bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny
Authors: Cui Yaoyao , Yan Chaochao , Sun Tianlin , Li Jing , Yue Bisong , Zhang Xiuyue , Li Jing 
Published: March 2016

AbstractChicken repeat 1 (CR1), a member of non‐LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.
High rates of phasing errors in highly polymorphic species with low levels of linkage disequilibrium
Authors: Bukowicki Marek , Franssen Susanne U. , Schlötterer Christian 
Published: March 2016

AbstractShort read sequencing of diploid individuals does not permit the direct inference of the sequence on each of the two homologous chromosomes. Although various phasing software packages exist, they were primarily tailored for and tested on human data, which differ from other species in factors that influence phasing, such as SNP density, amounts of linkage disequilibrium (LD) and sample sizes. Despite becoming increasingly popular for other species, the reliability of phasing in non‐human data has not been evaluated to a sufficient extent. We scrutinized the phasing accuracy for Drosophila melanogaster, a species with high polymorphism levels and reduced LD relative to humans. We phased two D. melanogaster populations and compared the results to the known haplotypes. The performance increased with size of the reference panel and was highest when the reference panel and phased individuals were from the same population. Full genomic SNP data and inclusion of sequence read information also improved phasing. Despite humans and Drosophila having similar switch error rates between polymorphic sites, the distances between switch errors were much shorter in Drosophila with only fragments <300–1500 bp being correctly phased with ≥95% confidence. This suggests that the higher SNP density cannot compensate for the higher recombination rate in D. melanogaster. Furthermore, we show that populations that have gone through demographic events such as bottlenecks can be phased with higher accuracy. Our results highlight that statistically phased data are particularly error prone in species with large population sizes or populations lacking suitable reference panels.
Experimental habitat restoration for conserved species using ecosystem engineers and vegetation management
Authors: McCullough Hennessy S. , Deutschman D. H. , Shier D. M. , Nordstrom L. A. , Lenihan C. , Montagne J.‐P. , Wisinski C. L. , Swaisgood R. R. 
Published: March 2016

AbstractWe experimentally address the theoretical potential for managing ecosystem engineer species to support suites of species in degraded habitats. Historically, the ecosystem engineer California ground squirrel Otospermophilus beecheyi supported a grassland food web through widespread burrowing activity. Currently, ground squirrels are not a threatened species, but like many other ecosystem engineers, they exist at densities too low to fulfill their engineering role in many locations. Our objective was to implement short‐term treatments, including squirrel translocation, to re‐establish key ecological processes on protected reserve lands. We manipulated vegetation and squirrels in a replicated, large‐scale field experiment for 2 years, and monitored through a third year. Vegetation mowing and soil decompaction treatments reduced grass density and thatch depth. Squirrel translocation accelerated squirrel settlement and activity in target sites. Of the more than 1000 burrow entrances remaining through the third year, nearly all burrows were concentrated in the plots that received squirrel translocation. We found significant additive effects of squirrel translocation and vegetation management on the spatial footprint of squirrel activity. Noteworthy and persistent engineering effects were achieved through squirrel activity, and both vegetation management and squirrel re‐establishment were needed to stimulate squirrel activity. The overarching goal of this experiment was to provide conservation managers with a cost‐effective tool for restoring degraded habitats to a hybrid ecosystem state with improved suitability for species of conservation concern, in this case, the western burrowing owl Athene cunicularia hypugaea.
Emergency assessment and treatment planning for traumatic dental injuries
Authors: Moule A , Cohenca N 
Published: March 2016

AbstractTrauma involving the dentoalveolar region is a frequent occurrence which can result in the fracturing and displacement of teeth, crushing and/or fracturing of bone and soft tissue injuries including contusions, abrasions and lacerations. This review describes the assessment of patients with these injuries, not in a didactic sense by repeating excellent already published classifications and treatment options, but by addressing questions that arise during assessment. It covers trauma first aid, examination of the patient, factors that affect treatment planning decisions, and the importance of communicating treatment options and prognosis to traumatized patients.
Responses of the pulp, periradicular and soft tissues following trauma to the permanent teeth
Authors: Yu CY , Abbott PV 
Published: March 2016

