bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sexually Transmitted Infection/HIV Testing Among Medicaid/Children’s Health Insurance Program–Insured Enrollees Aged 15 to 60 Years Who Were Diagnosed With High-Risk Sexual Behaviors With Their Opposite-Sex or Same-Sex Partners
Authors: Tao Guoyu , Patel Chirag 
Published: December 2020

Background
There is a lack of information on high-risk sexual behaviors (HRSB) related to gender of sex partner and associated sexually transmitted infection (STI)/HIV testing among Medicaid enrollees.

Methods
We used the 2016 Centers for Medicare & Medicaid Services Medicaid claims data to identify enrollees aged 15 to 60 years with HRSB by International Classification of Disease, Tenth Revision codes (Z72.51, Z72.52, and Z72.53). Enrollees diagnosed with HRSB were classified into 2 groups:(1) with same-sex partners and (2) with opposite-sex partners. The date when the initial diagnosis for HRSB was documented was used to define as the index date. We assessed chlamydia, gonorrhea, syphilis, and HIV testing on the index date, in the 6-month period before and after the index date (excluded the index date). HIV testing was limited to enrollees without documented HIV infection.

Results
Of 50 million Medicaid enrollees aged 15 to 60 years, 1.2% were identified as enrollees with HRSB in 2016. Of those enrollees with HRSB, 2.7% were enrollees with same-sex partners and 0.71% had documented HIV infection. Chlamydia, gonorrhea, syphilis, and HIV testing rates were 82.4%, 81.9%, 33.2%, and 44.3%, respectively, at the index date. The chlamydia testing rate was ≥90% among enrollees who resided in the West compared with 53% to 61% across other regions. HIV testing was more likely among males and among those with same-sex partners. Sexually transmitted infection/HIV testing was <30% in the 6-month periods before and after the index date.

Conclusions
Among Medicaid enrollees with HRSB, STI/HIV testing varied regionally. Many enrollees were not tested for STI/HIV at the index visit in which they were identified as HRSB.
Variables Associated With Perceived Risk of Contracting SARS-CoV-2 Infection During the COVID-19 Pandemic Among Patients With Systemic Rheumatic Diseases
Authors: Duculan Roland , Jannat-Khah Deanna , Mehta Bella , Mandl Lisa A. , Barbhaiya Medha , Bass Anne R. , Mancuso Carol A. 
Published: December 2020

Objective
The aim of this study was to assess patients' perceived risk of contracting SARS-CoV-2 at the peak of the pandemic in NYC in terms of their systemic rheumatic disease and medications.

Methods
With the approval of their rheumatologists, patients were interviewed by telephone and were asked about their perceived risk of contracting SARS-CoV-2 considering their rheumatic condition and whether medications increased this risk. Patients also completed surveys assessing beliefs about medication and multidimensions of physical/mental well-being. Information about current medications and rheumatologist-initiated changes in medications during the pandemic were reported by patients and verified from medical records.

Results
One hundred twelve patients (86% women; mean age, 50 years; 81% White, 15% Latino) with diverse diagnoses were enrolled. Fifty-four percent thought they were at “very much greater risk” of COVID-19 because of their rheumatic condition, and 57% thought medications “definitely” put them at greater risk. In multivariable analysis, the perception of “very much greater risk” was associated with greater belief that rheumatic disease medications were necessary, worse physical function, chronic pulmonary comorbidity, and more anxiety. In a separate model, the perception that medications “definitely” caused greater risk was associated with White race, not taking hydroxychloroquine, rheumatologists initiating change in medications, more anxiety, and taking biologics and corticosteroids.

Conclusions
Patients’ perceived increased risk of contracting SARS-CoV-2 was associated with beliefs about their rheumatic disease, medications, comorbidity, and anxiety. Clinicians should be aware of patients’ perceptions and foster self-management practices that will alleviate anxiety, minimize exposure to the virus, and optimize systemic rheumatic disease outcomes.
Declines, and Pronounced Regional Disparities, in Meperidine Use in the United States
Authors: Boyle John M. , McCall Kenneth L. , Nichols Stephanie D. , Piper Brian J. 
Published: December 2020

