bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Potential Impact of One-Time Routine HIV Screening on Prevention and Clinical Outcomes in the United States: A Model-Based Analysis
Authors: Rao Darcy White , Hughes James P. , Brady Kathleen , Golden Matthew R. 
Published: February 2020

Background
US guidelines recommend routine human immunodeficiency virus (HIV) screening of all adults and adolescents at least once. The population-level impact of this strategy is unclear and will vary across the country.

Methods
We constructed a static linear model to estimate the optimal ages and incremental impact of adding 1-time routine HIV screening to risk-based, prenatal, symptom-based, and partner notification testing. Using surveillance data and published studies, we parameterized the model at the national level and for 2 settings representing subnational variability in the rates and distribution of infection: King County, WA and Philadelphia County, PA. Screening strategies were evaluated in terms of the percent of tests that result in new diagnoses (test positivity), cumulative person-years of undiagnosed infection, and the number of symptomatic HIV/acquired immune deficiency syndrome cases.

Results
Depending on the frequency of risk-based screening, routine screening test positivity was maximized at ages 30 to 34 years in the national model. The optimal age for routine screening was higher in a setting with a lower proportion of cases among men who have sex with men. Across settings, routine screening resulted in incremental reductions of 3% to 8% in years of undiagnosed infection and 3% to 11% in symptomatic cases, compared with reductions of 36% to 69% and 41% to 76% attributable to risk-based screening.

Conclusions
Although routine HIV screening may contribute meaningfully to increased case detection in persons not captured by targeted testing programs in some settings, this strategy will have a limited impact on population-level outcomes. Our findings highlight the importance of a multipronged testing strategy with continued investment in risk-based screening programs.
Evaluation of BioPlex 2200 Syphilis Total With Automated Rapid Plasma Reagin: Experience From a Tertiary Medical Center
Authors: Tang Eric W. , Paiva Kimberly J. , Pytel-Parenteau Diane L. , Maynard Michaela A. , Chan Philip A. , Lu Shaolei 
Published: February 2020

BackgroundTreponema-specific assays are widely adopted in the first step of the reverse algorithm of serologic syphilis screening. The new BioPlex 2200 Syphilis Total and rapid plasma reagin (RPR) test is designed to perform the first 2 steps of the algorithm simultaneously. However, limited data regarding the BioPlex Syphilis Total and RPR in clinical practice exist.MethodsA total of 293 random samples at a tertiary medical center were tested by BioPlex Syphilis Total and RPR, BioPlex Syphilis IgG, Architect Syphilis TP, and BD Macro-Vue RPR card.Treponema pallidumparticle agglutination (TP-PA) assay and clinical chart review were used to resolve discrepancies. Comparisons were performed among treponemal-specific assays and between 2 RPR tests.ResultsGood overall agreements (>91%) were achieved between BioPlex Syphilis Total, BioPlex Syphilis IgG, and Architect Syphilis TP. Overall agreement between BioPlex RPR and BD RPR was 86.8% with positive percent agreement of 66.7% and negative percent agreement of 96.3%. There were 37 discordant samples including 30 with BD RPR+/BioPlex RPR− and 7 with BD RPR−/BioPlex RPR+. Negative BioPlex RPR results were observed in samples with reactive BD RPR: 10 (91%) of 11 for BD RPR 1:1, 13 (65%) of 20 for BD RPR 1:2, 6 (35%) of 17 for BD RPR 1:4, and 1 (7%) of 14 for BD RPR 1:8. The discordant samples were predominantly from patients with high-risk of syphilis reinfection and included 9 patients with an early reinfection.ConclusionsOur results demonstrated that BioPlex Syphilis Total and Architect Syphilis TP performed similarly. The BioPlex RPR missed a small number of early syphilis reinfections, and its implementation should depend on the patient population that the laboratory serves.
Subtracted Computed Tomography Angiography in the Evaluation of Coronary Arteries With Severe Calcification or Stents Using a 320-Row Computed Tomography Scanner
Authors: Chen Chun-Chi , Wu Patricia Wanping , Tsay Pei-Kwei , Wang Chun-Chieh , Toh Cheng-Hong , Wan Yung-Liang 
Published: February 2020

Purpose:
Coronary computed tomography angiography (CCTA) has its limitations in evaluating arteries with stents or heavy calcification. This study compares the diagnostic performance of subtracted coronary computed tomography angiography (SCCTA) and nonsubtracted coronary computed tomography angiography (NSCCTA) in evaluating coronary artery disease (CAD) and in-stent restenosis (ISR).

