bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neighborhood Characteristics and Frailty: A Scoping Review
Authors: Fritz Heather , Cutchin Malcolm P , Gharib Jamil , Haryadi Neehar , Patel Meet , Patel Nandit 
Published: May 2019

Abstract

Background and Objectives
Frailty is highly prevalent in later life and associated with early mortality and adverse health outcomes. The neighborhood has been identified as an important contributor to individual health, and neighborhood characteristics may contribute to frailty development. A scoping review was conducted of the peer-reviewed literature to better understand how physical and social neighborhood characteristics contribute to frailty.

Research Design and Methods
Following an established scoping review methodology, we searched four peer-reviewed databases for relevant studies published from January 1, 2008, to December 31, 2018. Data extracted from studies included study characteristics, operationalization of neighborhood, the conceptual model of the neighborhood–frailty relationship, operationalization of frailty, and study findings for associations among neighborhood variables and frailty indicators.

Results
A total of 522 articles were identified and 13 articles were included in the final data charting. Existing studies suggest that neighborhood characteristics are associated with frailty in later life. Few studies articulated a conceptual model identifying exact mechanisms through which neighborhood factors affected frailty. Studies designs were mostly cross-sectional. Longitudinal studies did not measure neighborhood characteristics over time. Studies varied considerably in how they operationalized the neighborhood. Frailty was most commonly assessed using a 5-point phenotype or a frailty index approach.

Discussion and Implications
Findings indicate that research on the relationship between neighborhood characteristics and frailty is an emerging area of inquiry. Additional studies are needed to more definitely explicate mechanisms through which neighborhoods contribute to, or protect older adults from, frailty.
Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood
Authors: Zhao Yi , Li Xiao , Zhao Weihua , Wang Jingwan , Yu Jiawei , Wan Ziyun , Gao Kai , Yi Gang , Wang Xie , Fan Bingbing , Wu Qinkai , Chen Bangwei , Xie Feng , Wu Jinghua , Zhang Wei , Chen Fang , Yang Huanming , Wang Jian , Xu Xun , Li Bin , Liu Shiping , Hou Yong , Liu Xiao 
Published: May 2019

Abstract

Background
For both pediatric and adult patients, umbilical cord blood (UCB) transplant is a therapeutic option for a variety of hematologic diseases, such as blood cancers, myeloproliferative disorders, genetic diseases, and metabolic disorders. However, the level of cellular heterogeneity and diversity of nucleated cells in UCB has not yet been assessed in an unbiased and systemic fashion. In the present study, nucleated cells from UCB were subjected to single-cell RNA sequencing to simultaneously profile the gene expression signatures of thousands of cells, generating a rich resource for further functional studies. Here, we report the transcriptomes of 17,637 UCB cells, covering 12 major cell types, many of which can be further divided into distinct subpopulations.

Results
Pseudotemporal ordering of nucleated red blood cells identifies wave-like activation and suppression of transcription regulators, leading to a polarized cellular state, which may reflect nucleated red blood cell maturation. Progenitor cells in UCB also comprise 2 subpopulations with activation of divergent transcription programs, leading to specific cell fate commitment. Detailed profiling of cytotoxic cell populations unveiled granzymes B and K signatures in natural killer and natural killer T-cell types in UCB.

Conclusions
Taken together, our data form a comprehensive single-cell transcriptomic landscape that reveals previously unrecognized cell types, pathways, and mechanisms of gene expression regulation. These data may contribute to the efficacy and outcome of UCB transplant, broadening the scope of research and clinical innovations.
A prototype knockoff filter for group selection with FDR control
Authors: Chen Jiajie , Hou Anthony , Hou Thomas Y 
Published: May 2019

