bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disparities Within the Disparity—Determining HIV Risk Factors Among Latino Gay and Bisexual Men Attending a Community-Based Clinic in Los Angeles, CA
Authors: Beymer Matthew R. , Weiss Robert E. , Halkitis Perry N. , Kapadia Farzana , Ompad Danielle C. , Bourque Linda , Bolan Robert K. 
Published: May 2016

Background:
Latino gay, bisexual, and other men who have sex with men (MSM) in the United States have a 50% greater incidence of HIV when compared with White MSM. Previous studies have analyzed factors contributing to condomless anal intercourse among Latino MSM, but few studies have followed cohorts of HIV-negative Latino MSM to determine circumstances for HIV infection. Informed by Syndemics theory, we examine behavioral, biological, and contextual factors associated with HIV infection for Latino MSM.

Methods:
Risk assessment and HIV testing data were analyzed for all initially HIV negative, Latino MSM (n = 3111) visiting a community-based clinic in Los Angeles, CA from January 2009 to June 2014. Survival analyses were used to determine characteristics of Latino MSM who became HIV positive during the study time frame.

Results:
Similar to previous studies of MSM, self-reported history of chlamydia, gonorrhea, and/or syphilis (adjusted hazard ratio (aHR): 1.97; CI: 1.28 to 3.04), receptive condomless anal intercourse (aHR: 1.7; CI: 1.16 to 2.49), and methamphetamine use (aHR: 1.99; CI: 1.15 to 3.43) predicted HIV infection. In addition, originating from Central America (aHR: 2.31; CI: 1.41 to 3.79), Latino ethnicity of the last sex partner (aHR: 1.67; CI: 1.16 to 2.39) and experiencing intimate partner violence (IPV) (aHR: 1.73; CI: 1.13 to 2.64) were also associated with HIV infection among Latino MSM.

Conclusions:
This is the first study to show independent associations between IPV and HIV infection among Latino MSM. This study shows that psychosocial conditions such as IPV fuel HIV incidence among Latino MSM, and psychosocial interventions should be considered to reduce HIV disparities among Latino MSM.
Chronic Morbidity Among Older Children and Adolescents at Diagnosis of HIV Infection
Authors: McHugh Grace , Rylance Jamie , Mujuru Hilda , Nathoo Kusum , Chonzi Prosper , Dauya Ethel , Bandason Tsitsi , Simms Victoria , Kranzer Katharina , Ferrand Rashida A. 
Published: May 2016

Background:
Substantial numbers of children with HIV present to health care services in older childhood and adolescence, previously undiagnosed. These “slow-progressors” may experience considerable chronic ill health, which is not well characterized. We investigated the prevalence of chronic morbidity among children aged 6–15 years at diagnosis of HIV infection.

Methods:
A cross-sectional study was performed at 7 primary care clinics in Harare, Zimbabwe. Children aged 6–15 years who tested HIV positive following provider-initiated HIV testing and counseling were recruited. A detailed clinical history and standardized clinical examination was undertaken. The association between chronic disease and CD4 count was investigated using multivariate logistic regression.

Results:
Of the 385 participants recruited [52% female, median age 11 years (interquartile range 8–13)], 95% were perinatally HIV infected. The median CD4 count was 375 (interquartile range 215–599) cells per cubic millimeter. Although 78% had previous contact with health care services, HIV testing had not been performed. There was a high burden of chronic morbidity: 23% were stunted, 21% had pubertal delay, 25% had chronic skin disease, 54% had a chronic cough of more than 1 month-duration, 28% had abnormal lung function, and 12% reported hearing impairment. There was no association between CD4 count of <500 cells per cubic millimeter or <350 cells per cubic millimeter with WHO stage or these chronic conditions.

Conclusions:
In children with slow-progressing HIV, there is a substantial burden of chronic morbidity even when CD4 count is relatively preserved. Timely HIV testing and prompt antiretroviral therapy initiation are urgently needed to prevent development of chronic complications.
Patient Comfort During Contrast Media Injection in Coronary Computed Tomographic Angiography Using Varying Contrast Media Concentrations and Flow Rates
Authors: Kok Madeleine , Mihl Casper , Hendriks Babs M.F. , Altintas Sibel , Eijsvoogel Nienke G. , Kietselaer Bas L.J.H. , Wildberger Joachim E. , Das Marco 
Published: May 2016

Purpose
Pain sensation and extravasation are potential drawbacks of contrast media (CM) injection during computed tomographic angiography. The purpose was to evaluate safety and patient comfort of higher flow rates in different CM protocols during coronary computed tomographic angiography.

