bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of methylglyoxal as a major mutagen in wood and bamboo pyroligneous acids
Authors: Onoda Aya , Asanoma Masaharu , Nukaya Haruo 
Published: February 2016

Abstract
To identify the major mutagen in pyroligneous acid (PA), 10 wood and 10 bamboo pyroligneous acids were examined using the Ames test in Salmonella typhimurium strains TA100 and TA98. Subsequently, the mutagenic dicarbonyl compounds (DCs), glyoxal, methylglyoxal (MG), and diacetyl in PA were quantified using high-performance liquid chromatography, and the mutagenic contribution ratios for each DC were calculated relative to the mutagenicity of PA. Eighteen samples were positive for mutagens and showed the strongest mutagenicity in TA100 in the absence of S9 mix. MG had the highest mutagenic contribution ratio, and its presence was strongly correlated with the specific mutagenicity of PA. These data indicate that MG is the major mutagen in PA.
A global assessment of a large monocot family highlights the need for group-specific analyses of invasiveness
Authors: Moodley Desika , Procheş Şerban , Wilson John R. U. 
Published: February 2016

Abstract
Significant progress has been made in understanding biological invasions recently, and one of the key findings is that the determinants of naturalization and invasion success vary from group to group. Here, we explore this variation for one of the largest plant families in the world, the Araceae. This group provides an excellent opportunity for identifying determinants of invasiveness in herbaceous plants, since it is one of the families most popular with horticulturalists, with species occupying various habitats and comprising many different life forms. We first developed a checklist of 3494 species of Araceae using online databases and literature sources. We aimed to determine whether invasiveness across the introduction–naturalization–invasion continuum is associated to particular traits within the family, and whether analyses focussed on specific life forms can reveal any mechanistic correlates. Boosted regression tree models were based on species invasion statuses as the response variables, and traits associated with human use, biological characteristics and distribution as the explanatory variables. The models indicate that biological traits such as plant life form and pollinator type are consistently strong correlates of invasiveness. Additionally, large-scale correlates such as the number of native floristic regions and number of introduced regions are also influential at particular stages in the invasion continuum. We used these traits to build a phenogram showing groups defined by the similarity of characters. We identified nine groups that have a greater tendency to invasiveness (including Alocasia , the Lemnoideae and Epipremnum ). From this, we propose a list of species that are not currently invasive for which we would recommend a precautionary approach to be taken. The successful management of plant invasions will depend on understanding such context-dependent effects across taxonomic groups, and across the different stages of the invasion process.
Prediction of missing sequences and branch lengths in phylogenomic data
Authors: Darriba Diego , Weiß Michael , Stamatakis Alexandros 
Published: February 2016

Abstract
Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition sequences is that the inferred phylogenies may exhibit extremely long branch lengths. We investigate if statistically predicting missing sequences for organisms by using information from genes/partitions that have data for these organisms alleviates the problem and improves phylogenetic accuracy.
Results: We present several algorithms for correcting excessively long branch lengths induced by missing data. We also present methods for predicting/imputing missing sequence data. We evaluate our algorithms by systematically removing sequence data from three empirical and 100 simulated alignments. We then compare the Maximum Likelihood trees inferred from the gappy alignments and on the alignments with predicted sequence data to the trees inferred from the original, complete datasets. The datasets with predicted sequences showed one to two orders of magnitude more accurate branch lengths compared to the branch lengths of the trees inferred from the alignments with missing data. However, prediction did not affect the RF distances between the trees.
Availability and implementation: https://github.com/ddarriba/ForeSeqs
Contact: diego.darriba@h-its.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Inference for the existence of hormetic dose–response relationships in toxicology studies
Authors: Kim Steven B. , Bartell Scott M. , Gillen Daniel L. 
Published: February 2016

AbstractIn toxicology studies hormesis refers to a dose–response relationship with a stimulatory response at low doses and an inhibitory response at high doses. In this manuscript, we particularly focus on a J-shaped dose–response relationship for binary cancer responses. We propose and examine two new flexible models for testing the hypothesis of hormesis in a Bayesian framework. The first model is parametric and enhances the flexibility of modeling a hormetic zone by using a non-linear predictor in a multistage model. The second model is non-parametric and allows multiple model specifications, weighting the contribution of each model via Bayesian model averaging (BMA). Simulation studies show that the non-parametric modeling approach with BMA provides robust sensitivity and specificity for detecting hormesis relative to the parametric approach, regardless of the shape of a hormetic zone.
Implantable cardioverter-defibrillators in adults with congenital heart disease: a systematic review and meta-analysis
Authors: Vehmeijer Jim T. , Brouwer Tom F. , Limpens Jacqueline , Knops Reinoud E. , Bouma Berto J. , Mulder Barbara J.M. , de Groot Joris R. 
Published: February 2016

Abstract

Aims
Sudden cardiac death is a major cause of mortality in adult congenital heart disease (ACHD) patients. The indications for implantable cardioverter-defibrillator (ICD) implantation in ACHD patients are still not well established. We aim to systematically review the literature on indications and outcome of ICD implantation in ACHD patients.

