationHospital medicineResidency ePublished: 17 December 2019 Issue Published: 17 December 2019 Copyright & PermissionsCopyright © 2019 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
The “now moment” is believed privileged because “now” is when happening is experienced
Authors: Ben Kenward, Michael Pilling
Journal: Behavioral and Brain Sciences (2019)

Abstract Hoerl &amp; McCormack risk misleading people about the cognitive underpinnings of the belief in a privileged “now moment” because they do not explicitly acknowledge that the sense of existing in the now moment is an intrinsically temporally dynamic one. The sense of happening that is exclusive to the now moment is a better candidate for the source of belief in a privileged now.
scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Authors: Jose Alquicira-Hernandez, Anuja Sathe, Hanlee P. Ji, Quan Nguyen, Joseph E. Powell
Journal: Genome biology (2019)

Abstract Single-cell RNA sequencing has enabled the characterization of highly specific cell types in many tissues, as well as both primary and stem cell-derived cell lines. An important facet of these studies is the ability to identify the transcriptional signatures that define a cell type or state. In theory, this information can be used to classify an individual cell based on its transcriptional profile. Here, we present scPred , a new generalizable method that is able to provide highly accurate classification of single cells, using a combination of unbiased feature selection from a reduced-dimension space, and machine-learning probability-based prediction method. We apply scPred to scRNA-seq data from pancreatic tissue, mononuclear cells, colorectal tumor biopsies, and circulating dendritic cells and show that scPred is able to classify individual cells with high accuracy. The generalized method is available at https://github.com/powellgenomicslab/scPred/ .
Machine learning to predict the long-term risk of myocardial infarction and cardiac death based on clinical risk, coronary calcium, and epicardial adipose tissue: a prospective study
Authors: Frederic Commandeur, Piotr J Slomka, Markus Goeller, Xi Chen, Sebastien Cadet, Aryabod Razipour, Priscilla McElhinney, Heidi Gransar, Stephanie Cantu, Robert J H Miller, Alan Rozanski, Stephan Achenbach, Balaji K Tamarappoo, Daniel S Berman, Damini Dey
Journal: Cardiovascular Research (2019)

Abstract Aims Our aim was to evaluate the performance of machine learning (ML), integrating clinical parameters with coronary artery calcium (CAC), and automated epicardial adipose tissue (EAT) quantification, for the prediction of long-term risk of myocardial infarction (MI) and cardiac death in asymptomatic subjects. Methods and results Our study included 1912 asymptomatic subjects [1117 (58.4%) male, age: 55.8 ± 9.1 years] from the prospective EISNER trial with long-term follow-up after CAC scoring. EAT volume and density were quantified using a fully automated deep learning method. ML extreme gradient boosting was trained using clinical co-variates, plasma lipid panel measurements, risk factors, CAC, aortic calcium, and automated EAT measures, and validated using repeated 10-fold cross validation. During mean follow-up of 14.5 ± 2 years, 76 events of MI and/or cardiac death occurred. ML obtained a significantly higher AUC than atherosclerotic cardiovascular disease (ASCVD) risk and CAC score for predicting events (ML: 0.82; ASCVD: 0.77; CAC: 0.77, P &amp;lt; 0.05 for all). Subjects with a higher ML score (by Youden’s index) had high hazard of suffering events (HR: 10.38, P &amp;lt; 0.001); the relationships persisted in multivariable analysis including ASCVD-risk and CAC measures (HR: 2.94, P = 0.005). Age, ASCVD-risk, and CAC were prognostically important for both genders. Systolic blood pressure was more important than cholesterol in women, and the opposite in men. Conclusions In this prospective study, machine learning used to integrate clinical and quantitative imaging-based variables significantly improves prediction of MI and cardiac death compared with standard clinical risk assessment. Following further validation, such a personalized paradigm could potentially be used to improve cardiovascular risk assessment.
Advanced Heart Failure in Adults With Congenital Heart Disease
Authors: Jonathan N. Menachem, Kelly H. Schlendorf, Jeremy A. Mazurek, David P. Bichell, D. Marshall Brinkley, Benjamin P. Frischhertz, Bret A. Mettler, Ashish S. Shah, Sandip Zalawadiya, Wendy Book, JoAnn Lindenfeld
Journal: JACC Heart Failure (2019)
E-cigarettes are independent risk factor for respiratory disease, study finds
Authors: Jacqui Wise
Journal: BMJ (2019)

