bluuebunny/crossref_metadata_2025_split huggingface dataset:
GAGA protein is essential for male germ cell development in Drosophila
Authors: Dorogova Natalia V. , Fedorova Elena V. , Bolobolova Elena Us. , Ogienko Anna A. , Baricheva Elina M. 
Published: May 2014

SummaryThe Drosophila Trithorax‐like (Trl) gene encodes a GAGA factor which regulates a number of developmentally important genes. In this study, we identify a new function for Drosophila GAGA factor in male germ cell development. Trl mutants carrying strong hypomorphic alleles display loss of primordial germ cells during their migration in embryogenesis and severe disruption in mitochondria structure during early spermatogenesis. The mutation resulted in small testes formation, a deficit of germ cells, abnormal mitochondrial morphogenesis, spermatocyte death through autophagy, and partial or complete male sterility. Pleiotropic mutation effects can be explained by the misexpression of GAGA factor target genes, the products of which are required for germ cell progression into mature sperm. genesis 52:738–751, 2014. © 2014 Wiley Periodicals, Inc.
Synthesis and characterization of polybutylacrylate viscosity index improver with anti‐wear function
Authors: Cai Guoxing , Zhang Letao , Ma Li , Eli Wumanjiang 
Published: May 2014

AbstractA new anti‐wear polybutylacrylate viscosity index improver was prepared and evaluated for lube oil. First, RAFT polymerization of n‐butyl acrylate was carried out, then the polymer intermediate was esterified with n‐butanol, and finally, the polybutylacrylate was obtained. Molecular weight test showed that the Reversible Addition‐Fragmentation Chain Transfer (RAFT) polymerization could obtain the expected molecular weight polymer by controlling the adding amount of RAFT agent. Rotary bomb oxidation test and thermogravimetric analysis demonstrated that this polybutylacrylate had excellent oxidation stability and thermal stability. Anti‐wear test and shear stability test showed that the polybutylacrylate had good anti‐wear property and shear stability. The effects on trihydroxymethyl propane triheptanoate showed that this polybutylacrylate not only could improve the viscosity index but also could improve the anti‐wear property of base oil. And the performance of this polybutylacrylate is affected by their molecular weight. Copyright © 2014 John Wiley & Sons, Ltd.
Apathy in Parkinson's disease is associated with nucleus accumbens atrophy: A magnetic resonance imaging shape analysis
Authors: Carriere Nicolas , Besson Pierre , Dujardin Kathy , Duhamel Alain , Defebvre Luc , Delmaire Christine , Devos David 
Published: May 2014

ABSTRACTApathy is characterized by lack of interest, loss of initiative, and flattening of affect. It is a frequent, very disabling nonmotor complication of Parkinson's disease (PD). The condition may notably occur when dopaminergic medications are tapered after the initiation of subthalamic stimulation and thus can be referred to as “dopaminergic apathy.” Even in the absence of tapering, some patients may develop a form of apathy as PD progresses. This form is often related to cognitive decline and does not respond to dopaminergic medications (dopa‐resistant apathy). We aimed at determining whether dopa‐resistant apathy in PD is related to striatofrontal morphological changes. We compared the shape of the striatum (using spherical harmonic parameterization and sampling in a three‐dimensional point distribution model [SPHARM‐PDM]), cortical thickness, and fractional anisotropy (using tract‐based spatial statistics) in 10 consecutive patients with dopamine‐refractory apathy, 10 matched nonapathetic PD patients and 10 healthy controls. Apathy in PD was associated with atrophy of the left nucleus accumbens. The SPHARM‐PDM analysis highlighted (1) a positive correlation between the severity of apathy and atrophy of the left nucleus accumbens, (2) greater atrophy of the dorsolateral head of the left caudate in apathetic patients than in nonapathetic patients, and (3) greater atrophy in the bilateral nucleus accumbens in apathetic patients than in controls. There were no significant intergroup differences in cortical thickness or fractional anisotropy. Dopa‐resistant apathy in PD was associated with atrophy of the left nucleus accumbens and the dorsolateral head of the left caudate. © 2014 International Parkinson and Movement Disorder Society
Urological fistulas after fetal cystoscopic laser ablation of posterior urethral valves: surgical technical aspects
Authors: Sananes N. , Favre R. , Koh C. J. , Zaloszyc A. , Braun M. C. , Roth D. R. , Moog R. , Becmeur F. , Belfort M. A. , Ruano R. 
Published: May 2014

