tbuckley/cabot-search huggingface dataset:
Risks of High Coronary Artery Calcium
Authors: Lewis H. Kuller
Journal: JAMA Cardiology (2019)

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Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Authors: Lin Zeng, Xiao-Long Tu, He Dai, Feng-Ming Han, Bing-She Lu, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiao-Long Li, Li-Li Ji, David M. Irwin, Hong Zhou, Min Liu, Hong-Kun Zheng, Ali Esmailizadeh, Dong-Dong Wu
Journal: Genome biology (2019)

Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.Here, we provide a draft de novo genome of pistachio as well as large-scale genome resequencing. Comparative genomic analyses reveal stress adaptation of pistachio is likely attributable to the expanded cytochrome P450 and chitinase gene families. Particularly, a comparative transcriptomic analysis shows that the jasmonic acid (JA) biosynthetic pathway plays an important role in salt tolerance in pistachio. Moreover, we resequence 93 cultivars and 14 wild P. vera genomes and 35 closely related wild Pistacia genomes, to provide insights into population structure, genetic diversity, and domestication. We find that frequent genetic admixture occurred among the different wild Pistacia species. Comparative population genomic analyses reveal that pistachio was domesticated about 8000 years ago and suggest that key genes for domestication related to tree and seed size experienced artificial selection.Our study provides insight into genetic underpinning of local adaptation and domestication of pistachio. The Pistacia genome sequences should facilitate future studies to understand the genetic basis of agronomically and environmentally related traits of desert crops.
THE EFFECTIVENESS OF EARLY ENDOSCOPIC ULTRASOUND-GUIDED DRAINAGE FOR POSTOPERATIVE FLUID COLLECTION AFTER PANCREATOBILIARY SURGERY
Authors: SS Lee, H Lee, D Oh, TJ Song, DH Park, SK Lee, MH Kim
Journal: Endoscopy (2019)

Postoperative abdominal fluid collection (PAFC) is a potentially fatal complication. Recently, EUS-guided drainage has been shown an effective way to treat PAFC more than 4 weeks old. The aim of this study was to assess the usefulness of earlier drainage of PAFC by using EUS-guidance.
Identifying Familial Hypercholesterolemia Using a Blood Donor Screening Program With More Than 1 Million Volunteer Donors
Authors: Candace L. Jackson, James Z. Keeton, Stephen J. Eason, Zahid A. Ahmad, Colby R. Ayers, M. Odette Gore, Darren K. McGuire, Merlyn H. Sayers, Amit Khera
Journal: JAMA Cardiology (2019)

Familial hypercholesterolemia is an autosomal-dominant disorder that often causes premature coronary artery disease. Unfortunately, familial hypercholesterolemia remains largely undiagnosed.To estimate the prevalence of familial hypercholesterolemia in a population of blood donors.This analysis of deidentified data from blood donors 16 years and older who donated to Carter BloodCare, one of the largest independent blood programs in the United States, between January 2002 and December 2016. Carter BloodCare, which serves a population of about 8 million in Texas, routinely measures total nonfasting serum cholesterol levels as part of a donor health screening program. Data analysis occurred from October 2017 to March 2019.Blood donation.Familial hypercholesterolemia was defined using the Make Early Diagnosis to Prevent Early Death general population criteria, with total nonfasting serum cholesterol thresholds of 270, 290, 340, and 360 mg/dL for donors younger than 20 years, 20 to 29 years, 30 to 39 years, and 40 years or older, respectively (to convert cholesterol values to mmol/L, multiply by 0.0259). For repeated donors, the maximum observed total cholesterol level was used for analyses.The study included 1 178 102 individual donors with a total of 3 038 420 blood donations. Of all individual donors (median total cholesterol level, 183 [interquartile range (IQR), 157-212] mg/dL; median age, 32 [IQR, 19-47] years; 619 583 [52.6%] women), a total of 3473 individuals (or 1 in every 339) met criteria for familial hypercholesterolemia. This group had a median (IQR) total cholesterol of 332 (297-377) mg/dL. Estimated prevalence was higher at younger ages (<30 years: 1:257) compared with older ages (≥30 years: 1:469; P < .001) and in men (1:327) compared with women (1:351; P = .03). Among 2219 repeated donors who met familial hypercholesterolemia criteria at least once, 3116 of 10 833 total donations (28.8%) met FH criteria.The prevalence of familial hypercholesterolemia using the Make Early Diagnosis to Prevent Early Death criteria in a large cohort of blood donors was similar to the estimated prevalence of this disorder in the general population. The blood donor screening program could be a novel strategy to detect and notify individuals with potential familial hypercholesterolemia, particularly younger individuals in whom early detection and treatment is especially helpful, as well as guide cascade screening.
Patterns of Neural Oscillations in Emotional Memory Discrimination
Authors: Marcelo G. Mattar, Deborah Talmi
Journal: Neuron (2019)