Materials and Methods:
Twelve patients with stents and 20 patients with heavy coronary calcifications (total Agatston’s score >400) underwent both SCCTA and invasive coronary angiography (ICA) with an interval of <3 months. Four subjects in the stented group also had heavy calcifications. Overall, 30 stented segments and 202 calcified segments were assessed to compare the diagnostic performance of SCCTA and NSCCTA in detecting ISR and CAD.

Results:
For the 30 stented segments, SCCTA/NSCCTA had a sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) (shown in %) of 66.7/100, 100/55.6, 96.7/60, 100/20, and 96.4/100 in diagnosing ISR, respectively. For the 202 calcified segments, SCCTA/NSCCTA had a sensitivity, specificity, accuracy, PPV, and NPV of 68.8/84.4, 97.6/76.5, 93.1/77.7, 84.6/40.3, and 94.3/96.3 in diagnosing CAD, respectively. For both stented and calcified segments, SCCTA was significantly superior to NSCCTA in specificity and accuracy. For the calcified segments, SCCTA was significantly superior to NSCCTA in PPV. There was no significant difference in the diagnostic performance of SCCTA between the stented and calcified segments.

Conclusions:
The diagnostic accuracy and specificity of SCCTA are significantly superior to those of NSCCTA in evaluating CAD and ISR. SCCTA shows no statistical difference in its diagnostic performance between the stented and calcified segments.
Opioid use and schizophrenia
Authors: Li Kevin J. , Chen Anderson , DeLisi Lynn E. 
Published: February 2020

Purpose of review
To summarize the current literature regarding comorbid schizophrenia and opioid use disorder (OUD).

Recent findings
Epidemiological evidence is unclear on whether patients with schizophrenia have a higher rate of OUD. Patients with OUD have been shown to have a higher risk of developing schizophrenia. However, it is clear that patients with both schizophrenia and OUD are less likely to receive standard of care including medication-assisted treatment (MAT) for opiate use disorder and have worse outcomes compared with patients with schizophrenia who do not abuse opioids. OUD significantly increases the risk of converting patients from prodromal schizophrenia states to schizophrenia or schizoaffective disorder. Shared pathophysiology involving the kappa opioid receptor may help explain the relationships between schizophrenia and OUD. Second-generation antipsychotics, long-acting injectables, and MAT for OUD should be utilized in a dual-diagnosis and treatment approach for patients with schizophrenia and OUD.

Summary
Exploration into the relationship between schizophrenia and opiate abuse is still in its infancy and requires a significant amount of future attention to clarify the epidemiology of this comorbidity, neurobiological relationship, shared genetic underpinnings, and possible treatments for both the psychotic symptoms and substance abuse.
Estimate number of individuals infected with the 2019-novel coronavirus in South Korea due to the influx of international students from countries with virus risk: a simulation study
Authors: Ryu Sukhyun , Ali Sheikh Taslim , Lim Jun-sik , Chun Byung Chul 
Published: February 2020

AbstractBackgroundIn March 2020, overall, 37,000 international students from the country at risk of the 2019-novel coronavirus (COVID-19) infection will arrive in Seoul, South Korea. Individuals from the country at risk of COVID-19 infection have been included in a home-quarantine program, but the efficacy of the program is uncertain.MethodsTo estimate the possible number of infected individuals within the large influx of international students, we used a deterministic compartmental model for epidemic and perform a simulation-based search of different rates of compliance with home-quarantine.ResultsUnder the home-quarantine program, the total number of the infected individuals would reach 24–53 from March 17–March 20, 50–86 from March 18– March 16, and 234– 343 from March 4– March 23 with the arrival of 0.1%, 0.2%, and 1% of pre-infectious individuals, in Seoul, South Korea, respectively. Our findings indicated when incoming international students showed strict compliance with quarantine, epidemics were less likely to occur in Seoul, South Korea.ConclusionTo mitigate possible epidemics, additional efforts to improve the compliance of home-quarantine are warranted along with other containment policies.
Risk map of the novel coronavirus (2019-nCoV) in China: proportionate control is needed
Authors: Li Xinhai , Zhao Xumao , Lou Yingqiang , Sun Yuehua 
Published: February 2020

