bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prescription Opioid Use Among Hispanics/Latinos With Arthritis Symptoms: Results From the Hispanic Community Health Study/Study of Latinos
Authors: Perez Hector R. , Starrels Joanna L. , Gonzalez Sara , Vidot Denise C. , Hua Simin , Strizich Garrett M. , Zeng Donglin , Daviglus Martha , Gellman Marc D. , Kaplan Robert C. 
Published: November 2019

Introduction: To determine the prevalence of prescription opioid (PO) use among Hispanics/Latinos with arthritis symptoms and to characterize how demographic and cultural factors are associated with PO use. Method: Cross-sectional analysis of baseline visit data during 2008 to 2011 from the Hispanic Community Health Study/Study of Latinos, a population-based cohort study of 16,415 Hispanics/Latinos living in Chicago, Illinois, Miami, Florida, Bronx, New York, and San Diego, California. Included participants self-reported painful inflammation or swelling in one or more joints. Multivariate models controlling for physical and mental health scores were constructed to assess how demographic and cultural factors were associated with PO use. Results: A total of 9.3% were using POs at the time of the baseline visit. In multivariate models, persons of Cuban background (adjusted odds ratio [AOR] = 0.42, 95% confidence interval [CI; 0.21, 0.81]) and of Dominican background (AOR = 0.38, 95% CI [0.18, 0.80]) were significantly less likely to use POs compared with a reference group of persons of Mexican background. Greater language acculturation was also negatively associated with PO use (AOR = 0.68, 95% CI [0.53, 0.87]). Conclusion: POs were used relatively uncommonly, and use showed marked variation between Hispanic/Latino groups. Future study should determine mechanisms for why greater use of English among Hispanics/Latinos might influence PO use.
Ischemic and bleeding outcomes of triple therapy in patients on chronic anticoagulation undergoing percutaneous coronary intervention: A meta-analysis of randomized trials
Authors: Dahal Khagendra , Mustafa Usman , Sharma Sharan P , Apte Nachiket , Bogabathina Hari , Hanna Magdy , Watti Hussam , Azrin Michael , Lee Juyong , Mina Goerge , Katikaneni Pavan , Modi Kalgi 
Published: November 2019

Background Triple therapy (TT) that includes oral anticoagulation and dual antiplatelet therapy is recommended in patients who are on chronic anticoagulation and undergo percutaneous coronary intervention (PCI). The randomized clinical trials (RCTs) comparing the effectiveness and safety of TT compared to double therapy (DT), which consists of an oral anticoagulation and one of the P2Y12 inhibitors, have shown increased risk of bleeding; however, none of the individual studies were powered to show a difference in ischemic outcomes. To compare the clinical outcomes of TT and DT, we performed this meta-analysis of RCTs. Methods Electronic search of PubMed, EMBASE and Cochrane CENTRAL databases was performed for RCTs comparing TT and DT in patients who were on oral anticoagulation (Vitamin K antagonist or non-vitamin K antagonist oral anticoagulant) who underwent PCI. All-cause and cardiovascular mortality, myocardial infarction (MI), stroke, stent thrombosis (ST) and TIMI major and minor bleeding were the major outcomes. Results An analysis of 5 trials including 10,592 total patients showed that TT, compared to DT, resulted in non-significant difference in risk of all-cause [odds ratio (OR); 1.14;95% confidence interval (CI):(0.80–1.63); P = 0.46) and cardiovascular mortality [1.43(0.58–3.36); P = 0.44], MI [0.88 (0.64–1.21); P = 0.42], stroke [1.10(0.75–1.62); P = 0.63] and ST [0.82(0.46–1.45); P = 0.49]. TT, compared to DT resulted in higher risk of TIMI major bleeding [1.61(1.09–2.37); P = 0.02], TIMI minor bleeding [1.85(1.23–2.79); P = 0.003] and TIMI major and minor bleeding [1.81 (1.38–2.38); P < 0.0001; I2 = 52%]. Conclusion Compared to DT, the patients receiving TT are at a higher risk of major and minor bleeding with no survival benefit or impact on thrombotic outcomes.
A Cadaveric Load Analysis of the Supramalleolar Osteotomy In The Setting of an Osteochondral Pseudolesion: Quantifying Chondral Off-loading
Authors: Tracey Joseph , Glisson Richard , Verschae Gregorio , Wagner Emilio , Gross Christopher , Easley Mark 
Published: November 2019