AbstractTrauma to the permanent teeth involves not only the teeth but also the pulp, the periodontal ligament, alveolar bone, gingiva and other associated structures. There are many variations in the types of injuries with varying severity and often a tooth may sustain more than one injury at the same time. In more severe trauma cases, there are many different cellular systems of mineralized hard and unmineralized soft tissues involved, each with varying potential for healing. Furthermore, the responses of the different tissues may be interrelated and dependent on each other. Hence, healing subsequent to dental trauma has long been known to be very complex. Because of this complexity, tissue responses and the consequences following dental trauma have been confusing and puzzling for many clinicians. In this review, the tissue responses are described under the tissue compartments typically involved following dental trauma: the pulp, periradicular and associated soft tissues. The factors involved in the mechanisms of trauma are analysed for their effects on the tissue responses. A thorough understanding of the possible tissue responses is imperative for clinicians to overcome the confusion and manage dental trauma adequately and conservatively in order to minimize the consequences following trauma.
The prevalence of functional gastrointestinal disorders in children in Panama: a school‐based study
Authors: Lu Peter L. , Saps Miguel , Chanis Ricardo A. , Velasco‐Benítez Carlos A. 
Published: March 2016

AbstractAimFunctional gastrointestinal disorders (FGIDs) are common in children, but the epidemiology of FGIDs is incompletely understood. Our aim was to perform a population‐based study using Rome III criteria to describe the prevalence of FGIDs in children in Panama.MethodsWe performed a cross‐sectional study of children attending three schools in Panama City, Panama. Children with organic medical diseases were excluded. Subjects provided demographic information and completed the Questionnaire on Pediatric Gastrointestinal Symptoms – Rome III Spanish version.ResultsA total of 321 subjects (61.1% female, median age 10 years, range 8–14 years) completed our study. A total of 92 subjects (28.7%) met criteria for an FGID. Gender, age and school type did not differ significantly between subjects with and without FGIDs. The most common FGIDs included functional constipation (15.9%), irritable bowel syndrome (5.6%), and functional abdominal pain or functional abdominal pain syndrome (4.0%). Abdominal pain‐related FGIDs were present in 12.1%.ConclusionFGIDs are common in school‐aged children in Panama. The prevalence of abdominal pain‐related FGIDs in children in Panama is similar to that described in other parts of the world. Further population‐based studies utilising Rome III criteria to measure FGID prevalence in children are needed to advance our understanding of the pathogenesis of FGIDs.
Assessing fundamental motor skills in Belgian children aged 3–8 years highlights differences to US reference sample
Authors: Bardid Farid , Huyben Floris , Lenoir Matthieu , Seghers Jan , De Martelaer Kristine , Goodway Jacqueline D. , Deconinck Frederik J. A. 
Published: March 2016

AbstractAimThis study aimed to understand the fundamental motor skills (FMS) of Belgian children using the process‐oriented Test of Gross Motor Development, Second Edition (TGMD‐2) and to investigate the suitability of using the United States (USA) test norms in Belgium.MethodsFMS were assessed using the TGMD‐2. Gender, age and motor performance were examined in 1614 Belgian children aged 3–8 years (52.1% boys) and compared with the US reference sample.ResultsMore proficient FMS performance was found with increasing age, from 3 to 6 years for locomotor skills and 3 to 7 years for object control skills. Gender differences were observed in object control skills, with boys performing better than girls. In general, Belgian children had lower levels of motor competence than the US reference sample, specifically for object control skills. The score distribution of the Belgian sample was skewed, with 37.4% scoring below average and only 6.9% scoring above average.ConclusionThis study supported the usefulness of the TGMD‐2 as a process‐oriented instrument to measure gross motor development in early childhood in Belgium. However, it also demonstrated that caution is warranted when using the US reference norms.
Pedometer intervention and weight loss in overweight and obese adults with Type 2 diabetes: a meta‐analysis
Authors: Cai X. , Qiu S. H. , Yin H. , Sun Z. L. , Ju C. P. , Zügel M. , Steinacker J. M. , Schumann U. 
Published: March 2016

