bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gender dysphoria in youth: a review of recent literature
Authors: Cartaya Julia , Lopez Ximena 
Published: November 2017

Purpose of review
Transgender individuals including pubertal young people require hormonal therapy, in conjunction with mental health support. These youths are a unique population, with specific and individual desires and needs as they move through the physical and mental transition to the gender with which they identify.

Recent findings
The number of transgender youth presenting for treatment is increasing rapidly. They continue to have a high prevalence of mental health disorders, though not when supported in their sex identities by family in younger age. Older children are more susceptible to peer support or lack thereof. Treatment with gonadotropin-releasing hormone agonists remains a mainstay of early therapy, but is associated with high costs and decrease in bone mineral density; androgenic progestogens could be used as a lower cost alternative. Fertility preservation is discussed with the majority of transgender youth, but use of such services is low.

Summary
Transgender youth are an increasingly identified population in need of medical and mental health treatment, as well as social support throughout life.
Potential mechanisms underlying the effect of bariatric surgery on eating behaviour
Authors: Zakeri Roxanna , Batterham Rachel L. 
Published: November 2017

Purpose of review
Reduced energy intake, resulting from favourable changes in eating behaviour, is the predominant driver of weight loss following bariatric surgery. Here we review the most recent studies examining the impact of Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy, the two most common bariatric procedures, upon eating behaviour and the suggested underlying biological mechanisms.

Recent findings
Following RYGB or sleeve gastrectomy, most people report subjective changes in appetite, taste and food preference, with decreased high-fat preference most commonly reported. Objective postsurgery changes in taste and olfactory acuity occur. A new phenomenon, ‘meal-size aversion’, may contribute to reduced postoperative energy intake. Recent studies provide evidence for peptide YY3–36, glucagon-like peptide-1, ghrelin, neurotensin and oleoylethanolamide as mediators of postoperative eating behaviour changes. Factors modulating these changes include sex, type 2 diabetes status, genetics and bariatric procedure. New studies implicate central dopaminergic and opioid receptor signalling as key neural mediators driving altered eating behaviour. Brain neuroimaging studies show that obesity-associated changes in food-cue responses, brain connectivity and structural abnormalities are normalized following bariatric surgery.

Summary
Understanding the biological mechanisms mediating the eating behaviour changes engendered by bariatric surgery may lead to the development of novel therapeutic strategies for people with obesity.
Update on endocrine aspects of childhood obesity
Authors: Baskaran Charumathi , Kandemir Nurgun 
Published: November 2017

Purpose of review
Although childhood obesity has leveled off in the last decade, ‘severe obesity’ continues to be on the rise. Various genetic, environmental and hormonal factors contribute to obesity. This article reviews the most current understanding of obesity's multifactorial origin and recent recommendations for its management in childhood and adolescence.

Recent findings
Epigenetics plays a key role in transmitting obesity risk to offspring. Single-nucleotide polymorphisms at genetic loci for adipokines and their receptors are associated with obesity. Gut microbiota is an important regulator of weight status, and Bifidobacterium species improves metabolic status. The incidence of comorbidities including prediabetes and type 2 diabetes has increased. Novel biomarkers such as alpha-hydroxybutyrate and branched-chain amino acids correlate with insulin sensitivity and predict glycemic control in adolescents. Lifestyle modifications and pharmacotherapy can produce small BMI changes. Bariatric surgery induces substantial weight loss and remission of comorbidities.