ABSTRACTObjectiveTo describe the surgical technical aspects associated with the development of urological fistulas after fetal antegrade cystoscopic laser fulguration of the posterior urethral valves (PUV).MethodsThe perioperative data for all fetal cystoscopies performed between January 2004 and August 2013 at three institutions in the USA, France and Brazil were reviewed, with particular emphasis on surgical technical aspects of the procedure and the complications encountered.ResultsA total of 40 fetal cystoscopies were performed at the three institutions. Laser fulguration of the PUV was performed in 23 of these cases, with a survival rate of 60.9% (14/23) and normal renal function in 85.7% (12/14) of these infants. Urological fistulas were diagnosed postnatally in four (10%) newborns. The presence of fistulas was associated with a higher gestational age at diagnosis of PUV (P < 0.01) and with the use of semi‐curved rather than curved sheaths (P < 0.01), the use of a diode laser (P < 0.01) and the use of higher laser power and energy (P < 0.01 and P < 0.01, respectively), as well as with less operator experience (P < 0.01) and with absence of fetal anesthesia/immobilization (P = 0.02).ConclusionUrological fistulas are a severe complication of fetal cystoscopic laser fulguration of PUV and are associated with type, energy and power settings of the laser and instrumentation. The use of appropriate technique and proper training of the operator are necessary to perform this fetal intervention safely. Copyright © 2014 ISUOG. Published by John Wiley & Sons Ltd.
Connection to parents and healthy separation during adolescence: A longitudinal perspective
Authors: Ponappa Sujata , Bartle‐Haring Suzanne , Day Randal 
Published: May 2014

ABSTRACTThe purpose of our study was to investigate how connection between parents and children influences the child's healthy separation during adolescence. We analyzed 3 waves of panel data from a study (Flourishing Families Project) of 500 families with children who were 10–13 years old at Time 1. This study includes information from the perspective of the child and his/her mother over a 4 year period for two‐parent families and mother‐headed households. Findings supported our hypothesis that a mutual sense of connection between mothers and adolescents supported the adolescent's healthy separation over time, with differences due to sex of the child, ethnicity and income. Pubertal maturation was negatively associated with the sense of connection between adolescents and mothers in our sample of young adolescents. We discuss these findings in relation to previous literature.
Three children with autism spectrum disorder learn to perform a three‐step communication sequence using an iPad®‐based speech‐generating device
Authors: Waddington Hannah , Sigafoos Jeff , Lancioni Giulio E. , O'Reilly Mark F. , van der Meer Larah , Carnett Amarie , Stevens Michelle , Roche Laura , Hodis Flaviu , Green Vanessa A. , Sutherland Dean , Lang Russell , Marschik Peter B. 
Published: May 2014

AbstractBackgroundMany children with autism spectrum disorder (ASD) have limited or absent speech and might therefore benefit from learning to use a speech‐generating device (SGD). The purpose of this study was to evaluate a procedure aimed at teaching three children with ASD to use an iPad®‐based SGD to make a general request for access to toys, then make a specific request for one of two toys, and then communicate a thank‐you response after receiving the requested toy.MethodA multiple‐baseline across participants design was used to determine whether systematic instruction involving least‐to‐most‐prompting, time delay, error correction, and reinforcement was effective in teaching the three children to engage in this requesting and social communication sequence. Generalization and follow‐up probes were conducted for two of the three participants.ResultsWith intervention, all three children showed improvement in performing the communication sequence. This improvement was maintained with an unfamiliar communication partner and during the follow‐up sessions.ConclusionWith systematic instruction, children with ASD and severe communication impairment can learn to use an iPad‐based SGD to complete multi‐step communication sequences that involve requesting and social communication functions.
PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM
Authors: Ghanat Bari Mehrab , Ma Xuepo , Zhang Jianqiu 
Published: May 2014

