bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)
Authors: Guinand Bruno , Vandeputte Marc , Dupont‐Nivet Mathilde , Vergnet Alain , Haffray Pierrick , Chavanne Hervé , Chatain Béatrice 
Published: March 2017

AbstractDescribing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.
Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting‐free algorithm
Authors: Goolsby Eric W. 
Published: March 2017

AbstractAncestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non‐Brownian models, missing data, and within‐species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time‐consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000‐species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within‐species variation, non‐Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time‐consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation‐Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars functions anc.recon and phylopars.
Gene expression profiling during the embryo‐to‐larva transition in the giant red sea urchin Mesocentrotus franciscanus
Authors: Gaitán‐Espitia Juan Diego , Hofmann Gretchen E. 
Published: March 2017

AbstractIn echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo‐to‐larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up‐regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.
Are whooping cranes destined for extinction? Climate change imperils recruitment and population growth
Authors: Butler Matthew J. , Metzger Kristine L. , Harris Grant M. 
Published: March 2017

SummaryIdentifying climatic drivers of an animal population's vital rates and locating where they operate steers conservation efforts to optimize species recovery. The population growth of endangered whooping cranes (Grus americana) hinges on juvenile recruitment. Therefore, we identify climatic drivers (solar activity [sunspots] and weather) of whooping crane recruitment throughout the species’ life cycle (breeding, migration, wintering). Our method uses a repeated cross‐validated absolute shrinkage and selection operator approach to identify drivers of recruitment. We model effects of climate change on those drivers to predict whooping crane population growth given alternative scenarios of climate change and solar activity. Years with fewer sunspots indicated greater recruitment. Increased precipitation during autumn migration signified less recruitment. On the breeding grounds, fewer days below freezing during winter and more precipitation during breeding suggested less recruitment. We predicted whooping crane recruitment and population growth may fall below long‐term averages during all solar cycles when atmospheric CO2concentration increases, as expected, to 500 ppm by 2050. Species recovery during a typical solar cycle with 500 ppm may require eight times longer than conditions without climate change and the chance of population decline increases to 31%. Although this whooping crane population is growing and may appear secure, long‐term threats imposed by climate change and increased solar activity may jeopardize its persistence. Weather on the breeding grounds likely affects recruitment through hydrological processes and predation risk, whereas precipitation during autumn migration may influence juvenile mortality. Mitigating threats or abating climate change should occur within ≈30 years or this wild population of whooping cranes may begin declining.
Genetic relationships among Eriobotrya species revealed by genome‐wide RAD sequence data
Authors: Yang Xianghui , Najafabadi Samaneh Kazemiani , Shahid Muhammad Qasim , Zhang Zhike , Jing Yi , Wei Weiling , Wu Jingcheng , Gao Yongshun , Lin Shunquan 
Published: March 2017

AbstractRestriction site‐associated DNA sequencing (RAD‐seq) was used to illuminate the genetic relationships among Eriobotrya species. The raw data were filtered, and 221 million clean reads were used for further analysis. A total of 1,983,332 SNPs were obtained from 23 Eriobotrya species and two relative genera. We obtained similar results by neighbor‐joining and maximum likelihood phylogenetic trees. All Eriobotrya plants grouped together into a big clade, and two out‐groups clustered together into a single or separate clade. Chinese and Vietnam accessions were distributed throughout the dendrogram. There was nonsignificant correlation between genotype and geographical distance. However, clustering results were correlated with leaf size to some extent. The Eriobotrya species could be divided into following three groups based on leaf size and phylogenetic analysis: group A and group B comprised of small leaves with <10 cm length except E. stipularis (16.76 cm), and group C can be further divided into two subgroups, which contained medium‐size leaves with a leaf length ranged from 10 to 20 cm and a leaf length bigger than 20 cm.
Defeating epilepsy: A global public health commitment
Authors: Saxena Shekhar , Li Shichuo 
Published: March 2017