Methods
Two hundred consecutive patients of a double-blind randomized controlled trial (NCT02462044) were analyzed. Patients were randomized to receive 94 mL of prewarmed iopromide 240 mg I/mL at 8.3 mL/s (group I), 75 mL of 300 mg I/mL at 6.7 mL/s (group II), or 61 mL of 370 mg I/mL at 5.4 mL/s (group III), respectively. Iodine delivery rate (2.0 g I/s) and total iodine load (22.5 g I) were kept identical. Outcome was defined as intravascular enhancement, patient comfort during injection, and injection safety, expressed as the occurrence of extravasation. Patients completed a questionnaire for comfort, pain, and stress during CM injection. Comfort was graded using a 5-point scale, 1 representing “very bad” and 5 “very well.” Pain was graded using a 10-point scale, 0 representing “no pain” and 10 “severe pain.” Stress was graded using a 5-point scale, 1 representing “no stress” and 5 “unsustainable stress.”

Results
Mean enhancement levels within the coronary arteries were as follows: 437 ± 104 Hounsfield units (HU) (group I), 448 ± 111 HU (group II), and 447 ± 106 HU (group III), with P ≥ 0.18. Extravasation occurred in none of the patients. Median (interquartile range) for comfort, pain, and stress was, respectively, 4 (4–5), 0 (0–0), and 1 (1–2), with P ≥ 0.68.

Conclusions
High flow rates of prewarmed CM were safely injected without discomfort, pain, or stress. Therefore, the use of high flow rates should not be considered a drawback for CM administration in clinical practice.
Mandibular Distraction in a Patient With Type II Collagenopathy
Authors: Garza Rebecca M. , Alyono Jennifer C. , Dorfman David W. , Wan Derrick C. 
Published: May 2016

Abstract
Kniest dysplasia is an extremely rare form of type II collagenopathy associated with cleft palate, micrognathia, shortened trunk, arms and legs, and club foot. The authors present a case of an infant with this disorder who also had micrognathia and respiratory distress for which mandibular distraction was performed. Although abnormal collagen and impaired endochondral ossification is noted with Kniest dysplasia, adequate bone formation was observed across the distraction gap. Nonetheless, despite stable mandibular advancement, failure to consider concomitant restrictive lung disease resulted in tracheostomy dependence. The authors demonstrate that while successful bone regeneration can be achieved through distraction of intramembranous facial bones, discretion must still be employed in patients with collagenopathies.
Urinary Incontinence and Health-Seeking Behavior Among White, Black, and Latina Women
Authors: Siddiqui Nazema Y. , Ammarell Natalie , Wu Jennifer M. , Sandoval Juan S. , Bosworth Hayden B. 
Published: May 2016

Objective
Fewer than half of women with urinary incontinence (UI) seek care for their condition. Our objective was to qualitatively assess the themes surrounding treatment-seeking behaviors.

Methods
We conducted 12 focus groups with women and, using purposive sampling, we stratified by racial or ethnic group (white, black, Latina) and by UI frequency. All sessions were transcribed and coded for common themes. Comparative thematic analysis was used to describe similarities and differences among groups.

Results
In total, 113 (39 white, 41 black, and 33 Latina) community-dwelling women participated in focus groups. There were no differences in treatment-seeking themes between groups with different UI frequency. However, certain themes emerged when comparing racial/ethnic groups. Women from all groups shared experiences of embarrassment and isolation because of UI, which were impediments to care seeking. White and black women described discussions with close friends or family that led to normalization of symptoms and prevented care seeking. Latina women maintained more secrecy about UI and reported the longest delays in seeking care. Women articulated a higher likelihood of seeking care if they had knowledge of treatment options, but white women were more likely to seek UI-related knowledge compared with black or Latina women. Physician communication barriers were identified in all groups.