Methods and results
We performed a comprehensive search in EMBASE, MEDLINE, and Google Scholar to identify all studies on ICD implantation in ACHD patients. We used random effects models to calculate proportions and 95% confidence intervals. Of 1356 articles, 24 studies with 2162 patients were included, with a mean follow-up of 3.6 ± 0.9 years. Half of patients had tetralogy of Fallot. Mean age at implantation was 36.5 ± 5.5 years old and 66% was male. Implantable cardioverter-defibrillators were implanted for primary prevention in 53% (43.5–62.7). Overall, 24% (18.6–31.3) of patients received one or more appropriate ICD interventions (anti-tachycardia pacing or shocks) during 3.7 ± 0.9 years: 22% (16.9–28.8) of patients with primary prevention in 3.3 ± 0.3 years and 35% (26.6–45.2) of patients with secondary prevention in 4.3 ± 1.2 years. Inappropriate shocks occurred in 25% (20.1–31.0) in 3.7 ± 0.8 years and other, particularly lead-related complications in 26% (18.9–33.6) of patients in 3.8 ± 0.8 years. All-cause mortality was 10% during 3.7 ± 0.9 years.

Conclusions
In ACHD, remarkably high rates of appropriate ICD therapy were reported, both in primary and secondary prevention. Because of the young age and lower death rates, the cumulative beneficial effects are likely greater in ACHD patients than in acquired heart disease patients. However, considering the high rates of inappropriate shocks and complications, case-by-case weighing of costs and benefits, remains essential.
CD4 + T-cell subsets in inflammatory diseases: beyond the T h 1/T h 2 paradigm
Authors: Hirahara Kiyoshi , Nakayama Toshinori 
Published: February 2016

AbstractCD4 + T cells are crucial for directing appropriate immune responses during host defense and for the pathogenesis of inflammatory diseases. In addition to the classical biphasic model of differentiation of T-helper 1 (T h 1) and T h 2 cells, unexpected increases in the numbers of CD4 + T-cell subsets, including T h 17, T h 9, T follicular-helper (T fh ) and T-regulatory (T reg ) cells, have been recognized. In the present review, we focus on how these various T-helper cell subsets contribute to the pathogenesis of immune-mediated inflammatory diseases. In particular, we focus on multiple sclerosis, psoriasis and asthma as typical model diseases in which multiple T-helper cell subsets have recently been suggested to play a role. We will also discuss various unique sub-populations of T-helper cells that have been identified. First, we will introduce the heterogeneous T-helper cell subsets, which are classified by their simultaneous expression of multiple key transcription factors. We will also introduce different kinds of memory-type T h 2 cells, which are involved in the pathogenesis of chronic type-2 immune-related diseases. Finally, we will discuss the molecular mechanisms underlying the generation of the plasticity and heterogeneity of T-helper cell subsets. The latest progress in the study of T-helper cell subsets has forced us to reconsider the etiology of immune-mediated inflammatory diseases beyond the model based on the T h 1/T h 2 balance. To this end, we propose another model—the pathogenic T-helper population disease-induction model—as a possible mechanism for the induction and/or persistence of immune-mediated inflammatory diseases.
Female philopatry and limited male-biased dispersal in the Ussuri tube-nosed bat, Murina ussuriensis
Authors: Flanders Jon , Inoue-Murayama Miho , Rossiter Stephen J. , Hill David A. 
Published: February 2016

