bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-exposure Prophylaxis Awareness and Use Among Cisgender Men Who Have Sex With Men and Use Methamphetamine in 3 Western US Cities
Authors: McMahan Vanessa M. , Moreno Courtney , Al-Tayyib Alia , Menza Timothy W. , Orellana Edwin Roberto , Bhattarai Amisha , Stekler Joanne D. , Glick Sara N. 
Published: January 2020

Background
In the United States, cisgender men who have sex with men (MSM) who use methamphetamine are at substantial risk for HIV and can benefit from pre-exposure prophylaxis (PrEP).

Methods
We used data from the National HIV Behavioral Surveillance 2017 survey from Seattle, WA; Portland, OR; and Denver, CO, to estimate PrEP awareness and use in the past 12 months among MSM who use methamphetamine. We then compared these estimates with participants who do not use methamphetamine but meet other criteria for PrEP use (i.e., condomless anal sex or a bacterial sexually transmitted infection). We explored reasons for not using PrEP and challenges using PrEP.

Results
Of the 1602 MSM who participated in the 2017 National HIV Behavioral Surveillance survey in Seattle, WA; Portland, OR; and Denver, CO, 881 met the inclusion criteria for this study, of whom 88 (10%) reported methamphetamine use in the past 12 months. Most (95%) participants had heard of PrEP, and 35% had used it in the past 12 months. Pre-exposure prophylaxis awareness was lower among MSM who used methamphetamine (P = 0.01), but use was not different (P = 0.26). Among those who had not used PrEP, the most common reason for not using it was not thinking one's HIV risk was high enough (51%). Men who have sex with men who used methamphetamine were more likely to report that they were not sure PrEP would prevent them from getting HIV (38% vs. 19%, P = 0.002).

Conclusions
These results highlight the need for continued efforts to educate and promote PrEP uptake among MSM, particularly those who use methamphetamine.
Anticoagulant chemoprophylaxis in patients with traumatic brain injuries: A systematic review
Authors: Spano Paul J. , Shaikh Saamia , Boneva Dessy , Hai Shaikh , McKenney Mark , Elkbuli Adel 
Published: January 2020

BACKGROUND
Traumatic brain injury (TBI) continues to be a deadly injury. Universally accepted guidelines regarding the use of venous thromboembolism (VTE) chemoprophylaxis in trauma patients presenting with TBI have not been established. The purpose of this review was to identify and review the current literature and present the evidence for anticoagulant chemoprophylaxis regimens in patients with TBI.

METHODS
A search of five databases including PubMed, Web of Science, Google Scholar, JAMA Network, and Cochrane Journals was conducted for studies evaluating the safety and efficacy of venous thromboembolism prophylaxis regimens according to the Preferred Reporting Items for Systematic reviews and Meta-analyses guidelines. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group criteria were used for quality of evidence assessment.

RESULTS
Seventeen studies were included in this review: 1 randomized controlled trial, 2 prospective observational studies, 10 retrospective reviews, and 5 systematic reviews. Most studies demonstrated that early chemoprophylactic administration is associated with a decreased incidence of VTE in patients with TBI without an increase in intracranial bleed.

CONCLUSION
For patients with TBI resulting in intracranial hemorrhages, administration of VTE chemoprophylaxis is warranted for those patients with stable repeat computed tomography scans. Early chemoprophylaxis, at 24 to 72 hours is associated with reduced VTE incidence without a corresponding increase or exacerbation of intracranial hemorrhage in patients with TBI who have a stable repeat head computed tomography scan. More studies are needed to establish guidelines for the safety and efficacy of VTE prophylaxis protocols in adult patients with TBI.