An exciting experiment by Zheng et al. (2019) in this issue of Neuron identifies neural signatures of successful and unsuccessful emotional memory discrimination. By examining human intracranial recordings with high spatial and temporal resolution, this study provides a novel link between rodent and human research on pattern separation.
Evaluation d'une nouvelle prothèse biliaire métallique de 12 mm de diamètre: une étude cas-témoins
Authors: C Decoster, M Pizzicannella, F Caillol, C Zemmour, J Winkler, A Debourdeau, JP Ratone, C Pesenti, E Bories, M Giovannini
Journal: Endoscopy (2019)

La mise en place d'une prothèse biliaire permet le drainage des voies biliaires de façon palliative ou préopératoire en cas de sténose maligne des voies biliaires, et un calibrage biliaire en cas de sténose bénigne. Actuellement, le calibre de ces prothèses est par accord d'expert de 10 mm pour les prothèses métalliques (1). Depuis 2017, des prothèses d'un calibre supérieur ont été mises sur le marché en France et sont agréées pour le drainage biliaire des sténoses biliaires bénignes et malignes. Ces nouvelles prothèses de 12 mm de diamètre pourraient diminuer le risque d'obstruction biliaire et donc augmenter la durée de vie des prothèses. L'objectif de notre étude était d'évaluer si la perméabilité des prothèses de 12 mm de diamètre était meilleure qu'une prothèse classique de 10 mm couverte ou non couverte selon l'indication.
THE EVOLUTION OF OESOPHAGEAL VARICES IN NON CIRRHOTIC PORTAL HYPERTENSION CAUSED BY PORTAL VEIN THROMBOSIS
Authors: H Boutallaka, I Benelbarhdadi, K Loubaris, F Zahra Ajana
Journal: Endoscopy (2019)

The aim of our study is to specify the evolution of oesogastric varices and thus haemorrhagic recurrence risk in patients with portal hypertension (PHT) by portal vein thrombosis (PVT).
DEGENERATED TODANI IA CHOLECOCHAL CYST
Authors: JF Sánchez Melgarejo, JM Rubio Mateos, MJ Sánchez Fernández, A Pérez Fernandez, A López Martín, E Pérez-Cuadrado Robles, E Pérez-Cuadrado Martínez
Journal: Endoscopy (2019)

Choledochal cysts are a very rare pathology and malignant transformation is the most serious complication (1).
Comparative Effectiveness of Carboplatin/Pemetrexed With Versus Without Bevacizumab for Advanced Nonsquamous Non–Small Cell Lung Cancer
Authors: Stephen J. Bagley, Suzanna Talento, Nandita Mitra, Neal J. Meropol, Roger B. Cohen, Corey J. Langer, Anil Vachani
Journal: Journal of the National Comprehensive Cancer Network (2019)