AbstractMale-biased dispersal and female philopatry are common traits among social mammals, often leading to elevated relatedness within social groups. However, exceptions do occur, with documented cases of female-biased dispersal, dispersal by both sexes, and philopatry of both sexes. In this study, we examined levels of dispersal and relatedness based on analyses of the mitochondrial D-loop and 12 nuclear microsatellite markers in the woodland specialist Ussuri tube-nosed bat ( Murina ussuriensis ), a relatively widespread, yet locally rare species that is thought to be threatened by loss of its forest habitats across its range. A total of 85 individuals were captured in lowland temperate forest on the island of Yakushima and 28 individuals in montane forest in Hokkaido, Japan. In the former, haplotypes showed extreme spatial clustering among females consistent with strong philopatry, but spatial mixing among males suggesting dispersal over short distances. These findings were broadly supported by microsatellite analyses, which indicated considerable genealogical structure within sampling locations but a lack of spatial structure, again indicating that some gene flow does occur in one or both sexes. The Hokkaido data, although limited, did not show these patterns and instead suggest that differences in environmental and behavioral variables may influence movement ecology of individuals at these 2 sites and consequently fine-scale genetic structure within this species.
An evaluation of hair-snaring devices for small-bodied carnivores in southwest China
Authors: Bu Hongliang , Hopkins John B. , Zhang Dan , Li Sheng , Wang Rongjiang , Yao Meng , Wang Dajun 
Published: February 2016

AbstractHuman population growth is a major threat to the biodiversity of mammals in China. Rapid development of infrastructure, pollution, and poor enforcement of environmental laws in China have altered the landscape and accelerated the extinction rates of mammals. To maintain biodiversity and conserve the mammals of China, it is essential to develop monitoring protocols for species of concern that are efficient, cost-effective, and current. It is now common practice for ecologists to survey mammals of interest using noninvasive sampling methods. These sampling techniques are affordable, require no handling of the target animals, and generally yield large samples. In China, such sampling methods have rarely been used and evaluated. For this study, we recorded the behavior of masked palm civets ( Paguma larvata ) and Siberian weasels ( Mustela sibirica ) to determine their relative preference for using different hair-snaring devices and evaluated the effectiveness of each device at collecting hair. Our goal was to determine which genetic sampling method(s) should be used to study masked palm civets and Siberian weasels in the future in Southwest China. In March–June of 2014, we monitored 13 hair-snare stations throughout the Main Valley of Laohegou Nature Reserve, Sichuan Province, China. Genetic analysis revealed that we collected 373 hair samples from civets and 47 hair samples from weasels over 104 and 26 sessions, respectively. Both civets and weasels seemed to prefer lure sticks to ground cubbies; however, the latter were more effective at collecting civet hair. Although glue sheets from lure sticks collected large samples of guard hair (&gt; 10), no device in its current design was consistently effective at collecting weasel hair. We suggest researchers in Southwest China use ground cubbies as described in this study to collect hair from masked palm civets and test other cubby designs (e.g., longer gun brushes or smaller in size) for collecting hair from Siberian weasels.人口增长是中国哺乳动物多样性危机的主要根源之一。在中国，基础建设的快速发展、环境污染，加之环境执法力度不足造成了哺乳动物的栖息地的退化，加速了动物的灭绝速率。为了维持生物多样性水平和保护中国的哺乳动物，有必要针对受关注的物种开发有效、低成本且通用的监测方法。现在，非损伤性取样方法正被生态学家普遍应用于哺乳动物的调查中。这些调查技术在成本上易于接受，不需要接触目标动物，并且通常可以得到大量可靠的样本。在中国，非损伤性取样方法的应用和评估还较少。本研究中，我们在四川省老河沟自然保护区评估了花面狸和黄鼬对毛发陷阱的访问偏好及陷阱收集动物毛发的有效性；目标是选出有效地遗传取样方法用于将来对花面狸和黄鼬的研究。从2014年3月到6月，我们在保护区主要山谷内设置了13个毛发陷阱站，在收集野生动物的毛发同时使用红外相机记录动物访问陷阱站时的行为。我们发现，相比于设置在地面的小室陷阱，花面狸和黄鼬都更喜欢访问直立的木桩陷阱，但是，小室陷阱能够更有效地收集花面狸的毛发。尽管固定有粘性薄片的木桩 陷阱能够少量收集带有直针毛的毛发（&gt;10根）,但是我们评估的毛发陷阱都不能有效地收集黄鼬的 毛发。根据研究，我们建议研究人员在中国西南可以应用固定有枪刷的小室陷阱（如本研究中所评估的）收集花面狸的毛发，而用更长的枪刷，或者更小的小室陷阱，并固定粘性薄片收集黄鼬的毛发。
Hepatitis C Screening in People With Human Immunodeficiency Virus: Lessons Learned From Syphilis Screening
Authors: Wurcel Alysse G. , Chen Daniel D. , Fitzpatrick Rosemary E. , Grasberger Paula E. , Kirshner Caleb H. , Anderson Jordan E. , Chui Kenneth K. H. , Knox Tamsin A. 
Published: February 2016