LEVEL OF EVIDENCE
Systematic review, level III.
Quality characteristics of Tenebrio molitor L. ingested yuzu supplemented feed
Authors: Park Sang-Jun , Na Ji-Hoon , Lee Chul-Gyo , Jeong Jae-Hee , Kim Cheol-Min , Han Hong-Bi , Kim Bok-Seon , Park Chang-Hee , Huh Chang-Ki 
Published: January 2020

In this study, we examined the quality of Tenebrio molitor L. that ingested yuzu supplemented feed at four feed compositions: C120 (120 g Chinese cabbage), C80+Y40 (80 g Chinese cabbage+40 g yuzu peel), C40+Y80 (40 g Chinese cabbage+80 g yuzu peel) and Y120 (120 g yuzu peel). Tenebrio molitor L. was fed for 90 d at a rate according to age, after which the moisture, crude protein, crude fat, and crude ash contents of the samples were determined to be 0.49-0.50%, 52.58-53.90%, 30.76-32.34%, and 3.32-3.45%, respectively. Color values, namely yellowness (b) and redness (a), were observed to decrease with increasing yuzu ingestion, and the C80+Y40 sample exhibited the highest lightness (L=36.28). The K and Mg contents were observed to increase with increasing yuzu content, and Pb and As were not detected in any Tenebrio molitor L. sample that ingested the yuzu supplemented feed. The free amino acid (serine and alanine) contents also increased with increasing yuzu content, while the histidine and arginine contents were observed to decrease with increasing yuzu ingestion. Naringin and hesperidin were detected at 1.77 mg%	and 1.63 mg% in sample Y120, respectively, while trace amounts were detected in samples C80+Y40 and C40+Y80, but none were detected in the control. The total polyphenol and flavonoid contents increased with increasing level of yuzu ingestion, and were highest in sample Y120 (123.11 mg% and 5.69 mg%, respectively).
Polygenic modelling of treatment effect heterogeneity
Authors: Xu Zhi Ming , Burgess Stephen 
Published: January 2020

AbstractMendelian randomization is the use of genetic variants to assess the effect of intervening on a risk factor using observational data. We consider the scenario in which there is a pharmacomimetic (that is, treatment-mimicking) genetic variant that can be used as a proxy for a particular pharmacological treatment that changes the level of the risk factor. If the association of the pharmacomimetic genetic variant with the risk factor is stronger in one subgroup of the population, then we may expect the effect of the treatment to be stronger in that subgroup. We test for gene–gene interactions in the associations of variants with a modifiable risk factor, where one genetic variant is treated as pharmacomimetic and the other as an effect modifier, to find genetic sub-groups of the population with different predicted response to treatment. If individual genetic variants that are strong effect modifiers cannot be found, moderating variants can be combined using a random forest of interaction trees method into a polygenic response score, analogous to a polygenic risk score for risk prediction. We illustrate the application of the method to investigate effect heterogeneity in the effect of statins on low-density lipoprotein cholesterol.
Population-based stroke surveillance using Big Data: epidemiological trends in admissions and mortality in Australia
Authors: Gattellari Melina , Goumas Chris , Jalaludin Bin , Worthington John M. 
Published: January 2020

AbstractBackgroundEpidemiological trends for major causes of death and disability, such as stroke, may be monitored using administrative data to guide public health initiatives and service delivery.MethodsWe calculated admissions rates for ischaemic stroke, intracerebral haemorrhage or subarachnoid haemorrhage between January 1, 2005 and December 31st, 2013 and rates of 30-day mortality and 365-day mortality in 30-day survivors to December 31st 2014 for patients aged 15 years or older from New South Wales, Australia (population 7.99 million). Annual Average Percentage Change in rates was estimated using negative binomial regression.ResultsOf 81,703 eligible admissions, 64,047 (78.4%) were ischaemic strokes and 13,302 (16.3%) and 4,778 (5.8%) were intracerebral and subarachnoid haemorrhages, respectively. Intracerebral haemorrhage admissions significantly declined by an average of 2.2% annually (95% Confidence Interval=-3.5% to −0.9%) (p<0.001). Thirty-day mortality rates significantly declined for ischaemic stroke (Average Percentage Change −2.9%, 95% Confidence Interval=-5.2% to −1.0%) (p=0.004) and subarachnoid haemorrhage (Average Percentage Change=-2.6%, 95% Confidence Interval=-4.8% to −0.2%) (p=0.04). Mortality at 365-days amongst 30-day survivors of ischaemic stroke and intracerebral haemorrhage was stable over time and increased in 30-day survivors of subarachnoid haemorrhage (Annual Percentage Change 6.2%, 95% Confidence Interval=-0.1% to 12.8%), although the increase was not statistically significant (p=0.05).ConclusionImproved prevention may have underpinned declining intracerebral haemorrhage rates while gains in survival suggest that innovations in stroke care are being successfully translated. Longer-term mortality in patients surviving the acute period is unchanged and may be increasing for subarachnoid haemorrhage warranting investment in post-discharge care and secondary prevention.
Assessment of Machine Learning Algorithms for Prediction of Breast Cancer Malignancy Based on Mammogram Numeric Data
Authors: Habib Peter T. , Alsamman Alsamman M. , Hassnein Sameh E. , Shereif Ghada A. , Hamwieh Aladdin 
Published: January 2020