AbstractIn many applications, we need to study a linear regression model that consists of a response variable and a large number of potential explanatory variables, and determine which variables are truly associated with the response. In Foygel Barber & Candès (2015, Ann. Statist., 43, 2055–2085), the authors introduced a new variable selection procedure called the knockoff filter to control the false discovery rate (FDR) and proved that this method achieves exact FDR control. In this paper, we propose a prototype knockoff filter for group selection by extending the Reid–Tibshirani (2016, Biostatistics, 17, 364–376) prototype method. Our prototype knockoff filter improves the computational efficiency and statistical power of the Reid–Tibshirani prototype method when it is applied for group selection. In some cases when the group features are spanned by one or a few hidden factors, we demonstrate that the Principal Component Analysis (PCA) prototype knockoff filter outperforms the Dai–Foygel Barber (2016, 33rd International Conference on Machine Learning (ICML 2016)) group knockoff filter. We present several numerical experiments to compare our prototype knockoff filter with the Reid–Tibshirani prototype method and the group knockoff filter. We have also conducted some analysis of the knockoff filter. Our analysis reveals that some knockoff path method statistics, including the Lasso path statistic, may lead to loss of power for certain design matrices and a specially designed response even if their signal strengths are still relatively strong.
From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics
Authors: Dulanto Chiang Augusto , Dekker John P 
Published: May 2019

AbstractNext-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
Humoral Immune Correlates for Prevention of Postnatal Cytomegalovirus Acquisition
Authors: Saccoccio Frances M , Jenks Jennifer A , Itell Hannah L , Li Shuk Hang , Berry Madison , Pollara Justin , Casper Corey , Gantt Soren , Permar Sallie R 
Published: May 2019

Abstract

Background
Development of a cytomegalovirus (CMV) vaccine is a high priority. However, the ability of antibodies to protect against CMV infection is not well characterized. Studies of maternal antibodies in infants offer the potential to identify humoral correlates of protection against postnatal acquisition.

Methods
This hypothesis-generating study analyzed 29 Ugandan mother-infant pairs that were followed weekly for CMV acquisition. Seventeen mothers and no infants were infected with human immunodeficiency virus (HIV). We evaluated the association between CMV-specific immunoglobulin G (IgG) responses in mothers at the time of delivery and their infants’ CMV status at 6 months of age. We also assessed levels of CMV-specific IgG in infants at 6 weeks of age. CMV-specific IgG responses in the mother-infant pairs were then analyzed on the basis of perinatal HIV exposure.

Results
We found similar levels of multiple CMV glycoprotein–specific IgG binding specificities and functions in mothers and infants, irrespective of perinatal HIV exposure or infant CMV status at 6 months of age. However, the glycoprotein B–specific IgG titer, measured by 2 distinct assays, was higher in infants without CMV infection and was moderately associated with delayed CMV acquisition.

Conclusions
These data suggest that high levels of glycoprotein B–specific IgG may contribute to the partial protection against postnatal CMV infection afforded by maternal antibodies, and they support the continued inclusion of glycoprotein B antigens in CMV vaccine candidates.
Prevalence, Concordance, and Transmission of Human Papillomavirus Infection Among Heterosexual Couples in Liuzhou, China: An Observational Perspective Study
Authors: Su Yingying , Wei Feixue , Huang Xiumin , Li Yafei , Qiu Lingxian , Hu Fangfang , Yang Chaoqi , Zhang Yuejing , Yin Kai , Li Mingqiang , Wu Ting , Xia Ningshao , Zhang Jun 
Published: May 2019

Abstract

Background
Knowledge of human papillomavirus (HPV) transmission dynamics, which have important public health implications for designing HPV vaccination strategies, is scarce in undeveloped areas.

Methods
From May to July 2014, 390 couples were enrolled from the general population in Liuzhou, China. Exfoliated cells from male penis shaft/glans penis/coronary sulcus (PGC) and perianal/anal canal (PA) sites and from female vaginal, vulvar, and PA sites were collected biannually for 1 year.