Summary
Alterations in genetics, epigenetics and microbiota influence childhood obesity. Lifestyle modification remains the mainstay of management and pharmacotherapy with Food and Drug Administration approved medications is recommended only for patients resistant to lifestyle changes and for comorbidities. Bariatric surgery produces sustained weight loss and cardiovascular benefits and is an effective option for adolescents with severe obesity.
Screening for Trichomonas vaginalis in a Large High-Risk Population: Prevalence Among Men and Women Determined by Nucleic Acid Amplification Testing
Authors: Schwebke Jane , Merriweather Anthony , Massingale Sharon , Scisney Mary , Hill Craig , Getman Damon 
Published: November 2017

Abstract
Men and women attending family planning and sexually transmitted disease clinics for sexually transmitted infection screening in 2012 to 2013 were tested for Trichomonas vaginalis (TV) using a sensitive nucleic acid amplification test. T. vaginalis prevalence in urogenital samples was 11.3% in 77,740 women and 6.1% in 12,604 men, and increased with age in both sexes.
End-Tidal Carbon Dioxide Use for Tracheal Intubation: Analysis From the National Emergency Airway Registry for Children (NEAR4KIDS) Registry
Authors: Langhan Melissa L. , Emerson Beth L. , Nett Sholeen , Pinto Matthew , Harwayne-Gidansky Ilana , Rehder Kyle J. , Krawiec Conrad , Meyer Keith , Giuliano John S. , Owen Erin B. , Tarquinio Keiko M. , Sanders Ron C. , Shepherd Michael , Bysani Gokul Kris , Shenoi Asha N. , Napolitano Natalie , Gangadharan Sandeep , Parsons Simon J. , Simon Dennis W. , Nadkarni Vinay M. , Nishisaki Akira 
Published: November 2017

Objective:
Waveform capnography use has been incorporated into guidelines for the confirmation of tracheal intubation. We aim to describe the trend in waveform capnography use in emergency departments and PICUs and assess the association between waveform capnography use and adverse tracheal intubation–associated events.

Design:
A multicenter retrospective cohort study.

Setting:
Thirty-four hospitals (34 ICUs and nine emergency departments) in the National Emergency Airway Registry for Children quality improvement initiative.

Patients:
Primary tracheal intubation in children younger than 18 years.

Interventions:
None.

Measurements and Main Results:
Patient, provider, and practice data for tracheal intubation procedure including a type of end-tidal carbon dioxide measurement, as well as the procedural safety outcomes, were prospectively collected. The use of waveform capnography versus colorimetry was evaluated in association with esophageal intubation with delayed recognition, cardiac arrest, and oxygen desaturation less than 80%. During January 2011 and December 2015, 9,639 tracheal intubations were reported. Waveform capnography use increased over time (39% in 2010 to 53% in 2015; p < 0.001), whereas colorimetry use decreased (< 0.001). There was significant variability in waveform capnography use across institutions (median 49%; interquartile range, 25–85%; p < 0.001). Capnography was used more often in emergency departments as compared with ICUs (66% vs. 49%; p < 0.001). The rate of esophageal intubation with delayed recognition was similar with waveform capnography versus colorimetry (0.39% vs. 0.46%; p = 0.62). The rate of cardiac arrest was also similar (p = 0.49). Oxygen desaturation occurred less frequently when capnography was used (17% vs. 19%; p = 0.03); however, this was not significant after adjusting for patient and provider characteristics.

Conclusions:
Significant variations existed in capnography use across institutions, with the use increasing over time in both emergency departments and ICUs. The use of capnography during intubation was not associated with esophageal intubation with delayed recognition or the occurrence of cardiac arrest.
HIV and Age Do Not Synergistically Affect Age-Related T-Cell Markers
Authors: Farhadian Shelli , Jalbert Emilie , Deng Yanhong , Goetz Matthew B. , Park Lesley S. , Justice Amy C. , Dubrow Robert , Emu Brinda 
Published: November 2017

Introduction:
Despite major progress in controlling HIV disease through antiretroviral therapy, changes in immune phenotype and function persist in individuals with chronic HIV, raising questions about accelerated aging of the immune system.

Methods:
We conducted a cross-sectional study (2005–2007) of HIV-infected (n = 111) and uninfected (n = 114) men from the Veterans Aging Cohort Study. All HIV-infected subjects were on antiretroviral therapy with VL <400 copies/mL for at least 3 years. T-cell markers were examined using flow cytometry. We evaluated the impact of HIV serostatus and age on T-cell phenotypes (expressed as percentages of the total CD4+ and CD8+ T-cell population) using multivariate linear regression, adjusted for smoking, alcohol, and race/ethnicity. We tested for interactions between HIV and age by including interaction terms.