Background: Despite recent advances in targeted therapy and immunotherapy for advanced non–small cell lung cancer (NSCLC), carboplatin/pemetrexed/bevacizumab remains a commonly used first-line regimen. However, it is unknown whether the addition of bevacizumab to carboplatin/pemetrexed improves overall survival (OS). Materials and Methods: Using nationally representative curated electronic health record data from Flatiron Health, we performed a retrospective cohort study of patients diagnosed with advanced nonsquamous NSCLC who received ≥1 cycle of carboplatin/pemetrexed ± bevacizumab as initial systemic therapy for stage IV or metastatic/recurrent disease. The OS impact of adding bevacizumab to carboplatin/pemetrexed was assessed using a Cox proportional hazards model to adjust for age, sex, race, original tumor stage, time between diagnosis of metastatic disease and start of chemotherapy, and performance status. In a secondary analysis of patients at a single academic institution, we also adjusted for the presence of brain metastases, hemoptysis, and anticoagulation. Results: A total of 4,724 patients were included, of which 2,759 patients (58%) received carboplatin/pemetrexed and 1,965 (42%) received carboplatin/pemetrexed/bevacizumab. Median OS was 12.1 months (95% CI, 11.2–12.9 months) in the carboplatin/pemetrexed/bevacizumab group compared with 8.6 months (95% CI, 8.1–9.1 months) in the carboplatin/pemetrexed group ( P &lt;.001). Bevacizumab use remained associated with improved OS in a multivariate model (hazard ratio, 0.80; 95% CI, 0.75–0.86; P &lt;.001). In the secondary, institutional analysis (N=539), the effect of bevacizumab was unchanged (hazard ratio, 0.75; 95% CI, 0.59–0.96; P =.02). Conclusions: In this large, real-world dataset, the addition of bevacizumab to first-line carboplatin/pemetrexed for metastatic nonsquamous NSCLC was associated with improved OS.
ANTEROGRADE BILIARY DRAINAGE AS SECOND STEP AFTER EUS HEPATICOGASTROSTOMY (ABD-HG) FOR MANAGING BENIGN BILIO-DIGESTIVE ANASTOMOTIC STRICTURES
Authors: JM Gonzalez, J Bodiou, M Gasmi, M Barthet
Journal: Endoscopy (2019)

Benign strictures of bilio-digestive anastomoses (ABDS) are classical complications after biliary surgery. We propose an approach in two consecutive steps:
Successful endoscopic management of Bouvaret syndrome using laser lithotripsy
Authors: Guru Trikudanathan, Dupinder Singh, Kyle Anderson, Eric Jensen, Robert Madoff, Martin L. Freeman
Journal: Endoscopy (2019)

A 64-year-old white woman, with a remote history of cervical cancer, for which she underwent hysterectomy, and diverticulosis with a colovaginal fistula in the distal sigmoid colon, presented with passage of a grape-sized stone per vagina. On chemical analysis, this was identified as being a cholesterol gallstone, which prompted further investigations.
Industry donated over £57m to UK patient organisations from 2012 to 2016
Authors: Gareth Iacobucci
Journal: BMJ (2019)

Drug companies donated over £57m (€65m; $72m) to UK patient organisations from 2012 to 2016, prioritising a small number of organisations that support commercially high profile conditions such as cancer, an analysis published by The BMJ has found.1

The researchers called for greater transparency to ensure that industry funding is not “unduly influenced” by commercial objectives.

The study team from the University of Bath, UK, and Lund University in Sweden examined disclosures of payments (a requirement since 2012) made to patient organisations from corporate members of the European and UK pharmaceutical industry association. The industry disclosed 4572 payments, worth £57.3m, to 508 UK patient organisations from 2012 to 2016, the analysis found.

This represented a modest proportion of the overall funding for healthcare professionals and organisations, which reached £340.3m …
An estimated one in seven babies is born with a low birthweight
Authors: Elisabeth Mahase
Journal: BMJ (2019)

Globally, 20.5 million babies were born with a low birthweight in 2015, and over 90% of these babies were born in low and middle income countries, according to the first worldwide estimates.1

The paper, published in The Lancet Global Health , found around one in seven babies were born with a low birthweight, defined as <2500 g or about 5.5 pounds, with most cases occurring in southern Asia (48%) and sub-Saharan Africa (24%).