Results
The HPV type-specific concordance rate between couples was 15.5% (95% confidence interval [CI], 8.5%–25.0%). For anogenital HPV transmission, the male-to-female transmission rate (11.5 [95% CI, 4.3–30.7] per 1000 person-months) was similar to the female-to-male transmission rate (11.3 [95% CI, 5.9–21.7] per 1000 person-months). The concordance rates between male PGC site and female vaginal, vulvar, and PA sites were 20.0%, 21.8%, and 14.9%, respectively, which were significantly higher than expected by chance. Infections transmitted from males to females seemed mainly originated from male genital sites, whereas for female-to-male transmission, the vaginal, vulvar, and PA sites might be all involved.

Conclusions
Among the heterosexual couples with relatively conservative sexual behavior, the anogenital HPV transmission rate for females to males is similar to that of males to females. In addition to the vagina and vulva, the female PA site is also an important reservoir for HPV transmission.
Enterococcus faecalis Escapes Complement-Mediated Killing via Recruitment of Complement Factor H
Authors: Ali Youssif M , Sim Robert B , Schwaeble Wilhelm , Shaaban Mona I 
Published: May 2019

AbstractBackgroundEnterococcus faecalis is considered to be the most important species of enterococci responsible for blood stream infections in critically ill patients. In blood, the complement system is activated via the classical pathway (CP), the lectin pathway (LP), or the alternative pathway (AP), and it plays a critical role in opsonophagocytosis of bacteria including E faecalis.MethodsIn a mouse model of enterococcus peritonitis, BALB-C mice were challenged with a high dose of E faecalis 12 hours after intraperitoneal administration of anti-Factor H (FH) antibodies or isotype control. Four hours later, control mice developed higher bacterial burden in blood and organs compared with mice treated with anti-FH antibodies.ResultsWe demonstrate that complement recognition molecules C1q, CL-11, and murine ficolin-A bind the enterococcus and drive the CP and the LP in human and mouse. We further describe that E faecalis evades the AP by recruitment of FH on its surface. Our results show a strong C3b deposition on E faecalis via both the CP and the LP but not through the AP.ConclusionsThese findings indicate that E faecalis avoids the complement phagocytosis by the AP via sequestering complement FH from the host blood.
First year of pre-exposure prophylaxis implementation in France with daily or on-demand tenofovir disoproxil fumarate/emtricitabine
Authors: Siguier M , Mera R , Pialoux G , Ohayon M , Cotte L , Valin N , Ghosn J , Cua E , Pintado C , Chas J , Barriere G , Durand F , Molina J M 
Published: May 2019

AbstractBackgroundIn January 2016, the French Medicine Agency initiated a Temporary Recommendation for Use (TRU) to allow the use of oral intake of tenofovir disoproxil fumarate and emtricitabine for pre-exposure prophylaxis (PrEP) in adults at high risk of HIV. We report the results of the first year of PrEP implementation in France.MethodsData were collected by physicians using a secured web subject-monitoring interface, with two forms: an initiation form, with patients’ baseline characteristics, and an HIV seroconversion form. Univariate and adjusted multivariate analysis using a logistic regression model were performed to identify baseline factors associated with on-demand PrEP regimen prescription.ResultsFrom 4 January 2016 to 28 February 2017, 3405 subjects were enrolled, with 2774 initiation forms completed; 98.1% were male and 96.9% were MSM. An on-demand regimen was prescribed to 57% of subjects. Older age (OR for participants older than 50 years = 1.76, 95% CI 1.35–2.3, P < 0.001) and site of prescription (OR of former IPERGAY sites = 2.28, 95% CI 1.84–2.83, P < 0.001) were associated with on-demand prescription. Those reporting sexually transmitted infection (STI) and condomless anal sex with at least two different partners were less likely to receive on-demand PrEP (OR = 0.68, 95% CI 0.57–0.82 and 0.75, 95% CI 0.57–0.98, respectively; P < 0.05 for all). Four breakthrough HIV infections were reported during the study, in the context of PrEP interruption or acute infection at the time of PrEP initiation.ConclusionsIn a real-life setting in France, PrEP was used, either daily or on-demand, mostly by MSM, with breakthrough infections being rare.
To Acclimate or Not to Acclimate? Simultaneous Positive and Negative Effects of Acclimation on Susceptibility of Tribolium confusum (Coleoptera: Tenebrionidae) and Oryzaephilus surinamensis (Coleoptera: Silvanidae) to Low Temperatures
Authors: Athanassiou Christos G , Arthur Frank H , Kavallieratos Nickolas G , Hartzer Kris L 
Published: May 2019