Abstractin 2019, estimated New Cases 268.600, Breast cancer has one of the most common cancers and is one of the world’s leading causes of death for women. Classification and data mining is an efficient way to classify information. Particularly in the medical field where prediction techniques are commonly used for early detection and effective treatment in diagnosis and research.These paper tests models for the mammogram analysis of breast cancer information from 23 of the more widely used machine learning algorithms such as Decision Tree, Random forest, K-nearest neighbors and support vector machine. The spontaneously splits results are distributed from a replicated 10-fold cross-validation method. The accuracy calculated by Regression Metrics such as Mean Absolute Error, Mean Squared Error, R2 Score and Clustering Metrics such as Adjusted Rand Index, Homogeneity, V-measure.accuracy has been checked F-Measure, AUC, and Cross-Validation. Thus, proper identification of patients with breast cancer would create care opportunities, for example, the supervision and the implementation of intervention plans could benefit the quality of long-term care. Experimental results reveal that the maximum precision 100%with the lowest error rate is obtained with Ada-boost Classifier.
Bimodal distribution and set point HBV DNA viral loads in chronic infection: retrospective analysis of cohorts from the UK and South Africa
Authors: Downs Louise O , Vawda Sabeehah , Bester Phillip Armand , Lythgoe Katrina A , Wang Tingyan , McNaughton Anna L , Smith David A , Maponga Tongai , Freeman Oliver , Várnai Kinga A , Davies Jim , Woods Kerrie , Fraser Christophe , Barnes Eleanor , Goedhals Dominique , Matthews Philippa C 
Published: January 2020

AbstractHepatitis B virus (HBV) DNA viral loads (VL) show wide variation between individuals with chronic hepatitis B (CHB) infection, and are used to determine treatment eligibility. There are few refined descriptions of VL distribution in CHB, and limited understanding of the biology that underpins these patterns. We set out to describe the VL distribution in independent cohorts from the UK and South Africa, to identify associated host characteristics, and to compare with VL in HIV-1 and hepatitis C (HCV) infection. We show the presence of a set-point in chronic HBV infection and report significant differences in the viral load distribution of HBV when compared to HIV and HCV.
DDIEM: Drug Database for Inborn Errors of Metabolism
Authors: Abdelhakim Marwa , McMurray Eunice , Syed Ali Raza , Kafkas Senay , Kamau Allan Anthony , Schofield Paul N , Hoehndorf Robert 
Published: January 2020