AbstractAimAlthough pedometer intervention is effective in increasing physical activity among adults with Type 2 diabetes, its impact on weight loss remains unclear. This meta‐analysis was aimed to assess whether pedometer intervention promotes weight loss.MethodsThree different databases were searched for randomized controlled trials (RCTs) published in English up to April 2015. Studies were included if they investigated the effects of pedometer intervention on weight loss, as measured by BMI or weight. Effect sizes were aggregated using a random‐effects model. Subgroup and meta‐regression analyses were used to identify potential moderators. Eleven RCTs with 1258 participants were included. All enrolled participants were overweight or obese.ResultsPedometer intervention led to significantly decreased BMI [weighted mean difference (WMD) −0.15 kg/m2, 95% confidence interval (CI) −0.29 to −0.02 kg/m2] and reduced weight (WMD −0.65 kg, 95% CI −1.12 to −0.17 kg). Dietary counselling seemed to be a key predictor of the observed changes. However, none of the following variables had a significant influence: step goal setting, baseline age, BMI, weight, sex distribution, disease duration, intervention duration, and baseline values or change scores for total or moderate‐to‐vigorous physical activity. After completion of the pedometer intervention, non‐significant declines in BMI and weight were observed during the follow‐up periods.ConclusionsPedometer intervention promotes modest weight loss, but its association with physical activity requires further clarification. Future studies are also required to document dietary and sedentary behaviour changes to facilitate the use of pedometers for weight loss in overweight and obese adults with Type 2 diabetes.
Impact of Septal Reduction on Left Atrial Size and Diastole in Hypertrophic Cardiomyopathy
Authors: Finocchiaro Gherardo , Haddad Francois , Kobayashi Yukari , Lee David , Pavlovic Aleksandra , Schnittger Ingela , Sinagra Gianfranco , Magavern Emma , Myers Jonathan , Froelicher Victor , Knowles Joshua W. , Ashley Euan 
Published: March 2016

Background and aimsBoth myectomy and alcohol septal ablation (ASA) can substantially reduce left ventricular (LV) outflow obstruction, relieve symptoms, and improve outcomes in hypertrophic cardiomyopathy (HCM). It is unclear whether septal reduction decreases left atrial (LA) size and improves diastolic function. The aim of this study was to analyze the consequences of septal reduction on LA size and diastolic function in a cohort of patients with HCM.MethodsForty patients (mean age: 50 ± 14, male sex 64%) with HCM who underwent septal reduction (myectomy or alcohol septal ablation) were studied. Retrospective analyses of echocardiograms preprocedure, postprocedure, and at 1 year of follow‐up were performed.ResultsThirty‐one patients had septal myectomy and 9 ASA. The degree of reduction in rest peak LV outflow tract gradient was significant (57 ± 32 vs. 23 ± 20 mmHg at 1 year, P < 0.001). Maximal interventricular septal thickness decreased from 22 ± 6 mm preprocedure to 19 ± 4 mm postprocedure (P < 0.001); moderate‐to‐severe mitral regurgitation (MR) was initially present in 34% of the sample and only 2% after the procedure. Average LA volume index (LAVI) decreased from 63 ± 20 to 55 ± 20 mL/m2 at the 1‐year follow‐up (P < 0.001). We did not observe a significant improvement in diastolic function at Doppler (E/A 1.2 ± 0.4 vs. 1.1 ± 0.5, P = 0.07; E’ 7.6 ± 3.6 vs. 6.9 ± 3.0, P = 0.4) pre‐ and postprocedure, respectively). At 1 year, only 5% of the patients were severely symptomatic (NYHA III). On multivariate analysis, a significant change in the LVOT gradient during stress (Δ gradient ≥30 mmHg) was the only variable independently associated with LAVI reverse remodeling >10 mL/m2 [OR = 6.4 (CI 95% 1.12–36.44), P = 0.04].ConclusionsSeptal reduction is effective in the relief of LV obstruction and symptoms in patients with HCM. The hemodynamic changes result in a significant LA reverse remodeling, but not in an improvement of diastolic function in these patients.
A single dose of lorazepam reduces paired‐pulse suppression of median nerve evoked somatosensory evoked potentials
Authors: Stude Philipp , Lenz Melanie , Höffken Oliver , Tegenthoff Martin , Dinse Hubert 
Published: March 2016

