tbuckley/cabot-search huggingface dataset:
Impact of oncology urgent care center on healthcare utilization.
Authors: Christopher Davella, Peter Whooley, Emily Milano, Brian L. Egleston, Martin Edelman, James Helstrom, Kenneth Patrick, Jessica Ruth Bauman
Journal: Journal of Clinical Oncology (2020)

7 Background: Studies suggest that many Emergency Department (ED) visits and hospitalizations for cancer patients may be preventable. CMS has made changes to the hospital outpatient reporting program (OP-35) targeting ED visits and admissions in treatment patients for preventable conditions. Oncologic urgent care centers aim to streamline care for this population. Fox Chase Cancer Center (FCCC) developed an urgent care center called the Direct Referral Unit (DRU) in July 2011. We sought to assess the impact of the DRU on care utilization. Methods: We abstracted visits to our adjacent hospital (Jeanes) ED and the DRU from January 2014-June 2018. Visit rates represent the ratio of visits over the total number of patients with a clinic visit at FCCC per year. ED and DRU visits were associated with both a cancer and visit diagnosis per the International Classification of Disease (ICD). Patient demographics were abstracted. We also analyzed visit charges, inpatient admission and 30-day therapy utilization (chemotherapy, immunotherapy, radiation). Results: A total of 13,210 visits were analyzed including 5,789 ED visits and 7,421 DRU visits. Visits to the Jeanes ED increased over time. The average age of patients at time of first visit was 63 and visits were most common in females and Caucasians. Hispanic and African American (AA) patients were more likely to visit the ED compared to the DRU (OR: 7.54 and 1.30). Patients with GI (27%) and thoracic (15%) malignancies had the most visits. Commercial insurance use was most common (48%) followed by Medicare (34%) and Medicaid (16%). DRU use was most frequent on Mondays (22%), while ED use occurred the most on Sundays (17%). The most common DRU visit diagnoses in order of prevalence were dehydration, nausea/vomiting, abdominal pain, fever, shortness of breath, fatigue, diarrhea, cellulitis/rash, constipation and anemia. Inpatient admission rates were similar between the two settings (p=.8176). Patients on active cancer treatment more frequently presented to the DRU in comparison to the ED (p&lt;.0001). The average charges were $2226.22 for a DRU visit vs. $10,253.44 for an ED visit. Conclusions: The increase in ED visits over time as well the more frequent ED use in Hispanic and AA patients both suggest a need for greater urgent care access. Many of the most common visit diagnoses to the DRU align with CMS’s list of preventable conditions, demonstrating the DRU’s success as a triage center targeting these conditions. DRU visits were associated with considerable cost savings, supporting the use of cancer urgent care centers as a cost-effective method to reduce acute care.
Impact of Comorbidities and Glycemia at Admission and Dipeptidyl Peptidase 4 Inhibitors in Patients With Type 2 Diabetes With COVID-19: A Case Series From an Academic Hospital in Lombardy, Italy
Authors: Marco Mirani, Giuseppe Favacchio, Flaminia Carrone, Nazarena Betella, Emilia Biamonte, Emanuela Morenghi, Gherardo Mazziotti, Andrea Gerardo Lania
Journal: Diabetes Care (2020)

