bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics from pool sequencing
Authors: Ferretti Luca , Ramos‐Onsins Sebastián E. , Pérez‐Enciso Miguel 
Published: October 2013

AbstractNext generation sequencing of pooled samples is an effective approach for studies of variability and differentiation in populations. In this paper we provide a comprehensive set of estimators of the most common statistics in population genetics based on the frequency spectrum, namely the Watterson estimator , nucleotide pairwise diversity Π, Tajima's D, Fu and Li's D and F, Fay and Wu's H, McDonald‐Kreitman and HKA tests and , corrected for sequencing errors and ascertainment bias. In a simulation study, we show that pool and individual θ estimates are highly correlated and discuss how the performance of the statistics vary with read depth and sample size in different evolutionary scenarios. As an application, we reanalyse sequences from Drosophila mauritiana and from an evolution experiment in Drosophila melanogaster. These methods are useful for population genetic projects with limited budget, study of communities of individuals that are hard to isolate, or autopolyploid species.
On minimizing assignment errors and the trade‐off between false positives and negatives in parentage analysis
Authors: Harrison Hugo B. , Saenz‐Agudelo Pablo , Planes Serge , Jones Geoffrey P. , Berumen Michael L. 
Published: October 2013

Genetic parentage analyses provide a practical means with which to identify parent–offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion‐Bayes theorem method was more susceptible to false‐positive and false‐negative assignments than other methods tested. Here, we analyse and discuss the trade‐off between type I and type II errors in parentage analyses. We show that controlling for false‐positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false‐positive and false‐negative assignments in parentage analyses.
Plum pox virus and sharka: a model potyvirus and a major disease
Authors: García Juan Antonio , Glasa Miroslav , Cambra Mariano , Candresse Thierry 
Published: October 2013

SummaryTaxonomic relationshipsPlum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains.Geographical distributionFirst discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents.Genomic structureTypical of potyviruses, the PPV genome is a positive‐sense single‐stranded RNA (ssRNA), with a protein linked to its 5′ end and a 3′‐terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N‐PIPO is predicted to be produced by a translational frameshift.Pathogenicity featuresPPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner.Sources of resistanceA few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, ‘HoneySweet’, transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.
Prevalence and epidemiological characteristics of vaginal candidiasis in the UAE
Authors: Hamad Mawieh , Kazandji Norair , Awadallah Samir , Allam Hilda 
Published: October 2013

SummaryVaginal candidiasis (VC) continues to be a health problem to women worldwide. Although the majority of VC cases are caused by Candida albicans (C. albicans), non‐albicans Candida spp. like C. glabrata and C. tropicalis are emerging as important and potentially resistant opportunistic agents of VC. The objective of this study was to evaluate the prevalence and epidemiology of VC in the UAE through retrospective analysis of pertinent data compiled by the microbiology and infection control unit at Latifa Hospital, Dubai between 2005 and 2011. The incidence of VC significantly increased from 10.76% in 2005 to 17.61% in 2011; average prevalence was 13.88%. C. albicans occurred at a frequency of 83.02%, C. glabrata at 16.5% and C. tropicalis at 1.2%. A single C. dubliniensis isolate was identified in the sample population. The percentage of C. albicans significantly decreased from 83.02% in the sample population as a whole to 60.8% in subjects over 45 years of age (P < 0.01) and that of C. glabrata, C. tropicalis and C. krusei significantly increased from 13.88%, 0.9% and 0.03% to 29.7%, 6.7% and 1.4% (P < 0.05) respectively. The incidence of VC in the UAE is on the rise and the frequency of non‐albicans Candida spp. is noticeably increasing especially in postmenopausal women.
Belief through Thick and Thin
Authors: Buckwalter Wesley , Rose David , Turri John 
Published: October 2013