Category: Ankle, Ankle Arthritis Introduction/Purpose: The supramalleolar osteotomy (SMO) serves as a means to alter joint load transmission and shield damaged areas of cartilage within the tibiotalar joint. The aim of this study was to directly measure the changes in pressure attributed to varying degrees of SMOs (varus and valgus); with and without an osteochondral (OCD) pseudolesion, and in multiple ankle alignments (Dorsiflexion, neutral, and plantarflexion). We hypothesize measurement metrics to be reduced with increasing degrees of SMO. Methods: 6 cadaver specimens were in included in the biomechanical study (sectioned at the mid-tibia). A pressure sensor was used to measure load, load area, and peak pressure within the tibiotalar joint. SMOs of 3,6,9, and 12 degrees in varus or valgus were performed. A servohydraulic machine was used to transmit 400 and 800 N through the specimens; in 10 degrees of dorsiflexion, neutral, or in 10 degrees of plantarflexion during load transmission. Measurements were performed in undisturbed joints, followed by re-measurement in the presence of a created 9 mm diameter pseudolesion. Results: Load was not changed (only significant changes reported) in the presence of a lesion. For the load, it was more influenceable at 800 N, changes were observed in higher degree SMOs, and changes were only observed in neutral and dorsiflexion. Changes in area were only observed when 12 degrees of varus or valgus SMOs were used. Peak Pressure was the only modifiable metric in the presence of a pseudo-lesion, reductions were more common at 800 N, and in the absence of a pseudolesion there was an incremental reduction in medial peak pressure when increasing varus SMOs were performed (dorsiflexion). Conclusion: Medial peak pressure tended to decrease with varus SMOs in neutral and dorsiflexion. Medial load tended to decrease with varus osteotomies in 10 degrees of dorsiflexion. A 12 degree varus SMO was the only SMO to influence a pseudolesion.
Antivascular Endothelial Growth Factor Treatment Might Be Continued Even After Vitrectomy for Endophthalmitis in Neovascular Age-Related Macular Degeneration
Authors: Michalewska Zofia , Nawrocki Jerzy 
Published: November 2019

Purpose: This article studies visual outcome and frequency of antivascular endothelial growth factor (anti-VEGF) injections continued in patients with neovascular age-related macular degeneration (AMD) who had an earlier vitrectomy for postinjection endophthalmitis. Methods: A retrospective interventional study was conducted reviewing our database for patients with a diagnosis of endophthalmitis in the course of anti-VEGF injections. Endophthalmitis diagnosis was made on clinical examination of pain, rapid decrease in visual acuity (VA), conjunctival hyperemia, hypopyon, and vitritis. In all eyes, core vitrectomy with intravitreal antibiotics was performed. Spectral-domain optical coherence tomography was performed monthly before and after surgery during follow-up. Anti-VEGF injections were continued after surgery in all cases. Results: Eight eyes with postinjection endophthalmitis were included. Mean VA immediately before endophthalmitis was 20/50 Snellen with a mean of 19 intravitreal anti-VEGF injections ( P = .45). At time of endophthalmitis diagnosis, mean VA was 20/1000 (range, 20/2000-20/200). Mean time from injection to when the patient noted first symptoms was 4.3 days (range, 1-8 days). Mean time from first symptoms to surgery was 12 hours (range, 2.5-26 hours). Final mean VA at the end of follow-up (range, 12-84 months) did not statistically differ from VA at the visit immediately before endophthalmitis diagnosis ( P = .69). Mean frequency of injections after vitrectomy did not significantly differ from the presurgical course of treatment ( P =.97). Conclusions: Anti-VEGF treatment might be continued after vitrectomy for endophthalmitis and results in satisfactory anatomical and visual outcome. Surgery did not influence the frequency of anti-VEGF injections for neovascular AMD.
Annot: a Django-based sample, reagent, and experiment metadata tracking system
Authors: Bucher Elmar , Claunch Cheryl J. , Hee Derrick , Smith Rebecca L. , Devlin Kaylyn , Thompson Wallace , Korkola James E. , Heiser Laura M. 
Published: November 2019

Abstract

Background
In biological experiments, comprehensive experimental metadata tracking – which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies – remains a challenge, especially when the experiment involves multiple laboratory scientists who execute different steps of the protocol. Here we describe Annot, a novel web application designed to provide a flexible solution for this task.

Results
Annot enforces the use of controlled vocabulary for sample and reagent annotation while enabling robust investigation, study, and protocol tracking. The cornerstone of Annot’s implementation is a json syntax-compatible file format, which can capture detailed metadata for all aspects of complex biological experiments. Data stored in this json file format can easily be ported into spreadsheet or data frame files that can be loaded into R (https://www.r-project.org/) or Pandas, Python’s data analysis library (https://pandas.pydata.org/). Annot is implemented in Python3 and utilizes the Django web framework, Postgresql, Nginx, and Debian. It is deployed via Docker and supports all major browsers.