OBJECTIVE Diabetes may unfavorably influence the outcome of coronavirus disease 19 (COVID-19), but the determinants of this effect are still poorly understood. In this monocentric study, we aimed at evaluating the impact of type 2 diabetes, comorbidities, plasma glucose levels, and antidiabetes medications on the survival of COVID-19 patients. RESEARCH DESIGN AND METHODS This was a case series involving 387 COVID-19 patients admitted to a single center in the region of Lombardy, the epicenter of the severe acute respiratory syndrome coronavirus 2 pandemic in Italy, between 20 February and 9 April 2020. Medical history, pharmacological treatments, laboratory findings, and clinical outcomes of patients without diabetes and patients with type 2 diabetes were compared. Cox proportional hazards analysis was applied to investigate risk factors associated with mortality. RESULTS Our samples included 90 patients (23.3%) with type 2 diabetes, who displayed double the mortality rate of subjects without diabetes (42.3% vs. 21.7%, P &amp;lt; 0.001). In spite of this, after correction for age and sex, risk of mortality was significantly associated with a history of hypertension (adjusted hazard ratio [aHR] 1.84, 95% CI 1.15–2.95; P = 0.011), coronary artery disease (aHR 1.56, 95% CI 1.04–2.35; P = 0.031), chronic kidney disease (aHR 2.07, 95% CI 1.27–3.38; P = 0.003), stroke (aHR 2.09, 95% CI 1.23–3.55; P = 0.006), and cancer (aHR 1.57, 95% CI 1.08–2.42; P = 0.04) but not with type 2 diabetes (P = 0.170). In patients with diabetes, elevated plasma glucose (aHR 1.22, 95% CI 1.04–1.44, per mmol/L; P = 0.015) and IL-6 levels at admission (aHR 2.47, 95% CI 1.28–4.78, per 1-SD increase; P = 0.007) as well as treatment with insulin (aHR 3.05, 95% CI 1.57–5.95; P = 0.001) and β-blockers (aHR 3.20, 95% CI 1.50–6.60; P = 0.001) were independently associated with increased mortality, whereas the use of dipeptidyl peptidase 4 inhibitors was significantly and independently associated with a lower risk of mortality (aHR 0.13, 95% CI 0.02–0.92; P = 0.042). CONCLUSIONS Plasma glucose levels at admission and antidiabetes drugs may influence the survival of COVID-19 patients affected by type 2 diabetes.
The association between Medicare’s next generation sequencing (NGS), national coverage decision (NCD), and NGS utilization.
Authors: William Bruce Wong, Daniel Sheinson, Sarika Ogale, Carlos Flores, Cary Philip Gross
Journal: Journal of Clinical Oncology (2020)

98 Background: In 2018, Medicare released a NGS NCD memo which would facilitate reimbursement for NGS tests for patients (pts) with advanced or metastatic cancer who had not been previously tested using NGS for the same cancer and genetic content. We examined the association between the NCD and: a) NGS utilization trends in commercially-insured and Medicare pts and b) repeat NGS testing. Methods: We conducted a retrospective study of pts with advanced non-small cell lung cancer (aNSCLC), metastatic colorectal cancer (mCRC), metastatic breast cancer (mBC) or advanced melanoma (aM), diagnosed 2011 (2013 for mCRC) through Dec. 2019 using the Flatiron Health EHR-derived de-identified database, comprising data from over 280 (largely community based) cancer clinics (~800 sites of care). Pts were classified as Medicare or Commercially insured based on age and insurance type, and grouped into quarters based on their advanced or metastatic diagnosis date. NGS testing rates per quarter were based on evidence of first NGS test within 60 days from diagnosis. We used an interrupted time series analysis to assess NGS utilization trends pre- and post-NCD policy effective date (March 2018). The frequency of repeat NGS testing was assessed among those pts with only 1 primary cancer. Results: The utilization analysis included 70,290 pts while the repeat NGS testing analysis included 51,385 pts. Across the 4 tumors combined, the use of NGS was &lt; 1% in 2011 (both insurance types) and increased to 41% in commercially-insured pts and 37% in Medicare in 2019. In each tumor, NGS utilization was &lt; 6% in Q1 2014; however, the rate of increase varied by tumor, with aNSCLC increasing to 58% in commercial and 48% in Medicare, while mBC and aM remained &lt; 20% in Q4 2019. Among pts with aNSCLC, mCRC, or mBC, the quarterly rate of increase in NGS testing was higher post-NCD compared to pre-NCD (p &lt; 0.05 for pre-post difference in rate of NGS increase within each cancer type). The difference in trends pre- and post-NCD was not significantly different between commercial and Medicare in any of the tumors (p &gt; 0.05 within each cancer type). Repeat NGS testing increased over time from 17.8% (in Q3 2014 to Q2 2016) to 29.6% (in Q2 2018 to Q4 2019). Conclusions: NGS utilization trends significantly changed post-NCD, however the rate of change was not significantly different by insurance, indicating private insurers may also be following the guidance of the NCD. We observed an increase in repeat NGS testing, despite the NCD not covering repeat testing with the same NGS test.
STAT3 couples with 14-3-3σ to regulate BCR signaling, B-cell differentiation, and IgE production
Authors: Zuochen Du, Anwei Chen, Lu Huang, Xin Dai, Qiuyue Chen, Di Yang, Liling Li, Heather Miller, Lisa Westerberg, Yuan Ding, Xuemei Tang, Masato Kubo, Liping Jiang, Xiaodong Zhao, Hua Wang, Chaohong Liu
Journal: Journal of Allergy and Clinical Immunology (2020)
Genomic Targets of Positive Selection in Giant Mice from Gough Island
Authors: Bret A Payseur, Peicheng Jing
Journal: Molecular Biology and Evolution (2020)