Motivation: In liquid chromatography–mass spectrometry/tandem mass spectrometry (LC-MS/MS), it is necessary to link tandem MS-identified peptide peaks so that protein expression changes between the two runs can be tracked. However, only a small number of peptides can be identified and linked by tandem MS in two runs, and it becomes necessary to link peptide peaks with tandem identification in one run to their corresponding ones in another run without identification. In the past, peptide peaks are linked based on similarities in retention time (rt), mass or peak shape after rt alignment, which corrects mean rt shifts between runs. However, the accuracy in linking is still limited especially for complex samples collected from different conditions. Consequently, large-scale proteomics studies that require comparison of protein expression profiles of hundreds of patients can not be carried out effectively.
Method: In this article, we consider the problem of linking peptides from a pair of LC-MS/MS runs and propose a new method, PeakLink (PL), which uses information in both the time and frequency domain as inputs to a non-linear support vector machine (SVM) classifier. The PL algorithm first uses a threshold on an rt likelihood ratio score to remove candidate corresponding peaks with excessively large elution time shifts, then PL calculates the correlation between a pair of candidate peaks after reducing noise through wavelet transformation. After converting rt and peak shape correlation to statistical scores, an SVM classifier is trained and applied for differentiating corresponding and non-corresponding peptide peaks.
Results: PL is tested in multiple challenging cases, in which LC-MS/MS samples are collected from different disease states, different instruments and different laboratories. Testing results show significant improvement in linking accuracy compared with other algorithms.
Availability and implementation: M files for the PL alignment method are available at http://compgenomics.utsa.edu/zgroup/PeakLink
Contact: Michelle.Zhang@utsa.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
compcodeR—an R package for benchmarking differential expression methods for RNA-seq data
Authors: Soneson Charlotte 
Published: May 2014

Summary: compcodeR is an R package for benchmarking of differential expression analysis methods, in particular, methods developed for analyzing RNA-seq data. The package provides functionality for simulating realistic RNA-seq count datasets, an interface to several of the most commonly used differential expression analysis methods and extensive functionality for evaluating and comparing different approaches on real and simulated data.
Availability and implementation: compcodeR is available from http://www.bioconductor.org/packages/release/bioc/html/compcodeR.html
Contact: Charlotte.Soneson@isb-sib.ch or charlottesoneson@gmail.com
Modelling the interaction between the host immune response, bacterial dynamics and inflammatory damage in comparison with immunomodulation and vaccination experiments
Authors: Jarrett Angela M. , Cogan N.G. , Shirtliff M.E. 
Published: May 2014

Abstract
The immune system is a complex system of chemical and cellular interactions that responds quickly to queues that signal infection and then reverts to a basal level once the challenge is eliminated. Here, we present a general, four-component model of the immune system's response to a Staphylococcal aureus (S. aureus) infection, using ordinary differential equations. To incorporate both the infection and the immune system, we adopt the style of compartmenting the system to include bacterial dynamics, damage and inflammation to the host, and the host response. We incorporate interactions not previously represented including cross-talk between inflammation/damage and the infection and the suppression of the anti-inflammatory pathway in response to inflammation/damage. As a result, the most relevant equilibrium of the system, representing the health state, is an all-positive basal level. The model is able to capture eight different experimental outcomes for mice challenged with intratibial osteomyelitis due to S. aureus, primarily involving immunomodulation and vaccine therapies. For further validation and parameter exploration, we perform a parameter sensitivity analysis which suggests that the model is very stable with respect to variations in parameters, indicates potential immunomodulation strategies and provides a possible explanation for the difference in immune potential for different mouse strains.
Factors Associated With Cancer Incidence and With All-Cause Mortality After Cancer Diagnosis Among Human Immunodeficiency Virus-Infected Persons During the Combination Antiretroviral Therapy Era
Authors: Patel Pragna , Armon Carl , Chmiel Joan S. , Brooks John T. , Buchacz Kate , Wood Kathy , Novak Richard M. 
Published: May 2014