AbstractPurposeThere have been increasing concerns about adverse effects and drug interactions with meperidine including removal from the World Health Organization’s list of essential medications. The goal of this study was to characterize pharmacoepidemiological patterns in meperidine use in the United States.MethodsMeperidine distribution data was obtained from the Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS). Medicare Part D Prescriber Public Use Files (PUF) were utilized to capture overall trends in national meperidine prescriptions.ResultsNational meperidine distribution decreased from 2001 to 2019 by 94.6%. In 2019 Arkansas, Alabama, Oklahoma, and Mississippi saw significantly greater distribution per person when compared to the average state (9.27, SD = 6.82). Meperidine per ten persons showed an eighteen-fold difference between the highest (Arkansas = 36.8 mg) and lowest (Minnesota = 2.1 mg) states. Five of the six lowest states were in the northeast. Meperidine distribution per state was significantly correlated with the prevalence of adult obesity (r(47) = +0.47,p< 0.001).Family medicine and internal medicine physicians accounted for 28.9% and 20.5% of Medicare Part D total daily supply (TDS) of meperidine in 2017. However, interventional pain management (5.66) and pain management (3.48) physicians accounted for the longest while family medicine (0.69) and internal medicine (0.40) accounted for the shortest TDS per provider.ConclusionUse of meperidine has been declining over the last two-decades. Meperidine distribution varied on a geographical level with south/south-central, and more obese, states showing appreciably greater distribution per person. Primary care doctors continue to account for the majority of meperidine daily supply, but specialists like interventional pain management were the most likely to prescribe meperidine to Medicare patients. Increasing knowledge of meperidine’s undesirable adverse effects (e.g. seizures) and serious drug-drug interactions likely are responsible for these pronounced reductions.
Detection of the Novel SARS-CoV-2 European Lineage B.1.177 in Ontario, Canada
Authors: Guthrie Jennifer L. , Teatero Sarah , Zittermann Sandra , Chen Yao , Sullivan Ashleigh , Rilkoff Heather , Joshi Esha , Sivaraman Karthikeyan , de Borja Richard , Sundaravadanam Yogi , Laszloffy Michael , Heisler Lawrence , Allen Vanessa G. , Simpson Jared T. , Fittipaldi Nahuel 
Published: December 2020

ABSTRACTBackgroundTravel-related dissemination of SARS-CoV-2 continues to contribute to the global pandemic. A novel SARS-CoV-2 lineage (B.1.177) reportedly arose in Spain in the summer of 2020, with subsequent spread across Europe linked to travel by infected individuals. Surveillance and monitoring through the use of whole genome sequencing (WGS) offers insights into the global and local movement of pathogens such as SARS-CoV-2 and can detect introductions of novel variants.MethodsWe analyzed the genomes of SARS-CoV-2 sequenced for surveillance purposes from specimens received by Public Health Ontario (Sept 6 – Oct 10, 2020), collected from individuals in eastern Ontario. Taxonomic lineages were identified using pangolin (v2.08) and phylogenetic analysis incorporated publicly available genomes covering the same time period as the study sample. Epidemiological data collected from laboratory requisitions and standard reportable disease case investigation was integrated into the analysis.ResultsGenomic surveillance identified a COVID-19 case with SARS-CoV-2 lineage B.1.177 from an individual in eastern Ontario in late September, 2020. The individual had recently returned from Europe. Genomic analysis with publicly available data indicate the most closely related genomes to this specimen were from Southern Europe. Genomic surveillance did not identify further cases with this lineage.ConclusionsGenomic surveillance allowed for early detection of a novel SARS-CoV-2 lineage in Ontario which was deemed to be travel related. This type of genomic-based surveillance is a key tool to measure the effectiveness of public health measures such as mandatory self-isolation for returned travellers, aimed at preventing onward transmission of newly introduced lineages of SARS-CoV-2.
Age-Specific Rates of Onset of Cannabis Use in Mexico
Authors: López-Méndez Mauricio , Ospina-Escobar Angélica , Iskandar Rowan , Alarid-Escudero Fernando 
Published: December 2020