AbstractPaired‐pulse behaviour in the somatosensory cortex is an approach to obtain insights into cortical processing modes and to obtain markers of changes of cortical excitability attributable to learning or pathological states. Numerous studies have demonstrated suppression of the response to the stimulus that follows a first one after a short interval, but the underlying mechanisms remain elusive, although there is agreement that GABAergic mechanisms seem to play a crucial role. We therefore aimed to explore the influence of the GABAA agonist lorazepam on paired‐pulse somatosensory evoked potentials (SEPs). We recorded and analysed SEPs after paired median nerve stimulation in healthy individuals before and after they had received a single dose of 2.5 mg of lorazepam as compared with a control group receiving placebo. Paired‐pulse suppression was expressed as a ratio of the amplitudes of the second and the first peaks. We found that, after lorazepam application, paired‐pulse suppression of the cortical N20 component remained unchanged, but suppression of the N20–P25 complex was significantly reduced, indicative of GABAergic involvement in intracortical processing. Our data suggest that lorazepam most likely enhances inhibition within the cortical network of interneurons responsible for creating paired‐pulse suppression, leading to reduced inhibitory drive with a subsequently reduced amount of suppression. The results provide further evidence that GABAA‐mediated mechanisms are involved in the generation of median nerve evoked paired‐pulse suppression.
Elevated atmospheric [CO2] can dramatically increase wheat yields in semi‐arid environments and buffer against heat waves
Authors: Fitzgerald Glenn J. , Tausz Michael , O'Leary Garry , Mollah Mahabubur R. , Tausz‐Posch Sabine , Seneweera Saman , Mock Ivan , Löw Markus , Partington Debra L. , McNeil David , Norton Robert M. 
Published: March 2016

AbstractWheat production will be impacted by increasing concentration of atmospheric CO2 [CO2], which is expected to rise from about 400 μmol mol−1 in 2015 to 550 μmol mol−1 by 2050. Changes to plant physiology and crop responses from elevated [CO2] (e[CO2]) are well documented for some environments, but field‐level responses in dryland Mediterranean environments with terminal drought and heat waves are scarce. The Australian Grains Free Air CO2 Enrichment facility was established to compare wheat (Triticum aestivum) growth and yield under ambient (~370 μmol−1 in 2007) and e[CO2] (550 μmol−1) in semi‐arid environments. Experiments were undertaken at two dryland sites (Horsham and Walpeup) across three years with two cultivars, two sowing times and two irrigation treatments. Mean yield stimulation due to e[CO2] was 24% at Horsham and 53% at Walpeup, with some treatment responses greater than 70%, depending on environment. Under supplemental irrigation, e[CO2] stimulated yields at Horsham by 37% compared to 13% under rainfed conditions, showing that water limited growth and yield response to e[CO2]. Heat wave effects were ameliorated under e[CO2] as shown by reductions of 31% and 54% in screenings and 10% and 12% larger kernels (Horsham and Walpeup). Greatest yield stimulations occurred in the e[CO2] late sowing and heat stressed treatments, when supplied with more water. There were no clear differences in cultivar response due to e[CO2]. Multiple regression showed that yield response to e[CO2] depended on temperatures and water availability before and after anthesis. Thus, timing of temperature and water and the crop's ability to translocate carbohydrates to the grain postanthesis were all important in determining the e[CO2] response. The large responses to e[CO2] under dryland conditions have not been previously reported and underscore the need for field level research to provide mechanistic understanding for adapting crops to a changing climate.
Tree‐mycorrhizal associations detected remotely from canopy spectral properties
Authors: Fisher Joshua B. , Sweeney Sean , Brzostek Edward R. , Evans Tom P. , Johnson Daniel J. , Myers Jonathan A. , Bourg Norman A. , Wolf Amy T. , Howe Robert W. , Phillips Richard P. 
Published: March 2016