AbstractBackgroundChina is running a national level antivirus campaign against the novel coronavirus (2019-nCoV). Strict control measures are being enforced in either the populated areas and remote regions. While the virus is closed to be under control, tremendous economic loss has been caused.Methods and findingsWe assessed the pandemic risk of 2019-nCoV for all cities/regions in China using the random forest algorithm, taking into account the effect of five factors: the accumulative and increased numbers of confirmed cases, total population, population density, and GDP. We defined four levels of the risk, corresponding to the four response levels to public health emergencies in China. The classification system has good consistency among cities in China, as the error rate of the confusion matrix is 1.58%.ConclusionsThe pandemic risk of 2019-nCoV is dramatically different among the 442 cities/regions. We recommend to adopt proportionate control policy according to the risk level to reduce unnecessary economic loss.
Inpainting as a Technique for Estimation of Missing Voxels in Chemical Shift Imaging
Authors: Torrado-Carvajal Angel , Albrecht Daniel S. , Lee Jeungchan , Andronesi Ovidiu C. , Ratai Eva-Maria , Napadow Vitaly , Loggia Marco L. 
Published: February 2020

AbstractIssues with model fitting (i.e. suboptimal standard deviation, linewidth/full-width-at-half-maximum, and/or signal-to-noise ratio) in multi-voxel MRI spectroscopy, or chemical shift imaging (CSI), can result in the significant loss of usable voxels. A potential solution to minimize this problem is to estimate the value of unusable voxels by utilizing information from reliable voxels in the same image. We assessed an image restoration method called inpainting as a tool to restore unusable voxels and compared it with traditional interpolation methods (nearest neighbor, trilinear interpolation and tricubic interpolation). We applied these techniques to N-acetylaspartate (NAA) spectroscopy maps from a CSI dataset. Inpainting exhibited superior performance (lower normalized root-mean-square errors, NRMSE) compared to all other methods considered (p’s<0.001). Inpainting maintained its superiority whether the previously unusable voxels were randomly distributed or located in regions most commonly affected by voxel loss in real-world data.Clinical RelevanceThe presence of missing voxels can be problematic, particularly when data are analyzed in standard space, given that only voxels that are contributed to by all participants can be interrogated in these analyses. Inpainting is a promising approach for recovering unusable or missing voxels in voxelwise analyses, particularly in imaging modalities characterized by low SNR such as CSI.
PCR procedures to amplify GC-rich DNA sequences ofMycobacterium bovis
Authors: Assal Nadia , Lin Min 
Published: February 2020

AbstractAmplification of high GC content genes by PCR is a major challenge during the creation of recombinant GC-rich DNA constructs. This may be due to the difficulty in DNA denaturation or the possibility of forming secondary structures from DNA templates. Tools have been described to address the technical problems associated with the amplification of shorter sequences (<1000 bp). However, obstacles of synthesizing larger-sized GC-rich sequences by PCR continue to exist. This study aims to investigate the amplification of long and high GC content genes by PCR from theMycobacterium bovis, a genome with GC content >60%, in comparison to amplifying a gene from theListeria monocytogenesgenome, a genome with a 37.8% GC content. Three PCR protocols were designed and experimented at various conditions with twoM. bovisgenes,Mb0129, a large gene of 1794 bp with 77.5% GC content,mpb83, a smaller gene of 663 bp in length with moderate GC content of 63%, together withLMHCC_RS00060, a largeL.monocytogenesgene of 1617 bp with a lower GC content of 41.53%. The result demonstrated the superiority of the 2-step PCR protocol over other protocols in PCR amplification ofMb0129when specific high fidelity DNA polymerases were used in the presence of an enhancer. The study highlighted the importance of manipulating the cycling conditions to perform the annealing and extension steps at higher temperatures for a successful PCR amplification of a large GC-rich DNA template. The PCR protocols developed in this study can be valuable tools for the amplification of long GC-rich DNA sequences for various downstream applications.
TREEasy: An automated workflow to infer gene trees, species trees, and phylogenetic networks from multilocus data
Authors: Mao Yafei , Hou Siqing , Shi Junfeng , Economo Evan P. 
Published: February 2020