Conclusions
Annot offers a robust solution to annotate samples, reagents, and experimental protocols for established assays where multiple laboratory scientists are involved. Further, it provides a framework to store and retrieve metadata for data analysis and integration, and therefore ensures that data generated in different experiments can be integrated and jointly analyzed. This type of solution to metadata tracking can enhance the utility of large-scale datasets, which we demonstrate here with a large-scale microenvironment microarray study.
Fibrin γ/γ' influences the secretion of fibrinolytic components and clot structure
Authors: Cantero Miriam , Rojas Héctor , Anglés-Cano Eduardo , Marchi Rita 
Published: November 2019

AbstractBackgroundIn healthy subjects fibrinogen γ/γ‘ circulates at 8–15% of the total plasma fibrinogen concentration. Elevated levels of this variant have been associated with arterial thrombosis, and its diminution with venous thrombosis. The aims of the present work were to analyze the structure of the fibrin network formed on the top of human dermal microvascular endothelial cells (HMEC-1) at different fibrinogen γ/γ‘ concentrations, as well as its influence on the secretion of fibrinolytic components.The kinetics of fibrin polymerization on top of HMEC-1 cells with 3, 10, and 30% fibrinogen γ/γ‘ was followed at 350 nm. The secretion of urokinase-type plasminogen activator (uPA) and plasminogen activator inhibitor type 1 (PAI 1) by HMEC-1 were measured in the supernatant and cell lysates, after incubation with 1 nM thrombin, fibrin with 3, and 30% fibrinogen γ/γ‘, using commercial kits. The influence of fibrinogen γ/γ‘ on fibrin structure on the surface of the HMEC-1 was followed with laser scanning confocal microscopy (LSCM).ResultsThe kinetics of fibrin formation on HMEC-1 with 3 and 10% fibrinogen γ/γ‘ were similar. However, with 30% fibrinogen γ/γ‘ both the slope and final turbity were approximately 50% less. The LSCM images showed the dramatic effects of increasing fibrinogen γ/γ‘ from 3 to 30%. The uPA and PAI 1 concentrations in culture supernatants HMEC-1 cells treated with thrombin or 30% γ/γ‘ fibrin were two-fold increased as compared to basal culture supernatants and 3% γ/γ‘ fibrin-treated HMEC-1. In all stimulatory conditions the intracellular concentration of uPA was higher than in supernatants. In contrast, the intracellular PAI 1 concentration was decreased as compared to that measured in the supernatant, including the basal condition.ConclusionA concentration of 30% fibrin γ/γ‘ alter drastically fibrin structure on the cell surface and affects the secretion of uPA and PAI 1 through its capacity to bind thrombin.
Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic
Authors: Ono Takaaki , Cruz Modesto , Jiménez Abreu José A. , Nagashima Hiroyuki , Subsomwong Phawinee , Hosking Celso , Shiota Seiji , Suzuki Rumiko , Yamaoka Yoshio 
Published: November 2019

AbstractBackgroundHelicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human,H. pyloriis used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography ofH. pyloriand its host human.MethodsWe examined bothH. pyloriDNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from culturedH. pyloriwere analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses.ResultsH. pyloristrains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both inH. pyloriand in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant inH. pyloriinfection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) ofH. pyloriwas not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent.ConclusionsGenetic features ofH. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy betweenH. pyloriand the host human genotypes support the hypothesis that adaptability of hspAmerindH. pyloristrains are weaker than hpEurope strains.H. pyloristrains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.
Genome-wide identification of microsatellite markers from cultivated peanut (Arachis hypogaea L.)
Authors: Lu Qing , Hong Yanbin , Li Shaoxiong , Liu Hao , Li Haifen , Zhang Jianan , Lan Haofa , Liu Haiyan , Li Xingyu , Wen Shijie , Zhou Guiyuan , Varshney Rajeev K. , Jiang Huifang , Chen Xiaoping , Liang Xuanqiang 
Published: November 2019

Abstract

Background
Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map.

Results
A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected.

Conclusions
The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.
A novel miniature transposon-like element discovered in the coding sequence of a gene that encodes for 5-formyltetrahydrofolate in wheat
Authors: Domb Katherine , Keidar-Friedman Danielle , Kashkush Khalil 
Published: November 2019

AbstractBackgroundTransposable elements (TEs) comprise over 80% of the wheat genome and usually possess unique features for specific super-families and families. However, the role of TEs in wheat evolution and reshaping the wheat genome remains largely unclear.ResultsIn this study, we discovered a miniature (307 bp in length) TE-like sequence in exon 6 of a gene that encodes for 5-formyltetrahydrofolate, in two accessions of wild emmer wheat (T. turgidumssp.dicoccoides) and has interfered with the gene translation by creating a shorter reading frame as a result of a stop codon. The sequence that was termedMariam,does not show any structural similarity to known TEs. It does not possess terminal inverted repeats (TIRs) that would allow us to assign this element to one of the TIR DNA super-families, and it does not possess characteristic features of SINE, such as a Pol-III promotor or a poly-A tail.In-silicoanalysis of five publicly available genome drafts ofTriticumandAegilopsspecies revealed thatMariamelement appears in a very low copy number (1–3 insertions) in diploid wheat species and ~ 12 insertions in tetraploid and hexaploidy wheat species. In addition,Mariamelement was found to be unique to wheat, as it was not found in other plant genomes. The dynamic nature ofMariamin the wheat genome was assessed by site-specific PCR analysis and revealed that it retained activity in wild emmer populations in a population-specific manner.ConclusionsThis study provides additional insight into the evolutionary impact of TEs in wheat.
Ghd8 controls rice photoperiod sensitivity by forming a complex that interacts with Ghd7
Authors: Wang Peng , Gong Rong , Yang Ying , Yu Sibin 
Published: November 2019

