bluuebunny/crossref_metadata_2025_split huggingface dataset:
Habitat predicts levels of genetic admixture inSaccharomyces cerevisiae
Authors: Tilakaratna Viranga , Bensasson Douda 
Published: December 2016

AbstractGenetic admixture can provide material for populations to adapt to local environments, and this process has played a crucial role in the domestication of plants and animals. The model yeast,Saccharomyces cerevisiae, has been domesticated multiple times for the production of wine, sake, beer and bread, but the high rate of admixture between yeast lineages has so far been treated as a complication for population genomic analysis. Here we make use of the low recombination rate at centromeres to investigate admixture in yeast using a classic Bayesian approach and a more conservative locus by locus phylogenetic approach developed here. Using both approaches, we find thatS. cerevisiaefrom stable oak woodland habitats are less likely to show recent genetic admixture compared with those isolated from transient habitats such as fruits, wine or human infections. When woodland yeast strains do show recent genetic admixture, the degree of admixture is lower than in strains from other habitats. Furthermore,S. cerevisiaepopulations from oak woodlands are genetically isolated from each other, with only occasional migration between woodlands and local fruit habitats. Application of our phylogenetic approach suggests that there is a previously undetected population in North Africa that is the closest outgroup to the EuropeanS. cerevisiae, including the domesticated Wine population. Thorough testing for admixture inS. cerevisiaetherefore leads to a better understanding of the underlying population structure of the species and will be important for understanding the selective processes underlying domestication in this economically important species.
RNAtor: an Android-based application for biologists to plan RNA sequencing experiments
Authors: Kane Shruti , Garg Himanshu , Krishnan Neeraja M. , Singh Aditya , Panda Binay 
Published: December 2016

AbstractRNA sequencing (RNA-seq) is a powerful technology for identification of novel transcripts (coding, non-coding and splice variants), understanding of transcript structures and estimation of gene and/or allelic expression. There are specific challenges that biologists face in determining the number of replicates to use, total number of sequencing reads to generate for detecting marginally differentially expressed transcripts and the number of lanes in a sequencing flow cell to use for the production of right amount of information. Although past studies attempted answering some of these questions, there is a lack of accessible and biologist-friendly mobile applications to answer these questions. Keeping this in mind, we have developedRNAtor, a mobile application for Android platforms, to aid biologists in correctly designing their RNA-seq experiments. The recommendations fromRNAtorare based on simulations and real data.Availability and ImplementationThe Android version ofRNAtoris available on Google Play Store and the code from GitHub (https://github.com/binaypanda/RNAtor).
The social evolution of siderophore production inPseudomonas aeruginosais environmentally determined
Authors: Harrison Freya , McNally Alan , da Silva Ana C. , Diggle Stephen P. 
Published: December 2016

AbstractBacteria secrete various exoproducts whose benefits can be shared by all cells in the vicinity. The potential importance of these “public goods” in bacterial evolutionary ecology has been extensively studied. Cheating by siderophore-null mutants of the opportunistic pathogenPseudomonas aeruginosahas received particular attention. The potential of siderophore mutants to attenuate virulence, and the possibility of exploiting this for clinical ends, have generated a wealth of publications. However, the possibility that genotype · environment interactions govern the evolutionary consequences of siderophore loss has been almost entirely ignored. A review of the available literature revealed (i) widespread use of an undefined mutant as a siderophore cheat; and (ii) a reliance on experiments conducted in iron-limited minimal medium. Whole genome sequencing of the undefined mutant revealed a range of mutations affecting phenotypes other than siderophore production. We then conducted cheating assays using defined deletion mutants, grown in conditions designed to model infected fluids and tissue in CF lung infection and non-healing wounds. Depending on the environment, we found that siderophore loss could lead to cheating, simple fitness defects, or no fitness effect at all. It is therefore crucial to develop appropriatein vitrogrowth conditions in order to better predict the social evolution of traitsin vivo.
Large-scale network dynamics of beta-band oscillations underlie auditory perceptual decision-making
Authors: Alavash Mohsen , Daube Christoph , Wöestmann Malte , Brandmeyer Alex , Obleser Jonas 
Published: December 2016