AbstractBackground.  The incidence of hepatitis C virus (HCV) infection is increasing in human immunodeficiency virus (HIV)-positive men who have sex with men (MSM). New guidelines recommend annual screening for HCV, similar to recommendations for syphilis screening with rapid plasma reagin (RPR).Methods.  This study compares the frequency of repeat HCV antibody (Ab) testing to repeat RPR testing in a retrospective chart review of 359 HCVAb-negative people living with HIV (PLWH) observed in an Infectious Diseases clinic. Patients were classified into risk groups based on sexual risk factors.Results.  Although 85% of PLWH had repeat syphilis screening, less than two thirds had repeat HCVAb screening. The MSM status was associated with increased HCVAb and RPR testing (adjusted odds ratio, 2.6 and 5.9, respectively). Seven persons had incident HCV infection: 3 were MSM, and 4 had symptoms or abnormal laboratory results to prompt testing.Conclusions.  Failure to find incident HCV infection in PLWH represents missed opportunities to cure HCV infection and prevent progressive liver disease. Further quality improvement studies are necessary to develop physician-focused interventions to increase HCV screening rates in PLWH.
Liver Fibrosis Regression Measured by Transient Elastography in Human Immunodeficiency Virus (HIV)-Hepatitis B Virus (HBV)-Coinfected Individuals on Long-Term HBV-Active Combination Antiretroviral Therapy
Authors: Audsley Jennifer , Robson Christopher , Aitchison Stacey , Matthews Gail V. , Iser David , Sasadeusz Joe , Lewin Sharon R. 
Published: February 2016

Abstract
Background.  Advanced fibrosis occurs more commonly in human immunodeficiency virus (HIV)-hepatitis B virus (HBV) coinfected individuals; therefore, fibrosis monitoring is important in this population. However, transient elastography (TE) data in HIV-HBV coinfection are lacking. We aimed to assess liver fibrosis using TE in a cross-sectional study of HIV-HBV coinfected individuals receiving combination HBV-active (lamivudine and/or tenofovir/tenofovir-emtricitabine) antiretroviral therapy, identify factors associated with advanced fibrosis, and examine change in fibrosis in those with &gt;1 TE assessment.
Methods.  We assessed liver fibrosis in 70 HIV-HBV coinfected individuals on HBV-active combination antiretroviral therapy (cART). Change in fibrosis over time was examined in a subset with more than 1 TE result (n = 49). Clinical and laboratory variables at the time of the first TE were collected, and associations with advanced fibrosis (≥F3, Metavir scoring system) and fibrosis regression (of least 1 stage) were examined.
Results.  The majority of the cohort (64%) had mild to moderate fibrosis at the time of the first TE, and we identified alanine transaminase, platelets, and detectable HIV ribonucleic acid as associated with advanced liver fibrosis. Alanine transaminase and platelets remained independently advanced in multivariate modeling. More than 28% of those with &gt;1 TE subsequently showed liver fibrosis regression, and higher baseline HBV deoxyribonucleic acid was associated with regression. Prevalence of advanced fibrosis (≥F3) decreased 12.3% (32.7%–20.4%) over a median of 31 months.
Conclusions.  The observed fibrosis regression in this group supports the beneficial effects of cART on liver stiffness. It would be important to study a larger group of individuals with more advanced fibrosis to more definitively assess factors associated with liver fibrosis regression.
A Critical Reappraisal of Prolonged Neutropenia as a Risk Factor for Invasive Pulmonary Aspergillosis
Authors: Abers Michael S. , Ghebremichael Musie S. , Timmons Allison K. , Warren H. Shaw , Poznansky Mark C. , Vyas Jatin M. 
Published: February 2016

Abstract
Prolonged neutropenia is generally thought to be the major factor for invasive pulmonary aspergillosis (IPA). In the present study, we characterize the frequency, severity, and duration of neutropenia that immediately precedes IPA. Prolonged neutropenia was identified in only one third of all IPA cases and occurred exclusively in hematologic patients.
Age-Related Changes in Binaural Interaction at Brainstem Level
Authors: Van Yper Lindsey N. , Vermeire Katrien , De Vel Eddy F. J. , Beynon Andy J. , Dhooge Ingeborg J. M. 
Published: February 2016

Objectives:
Age-related hearing loss hampers the ability to understand speech in adverse listening conditions. This is attributed to a complex interaction of changes in the peripheral and central auditory system. One aspect that may deteriorate across the lifespan is binaural interaction. The present study investigates binaural interaction at the level of the auditory brainstem. It is hypothesized that brainstem binaural interaction deteriorates with advancing age.