AbstractWe distinguish between two categories of belief—thin belief and thick belief—and provide evidence that they approximate genuinely distinct categories within folk psychology. We use the distinction to make informative predictions about how laypeople view the relationship between knowledge and belief. More specifically, we show that if the distinction is genuine, then we can make sense of otherwise extremely puzzling recent experimental findings on the entailment thesis (i.e. the widely held philosophical thesis that knowledge entails belief). We also suggest that the distinction can be applied to debates in the philosophy of mind and metaethics.
Facilitation as a ubiquitous driver of biodiversity
Authors: McIntire Eliot J. B. , Fajardo Alex 
Published: October 2013

SummaryModels describing the biotic drivers that create and maintain biological diversity within trophic levels have focused primarily on negative interactions (i.e. competition), leaving marginal room for positive interactions (i.e. facilitation). We show facilitation to be a ubiquitous driver of biodiversity by first noting that all species use resources and thus change the local biotic or abiotic conditions, altering the available multidimensional niches. This can cause a shift in local species composition, which can cause an increase in beta, and sometimes alpha, diversity. We show that these increases are ubiquitous across ecosystems. These positive effects on diversity occur via a broad host of disparate direct and indirect mechanisms. We identify and unify several of these facilitative mechanisms and discuss why it has been easy to underappreciate the importance of facilitation. We show that net positive effects have a long history of being considered ecologically or evolutionarily unstable, and we present recent evidence of its potential stability. Facilitation goes well beyond the common case of stress amelioration and it probably gains importance as community complexity increases. While biodiversity is, in part, created by species exploiting many niches, many niches are available to exploit only because species create them.

Contents

Summary
403

I.
Introduction
403

II.
Facilitative mechanisms increasing diversity
405

III.
Facilitation as an evolutionary driver in proximate interactions
410

IV.
Why has facilitation been just recently added to ecological theory?
411

V.
Facilitation and the plant functional trait programme
412

VI.
Predictability and testability
412

VII.
Conservation, restoration and management
413

VIII.
Conclusions and next steps
413

Acknowledgements
413

References
414
The circadian clock has transient plasticity of period and is required for timing of nocturnal processes in Arabidopsis
Authors: Dodd Antony N. , Dalchau Neil , Gardner Michael J. , Baek Seong‐Jin , Webb Alex A. R. 
Published: October 2013

Summary

A circadian rhythm matched to the phase and period of the day–night cycle has measurable benefits for land plants. We assessed the contribution of circadian period to the phasing of cellular events with the light : dark cycle. We also investigated the plasticity of circadian period within the Arabidopsis circadian oscillator.

We monitored the circadian oscillator in wild‐type and circadian period mutants under light : dark cycles of varying total duration. We also investigated changes in oscillator dynamics during and after the transition from light : dark cycles to free running conditions.

Under light : dark cycles, dawn and dusk were anticipated differently when the circadian period was not resonant with the environmental period (‘T cycle’). Entrainment to T cycles differing from the free‐running period caused a short‐term alteration in oscillator period. The transient plasticity of period was described by existing mathematical models of the Arabidopsis circadian network.

We conclude that a circadian period resonant with the period of the environment is particularly important for anticipation of dawn and the timing of nocturnal events; and there is short‐term and transient plasticity of period of the Arabidopsis circadian network.
Mineral trioxide aggregate enhances the odonto/osteogenic capacity of stem cells from inflammatory dental pulps via NF‐κB pathway
Authors: Wang Y , Yan M , Fan Z , Ma L , Yu Y , Yu J 
Published: October 2013