AbstractPerceptual decisions vary in the speed at which we make them. Evidence suggests that translating sensory information into behavioral decisions relies on distributed interacting neural populations, with decision speed hinging on power modulations of neural oscillations. Yet, the dependence of perceptual decisions on the large-scale network organization of coupled neural oscillations has remained elusive. We measured magnetoencephalography signals in human listeners who judged acoustic stimuli made of carefully titrated clouds of tone sweeps. These stimuli were used under two task contexts where the participants judged the overall pitch or direction of the tone sweeps. We traced the large-scale network dynamics of source-projected neural oscillations on a trial-by-trial basis using power envelope correlations and graph-theoretical network discovery. Under both tasks, faster decisions were predicted by higher segregation and lower integration of coupled beta-band (~16-28 Hz) oscillations. We also uncovered brain network states that promoted faster decisions and emerged from lower-order auditory and higher-order control brain areas. Specifically, decision speed in judging tone-sweep direction critically relied on nodal network configurations of anterior temporal, cingulate and middle frontal cortices. Our findings suggest that global network communication during perceptual decision-making is implemented in the human brain by large-scale couplings between beta-band neural oscillations.Author SummaryThe speed at which we make perceptual decisions varies. This translation of sensory information into behavioral decisions hinges on dynamic changes in neural oscillatory activity. However, the large-scale neural network embodiment supporting perceptual decision-making is unclear. Alavash et al. address this question by experimenting two auditory perceptual decision-making situations. Using graph-theoretical network discovery, they trace the large-scale network dynamics of coupled neural oscillations to uncover brain network states supporting the speed of auditory perceptual decisions. They find that higher network segregation of coupled beta-band oscillations supports faster auditory perceptual decisions over trials. Moreover, when auditory perceptual decisions are relatively difficult, the decision speed benefits from higher segregation of frontal cortical areas, but lower segregation and integration of auditory cortical areas.
Mortality prediction in sepsis via gene expression analysis: a community approach
Authors: Sweeney Timothy E , Perumal Thanneer M , Henao Ricardo , Nichols Marshall , Howrylak Judith A , Choi Augustine M , Bermejo-Martin Jesús F , Almansa Raquel , Tamayo Eduardo , Davenport Emma E , Burnham Katie L , Hinds Charles J , Knight Julian C , Woods Christopher W , Kingsmore Stephen F , Ginsburg Geoffrey S , Wong Hector R , Parnell Grant P , Tang Benjamin , Moldawer Lyle L , Moore Frederick E , Omberg Larsson , Khatri Purvesh , Tsalik Ephraim L , Mangravite Lara M , Langley Raymond J 
Published: December 2016

AbstractImproved risk stratification and prognosis in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal performance, and do not specifically reveal the underlying dysregulation of sepsis. Here three scientific groups were invited to independently generate prognostic models for 30-day mortality using 12 discovery cohorts (N=650) containing transcriptomic data collected from primarily community-onset sepsis patients. Predictive performance was validated in 5 cohorts of community-onset sepsis patients (N=189) in which the models showed summary AUROCs ranging from 0.765-0.89. Similar performance was observed in 4 cohorts of hospital-acquired sepsis (N=282). Combining the new gene-expression-based prognostic models with prior clinical severity scores led to significant improvement in prediction of 30-day mortality (p<0.01). These models provide an opportunity to develop molecular bedside tests that may improve risk stratification and mortality prediction in patients with sepsis, improving both resource allocation and prognostic enrichment in clinical trials.
Career adaptability as a strategic competence for career development
Authors: Bocciardi Federica , Caputo Andrea , Fregonese Chiara , Langher Viviana , Sartori Riccardo 
Published: December 2016

Purpose
In the current labour market, the competence to adapt is becoming significantly relevant for career development and career success. The construct of career adaptability, i.e. the capability to adapt to changing career-related circumstances and predict advancement in career development, seems to provide a fruitful scientific base for successful career intervention. The purpose of the study is exploratory, with the aim of providing new findings about the key predictors of this meta-competence that are relevant for career development.