Abstract A key challenge in understanding how organisms adapt to their environments is to identify the mutations and genes that make it possible. By comparing patterns of sequence variation to neutral predictions across genomes, the targets of positive selection can be located. We applied this logic to house mice that invaded Gough Island (GI), an unusual population that shows phenotypic and ecological hallmarks of selection. We used massively parallel short-read sequencing to survey the genomes of 14 GI mice. We computed a set of summary statistics to capture diverse aspects of variation across these genome sequences, used approximate Bayesian computation to reconstruct a null demographic model, and then applied machine learning to estimate the posterior probability of positive selection in each region of the genome. Using a conservative threshold, 1,463 5-kb windows show strong evidence for positive selection in GI mice but not in a mainland reference population of German mice. Disproportionate shares of these selection windows contain genes that harbor derived nonsynonymous mutations with large frequency differences. Over-represented gene ontologies in selection windows emphasize neurological themes. Inspection of genomic regions harboring many selection windows with high posterior probabilities pointed to genes with known effects on exploratory behavior and body size as potential targets. Some genes in these regions contain candidate adaptive variants, including missense mutations and/or putative regulatory mutations. Our results provide a genomic portrait of adaptation to island conditions and position GI mice as a powerful system for understanding the genetic component of natural selection.
Abstract 14133: CTRPs, A Novel Therapeutic Target Against Myocardial Ischemia/Reperfusion Injury
Authors: Yuexing Yuan, Erhe Gao, Yajing Wang, Xiaoliang Wang, Wei Yi, Wayne Bond Lau, William G Wong, Walter J Koch, Xin Ma
Journal: Circulation (2010)

The C1q/TNF-related proteins (CTRP1–10) are a group of newly identified adipocytokines that share structural similarity to adiponectin (APN), a potent cardioprotective molecule. Recent in vitro stu...
A Global and Integrated Analysis of CINSARC-Associated Genetic Defects
Authors: Tom Lesluyes, Frédéric Chibon
Journal: Cancer Research (2020)

The Complexity Index in Sarcomas (CINSARC) signature is a transcriptomic marker that identifies high-risk soft-tissue sarcomas and is associated with high metastatic potential. During the last decade, CINSARC has been successfully developed and validated and is currently being assessed in two prospective phase III clinical trials for stratification of therapy. Although the link between CINSARC expression and tumor aggressiveness is well established, questions remain about how CINSARC genes are regulated. In this study, we leveraged a The Cancer Genome Atlas multiomics study on sarcomas with complex genetics to appraise the association between CINSARC profile, genomic features, and two potential regulation mechanisms, DNA methylation and miRNA expression. CINSARC expression was associated with an increase of ploidy, intratumor heterogeneity, copy-number alteration, altered expression of 37 miRNAs, and a decrease of DNA methylation. These genetic changes are not independent, but rather act together to promote or repress CINSARC expression. These findings depict new insights into CINSARC regulation. SIGNIFICANCE: These findings demonstrate that CINSARC is associated with a variety of genomic aberrations that contribute to higher risk for metastasis and may serve as a prognostic factor in sarcomas and beyond.
Association of cancer history and medical financial hardship with mortality in the United States.
Authors: K Robin Yabroff, Xuesong Han, Weishan Song, Jingxuan Zhao, Ahmedin Jemal, Zhiyuan Zheng
Journal: Journal of Clinical Oncology (2020)