SummaryThis article points out that defeating epilepsy is a global public health commitment and a new challenge. This is because: epilepsy causes a heavy burden and very high treatment gap; in the field of life sciences and medicine, the 21st century would be the “Century of Brain Science”; a number of national brain research initiatives provide a great opportunity to reveal the secret of epilepsy; the Global Campaign against Epilepsy and the Mental Health Gap Action Programme made great contributions in the epilepsy control work worldwide; the historical WHA68.20 resolution gives great strength to promote defeating epilepsy.
Concentrated, ‘pulsed’ axial glacier flow: structural glaciological evidence from Kvíárjökull in SE Iceland
Authors: Phillips Emrys , Everest Jez , Evans David J.A. , Finlayson Andrew , Ewertowski Marek , Guild Ailsa , Jones Lee 
Published: March 2017

AbstractA detailed structural glaciological study carried out on Kvíárjökull in SE Iceland reveals that recent flow within this maritime glacier is concentrated within a narrow corridor located along its central axis. This active corridor is responsible for feeding ice from the accumulation zone on the south‐eastern side of Öræfajökull to the lower reaches of the glacier and resulted in a c. 200 m advance during the winter of 2013–2014 and the formation of a push‐moraine. The corridor comprises a series of lobes linked by a laterally continuous zone of highly fractured ice characterised by prominent flow‐parallel crevasses, separated by shear zones. The lobes form highly crevassed topographic highs on the glacier surface and occur immediately down‐ice of marked constrictions caused by prominent bedrock outcrops located on the northern side of the glacier. Close to the frontal margin of Kvíárjökull, the southern side of the glacier is relatively smooth and pock‐marked by a number of large moulins. The boundary between this slow moving ice and the active corridor is marked by a number of ice flow‐parallel strike‐slip faults and a prominent dextral shear zone which resulted in the clockwise rotation and dissection of an ice‐cored esker exposed on the glacier surface. It is suggested that this concentrated style of glacier flow identified within Kvíárjökull has affinities with the individual flow units which operate within pulsing or surging glaciers. © 2017 The Authors Earth Surface Processes and Landforms © 2017 John Wiley & Sons, Ltd.
Holocene fluvial valley fill sources of atmospheric mineral dust in the Skeleton Coast, Namibia
Authors: Thomas David S.G. , Durcan Julie A. , Dansie Andrew , Wiggs Giles F.S. 
Published: March 2017

AbstractWestern Namibia is a significant global source of atmospheric mineral dust. We investigate the relationship between dust and source sediments, assessing the sustainability of dust flux. Remote sensing studies have highlighted specific ephemeral fluvial systems as important contributors to dust flux, including highlighting sections of valleys that are the origins of dust plumes in the period 2005–2008. Little is known however about the specific within‐valley dust sediment sources, particularly whether dust is derived from modern ephemeral channel floors or older valley fill sediments, many of which have been reported in the region. As part of a region‐wide analysis of aeolian dust flux, we investigate the sediment properties of atmospheric dust samples and valley sediments from the Huab valley, one of the principal regional dust sources. Trapped dust samples contain up to 88% very fine sand and silt when collected samples are disaggregated prior to analysis. Valley fill surface samples comprise 80% very fine sand and silt, and the surface of the modern ephemeral channel 30%. Valley fill sediments were sampled at depths up to 3.6 m below the present surface and reveal Holocene depositional ages from 0.6 ± 0.03 ka back to 9.79 ± 0.73 ka. These sediments contain 30% to 6% very fine sand and silt, with levels decreasing with depth and age. Aeolian bedforms in the valley system (nebkhas on the fill surface and climbing dunes on valley margins) indicate that aeolian processes under the influence of strong seasonal easterly winds likely result in dust being winnowed out of the valley fill surfaces, with sandy bedforms being constructed from the coarser component of the fill sediments. The volume of valley fill sediment suggests dust sourced from Holocene sediments is likely to continue into the future regardless of flow conditions in the modern channel system. Copyright © 2017 John Wiley & Sons, Ltd.
Body mass index and prognosis in patients with head and neck cancer
Authors: Gama Ricardo Ribeiro , Song Yuyao , Zhang Qihuang , Brown M. Catherine , Wang Jennifer , Habbous Steven , Tong Li , Huang Shao Hui , O'Sullivan Brian , Waldron John , Xu Wei , Goldstein David , Liu Geoffrey 
Published: March 2017