Design/methodology/approach
Through a web-based survey, a convenience sample of 230 working participants completed an online questionnaire, including socio-demographic characteristics (age, gender, education), professional status (role seniority, sector of employment, professional role), professional development-related features (training, new professional assignments, financial incentives) and psychological factors (work self-efficacy, search for work self-efficacy and job satisfaction). Four-step hierarchical multiple regression analyses were conducted to understand which of these factors account for the most career adaptability variance.

Findings
Results highlight that work self-efficacy, search for work self-efficacy and education play a significant role in predicting career adaptability. Surprisingly, professional development-related features and professional status do not seem to have a relevant influence.

Practical implications
Training and career-development professionals can improve their understanding of which career-related skills and attitudes can increase one’s capability to cope with sudden changes and instability of the current labour market.

Originality/value
This study supports previous research, addressing the importance of career adaptability in times of dramatic change. It also provides some insight into the factors that could predict it.
Antihypertensive methyldopa, labetalol, hydralazine, and clonidine reversed tumour necrosis factor‐α inhibited endothelial nitric oxide synthase expression in endothelial‐trophoblast cellular networks
Authors: Xu Bei , Bobek Gabriele , Makris Angela , Hennessy Annemarie 
Published: December 2016

SummaryMedications used to control hypertension in pregnancy also improve trophoblast and endothelial cellular interaction in vitro. Tumour necrosis factor‐α (TNF‐α) inhibits trophoblast and endothelial cellular interactions and simultaneously decreases endothelial nitric oxide synthase (eNOS) expression. This study investigated whether antihypertensive medications improved these cellular interactions by modulating eNOS and inducible nitric oxide synthase (iNOS) expression. Human uterine myometrial microvascular endothelial cells (UtMVECs) were pre‐incubated with (or without) low dose TNF‐α (0.5 ng/mL) or TNF‐α plus soluble fms‐like tyrosine kinase‐1 (sFlt‐1) (100 ng/mL). The endothelial cells were cultured on Matrigel. After endothelial cellular networks appeared, trophoblast derived HTR‐8/SVneo cells were co‐cultured in the presence of clinically relevant doses of methyldopa, labetalol, hydralazine or clonidine for 24 hours. Cells were retrieved from the Matrigel to extract mRNA and eNOS and iNOS expression were examined by quantitative PCR. Methyldopa, labetalol, hydralazine and clonidine reversed the inhibitory effect of TNF‐α on eNOS mRNA expression. After pre‐incubating endothelial cells with TNF‐α and sFlt‐1, all the medications except methyldopa lost their effect on eNOS mRNA expression. In the absence of TNF‐α, antihypertensive medications did not change eNOS expression. The mRNA expression of iNOS was not affected by TNF‐α or any medications. This study shows that selected antihypertensive medications used in the treatment of hypertension in pregnancy increase eNOS expression in vitro when induced by the inflammatory TNF‐α. The anti‐angiogenic molecule sFlt‐1 may antagonise the potential benefit of these medications by interfering with the NOS pathway.
Online Hemodiafiltration Reduces Bisphenol A Levels
Authors: Quiroga Borja , Bosch Ricardo J. , Fiallos Ruth A. , Sánchez‐Heras Marta , Olea‐Herrero Nuria , López‐Aparicio Pilar , Muñóz‐Moreno Carmen , Pérez‐Alvarsan Miguel Angel , De Arriba Gabriel 
Published: December 2016