86 Background: Cancer survivors frequently experience medical financial hardship in the United States. Little is known, however, about its long-term health consequences. In this study, we examine the associations of cancer history, medical financial hardship and mortality in a large nationally representative sample. Methods: We identified cohorts of adults aged 18-64 years (n = 415,114) and 65-79 years (n = 73,571) from the 1997-2014 National Health Interview Survey (NHIS) and the NHIS Linked Mortality Files with vital status through December 31, 2015. Medical financial hardship was measured as problems affording care or delaying or forgoing any medical care due to cost in the past 12 months using survey questions consistently available in all NHIS years. Risk of mortality estimated with weighted Cox’s proportional hazards models with age as the time scale, controlling for the effects of sex, race/ethnicity, educational attainment, marital status, comorbid conditions, region, and survey year. Health insurance coverage was added separately to multivariable models. All estimates accounted for the complex survey design. Results: Among adults aged 18-64 years, 29.6% with and 21.3% without a cancer history reported financial hardship Among adults aged 65-79 years with and without a cancer history, the same percentage reported financial hardship: 11.1%. Among adults aged 18-64 years, cancer survivors with financial hardship had the highest adjusted mortality risk (hazard ratio [HR]: 2.14, 95% confidence interval [95CI]: 1.92-2.37); followed by cancer survivors without medical financial hardship (HR: 1.93, 95CI: 1.81-2.06); and adults without a cancer history with medical financial hardship (HR: 1.36; 95CI: 1.31-1.41) compared with adults with neither a cancer history nor financial hardship. Similar pattern was observed among adults aged 65-79 years: cancer survivors with (HR: 1.62, 95CI: 1.45-1.82) and without (HR: 1.34, 95CI: 1.28-1.24) medical financial hardship and adults without a cancer history with financial hardship (HR: 1.17, 95CI: 1.10-1.24) had elevated mortality risk. Further adjustment for health insurance coverage reduced the magnitude of association of financial hardship and mortality among adults 18-64 years, but further adjustment for insurance had little effect on mortality risk among those aged 65-79 years. Conclusions: Medical financial hardship was associated with increased risk of mortality among adults with and without a cancer history, highlighting the need for efforts to mitigate financial hardship in the United States.
ウイルス学的シナプスでの微小管形成中心を極性化するためにT細胞シグナル経路に作用するHTLV-1-TaxおよびICAM-1
Authors: Bangham Crm, Taylor Gp, Orth K, Tanaka Y, Mukherjee S, Negi Vs, Nejmeddine M
Journal: Blood (2009)
Relationship Between Quality of Life and Survival in Patients With Pancreatic and Periampullary Cancer: A Multicenter Cohort Analysis
Authors: Tara M. Mackay, Anouk E.J. Latenstein, Mirjam A.G. Sprangers, Lydia G. van der Geest, Geert-Jan Creemers, Susan van Dieren, Jan-Willem B. de Groot, Bas Groot Koerkamp, Ignace H. de Hingh, Marjolein Y.V. Homs, Evelien J.M. de Jong, I. Quintus Molenaar, Gijs A. Patijn, Lonneke V. van de Poll-Franse, Hjalmar C. van Santvoort, Judith de Vos-Geelen, Johanna W. Wilmink, Casper H. van Eijck, Marc G. Besselink, Hanneke W.M. van Laarhoven, _ _
Journal: Journal of the National Comprehensive Cancer Network (2020)

Background: A relationship between quality of life (QoL) and survival has been shown for several types of cancer, mostly in clinical trials with highly selected patient groups. The relationship between QoL and survival for patients with pancreatic or periampullary cancer is unclear. Methods: This study analyzed QoL data from a prospective multicenter patient-reported outcome registry in patients with pancreatic or periampullary carcinoma registered in the nationwide Netherlands Cancer Registry (2015–2018). Baseline and delta QoL, between baseline and 3-month follow-up, were assessed with the Happiness, EORTC Quality of Life Questionnaire-Core 30 (QLQ-C30), and QLQ-PAN26 questionnaires. The relationship between QoL and survival was assessed using Cox regression models, and additional prognostic value of separate items was assessed using Nagelkerke R 2 (explained variance). Results: For the baseline and delta analyses, 233 and 148 patients were available, respectively. Most were diagnosed with pancreatic adenocarcinoma (n=194; 83.3%) and had stage III disease (n=77; 33.0%), with a median overall survival of 13.6 months. Multivariate analysis using baseline scores indicated several scales to be of prognostic value for the total cohort (ie, happiness today, role functioning, diarrhea, pancreatic pain, and body image; hazard ratios all P &lt;.05) and for patients without resection (ie, overall satisfaction with life, physical and cognitive functioning, QLQ-C30 summary score, fatigue, pain, constipation, diarrhea, and body image; hazard ratios all P &lt;.05). Except for diarrhea, all QoL items accounted for &gt;5% of the additional explained variance and were of added prognostic value. Multivariate analysis using delta QoL revealed that only constipation was of prognostic value for the total cohort, whereas no association with survival was found for subgroups with or without resection. Conclusions: In a multicenter cohort of patients with pancreatic or periampullary carcinoma, QoL scores predicted survival regardless of patient, tumor, and treatment characteristics. QoL scores may thus be used for shared decision-making regarding disease management and treatment choice.
Gilbert’s syndrome, circulating bilirubin and lung cancer: a genetic advantage?
Authors: Heinz Freisling, Nazlisadat Seyed Khoei, Vivian Viallon, Karl-Heinz Wagner
Journal: Thorax (2020)