Results:
Among both HIV-infected and uninfected subjects, increasing age was associated with a decreased proportion of naive CD4+ T cells (P = 0.014) and CD8+ T cells (P < 0.0001). Both HIV infection and increasing age were associated with higher proportions of effector memory CD4+ T cells (P < 0.0001 for HIV; P = 0.04 for age) and CD8+ T cells (P = 0.0001 for HIV; P = 0.0004 for age). HIV infection, but not age, was associated with a higher proportion of activated CD8+ T cells (P < 0.0001). For all T-cell subsets tested, there were no significant interactions between HIV infection and age.

Conclusions:
Age and HIV status independently altered the immune system, but we found no conclusive evidence that HIV infection and advancing age synergistically result in accelerated changes in age-associated T-cell markers among virally suppressed individuals.
Can Urodynamic Parameters Predict Sling Revision for Voiding Dysfunction in Women Undergoing Synthetic Midurethral Sling Placement?
Authors: Linder Brian J. , Trabuco Emanuel C. , Gebhart John B. , Klingele Christopher J. , Occhino John A. , Elliott Daniel S. , Lightner Deborah J. 
Published: November 2017

Objective
The objective of the study was to evaluate the utility of urodynamic studies performed before primary midurethral sling placement for stress urinary incontinence in predicting the need for subsequent sling release for voiding dysfunction.

Methods
The health records of women managed with primary synthetic midurethral sling placement at Mayo Clinic (Rochester, MN) from January 1, 2002, to December 31, 2012, were reviewed. The primary outcome was surgical sling release for postoperative voiding dysfunction (ie, prolonged retention, elevated postvoid residual volumes with new voiding symptoms, or de novo onset or worsening of overactive bladder symptoms). Logistic regression models were used to evaluate associations between potential clinical risk factors and the primary outcome.

Results
Overall, 1629 women underwent primary synthetic midurethral sling placement during the study time frame, including 1081 patients (66%) who underwent a preoperative multichannel urodynamic evaluation. A sling release for voiding dysfunction was performed for 51 patients (3.1%) at a median of 1.9 months postoperatively (interquartile range, 1.3–9.3 months). Patients undergoing sling release were significantly more likely to have had retropubic sling placement (P = 0.003) and concomitant prolapse surgery (P = 0.005). On univariate analysis, no urodynamic parameters were associated with the risk of sling release; evaluated parameters included peak flow rate (P = 0.20), postvoid residual volume (P = 0.37), voiding without detrusor contraction (P = 0.96), and detrusor pressure at maximal flow (P = 0.23).

Conclusions
Sling release for voiding dysfunction was rare in our cohort. No urodynamic parameters were associated with the risk of sling release.
Origin of life in a digital microcosm
Authors: C G Nitash , LaBar Thomas , Hintze Arend , Adami Christoph 
Published: November 2017

While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry). We generated the exhaustive set of minimal-genome self-replicators and analysed the network structure of this fitness landscape. We further examined the evolvability of these self-replicators and found that the evolvability of a self-replicator is dependent on its genomic architecture. We also studied the differential ability of replicators to take over the population when competed against each other, akin to a primordial-soup model of biogenesis, and found that the probability of a self-replicator outcompeting the others is not uniform. Instead, progenitor (most-recent common ancestor) genotypes are clustered in a small region of the replicator space. Our results demonstrate how computational systems can be used as test systems for hypotheses concerning the origin of life.This article is part of the themed issue ‘Reconceptualizing the origins of life’.
The role of public goods in planetary evolution
Authors: McInerney James O. , Erwin Douglas H. 
Published: November 2017