AbstractSeveral uremic toxins have been identified and related to higher rates of morbidity and mortality in dialysis patients. Bisphenol A (BPA) accumulates in patients with chronic kidney disease. The aim of this study is to demonstrate the usefulness of online hemodiafiltration (OL‐HDF) in reducing BPA levels. Thirty stable hemodialysis patients were selected to participate in this paired study. During three periods of 3 weeks each, patients were switched from high‐flux hemodialysis (HF‐HD) to OL‐HDF, and back to HF‐HD. BPA levels were measured in the last session of each period (pre‐ and post‐dialysis) using ELISA and HPLC. Twenty‐two patients (mean age 73 ± 14 years; 86.4% males) were included. Measurements of BPA levels by HPLC and ELISA assays showed a weak but significant correlation (r = 0.218, P = 0.012). BPA levels decreased in the OL‐HDF period of hemodialysis, in contrast to the HF‐HD period when they remained stable (P = 0.002). In conclusion, OL‐HDF reduced BPA levels in dialysis patients.
Tracking the amphibian pathogensBatrachochytrium dendrobatidisandBatrachochytrium salamandrivoransusing a highly specific monoclonal antibody and lateral‐flow technology
Authors: Dillon Michael J. , Bowkett Andrew E. , Bungard Michael J. , Beckman Katie M. , O'Brien Michelle F. , Bates Kieran , Fisher Matthew C. , Stevens Jamie R. , Thornton Christopher R. 
Published: December 2016

SummaryThe fungusBatrachochytrium dendrobatidis(Bd) causes chytridiomycosis, a lethal epizootic disease of amphibians. Rapid identification of the pathogen and biosecurity is essential to prevent its spread, but current laboratory‐based tests are time‐consuming and require specialist equipment. Here, we describe the generation of an IgM monoclonal antibody (mAb), 5C4, specific toBdas well as the related salamander and newt pathogenBatrachochytrium salamandrivorans(Bsal). The mAb, which binds to a glycoprotein antigen present on the surface of zoospores, sporangia and zoosporangia, was used to develop a lateral‐flow assay (LFA) for rapid (15 min) detection of the pathogens. TheLFAdetects known lineages ofBdand alsoBsal, as well as the closely related fungusHomolaphlyctis polyrhiza, but does not detect a wide range of related and unrelated fungi and oomycetes likely to be present in amphibian habitats. When combined with a simple swabbing procedure, theLFAwas 100% accurate in detecting the water‐soluble 5C4 antigen present in skin, foot and pelvic samples from frogs, newts and salamanders naturally infected withBdorBsal. Our results demonstrate the potential of the portableLFAas a rapid qualitative assay for tracking these amphibian pathogens and as an adjunct test to nucleic acid‐based detection methods.
Midsagittal corpus callosum area and conversion to multiple sclerosis after clinically isolated syndrome: A multicentre Australian cohort study
Authors: Odenthal Cara , Simpson Steve , Oughton Justin , van der Mei Ingrid , Rose Stephen , Fripp Jurgen , Lucas Robyn , Taylor Bruce , Dear Keith , Ponsonby Anne‐Louise , Coulthard Alan ,   the Ausimmune AusLong Investigator Groups
Published: December 2016

AbstractIntroductionPatients presenting with clinically isolated syndrome (CIS) may proceed to clinically definite multiple sclerosis (CDMS). Midsagittal corpus callosum area (CCA) is a surrogate marker for callosal atrophy, and can be obtained from a standard MRI study. This study explores the relationship between CCA measured at CIS presentation (baseline) and at 5 years post presentation, with conversion from CIS to CDMS. The association between CCA and markers of disability progression is explored.MethodsCorpus callosum area was measured on MRI scans at presentation and 5‐year review following diagnosis of a first demyelinating event, or evidence of progressive MS, in 143 participants in the Ausimmune/AusLong Study. Relationships between CCA (at baseline and follow‐up) and clinical outcomes were assessed.ResultsMean CCA at baseline study was 6.63 cm2 (SD 1.01). Patients who converted to MS by 5‐year review (n = 100) had a significantly smaller mean CCA at follow‐up (6.22 vs. 6.74, P = 0.007). Greater CCA reduction was associated with higher annualized relapse rate over follow‐up.ConclusionBaseline CCA obtained from standard MRI protocols may be compared with subsequent MRI examinations as a surrogate for neurodegeneration and cerebral atrophy in patients with MS. This study demonstrates an association between CCA and disability in individuals presenting with CIS who convert to MS.
Identifying the plant‐associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery
Authors: Jackrel Sara L. , Owens Sarah M. , Gilbert Jack A. , Pfister Catherine A. 
Published: December 2016