Use of electronic cigarettes appears to be an independent risk factor for respiratory disease in addition to tobacco smoking, according to the first population based long term analysis to investigate the association.1

“We found that for e-cigarette users the odds of developing lung disease increased by about a third, even after controlling for their tobacco use and their clinical and demographic information,” said the lead author Stanton Glantz, professor of medicine at the University of California, San Francisco. “We concluded that e-cigarettes are harmful on their own, and the effects are independent of smoking conventional tobacco,” he added.

The study, published in the American Journal of Preventive Medicine , analysed …
Is survival improving in stage IV non-small cell lung cancer?
Authors: A. E. Birnbaum, T. Ng, B. O'Connor, A. Plette, D. Berz
Journal: Journal of Clinical Oncology (2009)

6577 Background: Non small cell lung cancer (NSCLC) represents the number one cause of cancer mortality in the United States. Over several decades clinical research has focused on the development of new, more active chemotherapeutic drugs to improve survival. Over the time period from 1994 to 2003 six drugs have been approved for the treatment of metastatic NSCLC. We are presenting a population based analysis of the survival in patients with metastatic NSCLC in the US from 1981–1990, 1991–1997 and 1998–2003. We also provide a pharmaco-economic view of this observation. Methods: We analyzed the SEER (Surveillance, Epidemiology, and End Results) program database for cancer specific survival rates in stage IV NSCLC patients who were diagnosed between 1980 and 2003 in the SEER catchment geographic areas. The primary exposure of interest was the year of diagnosis. Results: We identified 52,086 eligible patients in total. 8,950, 21,111 and 18,712 patients were diagnosed 1981 to1990, 1991 to 1997 and 1998 to 2003 respectively. The cox proportional hazard ratios were 0.97 (95% CI 0.94–0.99) and 0.85 (0.83–0.88) for the time periods 1991 to 1997 and 1998 to 2003, respectively, using the time period from 1981 to1990 as reference. This subtle increase in survival was strictly paralleled by increasing costs for the medical care of this patient population. Conclusions: The survival of stage IV NSCLC patients seems to be mildly improving, what is paralleled by increasing cost for the care of those patients. [Table: see text] No significant financial relationships to disclose.
Projected U.S. State-Level Prevalence of Adult Obesity and Severe Obesity
Authors: Zachary J. Ward, Sara N. Bleich, Angie L. Cradock, Jessica L. Barrett, Catherine M. Giles, Chasmine Flax, Michael W. Long, Steven L. Gortmaker
Journal: New England Journal of Medicine (2019)

Although the national obesity epidemic has been well documented, less is known about obesity at the U.S. state level. Current estimates are based on body measures reported by persons themselves that underestimate the prevalence of obesity, especially severe obesity.
Evaluation of in vivo chimeric antigen receptor (CAR) transgene levels in patients (pts) treated with tisagenlecleucel
Authors: Rakesh Awasthi, Karen Thudium Mueller, Gregory A Yanik, Constantine S Tam, Susana Rives, Joseph P McGuirk, Michael A Pulsipher, Michael W Boyer, Ulrich Jaeger, Andre Baruchel, Gary D Myers, Peter Borchmann, Stephen J Schuster, Heather Stefanski, Michael Bishop, Edward R Waldron, Ozlem Anak, Abhijit Chakraborty, Eric Bleickardt, Stephane Wong, Lida Bubuteishvili Pacaud, Edmund K Waller, Shannon L Maude
Journal: Cancer Research (2019)
Mucocutaneous Eruptions in Acutely Ill Pediatric Patients—Think of <i>Mycoplasma pneumoniae</i> (and Other Infections) First
Authors: Michele L. Ramien, Anna L. Bruckner
Journal: JAMA Dermatology (2019)