<h3>Abstract</h3> <h3>Background</h3> As antibiotic resistance is becoming a major problem nowadays in a treatment of infections, bacteriophages (also known as phages) seem to be an alternative. However, to be used in a therapy, their life cycle should be strictly lytic. With the growing popularity of Next Generation Sequencing (NGS) technology, it is possible to gain such information from the genome sequence. A number of tools are available which help to define phage life cycle. However, there is still no unanimous way to deal with this problem, especially in the absence of well-defined open reading frames. To overcome this limitation, a new tool is definitely needed. <h3>Results</h3> We developed a novel tool, called PhageAI, that allows to access more than 10 000 publicly available bacteriophages and differentiate between their major types of life cycles: lytic and lysogenic. The tool included life cycle classifier which achieved 98.90% accuracy on a validation set and 97.18% average accuracy on a test set. We adopted nucleotide sequences embedding based on the Word2Vec with Ship-gram model and linear Support Vector Machine with 10-fold cross-validation for supervised classification. PhageAI is free of charge and it is available at https://phage.ai/. PhageAI is a REST web service and available as Python package. <h3>Conclusions</h3> Machine learning and Natural Language Processing allows to extract information from bacteriophages nucleotide sequences for lifecycle prediction tasks. The PhageAI tool classifies phages into either virulent or temperate with a higher accuracy than any existing methods and shares interactive 3D visualization to help interpreting model classification results.
Case 31-2020: A 48-Year-Old Man with Lymphoma and Abdominal Pain
Authors: Michael K. Mansour, Olivia C. Smibert, Avinash Kambadakone, Maroun M. Sfeir
Journal: New England Journal of Medicine (2020)

A 48-year-old man with diffuse large B-cell lymphoma was evaluated in the oncology clinic because of pain in the bilateral inguinal regions and upper quadrants. CT revealed multiple new hypodense lesions throughout the liver and new bilateral pleural effusions. A diagnostic test was performed.
Blood Pressure Thresholds During Endovascular Therapy in Ischemic Stroke
Authors: Zhuyi Elizabeth Sun, Stelios Smirnakis, Steven Feske
Journal: JAMA Neurology (2020)

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 Neurology 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 Neurology journal
Do eligibility criteria restrict access to clinical trials?
Authors: Nessa Stefaniak, Jennifer Walker, Monica L. Murphy, Mishellene McKinney, Lu Liu, Stephen B. Edge
Journal: Journal of Clinical Oncology (2020)

94 Background: Stringent eligibility criteria may be a barrier to oncology clinical trial enrollment. We examined patients meeting basic trial eligibility criteria defined in a clinical pathway where the trial was not selected, and then performed a thorough review of full trial eligibility. Methods: Locally available trials are embedded into a pathways tool used at the point of care by medical oncologists at a tertiary cancer center. The physician can choose to have the patient fully screened for the recommended trial or bypass it. Patients where the physician bypassed the trial for eleven Phase 2 and 3 solid tumor trials from April 2018 to December 2019 were reviewed for trial eligibility. Basket trials and adoptive cellular therapy trials were excluded. Trials selected for the audit were presented for more than 20 patients and were bypassed in 80% or more cases. For each trial a random set of 20% of cases or a minimum of 15 cases minimum were reviewed. Results: Among the 184 cases reviewed, 149 (81%) were trial ineligible based upon one or more criteria. The most common reasons for patients' ineligibility were the wrong biomarker profile, prior drug treatment, and health conditions including co-morbidities, autoimmune diseases, other cancers and poor performance status. Conclusions: The majority of patients meeting basic eligibility in a clinical pathways system did not meet strict eligibility criteria. This suggests the trials may not be reflective of the needs of the cancer population being treated and may limit the applicability of trial results to the general cancer population. Use of the pathway program to define eligibility is limited by the numerous and nuanced eligibility criteria that cannot be programmed into the pathways system. Clinical trials eligibility criteria and pathway tools need to adapt to the patient population to help advance cancer research. [Table: see text]