ABSTRACTBackgroundBody mass index (BMI) has been associated variably with head and neck cancer outcomes. We evaluated the association between BMI at either diagnosis or at early adulthood head and neck cancer outcomes.MethodsPatients with invasive head and neck squamous cell cancer at Princess Margaret Cancer Centre in Toronto, Canada, were surveyed on tobacco and alcohol exposure, performance status, comorbidities, and BMI at diagnosis. A subset also had data collected for BMI at early adulthood.ResultsWith a median follow‐up of 2.5 years, in 1279 analyzed patients, being overweight (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.4–0.8; p = .001) at diagnosis was associated with improved survival when compared with individuals with normal weight. In contrast, underweight patients at diagnosis were associated with a worse outcome (HR, 1.89; 95% CI, 1.2–3.1; p < .01).ConclusionBeing underweight at diagnosis was an independent, adverse prognostic factor, whereas being overweight conferred better prognosis. BMI in early adulthood was not associated strongly with head and neck cancer outcomes. © 2017 Wiley Periodicals, Inc. Head Neck 39: 1226–1233, 2017
Risk assessment of parking lot management based on occupational injuries data
Authors: Jeong Byung Yong , Park Myoung Hwan 
Published: March 2017

AbstractThis study is concerned with the characteristics of occupational injuries and sick leaves for the workers doing parking lot management. Possible incidents and sick leaves have been identified and analyzed for 470 occupational accidents in the parking lot management process. Management level of accidents for prioritizing prevention measures is induced for the combination of the accident types and parking lot management processes. Accidents occurring during the specific parking lot management process showed different characteristics, depending on the type of accident and agency of accident. Most critical accidents that required corrective actions for prevention were being struck by an object in the “guide” process and slipping in the “valet parking” process. And, possible incidents predicted also as high level of management were slips in the “fee collection” and “cleaning” processes and falls to lower level in the “operating lift” and “repair” processes. Also, traffic accidents in the “guide” process, overexertion and bodily reaction and posture in the “patrol” process were ranked ‘high. The findings of this study can be used to develop more effective accident prevention policies to reduce occupational accidents in parking lot management.
Children's understanding of animal, plant, and artifact properties between 3 and 6 years
Authors: Fouquet Nathalie , Megalakaki Olga , Labrell Florence 
Published: March 2017

AbstractWe investigated the kinds of biological properties that children aged 3–6 years attribute to animals, plants, and artifacts by administering a property attribution task and eliciting explanations for the resulting property attributions. Findings indicated that, from the age of 3 years, children more frequently attribute properties to animals than they do to plants or artifacts. Moreover, attributions increased with age for animals, decreased for artifacts, and remained constant for plants. Concerning the conceptual development of animals and plants, results showed that the properties subtending children's initial conceptualization of animals are movement and nutrition, followed by growth, backed up by perceptual, biological, and categorical explanations. By contrast, for plants, the properties are growth and then movement, backed up by perceptual and biological arguments. These findings provide some support for the idea that both conceptual information and perceptual cues influence children's conceptual development.Highlights

This paper compares children's understanding of animals, plants, and artifacts between 3 and 6 years, in terms of property attributions and the spontaneous explanations of these objects.
With a property attribution task, children more frequently attribute properties to animals than they do to plants or artifacts.
Findings suggest that both conceptual information and perceptual cues influence children's conceptual development.
How fat are the tails of equity market indices?
Authors: Stoyanov Stoyan , Loh Lixia , Fabozzi Frank J. 
Published: March 2017