Abstract
Background.  Little is known about survival and factors associated with mortality after cancer diagnosis among persons infected with human immunodeficiency virus (HIV).
Methods.  Using Poisson regression, we analyzed incidence rates of acquired immune deficiency syndrome (AIDS)-defining cancers (ADC), non-AIDS-defining infection-related cancers (NADCI), and non-AIDS-defining noninfection-related cancers (NADCNI) among HIV Outpatient Study participants seen at least twice from 1996–2010. All-cause mortality within each cancer category and by calendar period (1996–2000, 2001–2005, 2006–2010) were examined using Kaplan-Meier survival methods and log-rank tests. We identified risk factors for all-cause mortality using multivariable Cox proportional hazard models.
Results.  Among 8350 patients, 627 were diagnosed with 664 cancers. Over the 3 time periods, the age- and sex-adjusted incidence rates for ADC and NADCNI declined (both P &lt; .001) and for NADCI did not change (P = .13). Five-year survival differed by cancer category (ADC, 54.5%; NADCI, 65.8%; NADCNI, 65.9%; P = .018), as did median CD4 cell count (107, 241, and 420 cells/mm3; P &lt; .001) and median log10 viral load (4.1, 2.3, and 2.0 copies/mL; P &lt; .001) at cancer diagnosis, respectively. Factors independently associated with increased mortality for ADC were lower nadir CD4 cell count (hazard ratio [HR] = 3.02; 95% confidence interval [CI], 1.39–6.59) and detectable viral load (≥400 copies/mL; HR = 1.72 [95% CI, 1.01–2.94]) and for NADCNI, age (HR = 1.50 [95% CI, 1.16–1.94]), non-Hispanic black race (HR = 1.92 [95% CI, 1.15–3.24]), lower nadir CD4 cell count (HR = 1.77 [95% CI, 1.07–2.94]), detectable viral load (HR = 1.96 [95% CI, 1.18–3.24]), and current or prior tobacco use (HR = 3.18 [95% CI, 1.77–5.74]).
Conclusions.  Since 1996, ADC and NADCNI incidence rates have declined. Survival after cancer diagnosis has increased with concomitant increases in CD4 cell count in recent years. Advances in HIV therapy, including early initiation of combination antiretroviral therapy, may help reduce mortality risk among HIV-infected persons with cancer.
Rates of Pneumococcal Disease in Adults With Chronic Medical Conditions
Authors: Shea Kimberly M. , Edelsberg John , Weycker Derek , Farkouh Raymond A. , Strutton David R. , Pelton Stephen I. 
Published: May 2014

AbstractBackground.  Although it is widely accepted that adults with immunocompromising conditions are at greatly increased risk of pneumococcal infection, the extent of risk among immunocompetent adults with chronic medical conditions is less certain, particularly in the current era of universal vaccination of children with pneumococcal conjugate vaccines.Methods.  We conducted a retrospective cohort study using data from 3 healthcare claims repositories (2006–2010) to compare rates of pneumococcal disease in immunocompetent adults with chronic medical conditions (“at-risk”) and immunocompromised adults (“high-risk”), with rates in adults without these conditions (“healthy”). Risk profiles and episodes of pneumococcal disease—all-cause pneumonia, pneumococcal pneumonia, and invasive pneumococcal disease (IPD)—were ascertained from diagnosis, procedure, and drug codes.Results.  Rates of all-cause pneumonia among at-risk persons aged 18–49 years, 50–64 years, and ≥65 years were 3.2 (95% confidence interval [CI], 3.1–3.2), 3.1 (95% CI, 3.1–3.1), and 3.0 (95% CI, 3.0–3.0) times the rates in age-matched healthy counterparts, respectively. We idetified rheumatoid arthritis, systemic lupus erythematosus, Crohn's disease, and neuromuscular or seizure disorders as additional at-risk conditions for pneumococcal disease. Among persons with at-risk conditions, the rate of all-cause pneumonia substantially increased with the accumulation of concurrent at-risk conditions (risk stacking): among persons 18–49 years, rate ratios increased from 2.5 (95% CI, 2.5–2.5) in those with 1 at-risk condition to 6.2 (95% CI, 6.1–6.3) in those with 2 conditions, and to 15.6 (95% CI, 15.3–16.0) in those with ≥3 conditions. Findings for pneumococcal pneumonia and IPD were similar.Conclusions.  Despite widespread use of pneumococcal conjugate vaccines, rates of pneumonia and IPD remain disproportionately high in adults with at-risk conditions, including those with conditions not currently included in the Advisory Committee on Immunization Practices’ guidelines for prevention and those with multiple at-risk conditions.
Endothelial Activation and Repair During Hantavirus Infection: Association with Disease Outcome
Authors: Connolly-Andersen Anne-Marie , Thunberg Therese , Ahlm Clas 
Published: May 2014

