tbuckley/cabot-search huggingface dataset:
Impact of depression and anxiety on cancer patients' perceptions of lifestyle behaviors.
Authors: Kathryn Corbett, Jingyue Huang, Sophia Liu, Elliot Charles Smith, Delaram Farzanfar, Karmugi Balaratnam, Dixon Pinto, Alexandra McCartney, RuiQi Chen, Amedra Basgaran, Devon Alton, M. Catherine Brown, Doris Howell, Madeline Li, Wei Xu, Geoffrey Liu, Lawson Eng
Journal: Journal of Clinical Oncology (2019)

141 Background: Health behaviors including tobacco use, alcohol consumption, and physical activity (PA) can impact outcomes in cancer survivors. While the peri-diagnostic period can be a "teachable moment" for behavior change, patients may face barriers including mental health comorbidities. We have previously identified that patient perceptions of behaviors can influence behavior change. Here, we evaluated the impact of anxiety and depression on patient perceptions of these behaviors. Methods: Cancer patients from all disease sites were surveyed (2016-17) on their smoking, alcohol habits, and PA, and perceptions of the impact of these behaviors on fatigue, survival, and quality of life (QofL). Survey data were linked with same day Edmonton Symptom Assessment Symptom (ESAS) anxiety and depression scores. Logistic regression models evaluated the impact of anxiety and depression on patient perceptions. Results: Of 496, 53% were male; median age, 60 years. At diagnosis, 20% were current smokers, 47% were current drinkers, and 67% were not meeting PA guidelines. 30% screened positive for anxiety (ESAS anxiety &gt; 3) and 34% screened positive for depression (ESAS depression &gt; 2); mean [standard deviation] scores were 1.9 [2.3] for anxiety and 1.5 [2.2] for depression. Most current smokers (&gt; 80%) perceived smoking to negatively impact fatigue, survival and QofL. Smokers screening positive for anxiety were more likely to perceive smoking as harmful on survival (OR=9.09, 95% CI (1.15-100), P=0.04); greater ESAS anxiety scores were associated with perceiving smoking to worsen survival (OR=1.51 per point, 95% CI (1.04-2.17), P=0.03). While those less physically active at diagnosis (&gt; 65%) felt that PA improves fatigue, survival and QofL and half of current drinkers (45%-50%) felt that alcohol worsens outcomes, anxiety and depression were not found associated with perceptions (P &gt; 0.10). Conclusions: Among current smokers, greater anxiety scores and those screening positive for anxiety were more likely to perceive continued smoking as harmful to survival. Mental health comorbidities were not found to have an impact on patient perceptions of the effect of alcohol consumption and PA on fatigue, survival, and QofL.
Comparative Safety Profile of the Fixed-Dose Combination Corticosteroid and Long-acting β2-Agonist Fluticasone Propionate/Formoterol Fumarate: A 36-Month Longitudinal Cohort Study in UK Primary Care
Authors: David B. Price, Victoria Carter, Jessica Martin, Elizabeth A. Gardener, Derek Skinner, Sen Yang, Matthias Hoffman, Jenna C. Willis, Andrew J. Cooper
Journal: Drugs (2019)
VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants
Authors: Eddie Ip, Gavin Chapman, David Winlaw, Sally L. Dunwoodie, Eleni Giannoulatou
Journal: Genomics Proteomics & Bioinformatics (2019)