AbstractA central challenge in global ecology is the identification of key functional processes in ecosystems that scale, but do not require, data for individual species across landscapes. Given that nearly all tree species form symbiotic relationships with one of two types of mycorrhizal fungi – arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi – and that AM‐ and ECM‐dominated forests often have distinct nutrient economies, the detection and mapping of mycorrhizae over large areas could provide valuable insights about fundamental ecosystem processes such as nutrient cycling, species interactions, and overall forest productivity. We explored remotely sensed tree canopy spectral properties to detect underlying mycorrhizal association across a gradient of AM‐ and ECM‐dominated forest plots. Statistical mining of reflectance and reflectance derivatives across moderate/high‐resolution Landsat data revealed distinctly unique phenological signals that differentiated AM and ECM associations. This approach was trained and validated against measurements of tree species and mycorrhizal association across ~130 000 trees throughout the temperate United States. We were able to predict 77% of the variation in mycorrhizal association distribution within the forest plots (P < 0.001). The implications for this work move us toward mapping mycorrhizal association globally and advancing our understanding of biogeochemical cycling and other ecosystem processes.
Do physicians correctly calculate thromboembolic risk scores? A comparison of concordance between manual and computer‐based calculation of CHADS2 and CHA2DS2‐VASc scores
Authors: Esteve‐Pastor M. A. , Marín F. , Bertomeu‐Martinez V. , Roldán‐Rabadán I. , Cequier‐Fillat Á. , Badimon L. , Muñiz‐García J. , Valdés M. , Anguita‐Sánchez M. ,   FANTASIIA Study Investigators
Published: March 2016

BackgroundClinical risk scores, CHADS2
and CHA2DS2‐VASc scores, are the established tools for assessing stroke risk in patients with atrial fibrillation (AF).AimThe aim of this study is to assess concordance between manual and computer‐based calculation of CHADS2
and CHA2DS2‐VASc scores, as well as to analyse the patient categories using CHADS2
and the potential improvement on stroke risk stratification with CHA2DS2‐VASc score.MethodsWe linked data from Atrial Fibrillation Spanish registry FANTASIIA. Between June 2013 and March 2014, 1318 consecutive outpatients were recruited. We explore the concordance between manual scoring and computer‐based calculation. We compare the distribution of embolic risk of patients using both CHADS2
and CHA2DS2‐VASc scoresResultsThe mean age was 73.8 ± 9.4 years, and 758 (57.5%) were male. For CHADS2
score, concordance between manual scoring and computer‐based calculation was 92.5%, whereas for CHA2DS2‐VASc score was 96.4%. In CHADS2
score, 6.37% of patients with AF changed indication on antithrombotic therapy (3.49% of patients with no treatment changed to need antithrombotic treatment and 2.88% of patients otherwise). Using CHA2DS2‐VASc score, only 0.45% of patients with AF needed to change in the recommendation of antithrombotic therapy.ConclusionWe have found a strong concordance between manual and computer‐based score calculation of both CHADS2 and CHA2DS2‐VASc risk scores with minimal changes in anticoagulation recommendations. The use of CHA2DS2‐VASc score significantly improves classification of AF patients at low and intermediate risk of stroke into higher grade of thromboembolic score. Moreover, CHA2DS2‐VASc score could identify ‘truly low risk’ patients compared with CHADS2 score.