Biological public goods are broadly shared within an ecosystem and readily available. They appear to be widespread and may have played important roles in the history of life on Earth. Of particular importance to events in the early history of life are the roles of public goods in the merging of genomes, protein domains and even cells. We suggest that public goods facilitated the origin of the eukaryotic cell, a classic major evolutionary transition. The recognition of genomic public goods challenges advocates of a direct graph view of phylogeny, and those who deny that any useful phylogenetic signal persists in modern genomes. Ecological spillovers generate public goods that provide new ecological opportunities.
This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Bayesian estimation of MSM population size in Côte d’Ivoire
Authors: Datta Abhirup , Lin Wenyi , Rao Amrita , Diouf Daouda , Kouame Abo , Edwards Jessie K , Bao Le , Louis Thomas A , Baral Stefan 
Published: November 2017

AbstractCôte d’Ivoire has one of the largest HIV epidemics in West Africa with around half million people living with HIV. Key populations like gay men and other men who have sex with men (MSM) are often disproportionately burdened with HIV due to specific acquisition and transmission risks. Quantifying the MSM population sizes at subnational level is critical to improving the HIV prevention interventions. While survey-based direct estimates of MSM numbers are available at a few urban centers in Cˆote d’Ivoire, no data on MSM population size exists at other areas without any community infrastructure to facilitate sufficient access to the MSM community. We use this limited data in a Bayesian regression setup to produce first empirically calculated estimates of the numbers of MSM in all areas of Cˆote d’Ivoire prioritized in the HIV response. Our hierarchical model imputes missing covariates using geospatial information and allows for proper uncertainty quantification leading to meaningful confidence bounds for the predicted MSM population size estimates. The intended impact of this process is to increase uptake and use of high quality, comprehensive epidemiologic and interventional data in program planning. These estimates will help design future surveys and support the planning of the scale and content of HIV prevention and treatment programs for MSM in Cˆote d’Ivoire.
Mitochondrial Genomes Of The Regionally Extinct Nittany Lion (Puma Concolor From Pennsylvania)
Authors: Evanitsky Maya N. , George Richard J. , Johnson Stephen , Dowell Stephanie , Perry George H. 
Published: November 2017

AbstractMountain lions (Puma concolor) were once endemic across the United States. The Northeastern population of mountain lions has been largely nonexistent since the early 1800s and was officially declared extinct in 2011. This regionally extinct mountain lion is Pennsylvania State University’s official mascot, where it is referred to as the ‘Nittany Lion’. Our goal in this study was to use recent methodological advances in ancient DNA and massively parallel sequencing to reconstruct complete mitochondrial DNA (mtDNA) genomes of multiple Nittany Lions by sampling from preserved skins. This effort is part of a broader Nittany Lion Genome project intended to involve undergraduates in ancient DNA and bioinformatics research and to engage the broader Penn State community in discussions about conservation biology and extinction. Complete mtDNA genome sequences were obtained from five individuals. When compared to previously published sequences, Nittany Lions are not more similar to each other than to individuals from the Western U.S. and Florida. Supporting previous findings, North American mountain lions overall were more closely related to each other than to those from South America and had lower genetic diversity. This result emphasizes the importance of continued conservation in the Western U.S. and Florida to prevent further regional extinctions.
Towards sustainable bioplastic production in resource limited environments using the photoferroautotrophic and photoelectroautotrophic bacteriumRhodopseudomonas palustrisTIE-1
Authors: Ranaivoarisoa Tahina Onina , Rengasamy Karthikeyan , Guzman Michael S. , Singh Rajesh , Bose Arpita 
Published: November 2017