AbstractBackgroundOver the previous two decades, the prevalence of cannabis use has risen among the population in Mexico.AimsTo estimate the sex- and age-specific rates of onset of cannabis use over time.DesignTime-to-event flexible parametric models with spline specifications of the hazard function. Stratified analysis by sex, and control for temporal trends by year of data collection or decennial birth-cohort.SettingMexico.ParticipantsPooled sample of 141,342 respondents aged between 12 and 65 years from five nationally representative cross-sectional surveys, the Mexican National Surveys of Addictions (1998, 2002, 2008, 2012) and the Mexican National Survey on Drugs, Alcohol, and Tobacco Consumption (2016).MeasurementsWe estimated age-specific rates of onset of cannabis as the conditional rate of consuming cannabis for the first time at a specific age.FindingsAge-specific rates of onset of cannabis use per 1,000 individuals increased over time for both females and males. Peak rates per 1,000 ranged from 0.935 (95%CI= [0.754,1.140]) in 1998, to 5.390 (95%CI= [4.910,5.960]) in 2016 for females; and from 7.510 (95%CI= [5.516, 10.355]) in 1998, to 26.100 (95%CI= [23.162,30.169]) in 2016 for males. Across decennial birth-cohorts, peak rates of onset of cannabis use per 1,000 individuals for females ranged from 0.342 (95%CI= [0.127,0.898]) for those born in the 1930s, to 14.600 (95%CI= [13.200,16.100]) for those born in the 1990s; and for males, from 4.900 (95%CI= [0.768, 7.947]) for those born in the 1930s, to 38.700 (95%CI= [32.553,66.341]) for those born in the 1990s.ConclusionRates of onset of cannabis use for males are higher than for females; however, the change across recent cohorts of the rates of onset has increased at a faster rate among females. Our findings can inform and improve the implementation of policies around cannabis use by identifying subpopulations by age, sex, and birth-cohort that are at the highest risk of initiating cannabis consumption.
Assessing deep learning algorithms incis-regulatory motif finding based on genomic sequencing data
Authors: Wang Yan , Zhang Shuangquan , Ma Anjun , Wang Cankun , Wu Zhenyu , Xu Dong , Ma Qin 
Published: December 2020

AbstractCis-regulatory motif finding is a crucial step in the detection of gene regulatory mechanisms using genomic data. Deep learning (DL) models have been utilized to denovoly identify motifs, and have been proven to outperform traditional methods. By 2020, twenty DL models have been developed to identify DNA and RNA motifs with diverse framework designs and implementation styles. Hence, it is beneficial to systematically compare their performances, which can facilitate researchers in selecting the appropriate tools for their motif analyses. Here, we carried out an in-depth assessment of the 20 models utilizing 1,043 genomic sequencing datasets, including 690 ENCODE ChIP-Seq, 126 cancer ChIP-Seq, 172 single-cell cleavages under targets and release using a nuclease, and 55 RNA CLIP-Seq. Four metrics were designed and investigated, including the accuracy of motif finding, the performance of DNA/RNA sequence classification, algorithm scalability, and tool usability. The assessment results demonstrated the high complementarity of the existing models, and it was determined that the most suitable model should primarily depend on the data size and type as well as the model outputs. A webserver was developed to allow efficient access of the identified motifs and effective utilization of high-performing DL models.
Liquid foam therapy (LiFT) for homogenous distribution of exogenous pulmonary surfactant in ARDS
Authors: Fishler Rami , Ostrovski Yan , Frenkel Avital , Dorfman Simon , Brod Vera , Haas Tali , Waisman Dan , Sznitman Josué 
Published: December 2020

AbstractLung surfactant dysfunction has a critical role in the pathophysiology of acute respiratory distress syndrome (ARDS). Yet, efforts to treat ARDS patients with liquid instillations of exogenous surfactant have so far failed. One of the ongoing challenges in surfactant therapy is obtaining a homogeneous distribution of surfactant within the lungs despite an inherent tendency to non-uniform spreading, owing amongst others to the influence of gravity. Here, we show that liquid foam therapy (LiFT), where surfactant is foamed prior to intratracheal administration, may improve notably surfactant distribution while maintaining safety and efficacy. We first show quantitatively that a foamed surrogate surfactant solution distributes more uniformly inex vivopig lungs compared to endotracheal instillations of the liquid solution, while maintaining pulmonary airway pressures within a safe range. Next, we demonstrate that a foamed commercial surfactant preparation (Infasurf) is effective in an establishedin vivorat lung lavage model of ARDS. Our results suggest that LiFT may be more effective than liquid instillations for treating ARDS and serve as a proof-of-principle towards large animal and clinical trials.
Sex, Competition and Mimicry : an eco-evolutionary model reveals how ecological interactions shape the evolution of phenotypes in sympatry
Authors: Grégoire Boussens-Dumon , Violaine Llaurens 
Published: December 2020