Abstract Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.
Effect of Co-Mutations and FLT3-ITD Variant Allele Frequency (VAF) on Response to Quizartinib or Salvage Chemotherapy (SC) in Relapsed/Refractory (R/R) Acute Myeloid Leukemia (AML)
Authors: Alexander E. Perl, Jorge E. Cortes, Siddhartha Ganguly, Samer K. Khaled, Alwin Krämer, Giovanni Martinelli, Nigel H. Russell, Ken CN Chang, Derek E. Mires, Kazunobu Kato, Yufen Zhang, Sergey Korkhov, Zhenyu Wang, Tobias Günnel, Hiroyuki Sumi, Takeshi Isoyama, Arnaud Lesegretain, Flora Berisha, Cedric E. Dos Santos, Mark J. Levis
Journal: Blood (2019)
Artificial intelligence-guided tissue analysis combined with immune infiltrate assessment predicts stage III colon cancer outcomes in PETACC08 study
Authors: Cynthia Reichling, Julien Taieb, Valentin Derangere, Quentin Klopfenstein, Karine Le Malicot, Jean-Marc Gornet, Hakim Becheur, Francis Fein, Oana Cojocarasu, Marie Christine Kaminsky, Jean Paul Lagasse, Dominique Luet, Suzanne Nguyen, Pierre-Luc Etienne, Mohamed Gasmi, Andre Vanoli, Hervé Perrier, Pierre-Laurent Puig, Jean-François Emile, Come Lepage, François Ghiringhelli
Journal: Gut (2019)

Objective Diagnostic tests, such as Immunoscore, predict prognosis in patients with colon cancer. However, additional prognostic markers could be detected on pathological slides using artificial intelligence tools. Design We have developed a software to detect colon tumour, healthy mucosa, stroma and immune cells on CD3 and CD8 stained slides. The lymphocyte density and surface area were quantified automatically in the tumour core (TC) and invasive margin (IM). Using a LASSO algorithm, DGMate (DiGital tuMor pArameTErs), we detected digital parameters within the tumour cells related to patient outcomes. Results Within the dataset of 1018 patients, we observed that a poorer relapse-free survival (RFS) was associated with high IM stromal area (HR 5.65; 95% CI 2.34 to 13.67; p&lt;0.0001) and high DGMate (HR 2.72; 95% CI 1.92 to 3.85; p&lt;0.001). Higher CD3+ TC, CD3+ IM and CD8+ TC densities were significantly associated with a longer RFS. Analysis of variance showed that CD3+ TC yielded a similar prognostic value to the classical CD3/CD8 Immunoscore (p=0.44). A combination of the IM stromal area, DGMate and CD3, designated ‘DGMuneS’, outperformed Immunoscore when used in estimating patients’ prognosis (C-index=0.601 vs 0.578, p=0.04) and was independently associated with patient outcomes following Cox multivariate analysis. A predictive nomogram based on DGMuneS and clinical variables identified a group of patients with less than 10% relapse risk and another group with a 50% relapse risk. Conclusion These findings suggest that artificial intelligence can potentially improve patient care by assisting pathologists in better defining stage III colon cancer patients’ prognosis.
Diagnosing With a Camera From a Distance—Proceed Cautiously and Responsibly
Authors: Mintu P. Turakhia
Journal: JAMA Cardiology (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 Cardiology 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 Cardiology journal
Annals Graphic Medicine - Dr. Mom: How Do You ...?
Authors: Grace E. Farris
Journal: Annals of Internal Medicine (2019)

Web Exclusives3 December 2019Annals Graphic Medicine - Dr. Mom: How Do You ...?FREEGrace E. Farris, MDGrace E. Farris, MDMount Sinai School of Medicine, New York, New York (G.E.F.)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/G19-0074 SectionsAboutVisual AbstractPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail Download figure Download PowerPoint Comments0 CommentsSign In to Submit A Comment Author, Article, and Disclosure InformationAffiliations: Mount Sinai School of Medicine, New York, New York (G.E.F.)Disclosures: The author has disclosed no conflicts of interest. The form can be viewed at www.acponline.org/authors/icmje/ConflictOfInterestForms.do?msNum=G18-0042.Author/Illustrator Information: Grace E. Farris, MD, is an assistant professor of medicine at Icahn School of Medicine at Mount Sinai and chief of hospital medicine at Mount Sinai West hospital in New York, New York. You can view her work at her Web site: www.farrisgrace.com.About Dr. Mom: In Dr. Mom, physician and cartoonist Grace Farris examines work–life balance while mothering and doctoring. Dr. Mom appears monthly in Annals Graphic Medicine at Annals.org. PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 3 December 2019Volume 171, Issue 11Page: W76-W77KeywordsConflicts of interestDisclosureHospital medicineHospitalists ePublished: 3 December 2019 Issue Published: 3 December 2019 Copyright & PermissionsCopyright © 2019 by American College of Physicians. All Rights Reserved.PDF downloadLoading ...
Defining a recovery-oriented cascade of care for opioid use disorder: A community-driven, statewide cross-sectional assessment
Authors: Jesse L. Yedinak, William C. Goedel, Kimberly Paull, Rebecca Lebeau, Maxwell S. Krieger, Cheyenne Thompson, Ashley L. Buchanan, Tom Coderre, Rebecca Boss, Josiah D. Rich, Brandon D. L. Marshall
Journal: PLoS Medicine (2019)