AbstractMultilocus genomic data sets can be used to infer a rich set of information about the evolutionary history of a lineage, including gene trees, species trees, and phylogenetic networks. However, user‐friendly tools to run such integrated analyses are lacking, and workflows often require tedious reformatting and handling time to shepherd data through a series of individual programs. Here, we present a tool written in Python—TREEasy—that performs automated sequence alignment (with MAFFT), gene tree inference (with IQ‐Tree), species inference from concatenated data (with IQ‐Tree and RaxML‐NG), species tree inference from gene trees (with ASTRAL, MP‐EST, and STELLS2), and phylogenetic network inference (with SNaQ and PhyloNet). The tool only requires FASTA files and nine parameters as inputs. The tool can be run as command line or through a Graphical User Interface (GUI). As examples, we reproduced a recent analysis of staghorn coral evolution, and performed a new analysis on the evolution of the “WGD clade” of yeast. The latter revealed novel patterns that were not identified by previous analyses. TREEasy represents a reliable and simple tool to accelerate research in systematic biology (https://github.com/MaoYafei/TREEasy).
Trends in suicide death risk in transgender people: results from the Amsterdam Cohort of Gender Dysphoria study (1972–2017)
Authors: Wiepjes C. M. , den Heijer M. , Bremmer M. A. , Nota N. M. , de Blok C. J. M. , Coumou B. J. G. , Steensma T. D. 
Published: February 2020

ObjectiveThis study explored the overall suicide death rate, the incidence over time, and the stage in transition where suicide deaths were observed in transgender people.MethodsA chart study, including all 8263 referrals to our clinic since 1972. Information on death occurrence, time, and cause of death was obtained from multiple sources.ResultsOut of 5107 trans women (median age at first visit 28 years, median follow‐up time 10 years) and 3156 trans men (median age at first visit 20 years, median follow‐up time 5 years), 41 trans women and 8 trans men died by suicide. In trans women, suicide deaths decreased over time, while it did not change in trans men. Of all suicide deaths, 14 people were no longer in treatment, 35 were in treatment in the previous two years. The mean number of suicides in the years 2013–2017 was higher in the trans population compared with the Dutch population.ConclusionsWe observed no increase in suicide death risk over time and even a decrease in suicide death risk in trans women. However, the suicide risk in transgender people is higher than in the general population and seems to occur during every stage of transitioning. It is important to have specific attention for suicide risk in the counseling of this population and in providing suicide prevention programs.
Cardiovascular risk factors are not present in adolescents with inflammatory bowel disease
Authors: Dorfman Lev , Ghersin Itai , Khateeb Neron , Daher Saleh , Shamir Raanan , Assa Amit 
Published: February 2020

AbstractAimDue to conflicting data, we aimed to investigate the association of inflammatory bowel disease (IBD) with cardiovascular disease (CVD) risk factors at late adolescence in a cross‐sectional population‐based study.MethodsA total of 1 144 213 Jewish Israeli adolescents who underwent a general health examination prior to enlistment at median age of 17.1 years from 1988 to 2016 were included. Covariate data included demographics, blood pressure, resting heart rate and risk factors associated with CVD.ResultsOverall, 2372 cases of IBD were identified, including 1612 cases of Crohn's disease (68%). Univariate analysis showed marginally lower systolic and diastolic blood pressure in patients with IBD with no difference following multivariate analysis. Diagnosis of Crohn's disease in males was associated with lower rates of overweight (15.8% vs 21.2%, P < .001) and obesity (3.7% vs 6.1% P = .003), whereas females with Crohn's disease had a lower rate of overweight (14.0% vs 17.9% P = .04) but not obesity. Patients with ulcerative colitis did not differ from controls in terms of overweight or obesity. Patients with Crohn's disease had an increased prevalence of hereditary hypercoagulability (odds ratio 16.9, 95% confidence interval 8.0‐35.7, P < .001).ConclusionSignificant risk factors for CVD were not present in adolescents with IBD.
Variation in the Human Leukocyte Antigen system and risk for endemic Burkitt lymphoma in northern Uganda
Authors: Kirimunda Samuel , Verboom Murielle , Otim Isaac , Ssennono Mark , Legason Ismail D. , Nabalende Hadijah , Ogwang Martin D. , Kerchan Patrick , Kinyera Tobias , Mwebaza Ivan , Joloba Moses , Ayers Leona W. , Reynolds Steven J. , Bhatia Kishor , Onabajo Olusegun O. , Hallensleben Michael , Biggar Robert J. , Prokunina‐Olsson Ludmila , Goedert James J. , Blasczyk Rainer , Mbulaiteye Sam M. 
Published: February 2020