1AbstractPhenotypic evolution in sympatric species can be strongly impacted by species interactions, either mutualistic or antagonistic, which may favour local phenotypic divergence or convergence. Interspecific sexual interactions between sympatric species has been shown to favour phenotypic divergence of traits used as sexual cues for example. Those traits may also be involved in local adaptation or in other types of species interactions resulting in complex evolution of traits shared by sympatric species. Here we focus on mimicry and study how reproductive interference may impair phenotypic convergence between species with various levels of defences. We use a deterministic model assuming two sympatric species and where individuals can display two different warning colour patterns. This eco-evolutionary model explores how ecological interactions shape phenotypic evolution within sympatric species. We investigate the effect of (1) the opposing density-dependent selections exerted on colour patterns by predation and reproductive behaviour, and (2) the impact of relative species and phenotype abundances on the fitness costs faced by each individual depending on their species and phenotype. Our model shows that reproductive interference may limit the convergent effect of mimetic interactions and may promote phenotypic divergence between Müllerian mimics. The divergent and convergent evolution of traits also strongly depends on the relative species and phenotype abundances and levels of trophic competition, highlighting how the eco-evolutionary feedbacks between phenotypic evolution and species abundances may result in strikingly different evolutionary routes.
A body map of somatic mutagenesis in morphologically normal human tissues
Authors: Li Ruoyan , Di Lin , Li Jie , Fan Wenyi , Liu Yachen , Guo Wenjia , Liu Weiling , Liu Lu , Li Qiong , Chen Liping , Chen Yamei , Miao Chuanwang , Liu Hongjin , Wang Yuqian , Ma Yuling , Xu Deshu , Lin Dongxin , Huang Yanyi , Wang Jianbin , Bai Fan , Wu Chen 
Published: December 2020

AbstractSomatic mutations accumulated in normal tissues are associated with aging and disease. Here, we performed a comprehensive genomic analysis of 1,737 morphologically normal tissue biopsies (~ 600 cells each), mostly from the epithelia, of nine organs from five donors. We found that somatic mutation accumulations and clonal expansions are widespread, although with variable extent, in morphologically normal human tissues. Somatic copy number alterations were rarely detected, except for tissues from esophagus and cardia. Endogenous mutational processes like SBS1 and SBS5 are ubiquitous among normal tissues though exhibiting different relative activities. Exogenous mutational processes like SBS22 were found in different tissues from the same donor. We reconstructed the spatial somatic clonal architecture with sub-millimeter resolution. In epithelial tissues from esophagus and cardia, macroscopic somatic clones expanded to several millimeters were frequently seen, whereas in tissues from colon, rectum, and duodenum somatic clones were microscopic in size and evolved independently. Our study depicted a body map of somatic mutations and clonal expansions from the same individuals, and it revealed that the degree of somatic clonal expansion and enrichment of driver mutations are highly organ specific.
Pollen source richness may be a poor predictor of bumblebee colony growth
Authors: Watrobska Cecylia M. , Rodrigues Ana Ramos , Arce Andres N. , Clarke Jessica , Gill Richard J. 
Published: December 2020

ABSTRACTAgricultural intensification has drastically altered foraging landscapes for bees, with large-scale crop monocultures associated with floral diversity loss.Research on bumblebees and honeybees has shown individuals feeding on pollen from a low richness of floral sources can experience negative impacts on health and longevity relative to higher pollen source richness of similar protein concentrations. Florally rich landscapes are thus generally assumed to better support social bees. Yet, little is known about whether the effects of reduced pollen source richness can be mitigated by feeding on pollen with higher crude protein concentration, and importantly how variation in diet affects whole colony growth, rearing decisions and sexual production.Studying queen-right bumblebee (Bombus terrestris) colonies, we monitored colony development under polyfloral pollen diet or monofloral pollen diet with 1.5-1.8 times higher crude protein concentration.Over six weeks, we found monofloral colonies performed better for all measures, with no apparent long-term effects on colony mass or worker production, and a higher number of pupae in monofloral colonies at the end of the experiment. Unexpectedly, polyfloral colonies showed higher mortality, and little evidence of any strategy to counteract the effects of reduced protein; with fewer and lower mass workers being reared, and males showing a similar trend.Our findings i) provide well-needed daily growth dynamics of queenright colonies under varied diets, and ii) support the view that pollen protein content in the foraging landscape rather than floral species richness per se is likely a key driver of colony success.
Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models
Authors: Yang Xue , Mao Zhitao , Zhao Xin , Wang Ruoyu , Zhang Peiji , Cai Jingyi , Ma Hongwu 
Published: December 2020