AbstractUsing a generalized autoregressive conditional heteroskedasticity model to explain away the volatility clustering of volatility effect and extreme value theory to analyse the residuals' left and right tails, we study the tail thickness of 22 developed and 19 emerging equity market indices. In‐sample and out‐of‐sample tests indicate that exponential tails of the residuals cannot be strongly rejected. We study the dispersion of extremes of developed and emerging markets, and we report a statistically significant tail asymmetry in both types of markets and a significant change in both tail risk and tail asymmetry of emerging markets after the financial crisis of 2008.
Segmentation of brain MRI using active contour model
Authors: Ben Rabeh Amira , Benzarti Faouzi , Amiri Hamid 
Published: March 2017

ABSTRACTAlzheimer disease is a neurodegenerative disorder that impairs memory, cognitive function, and gradually leads to dementia, physical deterioration, loss of independence, and death of the affected individual. In this context, segmentation of medical images is a very important technique in the field of image analysis and Computer‐Assisted Diagnosis. In this article, we introduce a new automatic method of brain images’ segmentation based on the Active Contour (AC) model to extract the Hippocampus and the Corpus Callosum (CC). Our contribution is to combine the geometric method with the statistical method of the AC. We used the Caselle Level Set and added a learning phase to build an average shape and to make the initialization task automatic. For the step of contour evolution, we used the principle of Level set and we added to it the a priori knowledge. Experimental results are very promising. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 3–11, 2017
A novel Markov random field model based on region adjacency graph for T1 magnetic resonance imaging brain segmentation
Authors: Ahmadvand Ali , Yousefi Sahar , Manzuri Shalmani M. T. 
Published: March 2017

ABSTRACTTissue segmentation in magnetic resonance brain scans is the most critical task in different aspects of brain analysis. Because manual segmentation of brain magnetic resonance imaging (MRI) images is a time‐consuming and labor‐intensive procedure, automatic image segmentation is widely used for this purpose. As Markov Random Field (MRF) model provides a powerful tool for segmentation of images with a high level of artifacts, it has been considered as a superior method. But because of the high computational cost of MRF, it is not appropriate for online processing. This article has proposed a novel method based on a proper combination of MRF model and watershed algorithm in order to alleviate the MRF's drawbacks. Results illustrate that the proposed method has a good ability in MRI image segmentation, and also decreases the computational time effectively, which is a valuable improvement in the online applications. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 78–88, 2017
Neuroimage‐based clinical prediction using machine learning tools
Authors: Demirhan Ayşe 
Published: March 2017

ABSTRACTClassification of structural brain magnetic resonance (MR) images is a crucial task for many neurological phenotypes that machine learning tools are increasingly developed and applied to solve this problem in recent years. In this study binary classification of T1‐weighted structural brain MR images are performed using state‐of‐the‐art machine learning algorithms when there is no information about the clinical context or specifics of neuroimaging. Image derived features and clinical labels that are provided by the International Conference on Medical Image Computing and Computer‐Assisted Intervention 2014 machine learning challenge are used. These morphological summary features are obtained from four different datasets (eachN > 70) with clinically relevant phenotypes and automatically extracted from the MR imaging scans using FreeSurfer, a freely distributed brain MR image processing software package. Widely used machine learning tools, namely; back‐propagation neural network, self‐organizing maps, support vector machines and k‐nearest neighbors are used as classifiers. Clinical prediction accuracy is obtained via cross‐validation on the training data (N = 150) and predictions are made on the test data (N = 100). Classification accuracy, the fraction of cases where prediction is accurate and area under the ROC curve are used as the performance metrics. Accuracy and area under curve metrics are used for tuning the training hyperparameters and the evaluation of the performance of the classifiers. Performed experiments revealed that support vector machines show a better success compared to the other methods on clinical predictions using summary morphological features in the absence of any information about the phenotype. Prediction accuracy would increase greatly if contextual information is integrated into the system. © 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27, 89–97, 2017