AbstractPlants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free‐living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16SrRNAsequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host‐associated sequences. We assessed the efficacy of chloroplast and mitochondria‐blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal‐associated microbiota, Proteobacterial 16SrRNAbinds to the chloroplast‐blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14‐bp sequence in the Proteobacteria that matches the 17‐bp chloroplast‐blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14‐bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle‐blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n‐mer oligonucleotides of eachPNAsequence.
Lower cognitive functioning as a predictor of weight gain in bipolar disorder: a 12‐month study
Authors: Bond D. J. , Torres I. J. , Lee S. S. , Kozicky J.‐M. , Silveira L. E. , Dhanoa T. , Lam R. W. , Yatham L. N. 
Published: December 2016

ObjectiveIn cross‐sectional studies, elevated body mass index (BMI) is associated with cognitive impairment in bipolar disorder (BD). We investigated the direction of this association by prospectively examining changes in BMI and cognition.MethodWe measured BMI and performance in six cognitive domains over 12 months in 80 adolescent and young adult BD patients and 46 healthy comparison subjects (HS). Ninety‐three percent of patients received pharmacotherapy and 84% were euthymic. We used repeated‐measuresancovaand longitudinal mixed models to investigate whether (i) higher BMI and increasing BMI over time predicted lower subsequent cognitive functioning, and (ii) lower cognitive functioning and changes in cognition predicted increasing BMI.ResultsNeither baseline BMI nor BMI change predicted lower cognitive functioning. Lower baseline scores in attention, verbal memory, working memory, and a composite measure of global cognition predicted increasing BMI in patients and HS. In patients, lower cognitive functioning remained associated with increasing BMI when clinical and treatment variables were adjusted for. Improvement in working memory predicted a smaller subsequent BMI increase in patients.ConclusionLower cognitive functioning in specific domains predicts increasing BMI in patients with BD and healthy young adults. Targeting cognition may be important for minimizing weight gain in BD.
Exposure to violence, a risk for suicide in youths and young adults. A meta‐analysis of longitudinal studies
Authors: Castellví P. , Miranda‐Mendizábal A. , Parés‐Badell O. , Almenara J. , Alonso I. , Blasco M. J. , Cebrià A. , Gabilondo A. , Gili M. , Lagares C. , Piqueras J. A. , Roca M. , Rodríguez‐Marín J. , Rodríguez‐Jimenez T. , Soto‐Sanz V. , Alonso J. 
Published: December 2016

ObjectiveTo assess the association and magnitude of the effect of early exposure to different types of interpersonal violence (IPV) with suicide attempt and suicide death in youths and young adults.MethodWe searched six databases until June 2015. Inclusion criteria were as follows: (1) assessment of any type of IPV as risk factor of suicide attempt or suicide: (i) child maltreatment [childhood physical, sexual, emotional abuse, neglect], (ii) bullying, (iii) dating violence, and (iv) community violence; (2) population‐based case–control or cohort studies; and (3) subjects aged 12–26 years. Random models were used for meta‐analyses (Reg: CRD42013005775).ResultsFrom 23 682 articles, 29 articles with 143 730 subjects for meta‐analyses were included. For victims of any IPV, OR of subsequent suicide attempt was 1.99 (95% CI: 1.73–2.28); for child maltreatment, 2.25 (95% CI: 1.85–2.73); for bullying, 2.39 (95% CI: 1.89–3.01); for dating violence, 1.65 (95% CI: 1.40–1.94); and for community violence, 1.48 (95% CI: 1.16–1.87). Young victims of IPV had an OR of suicide death of 10.57 (95% CI: 4.46–25.07).ConclusionEarly exposure to IPV confers a risk of suicide attempts and particularly suicide death in youths and young adults. Future research should address the effectiveness of preventing and detecting early any type of IPV exposure in early ages.