AbstractBackgroundInborn errors of metabolism (IEM) represent a subclass of rare inherited diseases caused by a wide range of defects in metabolic enzymes or their regulation. Of over a thousand characterized IEMs, only about half are understood at the molecular level, and overall the development of treatment and management strategies has proved challenging. An overview of the changing landscape of therapeutic approaches is helpful in assessing strategic patterns in the approach to therapy, but the information is scattered throughout the literature and public data resources.ResultsWe gathered data on therapeutic strategies for 299 diseases into the Drug Database for Inborn Errors of Metabolism (DDIEM). Therapeutic approaches, including both successful and ineffective treatments, were manually classified by their mechanisms of action using a new ontology.ConclusionsWe present a manually curated, ontologically formalized knowledgebase of drugs, therapeutic procedures, and mitigated phenotypes. DDIEM is freely available through a web interface and for download athttp://ddiem.phenomebrowser.net.
Portable Automated Rapid Testing (PART) for auditory assessment: Validation in a young adult normal-hearing population
Authors: de Larrea-Mancera E. Sebastian Lelo , Stavropoulos Trevor , Hoover Eric C. , Eddins David A. , Gallun Frederick J. , Seitz Aaron R. 
Published: January 2020

AbstractThis study aims to determine the degree to which Portable Automated Rapid Testing (PART), a freely-available program running on a tablet computer, is capable of reproducing standard laboratory results. Undergraduate students were assigned to one of three within-subject conditions that examined repeatability of performance on a battery of psychoacoustical tests of temporal fine structure processing, spectro-temporal amplitude modulation, and targets in competition. The Repeatability condition examined test/retest with the same system, the Headphones condition examined the effects of varying headphones (passive and active noise-attenuating), and the Noise condition examined repeatability in the presence of recorded cafeteria noise. In general, performance on the test battery showed high repeatability, even across manipulated conditions, and was similar to that reported in the literature. These data serve as validation that suprathreshold psychoacoustical tests can be made accessible to run on consumer-grade hardware and performed in less controlled settings. This dataset also provides a distribution of thresholds that can be used as a normative baseline against which auditory dysfunction can be identified in future work.
Phosphoglycerol-type wall- and lipoteichoic acids are enantiomeric polymers differentially cleaved by the stereospecific glycerophosphodiesterase GlpQ
Authors: Walter Axel , Unsleber Sandra , Rismondo Jeanine , Jorge Ana Maria , Peschel Andreas , Gründling Angelika , Mayer Christoph 
Published: January 2020

ABSTRACTThe cell envelope of Gram-positive bacteria generally comprises two types of polyanionic polymers, either linked to peptidoglycan, wall teichoic acids (WTA), or to membrane glycolipids, lipoteichoic acids (LTA). In some bacteria, includingBacillus subtilisstrain 168, WTA and LTA both are glycerolphosphate polymers, yet are synthesized by different pathways and have distinct, although not entirely understood morphogenetic functions during cell elongation and division. We show here that the exo-lyticsn-glycerol-3-phosphodiesterase GlpQ can discriminate betweenB. subtilisWTA and LTA polymers. GlpQ completely degrades WTA, lacking modifications at the glycerol residues, by sequentially removing glycerolphosphates from the free end of the polymer up to the peptidoglycan linker. In contrast, GlpQ is unable to cleave unmodified LTA. LTA can only be hydrolyzed by GlpQ when the polymer is partially pre-cleaved, thereby allowing GlpQ to get access to the end of the polymer that is usually protected by a connection to the lipid anchor. This indicates that WTA and LTA are enantiomeric polymers: WTA is made ofsn-glycerol-3-phosphate and LTA is made ofsn-glycerol-1-phosphate. Differences in stereochemistry between WTA and LTA were assumed based on differences in biosynthesis precursors and chemical degradation products, but so far had not been demonstrated directly by differential, enantioselective cleavage of isolated polymers. The discriminative stereochemistry impacts the dissimilar physiological and immunogenic properties of WTA and LTA and enables independent degradation of the polymers, while appearing in the same location; e.g. under phosphate limitation,B. subtilis168 specifically hydrolyzes WTA and synthesizes phosphate-free teichuronic acids in exchange.
Nα-acetylation of EsxA is required for mycobacterial cytosolic translocation and virulence
Authors: Aguilera Javier , Karki Chitra B. , Li Lin , Vazquez-Reyes Salvador , Zhang Qi , Arico Chenoa D. , Ouellet Hugues , Sun Jianjun 
Published: January 2020