Abstract
Laboratory tests on acclimated and nonacclimated life stages of Tribolium confusum Jacquelin du Val (Coleoptera: Tenebrionidae) (adults, pupae, larvae, and eggs) and Oryzaephilus surinamensis (L.) (Coleoptera: Silvanidae) (adults, larvae, and eggs) were conducted at 0, –5, –10, and –15°C to evaluate effects of acclimation on susceptibility to cold treatment. Acclimation of all tested life stages for 7 d at 15°C affected susceptibility of both species to the cold temperatures. After 1 d exposures for ≥2 h, acclimated adults had a noticeable increase in cold tolerance compared with nonacclimated adults for both tested species. Nonacclimated pupae of T. confusum were equally susceptible to cold compared with acclimated pupae at short exposures to low temperatures. Exposure of nonacclimated life stages of T. confusum, at –10°C for 1 d gave 0% survival. Similarly, almost all (99.6%) nonacclimated individuals of O. surinamensis died at –10°C. At 0°C, nonacclimated larvae were more cold tolerant than acclimated larvae, but this trend was reversed when larvae were exposed to –5°C. Mixed results were obtained for larvae of O. surinamensis because in some of the combinations tested, nonacclimated larvae were more tolerant, even at temperatures that were lower than 0°C. In contrast to O. surinamensis, eggs of T. confusum that had not been exposed to cold were not affected by acclimation, while exposure to cold showed increased cold hardiness in acclimated eggs. Results show that individual stored-product insect species may have mixed susceptibility to cold temperatures, which must be taken into account when using cold treatment as a management strategy.
Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning
Authors: Ab Ghani Nur Syatila , Ramlan Effirul Ikhwan , Firdaus-Raih Mohd 
Published: May 2019

AbstractA common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins with similar binding sites may bind to similar drugs, the 3D substructure similarity data can be used to identify similar sites in other proteins that are not known targets. The Drug ReposER (DRug REPOSitioning Exploration Resource) web server is designed to identify potential targets for drug repurposing based on sub-structural similarity to the binding interfaces of known drug binding sites. The application has pre-computed amino acid arrangements from protein structures in the Protein Data Bank that are similar to the 3D arrangements of known drug binding sites thus allowing users to explore them as alternative targets. Users can annotate new structures for sites that are similarly arranged to the residues found in known drug binding interfaces. The search results are presented as mappings of matched sidechain superpositions. The results of the searches can be visualized using an integrated NGL viewer. The Drug ReposER server has no access restrictions and is available at http://mfrlab.org/drugreposer/.
Is hypovitaminosis D associated with fibromyalgia? A systematic review
Authors: Martins Yandara A , Cardinali Camila A E F , Ravanelli Maria Ida , Brunaldi Kellen 
Published: May 2019

Abstract

Context
Recent findings have suggested a high prevalence of vitamin D deficiency or insufficiency in fibromyalgia (FM) patients despite the lack of clinical and pathophysiological evidence.

Objective
A systematic review was conducted to examine the association between vitamin D status and FM, including the effect of vitamin D supplementation.

Data source
PubMed, LILACS, Scopus, SciELO, Cochrane, and EMBASE were searched, from January 2000 to July 2018, using the descriptors “Fibromyalgia” and “Vitamin D.”

Study selection
Trials including FM patients in whom vitamin D levels were assessed were eligible for inclusion.

Data extraction
Data comprised age, gender, country, aims, bias, diagnosis criteria, cutoff point, and status of vitamin D, together with FM symptoms and vitamin D supplementation protocol.

Results
A total of 26 articles were selected. Most of the studies were found to present unreliable control groups and small samples. Experimental data on vitamin D supplementation indicated improvement in certain FM symptoms.