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 Dermatology 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 Dermatology journal
Multiplex IHC panel development for adenosine pathway markers and TIL in human cancer specimens
Authors: A. Pabois, V. Bodo, A. Boisson, S. Crosignani, O. De Henau, M. Detheux, S. Garaud, J. Lager, C. Martinoli, M. Mercier, C. Naveaux, N. Thomas, N. Wald, A. Vezzu, K. Willard-Gallo, E. Houthuys
Journal: Annals of Oncology (2019)
Influence of family history on risk of second primary cancers and survival in patients with squamous cell skin cancer
Authors: S. Chattopadhyay, G. Zheng, A. Hemminki, A. Försti, K. Sundquist, J. Sundquist, K. Hemminki
Journal: British Journal of Dermatology (2019)

Patients with squamous cell skin cancer (SCC) have an excellent prognosis but second primary cancers (SPCs) weaken survival prospects. Family history is a known risk factor for cancer but whether it is a risk factor for SPC in patients with SCC is not known.To quantify the risk of family history on SPCs in patients with SCC and estimate survival probabilities of patients with SPCs depending on family history.With 13 945 histologically verified SCCs, relative risks (RRs) were estimated for family history using a generalized regression model. For survival analysis, hazard ratios (HRs) were assessed using a multivariable Cox proportional-hazards model.Family history of invasive SCC increased risk of second invasive SCC [RR = 42·92, 95% confidence interval (CI) 33·69-50·32] compared with risk without family history (RR 19·12, 95% CI 17·88-21·08). Family history of any nonskin cancer in invasive SCC increased risk of the same cancers to be diagnosed as SPC (RRFH = 1·48, 95% CI 1·35-1·61 vs. RRno FH = 1·40, 95% CI 1·32-1·48); significant increases were observed for seven different nonskin cancers. Most results were replicated for in situ SCC. SPC was deleterious for survival irrespective of family history; HR for patients with SPC was 4·28 (95% CI 3·83-4·72) vs. those without SPC (1·04).Family history of nonskin cancer was associated with approximately a doubling of risk for SPCs in patients with SCC. SPC increases the death rate in patients with SCC 3-4 times, irrespective of family history. Taking family history into account at SCC diagnosis may help prevention or early detection of SPCs. What's already known about this topic? Second primary cancers (SPCs) are frequently diagnosed in patients with invasive and in situ squamous cell carcinoma (SCC); some epidemiological studies suggest a link to immune dysfunction. Family history of cancer is a risk factor for practically all first primary cancers but whether it also influences risk of SPCs in patients with SCC is not known. The possible influence of family history on survival in patients with SCC remains to be established. Linked Comment: Youlden and Baade. Br J Dermatol 2020; 183:414-415.
Meat intake increases the risk for pancreatic cancer: The Multiethnic Cohort
Authors: Ute Nöthlings, Lynne R. Wilkens, Suzanne P. Murphy, Brian E. Henderson, Laurence N. Kolonel
Journal: Cancer Research (2005)

5821  Meat intake has been associated with risk for cancer of the exocrine pancreas in several case-control studies. This finding has been attributed to the fat and cholesterol content of meats, or to food preparation methods. However, the results to-date are inconsistent, and data from prospective studies are lacking. We analyzed data from the Multiethnic Cohort Study in Hawaii and Los Angeles to investigate associations between meat, other animal products, fat, and cholesterol intake, and pancreatic cancer risk. Data from 190,545 men and women of African-American, Japanese-American, Caucasian, Latino and Native Hawaiian origin were included in the analysis, and yielded 482 incident cases of pancreatic cancer after an average follow-up of 7 years. Dietary intake was assessed at baseline using a quantitative food frequency questionnaire specially designed for use in this multiethnic population. Cox proportional hazards models, stratified by gender and follow-up time, were calculated, adjusted for age at cohort entry, smoking status, history of diabetes mellitus, familial history of pancreatic cancer, and ethnicity. Pancreatic cancer cases were on average 5 years older than non-cases. A significantly higher proportion of cases were male, current smokers, diagnosed with diabetes mellitus prior to baseline, and reported a familial history of pancreatic cancer. The most pronounced risk factor was processed meat, with a 67% increase in risk for the fifth relative to the first quintile (Rate ratio (RR) 1.67; 95% C.I. 1.35-2.07; p for trend = 0.002). Pork and total red meat intake also increased risk by about 50% (p for trend
Role of AID in the temporal pattern of acquisition of driver mutations in multiple myeloma
Authors: Francesco Maura, Even H. Rustad, Venkata Yellapantula, Marta Łuksza, David Hoyos, Kylee H. Maclachlan, Benjamin T. Diamond, Benjamin D. Greenbaum, Gareth Morgan, Alexander Lesokhin, Elli Papaemmanuil, Ola Landgren
Journal: Leukemia (2019)
Role of inflammasomes in the pathogenesis of periodontal disease and therapeutics
Authors: Julie T. Marchesan, Mustafa Saadat Girnary, Kevin Moss, Eugenia Timofeev Monaghan, Grant Joseph Egnatz, Yizu Jiao, Shaoping Zhang, Jim Beck, Karen V. Swanson
Journal: Periodontology 2000 (2019)