Researchers warned that progress to reduce prevalence of low birthweight has been slow in high income countries, with almost no change between 2000 and 2015 in countries including Australia, Finland, France, Germany, …
Clinical Guidelines and PTH Measurement: Does Assay Generation Matter?
Authors: Marjon A Smit, Caroline M J van Kinschot, Joke van der Linden, Charlotte van Noord, Snježana Kos
Journal: Endocrine Reviews (2019)

PTH is an important regulator of calcium and phosphate homeostasis and bone remodeling. It is metabolized into PTH fragments, which are measured to a different extent by PTH assays of different generations because of differences in fragments recognized and lack of assay standardization. PTH is measured in the workup of several conditions, and clinical guidelines provide recommendations concerning these measurements. This review provides an overview of the impact of differences between PTH assays, applying distinct clinical guidelines for primary and secondary hyperparathyroidism and perioperative use of PTH measurements. Guidelines deal with PTH measurement in different ways, recommending either trend monitoring, the use of a fold increase of the upper reference limit, or an absolute PTH cutoff value. For classic primary hyperparathyroidism (PHPT), the type of PTH assay used will not affect diagnosis or management because the precise concentration of PTH is less relevant. In chronic kidney disease, the guideline recommends treating secondary hyperparathyroidism above a twofold to ninefold PTH increase, which will result in different clinical decisions depending on the assay used. For patients after bariatric surgery, guidelines state absolute cutoff values for PTH, but the impact of different generation assays is unknown because direct comparison of PTH assays has never been performed. During parathyroid surgery, PTH measurements with a third-generation assay reflect treatment success more rapidly than second-generation assays. Increased awareness among clinicians regarding the complexity of PTH measurements is warranted because it can affect clinical decisions.
DUODENO-JEJUNAL BYPASS LINER FOR THE TREATMENT OF DIABETES MELLITUS IN OBESE PATIENTS: COMPLETENESS OF DUODENAL BLINDING AS THE KEY FACTOR FOR EFFICACY
Authors: M Benes, T Hucl, P Drastich, M Haluzik, J Spicak
Journal: Endoscopy (2019)

The global increase in obesity incidence results in an increase of type 2 diabetes mellitus (T2DM). Surgical treatment has proven to be effective, however it carries a high risk of complications. The duodenal-jejunal bypass liner (EndoBarrier, GI Dynamics, EB) is an endoscopic implant that mimics the intestinal bypass portion of the Roux-en-Y Gastric Bypass. It results in weight loss and improvements in glucose control in obese patients with T2 diabetes mellitus (T2DM). We aimed to identify factors associated with an outcome of EB for T2DM.
WNT, Hedgehog and NOTCH signaling pathways in triple negative breast cancer with high and low content of cancer stem cells
Authors: A. Brilliant, Y. Brilliant, S. Sazonov
Journal: Annals of Oncology (2019)

Background: Triple negative breast cancer is at the greatest interest for the study. Cells of this type of breast cancer do not have receptors for steroid hormones or tyrosine kinases. For successful treatment of triple negative cases additional points of application are needed. Such targets could be cancer stem cells. For these types of cells, as well as for other stem cells, there are three main cascades are typical - WNT, Hedgehog and NOTCH. However, the conducted studies indicate the existence of other signaling mechanisms of regulation. In our work, we investigated the expression of the NF-kB, PI3K signaling pathways, as well as WNT, Hedgehog, NOTCH in cells of triple negative breast cancer with high and low content of cancer stem cells (ALDH1A1 level). Methods: The material of 54 cases of infiltrative breast cancer was used. To determine the presence of stem cells in tumor population, the presence of ALDH1A1 protein in cancer cells was investigated. Expression of steroid hormone receptors, HER-2 and Ki-67 was studied by immunohistochemical method to identify cases of triple negative breast cancer. The expression of signaling molecules PI3K, NF-kB, WNT, Notch, Hedgehog was also explored by innunohistochemical method. Results: All cases were investigated for ALDH1A1 expression and were divided into two groups - with low (expression of ALDH1A1 was estimated as 0 and 1+) and high (expression of ALDH1A1 was estimated as 2+ and 3+) content of cancer stem cells. It was found that 20% of cases of triple negative breast cancer are positive for ALDH1A1. Expression of explored signaling molecules in cases with high and low content of cancer stem cells is shown in the table. Table40PNF-kBPI3KPTENNOTCHWNTHHhigh ALDH1A1100%100%33%11%11%0%low ALDH1A1100%100%20%25%33%14% Open table in a new tab Conclusions: It was found that cases with high content of cancer stem cells are less regulated by signaling pathways NOTCH and WNT. Expression of NF-Kb and PI3K signaling molecules (which are responsible for activation of eponymous signaling pathways) appeared in all studied cases, while expression of PTEN phosphatase, which inhibits PI3K signaling pathway, was more common for cases with high content of cancer stem cells. Legal entity responsible for the study: Institute of Medical Cell Technologies, Ekaterinburg, Russian Federation. Funding: Ministry of Healthcare of Sverdlovsk Region of Russian Federation. Disclosure: All authors have declared no conflicts of interest.
CAPSULE RETENTION IN CROHN DISEASE: A META-ANALYSIS
Authors: SF Pasha, M Pennazio, E Rondonotti, D Wolf, MR Buras, JG Albert, SA Cohen, J Cotter, G D'Haens, R Eliakim, DT Rubin, JA Leighton
Journal: Endoscopy (2019)