ABSTRACTBioplastics are an attractive alternative to petroleum-derived plastics because of the harmful environmental effects of conventional plastics and the impending fossil fuel crisis. Polyhydroxybutyrate (PHB) is a well-known bioplastic that is produced by several microbes using organic carbon sources. Autotrophic (using carbon dioxide or CO2) PHB production is reported for only a few organisms. Sustainable PHB bioproduction using other autotrophic microbes needs to be explored.Rhodopseudomonas palustris, a metabolically versatile purple non-sulfur bacterium (PNSB) is known to produce PHBs under photoheterotrophic conditions.Rhodopseudomonas palustrisstrain TIE-1 demonstrates extended metabolic versatility by using electron sources such as ferrous iron and poised electrodes for photoautotrophy. Here we report the ability of TIE-1 to produce PHB under photoferroautotrophic (light - energy source, ferrous iron - electron source and CO2- carbon source) and photoelectroautotrophic (light - energy source, poised electrodes - electron source and CO2- carbon source) growth conditions. PHB accumulation was observed both under nitrogen (N2) fixing and non-N2fixing conditions. For comparison, we determined PHB production under chemoheterotrophic, photoheterotrophic and photoautotrophic conditions using hydrogen as the electron donor. Photoferroautotrophic and photoelectroautotrophic PHB production was on par with that observed from organic carbon substrates such as butyrate. PHB production increased during N2fixation under photoheterotrophic conditions but not during photoautotrophic growth. Electron microscopy confirmed that TIE-1 cells accumulate PHBs internally under the conditions that showed highest production. However, gene expression analysis suggests that PHB cycle genes are not differentially regulated despite observable changes in biopolymer production.
The Distribution of Bacterial Doubling Times in the Wild
Authors: Gibson Beth , Wilson Daniel , Feil Edward , Eyre-Walker Adam 
Published: November 2017

AbstractGeneration time varies widely across organisms and is an important factor in the life cycle, life history and evolution of organisms. Although the doubling time (DT), has been estimated for many bacteria in the lab, it is nearly impossible to directly measure it in the natural environment. However, an estimate can be obtained by measuring the rate at which bacteria accumulate mutations per year in the wild and the rate at which they mutate per generation in the lab. If we assume the mutation rate per generation is the same in the wild and in the lab, and that all mutations in the wild are neutral, an assumption that we show is not very important, then an estimate of the DT can be obtained by dividing the latter by the former. We estimate the DT for four species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the lab, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.
Arteria: An automation system for a sequencing core facility
Authors: Dahlberg Johan , Hermansson Johan , Sturlaugsson Steinar , Larsson Pontus 
Published: November 2017

AbstractArteria is an automation system aimed at sequencing core facilities. It is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. Herein we describe the Arteria system and elaborate on the underlying conceptual framework. The Arteria system breaks down into three conceptual levels; orchestration, process and execution. At the orchestration level it utilizes an event-based model of automation. It models processes, e.g. the steps involved in processing sequencing data, as workflows and executes these in a micro-service based environment. This creates a system which is both flexible and scalable. The Arteria Project code is available as open source software at http://www.github.com/arteria-project.
Variation in competitive ability with mating system, ploidy and range expansion in fourCapsellaspecies
Authors: Yang Xuyue , Lascoux Martin , Glémin Sylvain 
Published: November 2017

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (https://dx.doi.org/10.24072/pci.evolbiol.100054)Self-fertilization is often associated with ecological traits corresponding to the ruderal strategy in Grime’s Competitive-Stress-tolerant-Ruderal (CSR) classification of ecological strategies. Consequently, selfers are expected to be less competitive than outcrossers, either because of a colonization/competition trade-off or because of the deleterious genetic effects of selfing. Range expansion could reduce further competitive ability while polyploidy could mitigate the effects of selfing. Although suggested by meta-analyses, these predictions have not been directly tested yet. We compared the competitive ability of fourCapsellaspecies differing by their mating system and ploidy level. For vegetative traits we found no difference in competitive ability neither among species nor among populations. For flower production, we found that the two diploid selfing species (C. rubellaandC. orientalis) were more sensitive to competition than the diploid outcrosser (C. grandiflora), and that the tetraploid selfer (C. bursa-pastoris) was intermediate. WithinC. bursa-pastoris, we also found that sensitivity to competition increased in parallel to range expansion. These results highlight the possible roles of ecological context and ploidy in the evolutionary trajectories of selfing species.