Abstract Inflammasomes are a group of multimolecular intracellular complexes assembled around several innate immune proteins. Recognition of a diverse range of microbial, stress and damage signals by inflammasomes results in direct activation of caspase‐1, which subsequently induces the only known form of secretion of active interleukin‐1β and interleukin‐18. Although the importance of interleukin‐1β in the periodontium is not questioned, the impact of inflammasomes in periodontal disease and its potential for therapeutics in periodontology is still in its very early stages. Increasing evidence in preclinical models and human data strongly implicate the involvement of inflammasomes in a number of inflammatory, autoinflammatory and autoimmune disorders. Here we review: (a) the currently known inflammasome functions, (b) clinical/preclinical data supporting inflammasome involvement in the context of periodontal and comorbid diseases and (c) potential therapies targeting inflammasomes. To clarify further the inflammasome involvement in periodontitis, we present analyses of data from a large clinical study (n = 5809) that measured the gingival crevicular fluid‐interleukin‐1β and grouped the participants based on current periodontal disease classifications. We review data on 4910 European‐Americans that correlate 16 polymorphisms in the interleukin‐1B region with high gingival crevicular fluid‐interleukin‐1β levels. We show that inflammasome components are increased in diseased periodontal tissues and that the caspase‐1 inhibitor, VX ‐765, inhibits ~50% of alveolar bone loss in experimental periodontitis. The literature review further supports that although patients clinically present with the same phenotype, the disease that develops probably has different underlying biological pathways. The current data indicate that inflammasomes have a role in periodontal disease pathogenesis. Understanding the contribution of different inflammasomes to disease development and distinct patient susceptibility will probably translate into improved, personalized therapies.
Evaluation of Plasma Microbial Cell-Free DNA Sequencing to Predict Bloodstream Infection in Pediatric Patients With Relapsed or Refractory Cancer
Authors: Kathryn P. Goggin, Veronica Gonzalez-Pena, Yuki Inaba, Kim J. Allison, David K. Hong, Asim A. Ahmed, Desiree Hollemon, Sivaraman Natarajan, Ousman Mahmud, William Kuenzinger, Sarah Youssef, Abigail Brenner, Gabriela Maron, John Choi, Jeffrey E. Rubnitz, Yilun Sun, Li Tang, Joshua Wolf, Charles Gawad
Journal: JAMA Oncology (2019)

Bloodstream infection (BSI) is a common, life-threatening complication of treatment for cancer. Predicting BSI before onset of clinical symptoms would enable preemptive therapy, but there is no reliable screening test.
Colorectal cancer incidence in younger adults in India
Authors: Aju Mathew, Basil Baby, Kevin Wang, Bhawna Sirohi, Feintong Lei, Quan Chen, Bin Huang
Journal: Gut (2019)

Siegel et al 1 described patterns of colorectal cancer (CRC) incidence in young adults worldwide. In India, their estimates were based on data from a single population-based cancer registry (PBCR) in the southern Indian state of Tamil Nadu, representing 0.5% of Indian population (Chennai PBCR). India is a large country of more than a billion people. We analysed data from 14 PBCRs, representing 65 million people (5% of Indian population).2 PBCRs included in our study were Ahmedabad, Bangalore, Barshi, Bhopal, Chennai, Delhi, Dibrugarh, Kamrup, Kolkata, Manipur, Mizoram, Mumbai, Sikkim and Thiruvananthapuram.

We calculated age-standardised incidence rates (according to WHO World Standard Population 2000) for 5-year age groups for periods of diagnosis (2004–2005, 2006–2008, 2009–2011, 2012–2014), and categorised them as …