Conclusions
Despite similar experiences, there are different perceptions about care seeking among white, black, and Latina women. Culturally relevant educational resources that focus on a range of treatment options may improve knowledge and thus improve care-seeking behaviors in women with UI.
Results of the TOP Study: Prospectively Randomized Multicenter Trial of an Ex Vivo Tacrolimus Rinse Before Transplantation in EDC Livers
Authors: Pratschke Sebastian , Arnold Hannah , Zollner Alfred , Heise Michael , Pascher Andreas , Schemmer Peter , Scherer Marcus N. , Bauer Andreas , Jauch Karl-Walter , Werner Jens , Guba Markus , Angele Martin K. 
Published: May 2016

Background
Organ shortage results in the transplantation of extended donor criteria (EDC) livers which is associated with increased ischemia-reperfusion injury (IRI). Experimental studies indicate that an organ rinse with the calcineurin inhibitor tacrolimus before implantation protects against IRI. The tacrolimus organ perfusion study was initiated to examine the effects of ex vivo tacrolimus perfusion on IRI in transplantation of EDC livers.

Methods
A prospective randomized multicenter trial comparing ex vivo perfusion of marginal liver grafts (≥2 EDC according to Eurotransplant manual) with tacrolimus (20 ng/mL) or histidine-tryptophane-ketoglutarate solution (control) was carried out at 5 German liver transplant centers (Munich Ludwig-Maximilians University, Berlin, Heidelberg, Mainz, Regensburg) between October 2011 and July 2013. Primary endpoint was the maximum alanine transaminase (ALT) level within 48 hours after transplantation. Secondary endpoints were aspartate transaminase (AST), prothrombine ratio, and graft-patient survival within an observation period of 1 week. After an interim analysis, the study was terminated by the scientific committee after the treatment of 24 patients (tacrolimus n = 11, Control n = 13).

Results
Tacrolimus rinse did not reduce postoperative ALT peaks compared with control (P = 0.207; tacrolimus: median, 812; range, 362-3403 vs control: median, 652; range, 147-2034). Moreover, ALT (P = 0.100), prothrombine ratio (P = 0.553), and bilirubin (P = 0.815) did not differ between the groups. AST was higher in patients treated with tacrolimus (P = 0.011). Survival was comparable in both groups (P > 0.05).

Conclusions
Contrary to experimental findings, tacrolimus rinse failed to improve the primary endpoint of the study (ALT). Because 1 secondary endpoint (AST) was even higher in the intervention group, the study was terminated prematurely. Thus, tacrolimus rinse cannot be recommended in transplantation of EDC livers.
How human behavior drives the propagation of an emerging infection: the case of the 2014 Chikungunya outbreak in Martinique
Authors: Roche Benjamin , Gaillard Béatrice , Léger Lucas , Moutenda Renélise , Sochacki Thomas , Cazelles Bernard , Ledrans Martine , Blateau Alain , Fontenille Didier , Etienne Manuel , Simard Frédéric , Salathé Marcel , Yébakima André 
Published: May 2016

AbstractUnderstanding the spatio-temporal dynamics of endemic infections is of critical importance for a deeper understanding of pathogen transmission, and for the design of more efficient public health strategies. However, very few studies in this domain have focused on emerging infections, generating a gap of knowledge that hampers epidemiological response planning. Here, we analyze the case of a Chikungunya outbreak that occurred in Martinique in 2014. Using time series estimates from a network of sentinel practitioners covering the entire island, we first analyze the spatio-temporal dynamics and show that the largest city has served as the epicenter of this epidemic. We further show that the epidemic spread from there through two different propagation waves moving northwards and southwards, probably by individuals moving along the road network. We then develop a mathematical model to explore the drivers of the temporal dynamics of this mosquito-borne virus. Finally, we show that human behavior, inferred by a textual analysis of messages published on the social network Twitter, is required to explain the epidemiological dynamics over time. Overall, our results suggest that human behavior has been a key component of the outbreak propagation, and we argue that such results can lead to more efficient public health strategies specifically targeting the propagation process.
Maftools: Efficient analysis, visualization and summarization of MAF files from large-scale cohort based cancer studies
Authors: Mayakonda Anand , Koeffler H Phillip 
Published: May 2016