ObjectiveThis study was designed to investigate the effects of mineral trioxide aggregate (MTA) on the osteo/odontogenic differentiation of inflammatory dental pulp stem cells (iDPSCs).Materials and Methodsinflammatory DPSCs were isolated from the inflammatory pulps of rat incisors and cocultured with MTA‐conditioned medium. MTT assay and flow cytometry were performed to evaluate the proliferation of iDPSCs. Alkaline phosphatase (ALP) activity, alizarin red staining, real‐time RT‐PCR, and Western blot assay were used to investigate the differentiation capacity as well as the involvement of NF‐κB pathway in iDPSCs.ResultsMineral trioxide aggregate‐treated iDPSCs demonstrated the higher ALP activity and formed more mineralized nodules than the untreated group. The odonto/osteoblastic markers (Alp, Runx2/RUNX2, Osx/OSX, Ocn/OCN, and Dspp/DSP, respectively) in MTA‐treated iDPSCs were significantly upregulated as compared with untreated iDPSCs. Mechanistically, cytoplastic phos‐P65 and nuclear P65 in MTA‐treated iDPSCs were significantly increased in a time‐dependent manner. Moreover, the inhibition of NF‐κB pathway suppressed the MTA‐induced odonto/osteoblastic differentiation of iDPSCs, as indicated by decreased ALP levels, weakened mineralization capacity and downregulated levels of odonto/osteoblastic genes (Osx, Ocn, and Dspp).ConclusionsMineral trioxide aggregate enhances the odonto/osteogenic capacity of DPSCs from inflammatory sites via activating the NF‐κB pathway.
Impact of Fluoroscopy Unit on the Accuracy of a Magnet‐Based Electroanatomic Mapping and Navigation System: An In Vitro and In Vivo Validation Study
Authors: AHMAD GHADA , HUSSEIN AYMAN A. , MESUBI OLUROTIMI , TIAN JING , FERIEG HANAA , ELMAATY MERVAT A. , HAMDY AMAL , EGO‐OSUALA KELECHI , JIMENEZ ALEJANDRO , SEE VINCENT , SALIARIS ANASTASIOS , SHOROFSKY STEPHEN , DICKFELD TIMM 
Published: October 2013

IntroductionDuring mapping and ablation procedures, the movement of large ferromagnetic items (i.e., fluoroscopic equipment) introduce heterogeneities in the electromagnetic field, which may affect the accuracy of electromagnet‐based navigation. We aimed to assess the impact of common periprocedural fluoroscopic equipment movement on the accuracy of an electromagnet‐based navigation system.Methods and ResultsThe impact of fluoroscopic equipment movement on the accuracy of the Carto® 3 System (Biosense Webster, Inc., Diamond Bar, CA, USA) was assessed both in vitro (n = 20 patients, phantom model) and in vivo (n = 18 patients). Location recordings were obtained with unchanged catheter position for fluoroscopic equipment rotational movements (RMs) and maximal to closest distance (MD to CD) to phantom/patient. The effects of both single‐ and biplane fluoroscopy were assessed. In vitro, the movement of fluoroscopic equipment resulted in an average catheter location estimation error of 0.8 mm (interquartile range 0.3–1.3). The maximal location estimation errors with MD to CD movement and RM were 2.3 mm and 1.3 mm, respectively. Changing from single‐plane to biplane setup resulted in an average location estimation change of 1.5 mm (maximum 2.1). Larger location changes were observed in vivo (2.9 mm vs 0.8 mm, P < 0.0001) with 28.7% of these exceeded 4 mm versus none of the in vitro measurements (P < 0.0001).ConclusionAlthough fluoroscopy manipulation affected the accuracy of the Carto® 3 System, the in vitro data suggest that these inaccuracies are likely of limited clinical consequences. The larger in vivo inaccuracies are most likely due to nonferromagnetic interferences, such as respiratory or cardiac movements.
Combination Drug Therapy for Patients with Intractable Ventricular Tachycardia Associated with Right Ventricular Cardiomyopathy
Authors: ERMAKOV SIMON , HOFFMAYER KURT S. , GERSTENFELD EDWARD P. , SCHEINMAN MELVIN M. 
Published: October 2013