Design:
Forty-two subjects of various age participated in the study. Auditory brainstem responses (ABRs) were recorded using clicks and 500 Hz tone-bursts. ABRs were elicited by monaural right, monaural left, and binaural stimulation. Binaural interaction was investigated in two ways. First, grand averages of the binaural interaction component were computed for each age group. Second, wave V characteristics of the binaural ABR were compared with those of the summed left and right ABRs.

Results:
Binaural interaction in the click ABR was demonstrated by shorter latencies and smaller amplitudes in the binaural compared with the summed monaural responses. For 500 Hz tone-burst ABR, no latency differences were found. However, amplitudes were significantly smaller in the binaural than summed monaural condition. An age-effect was found for 500 Hz tone-burst, but not for click ABR.

Conclusions:
Brainstem binaural interaction seems to decline with age. Interestingly, these changes seem to be stimulus-dependent.
Herpesvirus Infections and Transglutaminase Type 2 Antibody Positivity in Childhood
Authors: Jansen Michelle A.E. , van den Heuvel Diana , van der Zwet Kirsten V.M. , Jaddoe Vincent W.V. , Hofman Albert , Escher Johanna C. , Fraaij Pieter L.A. , Hooijkaas Herbert , van Zelm Menno C. , Moll Henriette A. 
Published: February 2016

ABSTRACTObjectives:Persistent viral infections have been implicated in the etiology of autoimmune diseases in adulthood, but it is not known whether herpesviruses are associated with the development of celiac disease autoimmunity in childhood. We assessed whether herpesvirus infections are associated with transglutaminase type 2 antibody (TG2A) concentrations in children at 6 years of age.Methods:The present study was embedded within a population‐based prospective cohort study. Serum immunoglobulin G levels against Epstein‐Barr virus, cytomegalovirus (CMV), and herpes simplex virus type 1 were measured by enzyme‐linked immunosorbent assay , and TG2A concentrations with fluorescence enzyme immunoassay in 4420 children at 6 years of age. Children were categorized based on TG2A concentrations into negative (<7 U/mL), positive (≥7–70 U/mL), and strongly positive (≥70 U/mL), that is, 10 times upper limit normal.Results:Fifty‐nine children (1.3%) were TG2A positive, and of these 31 (53%) had concentrations 70 U/mL or more. Children with TG2A concentrations 70 U/mL or more were less often infected with CMV (adjusted odds ratio (aOR) 0.38, 95% CI 0.14–0.98, P = 0.04) and with any of the 3 viruses (aOR 0.38, 95% CI 0.18–0.78, P < 0.01) than children with TG2A negative concentrations. In addition, children with TG2A concentrations 70 U/mL or more were less often infected with 2 or more viruses than children with TG2A negative concentrations (aOR 0.15, 95% CI 0.03–0.65, P = 0.01).Conclusions:Both CMV single infection and combined CMV, Epstein‐Barr virus and/or herpes simplex virus type 1 infections are inversely associated with strongly TG2A positivity. This may indicate a protective effect of herpesvirus infections in the pathogenesis of celiac disease autoimmunity.
Quality of Reporting Nutritional Randomized Controlled Trials in Patients With Cystic Fibrosis
Authors: Daitch Vered , Babich Tanya , Singer Pierre , Leibovici Leonard 
Published: February 2016

AbstractObjective:Randomized controlled trials (RCTs) have a major role in the making of evidence‐based guidelines. The aim of the present study was to critically appraise the RCTs that addressed nutritional interventions in patients with cystic fibrosis.Methods:Embase, PubMed, and the Cochrane Library were systematically searched until July 2015. Methodology and reporting of nutritional RCTs were evaluated by the Consolidated Standards of Reporting Trials (CONSORT) checklist and additional dimensions relevant to patients with CF.Results:Fifty‐one RCTs were included. Full details on methods were provided in a minority of studies. The mean duration of intervention was <6 months. 56.9% of the RCTs did not define a primary outcome; 70.6% of studies did not provide details on sample size calculation; and only 31.4% reported on the subgroup or separated between important subgroups.Conclusions:The examined RCTs were characterized by a weak methodology, a small number of patients with no sample size calculations, a relatively short intervention, and many times did not examine the outcomes that are important to the patient. Improvement over the years has been minor.