AbstractMutation Annotation Format (MAF) has become a standard file format for storing somatic/germline variants derived from sequencing of large cohort of cancer samples. MAF files contain a list of all variants detected in a sample along with various annotations associated with the putative variant. MAF file forms the basis for many downstream analyses and provides complete landscape of the cohort. Here we introduce maftools–an R package that provides rich source of functions for performing various analyses, visualizations and summarization of MAF files. Maftools uses data.table library for faster processing/summarization and ggplot2 for generating rich and publication quality visualizations. Maftools also takes advantages of S4 class system for better data representation, with easy to use and flexible functions.Availability and Implementationmaftools is implemented as an R package available athttps://github.com/PoisonAlien/maftoolsContactcsiamt@nus.edu.sg
Robust high throughput prokaryotede novoassembly and improvement pipeline for Illumina data
Authors: Page Andrew J. , De Silva Nishadi , Hunt Martin , Quail Michael A. , Parkhill Julian , Harris Simon R. , Otto Thomas D. , Keane Jacqueline A. 
Published: May 2016

ABSTRACTThe rapidly reducing cost of bacterial genome sequencing has lead to its routine use in large scale microbial analysis. Though mapping approaches can be used to find differences relative to the reference, many bacteria are subject to constant evolutionary pressures resulting in events such as the loss and gain of mobile genetic elements, horizontal gene transfer through recombination and genomic rearrangements.De novoassembly is the reconstruction of the underlying genome sequence, an essential step to understanding bacterial genome diversity. Here we present a high throughput bacterial assembly and improvement pipeline that has been used to generate nearly 20,000 draft genome assemblies in public databases. We demonstrate its performance on a public data set of 9,404 genomes. We find all the genes used in MLST schema present in 99.6% of assembled genomes. When tested on low, neutral and high GC organisms, more than 94% of genes were present and completely intact. The pipeline has proven to be scalable and robust with a wide variety of datasets without requiring human intervention. All of the software is available on GitHub under the GNU GPL open source license.DATA SUMMARYThe assembly pipeline software is available from Github under the GNU GPL open source license; (url -https://github.com/sanger-pathogens/vr-codebase)The assembly improvement software is available from Github under the GNU GPL open source license; (url -https://github.com/sanger-pathogens/assembly_improvement)Accession numbers for 9,404 assemblies are provided in the supplementary material.TheBordetella pertussissample has sample accession ERS1058649, sequencing reads accession ERR1274624 and assembly accessions FJMX01000001-FJMX01000249.TheSalmonella enterica subsp. enterica serovarPullorum sample has sample accession ERS1058652, sequencing reads accession ERR1274625 and assembly accession FJMV01000001-FJMV01000026.TheStaphylococcus aureussample has sample accession ERS1058648, sequencing reads accession ERR1274626 and assembly accessions FJMW01000001-FJMW01000040.I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.☑IMPACT STATEMENTThe pipeline described in this paper has been used to assemble and annotate 30% of all bacterial genome assemblies in GenBank (18,080 out of 59,536, accessed 16/2/16). The automated generation ofde novoassemblies is a critical step to explore bacterial genome diversity. MLST genes are found in 99.6% of cases, making it at least as good as existing typing methods. In the test genomes we present, more than 94% of genes are correctly assembled into intact reading frames.
Efficient Maximum-Likelihood Inference For The Isolation-With-Initial-Migration Model With Potentially Asymmetric Gene Flow
Authors: Costa Rui J. , Wilkinson-Herbots Hilde 
Published: May 2016

AbstractThe isolation-with-migration (IM) model is commonly used to make inferences about gene flow during speciation, using polymorphism data. However, Becquet and Przeworski (2009) report that the parameter estimates obtained by fitting the IM model are very sensitive to the model's assumptions (including the assumption of constant gene flow until the present). This paper is concerned with the isolation-with-initial-migration (IIM) model of Wilkinson-Herbots (2012), which drops precisely this assumption. In the IIM model, one ancestral population divides into two descendant subpopulations, between which there is an initial period of gene flow and a subsequent period of isolation. We derive a very fast method of fitting an extended version of the IIM model, which also allows for asymmetric gene flow and unequal population sizes. This is a maximum-likelihood method, applicable to data on the number of segregating sites between pairs of DNA sequences from a large number of independent loci. In addition to obtaining parameter estimates, our method can also be used to distinguish between alternative models representing different evolutionary scenarios, by means of likelihood ratio tests. We illustrate the procedure on pairs of Drosophila sequences from approximately 30,000 loci. The computing time needed to fit the most complex version of the model to this data set is only a couple of minutes. The R code to fit the IIM model can be found in the supplementary files of this paper.
Can healthcare servicescape affect customer’s attitude? A study of the mediating role of image congruence and moderating role of customer’s prior experience
Authors: S. Sreejesh , Sahoo Debjani , Mitra Amarnath 
Published: May 2016