AbstractStoichiometric genome-scale metabolic network models (GEMs) have been widely used to predict metabolic phenotypes. In addition to stoichiometric ratios, other constraints such as enzyme availability and thermodynamic feasibility can also limit the phenotype solution space. Extended GEM models considering either enzymatic or thermodynamic constraints have been shown to improve prediction accuracy. In this paper, we propose a novel method that integrates both enzymatic and thermodynamic constraints in a single Pyomo modeling framework (ETGEMs). We applied this method to construct the EcoETM, theE. colimetabolic model iML1515 with enzymatic and thermodynamic constraints. Using this model, we calculated the optimal pathways for cellular growth and the production of 22 metabolites. When comparing the results with those of iML1515 and models with one of the two constraints, we observed that many thermodynamically unfavorable and/or high enzyme cost pathways were excluded from EcoETM. For example, the synthesis pathway of carbamoyl-phosphate (Cbp) from iML1515 is both thermodynamically unfavorable and enzymatically costly. After introducing the new constraints, the production pathways and yields of several Cbp-derived products (e.g. L-arginine, orotate) calculated using EcoETM were more realistic. The results of this study demonstrate the great application potential of metabolic models with multiple constraints for pathway analysis and phenotype predication.
Nutraceutical profiles of apricots (Prunus armeniacaL.) as a source of fruit quality traits for breeding
Authors: Gómez-Martínez Helena , Bermejo Almudena , Badenes María Luisa , Zuriaga Elena 
Published: December 2020

SummaryIn a social context of increasingly concern about healthy diets, the development of new varieties with enhanced content in nutraceutical compounds is an increasingly important objective of the fruit breeding programs currently developed. In this sense, apricot is a fruit crop very appreciated by consumers due to its organoleptic characteristics, but also plays an important role in human nutrition due to its contain of phytocompounds as sugars, organic acids, vitamins and polyphenols. In this work, new selections from the apricot breeding program carried out at the Instituto Valenciano de Investigaciones Agrarias (IVIA) and traditional varieties have been analysed aimed at identifying sources of genetic variation for fruit quality. For this purpose, sugar content, organic acids and ascorbic acid were studied during two crop years. Results revealed sucrose and glucose as the major sugars, malic and citric acid as the main organic acids, and diverse ascorbic acid content among the cultivars studied. Results obtained pointed some accessions as potential sources to increase fruit quality. In addition, the study showed that apricot peel is an excellent source of nutraceutical compounds. Moreover, this study opens up new possibilities for future work to study the genetic control of these traits in apricot.
Female mice are more prone to develop an addictive-like phenotype for sugar consumption
Authors: Wei Shoupeng , Hertle Sarah , Spanagel Rainer , Bilbao Ainhoa 
Published: December 2020

AbstractBackgroundThe concept of “sugar addiction” is gaining increasing attention in both the lay media and scientific literature. However, the concept of sugar addiction is controversial and only a few studies have attempted to determine the “addictive” properties of sugar using rigorous scientific criteria.ObjectiveHere we set out to systematically test the addictive properties of sugar in male and female mice using established paradigms and models from the drug addiction field.MethodsMale and female C57BL/6N (8-10 weeks old) were evaluated in 4 experimental procedures to study the addictive properties of sugar: (i) a drinking in the dark (DID) procedure to model sugar binging; (ii) a long-term free choice home cage drinking procedure measuring the sugar deprivation effect (SDE) following an abstinence phase; (iii) a long-term operant sugar self-administration with persistence, motivation and compulsivity measures and (iv) intracranial self-administration (ICSS).ResultsFemale mice were more vulnerable to the addictive properties of sugar than male mice, showing higher binge and long-term, excessive drinking, a more pronounced relapse-like drinking following deprivation, and higher persistence and motivation for sugar. No sex differences were seen in a compulsivity test or reward sensitivity measured using ICSS following extended sugar consumption.ConclusionThis study demonstrates the occurrence of an addictive-like phenotype for sugar in male and female mice, similar to drugs of abuse, and suggests sex-dependent differences in the development of sugar addiction.