Background In light of the accelerating and rapidly evolving overdose crisis in the United States (US), new strategies are needed to address the epidemic and to efficiently engage and retain individuals in care for opioid use disorder (OUD). Moreover, there is an increasing need for novel approaches to using health data to identify gaps in the cascade of care for persons with OUD. Methods and findings Between June 2018 and May 2019, we engaged a diverse stakeholder group (including directors of statewide health and social service agencies) to develop a statewide, patient-centered cascade of care for OUD for Rhode Island, a small state in New England, a region highly impacted by the opioid crisis. Through an iterative process, we modified the cascade of care defined by Williams et al. for use in Rhode Island using key national survey data and statewide health claims datasets to create a cross-sectional summary of 5 stages in the cascade. Approximately 47,000 Rhode Islanders (5.2%) were estimated to be at risk for OUD (stage 0) in 2016. At the same time, 26,000 Rhode Islanders had a medical claim related to an OUD diagnosis, accounting for 55% of the population at risk (stage 1); 27% of the stage 0 population, 12,700 people, showed evidence of initiation of medication for OUD (MOUD, stage 2), and 18%, or 8,300 people, had evidence of retention on MOUD (stage 3). Imputation from a national survey estimated that 4,200 Rhode Islanders were in recovery from OUD as of 2016, representing 9% of the total population at risk. Limitations included use of self-report data to arrive at estimates of the number of individuals at risk for OUD and using a national estimate to identify the number of individuals in recovery due to a lack of available state data sources. Conclusions Our findings indicate that cross-sectional summaries of the cascade of care for OUD can be used as a health policy tool to identify gaps in care, inform data-driven policy decisions, set benchmarks for quality, and improve health outcomes for persons with OUD. There exists a significant opportunity to increase engagement prior to the initiation of OUD treatment (i.e., identification of OUD symptoms via routine screening or acute presentation) and improve retention and remission from OUD symptoms through improved community-supported processes of recovery. To do this more precisely, states should work to systematically collect data to populate their own cascade of care as a health policy tool to enhance system-level interventions and maximize engagement in care.
Lenalidomide Plus Bortezomib and Dexamethasone in the Treatment of Newly Diagnosed Multiple Myeloma: Results from a Canadian Cost-Effectiveness Analysis
Authors: Michael Sebag, Julie Stakiw, Thomas J. Stephens, Amie Padhiar, Tony Kim, Jane Shum, Sujith Dhanasiri, Suzanne Trudel
Journal: Blood (2019)
Genomic and transcriptomic profiling of carcinogenesis in patients with familial adenomatous polyposis
Authors: Jingyun Li, Rui Wang, Xin Zhou, Wendong Wang, Shuai Gao, Yunuo Mao, Xinglong Wu, Limei Guo, Haijing Liu, Lu Wen, Wei Fu, Fuchou Tang
Journal: Gut (2019)