AbstractBackground.  Endothelial activation and dysfunction play a central role in the pathogenesis of sepsis and viral hemorrhagic fevers. Hantaviral disease is a viral hemorrhagic fever and is characterized by capillary dysfunction, although the underlying mechanisms for hantaviral disease are not fully elucidated.Methods.  The temporal course of endothelial activation and repair were analyzed during Puumala hantavirus infection and associated with disease outcome and a marker for hypoxia, insulin-like growth factor binding protein 1 (IGFBP-1). The following endothelial activation markers were studied: endothelial glycocalyx degradation (syndecan-1) and leukocyte adhesion molecules (soluble vascular cellular adhesion molecule 1, intercellular adhesion molecule 1, and endothelial selectin). Cytokines associated with vascular repair were also analyzed (vascular endothelial growth factor, erythropoietin, angiopoietin, and stromal cell-derived factor 1).Results.  Most of the markers we studied were highest during the earliest phase of hantaviral disease and associated with clinical and laboratory surrogate markers for disease outcome. In particular, the marker for glycocalyx degradation, syndecan-1, was significantly associated with levels of thrombocytes, albumin, IGFBP-1, decreased blood pressure, and disease severity.Conclusions.  Hantaviral disease outcome was associated with endothelial dysfunction. Consequently, the endothelium warrants further investigation when designing future medical interventions.
Gender, Competitiveness, and Career Choices *
Authors: Buser Thomas , Niederle Muriel , Oosterbeek Hessel 
Published: May 2014

AbstractGender differences in competitiveness have been hypothesized as a potential explanation for gender differences in education and labor market outcomes. We examine the predictive power of a standard laboratory experimental measure of competitiveness for the later important choice of academic track of secondary school students in the Netherlands. Although boys and girls display similar levels of academic ability, boys choose substantially more prestigious academic tracks, where more prestigious tracks are more math- and science-intensive. Our experimental measure shows that boys are also substantially more competitive than girls. We find that competitiveness is strongly positively correlated with choosing more prestigious academic tracks even conditional on academic ability. Most important, we find that the gender difference in competitiveness accounts for a substantial portion (about 20%) of the gender difference in track choice.
Spatial variation in water loss predicts terrestrial salamander distribution and population dynamics
Authors: Peterman W.E. , Semlitsch R.D. 
Published: May 2014

AbstractMany patterns observed in ecology, such as species richness, life history variation, habitat use, and distribution have physiological underpinnings. For many ectothermic organisms temperature relations shape these patterns, but for terrestrial amphibians, water balance may supersede temperature as the most critical physiologically-limiting factor. Many amphibian species have little resistance to water loss, which restricts them to moist microhabitats and may significantly affect foraging, dispersal, and courtship. Using plaster models as surrogates for terrestrial plethodontid salamanders, we measured water loss under ecologically-relevant field conditions to estimate the duration of surface activity time across the landscape. Surface activity time was significantly affected by topography, solar exposure, canopy cover, maximum air temperature, and time since rain. Spatially, surface activity times were highest in ravine habitats and lowest on ridges. Surface activity time was a significant predictor of salamander abundance, as well as a predictor of successful recruitment; the probability of a juvenile salamander occupying an area with high surface activity time was two times greater than an area with limited predicted surface activity. Our results suggest that survival, recruitment, or both are demographic processes that are affected by water loss and the ability of salamanders to be surface active. Results from our study extend our understanding of plethodontid salamander ecology, emphasize the limitations imposed by their unique physiology, and highlight the importance of water loss to spatial population dynamics. These findings are timely to understanding the effects that fluctuating temperature and moisture conditions predicted for future climates will have on plethodontid salamanders.