BackgroundDrug therapy for patients with right ventricular (RV) cardiomyopathy refractory to single‐drug therapy and ablation has not been well defined.MethodsWe reviewed our entire RV cardiomyopathy database (31 patients) and found four patients presenting with ventricular arrhythmias of RV origin refractory to single‐drug therapy. These patients underwent complete evaluation for arrhythmogenic right ventricular cardiomyopathy (ARVC).ResultsFollowing the revised 2010 task force criteria, of these four patients, three were diagnosed with ARVC, and one with cardiac sarcoidosis. These patients proved to be refractory to drug monotherapy and either failed or deemed to not be candidates for endocardial ablation. Their arrhythmias were ultimately controlled with combinations of sotalol, flecainide, and mexiletine.ConclusionsIn our experience, combination drug therapy is an effective treatment strategy for patients with ventricular tachycardia refractory to monotherapy and, in some cases, ablation. In addition, flecainide appears to be safe and effective for those with RV cardiomyopathy without significant left ventricular dysfunction.
The SNAP index does not correlate with the State Behavioral Scale in intubated and sedated children
Authors: Thompson Cecilia , Shabanova Veronika , Giuliano John S. 
Published: October 2013

SummaryBackgroundEnsuring appropriate levels of sedation for critically ill children is integral to pediatric critical care. Traditionally, clinicians have used subjective scoring tools to assess sedation levels. The SNAP II uses dual frequency processed electroencephalography to evaluate brain activity and may provide an objective assessment of sedation levels.ObjectiveThis study attempts to find an objective method to monitor sedation in critically ill pediatric patients. We compared the SNAP II, a processed electroencephalography device, with the State Behavioral Scale (SBS), a subjective sedation scoring tool. We hypothesize that the SNAP II correlates with the SBS and has less observer bias.MethodsThis was an IRB approved prospective, observational study. Patients receiving intravenous sedation while being mechanically ventilated were enrolled after informed consent. After the SNAP II monitoring electrodes were attached, blinded bedside nurses assessed sedation levels using the SBS. SNAP indices were collected and compared with SBS scores to determine correlation.ResultsWe compared 417 paired data points from 15 patients using Pearson's correlation and least squares means to determine correlation between the SBS and SNAP indices. No correlation was observed. Using covariance model patterning for repeated measures to adjust for covariates again showed no correlation.ConclusionThe SNAP index does not correlate with SBS scores in our pediatric intensive care unit (PICU). Its use cannot be recommended to measure levels of sedation in our population. Future research should continue to explore objective ways of measuring sedation in critically ill children.
Increased pituitary volume in subjects at risk for psychosis and patients with first‐episode schizophrenia
Authors: Takahashi Tsutomu , Nakamura Kazue , Nishiyama Shimako , Furuichi Atsushi , Ikeda Eiji , Kido Mikio , Nakamura Yumiko , Kawasaki Yasuhiro , Noguchi Kyo , Seto Hikaru , Suzuki Michio 
Published: October 2013

AimEnlarged pituitary gland has been reported in schizophrenia, possibly reflecting hypothalamic–pituitary–adrenal hyperactivity. The aim of the present study was to examine whether individuals at risk of psychosis also have similar changes.MethodsMagnetic resonance imaging was used to examine the pituitary volume in 22 individuals with at‐risk mental state (ARMS; 11 male, 11 female), 64 first‐episode patients with schizophrenia (FESz; 37 male, 27 female), and 86 healthy controls. The control subjects were divided into age‐ and gender‐matched controls for ARMS (11 male, 11 female) and FESz (37 male, 27 female).ResultsBoth the ARMS and FESz groups had a larger pituitary volume compared with matched controls, but no difference was found between the ARMS and FESz subjects. There was no association between the pituitary volume and clinical variables (symptommeasures at scanning, daily dosage or duration of antipsychotic medication) in either clinical group. The pituitary volume did not differ significantly between the ARMS individuals who later developed schizophrenia (n = 5) and those who did not (n = 17). The pituitary volume was larger in women than in men for all diagnostic groups.ConclusionThe finding of increased pituitary volume in both ARMS and FESz subjects may reflect a common vulnerability to stress in early psychosis. Further work in a larger ARMS sample is required to examine the possible relationship between pituitary volume and emergence of psychosis.
Intimate Partner Violence and the CDC's Best‐Evidence HIV Risk Reduction Interventions
Authors: Prowse Kayleigh M. , Logue Christine E. , Fantasia Heidi C. , Sutherland Melissa A. 
Published: October 2013