Objective Familial adenomatous polyposis (FAP) is characterised by the development of hundreds to thousands of adenomas at different evolutionary stages in the colon and rectum that will inevitably progress to adenocarcinomas if left untreated. Here, we investigated the genetic alterations and transcriptomic transitions from precancerous adenoma to carcinoma. Design Whole-exome sequencing, whole-genome sequencing and single-cell RNA sequencing were performed on matched adjacent normal tissues, multiregionally sampled adenomas at different stages and carcinomas from six patients with FAP and one patient with MUTYH -associated polyposis (n=56 exomes, n=56 genomes and n=8,757 single cells). Genomic alterations (including copy number alterations and somatic mutations), clonal architectures and transcriptome dynamics during adenocarcinoma carcinogenesis were comprehensively investigated. Results Genomic evolutionary analysis showed that adjacent lesions from the same patient with FAP can originate from the same cancer-primed cell. In addition, the tricarboxylic acid cycle pathway was strongly repressed in adenomas and was then slightly alleviated in carcinomas. Cells from the ‘normal’ colon epithelium of patients with FAP already showed metabolic reprogramming compared with cells from the normal colon epithelium of patients with sporadic colorectal cancer. Conclusions The process described in the previously reported field cancerisation model also occurs in patients with FAP and can contribute to the formation of adjacent lesions in patients with FAP. Reprogramming of carbohydrate metabolism has already occurred at the precancerous adenoma stage. Our study provides an accurate picture of the genomic and transcriptomic landscapes during the initiation and progression of carcinogenesis, especially during the transition from adenoma to carcinoma.
Epigenetic modifications of histones in cancer
Authors: Zibo Zhao, Ali Shilatifard
Journal: Genome biology (2019)

Abstract The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.
Comment on Kiviniemi et al. Prediabetes and Risk for Cardiac Death Among Patients With Coronary Artery Disease: The ARTEMIS Study. Diabetes Care 2019;42:1319–1325
Authors: Sudipta Chattopadhyay, Joseph John
Journal: Diabetes Care (2019)

We read with interest the results of the Innovation to Reduce Cardiovascular Complications of Diabetes at the Intersection (ARTEMIS) study (1). The authors conclude that cardiac events in patients with coronary artery disease and prediabetes (revascularized or medically treated) were similar to those in patients with normal glucose tolerance.

The study includes a rather low-risk population with prediabetes. About 46% of patients had stable angina (patients who have very low event rates), and the rest had remote acute coronary syndrome (ACS). Recruitment 3–6 months after the coronary angiography with or without revascularization excluded the highest-risk ACS patients who are expected to have events early. Without the baseline Global Registry of Acute Coronary Events (GRACE) or Thrombolysis …
Clinical outcomes in elderly patients with advanced non-small cell lung cancer: A prospective multicenter study of the National Hospital Organization in Japan
Authors: M. Shimada, M. Kanazu, M. Shimokawa, R. Saito, M. Mori, A. Tamura, Y. Okano, Y. Fujita, T. Endo, M. Motegi, S. Takata, T. Kita, N. Sukoh, M. Takenoyama, S. Atagi
Journal: Annals of Oncology (2019)
The Intermediate Dose Verse Conventional Dose Cytarabine in Induction Therapy in Adult Acute Myeloid Leukemia: A Phase III Randomized Controlled Trial
Authors: Hui Wei, Ying Wang, Dong Lin, Chunlin Zhou, Bingcheng Liu, Shaowei Qiu, Benfa Gong, Kaiqi Liu, Guangji Zhang, Shuning Wei, Xiaoyuan Gong, Yuntao Liu, Yan Li, Yingchang Mi, Jianxiang Wang
Journal: Blood (2017)
Survival outcomes and survival predictors in recurrent and metastatic head and neck squamous cell cancer (R/M-HNSCC) patients treated with chemotherapy (CT) plus cetuximab as first-line therapy in a real-world study
Authors: F. Pontes, I. Rego, I.C. Domingues, L. Pinto, R. Garcia, M.M. Teixeira, T. Serra, L. Khoury, M. Mariano, G.M. Sousa
Journal: Annals of Oncology (2019)
Estimates of the global population of children who are HIV-exposed and uninfected, 2000–18: a modelling study
Authors: Amy L Slogrove, Kathleen M Powis, Leigh F Johnson, John Stover, Mary Mahy
Journal: The Lancet Global Health (2019)