To evaluate capsule retention rates in adult and pediatric Crohn disease (CD) and determine if retention risk can be reduced in established CD (ECD) with patency capsule (PC) or dedicated small bowel (SB) cross sectional imaging (MR/CT enterography) using meta-analysis.
Abstract 13004: Continuous Quality Review of ICU CPR Events: Performance, Outcomes and Effect of Systems-Level Changes
Authors: Michael-Alice Moga, Eva Seligman, Genevieve Frey, Soyang Kwon, Eric Wald
Journal: Circulation (2016)

Introduction: Outcomes of in-hospital cardiac arrest remain disappointing. Continuous quality review (CQR) has been used to improve provider, team and systems performance during CPR. Little data exists on the incidence of individual, team and systems errors during in-hospital CPR and the influence of errors and systems-level changes on outcomes are equally unexplored. Hypothesis: CQR will identify consistent errors in three performance domains (technical, team, systems). Environmental factors and systems changes will affect code quality and outcomes. Methods: Analysis of prospectively collected data describing all ICU CPR events from September 2009-December 2014 in a tertiary care children’s hospital. Monthly quality review by a multidisciplinary team focused on three quality metrics (noise, leadership and equipment failure) and was later expanded to six metrics (communication, technical or systems errors). Results: There were 243 arrests in 193 patients, most of whom had primary cardiac (39%) or pulmonary disease (23%). Most events occurred during the day (7am-7pm); 27% occurred on a weekend or holiday. Median compression time was 5 minutes (IQR 2-15min). Event survival was 80% (70% ROSC, 10% ECMO) and 48% of hospitalizations ended in death. Excess noise (19%), leadership confusion (11%) and equipment failure (6%) were common. Quality CPR (all 3 elements) occurred 74% of the time and was not associated with event survival. Excess noise (p&lt;0.01) and leadership confusion (p=0.02) were more common during the day. A more recent cohort (n=34) demonstrated frequent communication, systems and technical errors (15%, 21% and 21% respectively). Only 38% of arrests had all 6 quality elements. In multivariable analysis, leadership confusion was associated with ICU survival (OR 2.2; 0.66-1). Statistical process control (SPC) only showed special cause variation in single quality metrics despite multiple systems level changes. Code incidence trended down after opening a new hospital and creation of a separate cardiac ICU service (p=0.07). Conclusion: Individual, team and systems errors are common during CPR in critically ill children. CQR incorporating SPC should be used to track performance and monitor the impact of QI initiatives and systems changes.
Nasal High-Flow Therapy for Newborn Infants in Special Care Nurseries
Authors: Brett J. Manley, Gaston R.B. Arnolda, Ian M.R. Wright, Louise S. Owen, Jann P. Foster, Li Huang, Calum T. Roberts, Tracey L. Clark, Wei-Qi Fan, Alice Y.W. Fang, Isaac R. Marshall, Rosalynn J. Pszczola, Peter G. Davis, Adam G. Buckmaster
Journal: New England Journal of Medicine (2019)

Nasal high-flow therapy is an alternative to nasal continuous positive airway pressure (CPAP) as a means of respiratory support for newborn infants. The efficacy of high-flow therapy in nontertiary special care nurseries is unknown.