AbstractObjectivesIntimate partner violence (IPV) is a prevalent health burden in the United States and is a risk factor for HIV (human immunodeficiency virus) transmission. Despite the association between IPV and HIV risk, IPV is often omitted from HIV prevention research and interventions. This review analyzes the Centers for Disease Control and Prevention's best‐evidence HIV risk reduction interventions and their incorporation of IPV assessment, education and evaluation.Design and SampleThe Centers for Disease Control and Prevention's best‐evidence HIV risk reduction interventions (n = 44) were reviewed for inclusion of IPV content.ResultsOf the 44 best evidence interventions, 5 addressed IPV. These 5 interventions were further examined for method, measurement and uniformity.ConclusionsJustification for IPV integration in HIV risk reduction programs is explored and supported by evidence‐based research and practice.
The Phenomenology of Face‐to‐Face Mindreading
Authors: Smith Joel 
Published: October 2013

AbstractI defend a perceptual account of face‐to‐face mindreading. I begin by proposing a phenomenological constraint on our visual awareness of others' emotional expressions. I argue that to meet this constraint we require a distinction between the basic and non‐basic ways people, and other things, look. I offer and defend just such an account.
The Origin of Amniotic Polymorphonuclear Leucocytes in the Mare
Authors: Hemberg E , Einarsson S , Jones B , Mikko S 
Published: October 2013

ContentsThe objective of this study was to investigate the presence and origin of polymorphonuclear leucocytes (PMNLs) in the amniotic fluid of mares giving birth to healthy foals. Material from 25 mares was included. Amniotic fluid was collected during parturition before breakage of the amniotic vesicle. Manual microscopic cytologic evaluation was made on cytospin preparations after staining. PMNLs were found in all amniotic samples examined. The genomic DNA was extracted from 12 of the amniotic fluid samples and was genotyped. The results indicate that the PMNLs originate from the foetus.
Space–Time Modelling of Extreme Events
Authors: Huser R. , Davison A. C. 
Published: October 2013

SummaryMax-stable processes are the natural analogues of the generalized extreme value distribution when modelling extreme events in space and time. Under suitable conditions, these processes are asymptotically justified models for maxima of independent replications of random fields, and they are also suitable for the modelling of extreme measurements over high thresholds. The paper shows how a pairwise censored likelihood can be used for consistent estimation of the extremes of space–time data under mild mixing conditions and illustrates this by fitting an extension of a model due to Schlather to hourly rainfall data. A block bootstrap procedure is used for uncertainty assessment. Estimator efficiency is considered and the choice of pairs to be included in the pairwise likelihood is discussed. The model proposed fits the data better than some natural competitors.
Rural Environmental Concern: Effects of Position, Partisanship, and Place
Authors: Hamilton Lawrence C. , Hartter Joel , Safford Thomas G. , Stevens Forrest R. 
Published: October 2013

Abstract The social bases of environmental concern in ruralAmerica resemble those for the nation as a whole, but also reflect the influence of place. Some general place characteristics, such as rates of population growth or resource‐industry employment, predict responses across a number of environmental issues. Other unique or distinctive aspects of local society and environment matter as well. We extend earlier work on both kinds of place effects, first by analyzing survey data from northeastOregon. Results emphasize that “environmental concern” has several dimensions. Second, we contextualize theOregon results using surveys from other regions. Analysis of an integrated dataset (up to 12,000 interviews in 38 U.S. counties) shows effects from respondent characteristics and political views, and from county rates of population growth and resource‐based employment. There also are significant place‐to‐place variations that are not explained by variables in the models. To understand some of these we return to the local scale. In northeastOregon, residents describe how perceptions of fire danger from unmanaged forest lands shape their response to the wordconservation. Their local interpretation contrasts with more general and urban connotations of this term, underlining the importance of place for understanding rural environmental concern.