Conclusion
Prevalence of hypovitaminosis D in the FM population and the cause-effect relationship were inconclusive. Nevertheless, vitamin D supplementation may be considered as a co-adjuvant in FM therapy.
Interaction between molecular clouds and MeV–TeV cosmic-ray protons escaped from supernova remnants
Authors: Makino Ken , Fujita Yutaka , Nobukawa Kumiko K , Matsumoto Hironori , Ohira Yutaka 
Published: May 2019

Abstract
Recent discovery of the X-ray neutral iron line (Fe  i Kα at 6.40 keV) around several supernova remnants (SNRs) show that MeV cosmic-ray (CR) protons are distributed around the SNRs and are interacting with neutral gas there. We propose that these MeV CRs are the ones that have been accelerated at the SNRs together with GeV–TeV CRs. In our analytical model, the MeV CRs are still confined in the SNR when the SNR collides with molecular clouds. After the collision, the MeV CRs leak into the clouds and produce the neutral iron line emissions. On the other hand, GeV–TeV CRs had already escaped from the SNRs and emitted gamma-rays through interaction with molecular clouds surrounding the SNRs. We apply this model to the SNRs W 28 and W 44 and show that it can reproduce the observations of the iron line intensities and the gamma-ray spectra. This could be additional support of the hadronic scenario for the gamma-ray emissions from these SNRs.
A Solidaristic Approach to Workers’ Compensation Reform in Taiwan
Authors: Yeh Ming-Jui 
Published: May 2019

Abstract
The workers’ compensation system in Taiwan cannot provide sufficient coverage for all workers. This essay adopts a solidaristic approach to address this issue by analyzing the reasons why workers’ compensation is underdeveloped in Taiwan and what could be done to persuade more key actors to support the reform for a more just policy arrangement. First, through comparison with the healthcare system, it is argued that the lack of solidarity and the perception of relevant similarities could explain the underdevelopment of workers’ compensation. Second, the essay turns to the normative aspect of the issue. Compared with other normative political theories, Iris M. Young’s social connection model provides specific normative guidance that is useful for justifying the allocation of responsibility for a more just workers’ compensation reform.
Channel Flow Past A Near-Wall Body
Authors: Smith F T , Servini P 
Published: May 2019

Summary
Near-wall behaviour arising when a finite sized body moves in a channel flow is investigated for high flow rates. This is over the interactive-flow length scale that admits considerable upstream influence. The focus is first on quasi-steady two-dimensional flow past a thin body in the outer reaches of one of the viscous wall layers. The jump conditions near the front of the body play an important part in the whole solution which involves an unusual multi-structured flow due to the presence of the body: flows above, below, ahead of and behind the body interact fully. Analytical solutions are presented and the repercussions for shorter and longer bodies are then examined. Second, implications are followed through for the movement of a free body in a dynamic fluid–body interaction. Particular key findings are that instability persists for all body lengths, the growth rate decreases like the $1/4$ power of distance as the body approaches the wall, and lift production on the body is dominated by high pressures from an unexpected flow region emerging on the front of the body.
Pairwise Kidney Exchange over the Blood Group Barrier
Authors: Andersson Tommy , Kratz Jörgen 
Published: May 2019

AbstractAdvances in medical technology have made kidney transplants over the blood group barrier feasible. This article investigates how such technology should be implemented when designing pairwise kidney exchange programs. The possibility to receive a kidney transplant from a blood group incompatible donor motivates an extension of the preference domain, allowing patients to distinguish between compatible donors and half-compatible donors (i.e. blood group incompatible donors that only become compatible after undergoing an immunosuppressive treatment). It is demonstrated that the number of transplants can be substantially increased by providing an incentive for patients with half-compatible donors to participate in kidney exchange programs. The results also suggest that the technology is beneficial for patient groups that are traditionally disadvantaged in kidney exchange programs (e.g. blood group O patients). The positive effect of allowing transplants over the blood group barrier is larger than the corresponding effects of including altruistic patient–donor pairs or of allowing three-way exchanges in addition to pairwise exchanges.