BackgroundChildren who are HIV-exposed uninfected (HEU) have higher morbidity and mortality than children who are HIV-unexposed and uninfected despite safer breastfeeding and improved maternal health with maternal antiretroviral therapy. We present the first global estimates of the population of children who are HEU (aged 0–14 years) and the geographical and temporal trends in HIV high-burden countries between 2000 and 2018.MethodsThe Spectrum AIDS Impact Module developed by Avenir Health, UNAIDS, and partners is used to estimate key HIV epidemic indicators from mathematical models. We used 2019 UNAIDS global estimates of children (aged 0–14 years) who are HEU generated by Spectrum and 2017 UN Population Division estimates of the number of all children in each region or country to estimate the regional or national prevalence of children who were HEU, the regional or national contribution of children who were HEU to the global population of children who were HEU, and the proportion of children who were HEU and exposed to antiretrovirals for six UNAIDS regions and 21 HIV high-burden countries in 2018. We also estimated the percentage change in the global population of children who were HEU between 2000 and 2018.FindingsIn 2018, there were an estimated 14·8 million (lower estimate 11·1–upper estimate 18·3) children who were HEU, 13·2 million (9·8–16·3; 90%) of whom resided in sub-Saharan Africa and 760 000 (640 000–970 000; 5%) of whom resided in the Asia and Pacific region. Five countries accounted for 50% of all 14·8 million children who were HEU globally: South Africa (3·5 million [23·8%]), Uganda (1·1 million [7·5%]), Mozambique (1·0 million [6·6%]), Tanzania (910 000 [6·1%]); and Nigeria (880 000 [6·0%]). In five southern African countries, the prevalence of children who were HEU exceeded 15% of the general child population: eSwatini (32·4%), Botswana (27·4%), South Africa (21·6%), Lesotho (21·1%), and Namibia (16·4%).InterpretationThe global population of children who are HEU is substantial, requiring a coordinated strategy to reduce HIV exposure in children and ensure optimal health and wellbeing of children who are HEU and their families. Future research and programmatic funding investments must be aligned with the geographical distribution of children who are HEU.FundingNational Institutes of Health, International AIDS Society.
Single-Cell Pathway Enrichment and Regulatory Profiling of Multiple Myeloma across Disease Stages
Authors: Tianjiao Wang, Hua Sun, Daniel Cui Zhou, Ruiyang Liu, Lijun Yao, Mark A. Fiala, Daniel R. Kohnen, Julie O'Neal, Michael P. Rettig, Jared S Fowles, Stephen T. Oh, Reyka G Jayasinghe, Ravi Vij, John F. DiPersio, Li Ding
Journal: Blood (2019)
Correlation of circulating tumour cells with PET-CT in metastatic breast cancer
Authors: V.P.B. Koyyala, S.D. Saini, D.C. Doval, A. Mehta, M. Suryavanshi, P. Goyal, U.D. Maheshwari, A. Jajodia, M. Sharma, S. Goyal
Journal: Annals of Oncology (2019)
EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation
Authors: Priscillia Lhoumaud, Gunjan Sethia, Franco Izzo, Theodore Sakellaropoulos, Valentina Snetkova, Simon Vidal, Sana Badri, Macintosh Cornwell, Dafne Campigli Di Giammartino, Kyu-Tae Kim, Effie Apostolou, Matthias Stadtfeld, Dan Avi Landau, Jane Skok
Journal: Genome biology (2019)

Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or transcription factor (TF) binding if assays are performed separately. We developed a fast, low-input, low sequencing depth method, EpiMethylTag, that combines ATAC-seq or ChIP-seq (M-ATAC or M-ChIP) with bisulfite conversion, to simultaneously examine accessibility/TF binding and methylation on the same DNA. Here we demonstrate that EpiMethylTag can be used to study the functional interplay between chromatin accessibility and TF binding (CTCF and KLF4) at methylated sites.