SummaryEndemic Burkitt lymphoma (eBL) is an aggressive childhood B‐cell lymphoma associated with Plasmodium falciparum (Pf) malaria and Epstein–Barr virus (EBV) infections. Variation in the Human Leukocyte Antigen (HLA) system is suspected to play a role, but assessments using less accurate serology‐based HLA typing techniques in small studies yielded conflicting results. We studied 200 eBL cases and 400 controls aged 0–15 years enrolled in northern Uganda and typed by accurate high‐resolution HLA sequencing methods. HLA results were analyzed at one‐ or two‐field resolution. Odds ratios and 95% confidence intervals (aOR, 95% CI) for eBL risk associated with common HLA alleles versus alleles that were rare (<1%) or differed by <2% between the cases and controls as the reference category, were estimated using multiple logistic regression adjusting for age, sex, microgeography, region, malaria positivity and treatment history, and genetic variants associated with eBL. Compared to the controls, eBL cases had a lower frequency of HLA‐A*02 (aOR = 0·59, 95% CI 0·38–0·91), HLA‐B*41 (aOR = 0·36, 95% CI 0·13–1·00), and HLA‐B*58 alleles (aOR = 0·59, 95% CI 0·36–0·97). eBL cases had a lower frequency of HLA‐DPB1 homozygosity (aOR = 0·57, 95% CI 0·40–0·82) but a higher frequency of HLA‐DQA1 homozygosity (aOR = 2·19, 95% CI 1·42–3·37). Our results suggest that variation in HLA may be associated with eBL risk.
Does democracy die in recessions? A descriptive analysis of aggregate demand shortfalls and regime transition
Authors: Murphy Ryan H 
Published: February 2020

AbstractCan a central bank accidentally provoke changes to a country's political regime? Sumner (2015) proposes that macroeconomic mismanagement on the part of central bank authorities, leading to declines in nominal output, can cause voters to respond with populism at the ballot box. Murphy and Smith (2018) have found evidence for this hypothesis, with populism interpreted as movements away from liberal market institutions. This article extends the hypothesis to macroeconomic mismanagement and its relationship with democratic political institutions. It finds both that recessions foreshadow a lower probability of a dictatorship becoming a democracy, and that a democracy is more likely to become a dictatorship. The relationship with autocratisation is most visible after 15 years, while the negative relationship with democratisation is far more persistent over time. These findings, it must be stressed, are historical and descriptive, not necessarily causal.
Angiographic characteristics in Moyamoya disease with the p.R4810K variant: a propensity score‐matched analysis
Authors: Ge P. , Zhang Q. , Ye X. , Liu X. , Deng X. , Wang J. , Wang R. , Zhang Y. , Zhang D. , Zhao J. 
Published: February 2020

Background and purposeThe p.R4810K variant was identified as a strong susceptibility in patients with Moyamoya disease (MMD). The aim of this study was to investigate the angiographic characteristics in MMD with the p.R4810K variant.MethodsAngiographic characteristics were compared between patients with wild‐type p.R4810K variant (GG) and patients with heterozygous p.R4810K variant (GA) after 1:1 propensity score matching, including Suzuki stage, collateral circulation and external carotid artery (ECA) collateral. Collateral circulation was graded with scores ranging from 0 to 12: posterior collateral circulation from the posterior cerebral artery to the middle cerebral artery and anterior cerebral artery was scored from 0 to 6; anterior collateral circulation was scored as 6 to 0 corresponding to Suzuki stages 0 to 6.ResultsA total of 489 patients were screened; 133 pairs were obtained after 1:1 propensity score matching. Compared with the patients in the GA group, unilateral MMD was more frequent in the GG group (P = 0.026). Hemispheres in the GA group (86/266) had more posterior cerebral artery involvement than hemispheres in the GG group (48/266) (P < 0.001). Hemispheres in the GA group had a lower grade in collateral circulation than hemispheres in the GG group (P = 0.011), but ECA collateral was more frequently observed in the GA group than in the GG group (53.4% vs. 39.8%, P = 0.002). Superficial temporal artery and occipital artery collateral was more frequently observed in the GA group than in the GG group (P < 0.05).ConclusionsPatients in the GA group had lower grades in collateral circulation than patients in the GG group, but ECA collateral was more frequently observed in the GA group than in the GG group.