AbstractBackgroundFlowering time is one of the most important agronomic characteristics that ultimately determine yield potential and eco-geographical adaptation in crops.Ghd8andGhd7, two major flowering genes, have similar functions and large pleiotropic effects in controlling the heading date, plant height and grain yield of rice. However, these gene interactions at the genetic and molecular levels have not been determined to date.ResultsIn this study, we investigated the genetic interaction betweenGhd8andGhd7by using a set of near-isogenic lines and a panel of natural germplasm accessions in rice. We found thatGhd8affected multiple agronomic traits in a functionalGhd7-dependent manner.Both functionalGhd8andGhd7are pivotal for rice photoperiod sensitivity controlled byHd1andHd3a. GHD8 could form a heterotrimeric complex with HD1 and OsHAP5b to activate the transcription ofGhd7by binding directly to the promoter region ofGhd7, which contains the CCAAT-box motif.ConclusionsThe results of this study help to elucidate the genetic and molecular bases ofGhd8andGhd7interactions, indicating thatGhd8acts upstream ofGhd7to activate its transcription, which inhibitsHd3aexpression and thus affects flowering time and rice adaptation.
Design of the ZWOT-CASE study: an observational study on the effectiveness of an integrated programme for cardiovascular risk management compared to usual care in general practice
Authors: Marchal Suzanne , Hollander Monika , Schoenmakers Marieke , Schouwink Michiel , Timmer Jorik R. , Bilo Henk J. G. , Schwantje Olof , van ’t Hof Arnoud W. J. , Hoes Arno W. 
Published: November 2019

Abstract

Background
Cardiovascular diseases (CVD) contribute considerably to mortality and morbidity. Prevention of CVD by lifestyle change and medication is important and needs full attention.
In the Netherlands an integrated programme for cardiovascular risk management (CVRM), based on the Chronic Care Model (CCM), has been introduced in primary care in many regions in recent years, but its effects are unknown.
In the ZWOT-CASE study we will assess the effect of integrated care for CVRM in the region of Zwolle on two major cardiovascular risk factors: systolic blood pressure (SBP) and low-density lipoprotein cholesterol (LDL-cholesterol) in patients with or at high risk of CVD.

Methods
This study is a pragmatic observational study comparing integrated care for CVRM with usual care among patients aged 40–80 years with CVD (n = 370) or with a high CVD risk (n = 370) within 26 general practices. After 1 yr follow-up, primary outcomes (SBP and LDL-cholesterol level) are measured. Secondary outcomes include lifestyle habits (smoking, dietary habits, alcohol use, physical activity), risk factor awareness, 10-year risk of cardiovascular morbidity or mortality, health care consumption, patient satisfaction and quality of life.

Conclusion
The ZWOT-CASE study will provide insight in the effects of integrated care for CVRM in general practice in patients with CVD or at high CVD risk.

Trial registration
The ZWOlle Transmural Integrated Care for CArdiovaScular Risk Management Study; ClinicalTrials.gov; Identifier: NCT03428061; date of registration: 09-02-2018; This study has been retrospectively registered.
Tracheobronchitis in ulcerative colitis: a case report of therapeutic response with infliximab and review of the literature
Authors: Horgan Lisa , Mulrennan Siobhain , D’Orsogna Lloyd , McLean-Tooke Andrew 
Published: November 2019

Abstract

Background
The extra-intestinal manifestation of tracheobronchitis is a rare complication of ulcerative colitis (UC). Here, we present a case of UC-related tracheobronchitis wherein the positive clinical effects of infliximab are demonstrated.

Case presentation
We report the case of a 39-year old woman who presented with a chronic productive cough on a distant background of surgically managed ulcerative colitis (UC). Our patient failed to achieve a satisfactory clinical improvement despite treatment with high dose inhaled corticosteroids, oral corticosteroids and azathioprine. Infliximab therapy was commenced and was demonstrated to achieve macroscopic and symptomatic remission of disease.

Conclusions
We present the first case report documenting the benefits of infliximab in UC-related tracheobronchitis.