Purpose
– The purpose of this paper is twofold. First, develop and test a conceptual model to understand the relationship between customers’ servicescape perceptions, self-image congruity and attitude in healthcare context. Second, to examine the extent to which the relationship between customers’ self-image congruity to attitude in a fully mediated model is moderated by their prior experience.

Design/methodology/approach
– Utilizing a self-administered survey of 320 customers, the study tested the proposed relationships with robust data analytic techniques.

Findings
– The results show that favorable servicescape perceptions help customers to form image congruence in terms of symbolic and functional elements and thereby strengthen their attitude. Further, servicescape accentuated image congruence have varying effects on customers’ attitude depending up on customers’ prior experience.

Research limitations/implications
– This study emphasized the role of servicescape on self-image congruity formation and customer attitude in a new service context (healthcare), and contribute to the body of existing knowledge on servicescapes and image congruity and further verify the soundness and robustness of the integrative theoretical framework.

Practical implications
– Favorable servicescape perceptions may encourage customers to form image congruence and attitude. In this respect, managers should make efforts to signal desired servicescape perceptions in order to retain existing customers and attract new ones.

Originality/value
– This study was the first to apply an integrative perspective of inference theory and image congruity theory to the context of hospital services to understand the relationship between servicescape, image-congruity and customer attitude.
Determinants of acquisitions in Chinese technology firms: an empirical investigation
Authors: Das Arindam , kapil sheeba 
Published: May 2016

Purpose– Globalization, increasing intensity of competition and access to capital markets have enabled emerging market firms to explore inorganic growth through merger and acquisitions (M & A) over the past two decades. The purpose of this paper is to analyze the role of firm-specific factors on M & A propensity in Chinese technology firms.Design/methodology/approach– The authors analyze data on 152 firms from Mainland China, Hong Kong and Taiwan over a period of 2001-2011 using logistic and count data regression.Findings– The authors find that the factors that influence M & As in these firms differ from the established factors found in M & A in developed economies. Large, low-debt firms have higher acquisition propensity irrespective of their technological strength and they tend to be serial acquirer too.Originality/value– The findings provide new insights into inorganic growth behavior of emerging market technology firms and indicate presence of both exploitative and exploratory motives.
“Raw, free”, and “almost rude”: educating warders’ children on St Helena Penal Establishment
Authors: Brady Tony James 
Published: May 2016

Purpose
– The purpose of this paper is to examine the education of children at St Helena Penal Establishment in Queensland and the trials faced by the educators that delivered their formal schooling. The paper will add to the growing research into the prison island and will provide an insight into a unique facet of education in the newly established Australian State of Queensland.

Design/methodology/approach
– The historical analysis draws on original documents and published works to chronicle the provision of education to the children of warders at the St Helena Penal Establishment.

Findings
– The establishment of the Department of Public Instruction and the introduction of the State Education Act of 1875 were intended to provide Queensland children from 6 to 12 years of age with free, compulsory, and secular primary education. The full implementation of the Act took until 1900, and in the process, initiatives like St Helena State School No. 12, through issues of administrative control, saw teachers excluded from the Department of Public Instruction in order to include schoolchildren under the auspices of the same department.

Research limitations/implications
– The research paper is an initial investigation into the subject and limited by the paucity of primary data available on the topic.

Originality/value
– The case study adds to the growing literature on other aspects of the prison at St Helena, Queensland and adds to knowledge of life on the island. Furthermore, the aspects of control over staff on the island and the requirement for the teachers to double as guards, ready to take up arms in defence of the prison, provides new insights into the obligations placed on some early educators.