AbstractMycobacterium tuberculosisvirulence factors, EsxA and EsxB, are secreted as a heterodimer (EsxA:B) and play an essential role in mycobacterial phagosomal escape and cytosolic translocation. Current studies support a model that EsxA must dissociate from its chaperon EsxB at low pH in order for EsxA to interact with host membranes. However, the mechanism of the heterodimer separation is not clear. In the present study, we have obtained evidence that the Nα-acetylation of Thr2 on EsxA, a post-translational modification that is present in mycobacteria, but absent inE. coli, is required for the heterodimer separation. The point mutations at Thr2 without Nα-acetylation inhibited the heterodimer separation and hence prevented EsxA from interacting with the membranes, which resulted in attenuated mycobacterial cytosolic translocation and virulence. Molecular dynamic simulation showed that at low pH the Nα-acetylated Thr2 made direct and frequent “bind-and-release” contacts with EsxB, which generates a dragging force to pull EsxB away from EsxA.
Species tree disequilibrium positively misleads models of gene family evolution
Authors: Lauterbur M. Elise , Heder Sarah , Yohe Laurel R. , Dávalos Liliana M. 
Published: January 2020

AbstractGene duplication is a key source of evolutionary innovation, and multigene families evolve in a birth-death process, continuously duplicating and pseudogenizing through time. To empirically test hypotheses about adaptive expansion and contraction of multigene families across species, models infer gene gain and loss in light of speciation events and these inferred gene family expansions may lead to interpretations of adaptations in particular lineages. While the relative abundance of a gene subfamily in the subgenome may reflect its functional importance, tests based on this expectation can be confounded by the complex relationship between the birth-death process of gene subfamily evolution and the species phylogeny. Using simulations, we confirmed tree heterogeneity as a confounding factor in inferring multi-gene adaptation, causing spurious associations between shifts in birth-death rate and lineages with higher branching rates. We then used theolfactory receptor(OR) repertoire, the largest gene family in the mammalian genome, of different bat species with divergent diets to test whether expansions in olfactory receptors are associated with shifts to frugivorous diets. After accounting for tree heterogeneity, we robustly inferred that certainORsubfamilies exhibited expansions associated with dietary shifts to frugivory. Taken together, these results suggest ecological correlates of individualORgene subfamilies can be identified, setting the stage for detailed inquiry into within-subfamily functional differences.
A cortical wiring space links cellular architecture, functional dynamics and hierarchies in humans
Authors: Paquola Casey , Seidlitz Jakob , Benkarim Oualid , Royer Jessica , Klimes Petr , Bethlehem Richard A. I. , Larivière Sara , Vos de Wael Reinder , Hall Jeffery A. , Frauscher Birgit , Smallwood Jonathan , Bernhardt Boris C. 
Published: January 2020

AbstractThe vast net of fibres within and underneath the cortex is optimised to support the convergence of different levels of brain organisation. Here we propose a novel coordinate system of the human cortex based on an advanced model of its connectivity. Our approach is inspired by seminal, but so far largely neglected models of cortico-cortical wiring established by post mortem anatomical studies and capitalizes on cutting-edge neuroimaging and machine learning. The new model expands the currently prevailing diffusion MRI tractography approach by incorporation of additional features of cortical microstructure and cortico-cortical proximity. Studying several datasets, we could show that our coordinate system robustly recapitulates established sensory-limbic and anterior-posterior dimensions of brain organisation. A series of validation experiments showed that the new wiring space reflects cortical microcircuit features (including pyramidal neuron depth and glial expression) and allowed for competitive simulations of functional connectivity and dynamics across a broad range contexts (based on resting-state fMRI, task-based fMRI, and human intracranial EEG coherence). Our results advance our understanding of how cell-specific neurobiological gradients produce a hierarchical cortical wiring scheme that is concordant with increasing functional sophistication of human brain organisation. Our evaluations demonstrate the cortical wiring space bridges across scales of neural organisation and can be easily translated to single individuals.