bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending phylogeography to account for lineage fusion
Authors: Garrick Ryan C. , Banusiewicz John D. , Burgess Stephanie , Hyseni Chaz , Symula Rebecca E. 
Published: January 2019

AbstractSecondary contact between long isolated populations has several possible outcomes. These include the strengthening of preexisting reproductive isolating mechanisms via reinforcement, the emergence of a hybrid lineage that is distinct from its extant parental lineages and which occupies a spatially restricted zone between them, or complete merging of two populations such that parental lineages are no longer extant (“lineage fusion” herein). The latter scenario has rarely been explicitly considered in single‐species and comparative phylogeographic studies, yet it has the potential to impact inferences about population history and levels of congruence. In this paper, we explore the idea that insights into past lineage fusion may now be possible, owing to the advent of next‐generation sequencing. Using simulated DNA sequence haplotype datasets (i.e., loci with alleles comprised of a set of linked nucleotide polymorphisms), we examined basic requirements (number of loci and individuals sampled) for identifying cases when a present‐day panmictic population is the product of lineage fusion, using an exemplar statistical framework—approximate Bayesian computation. We found that with approximately 100 phased haplotype loci (each 400 bp long) and modest sample sizes of individuals (10 per population), lineage fusion can be detected under rather challenging scenarios. This included some scenarios where reticulation was fully contained within a Last Glacial Maximum timeframe, provided that mixing was symmetrical, ancestral gene pools were moderately to deeply diverged, and the lag time between the fusion event and gene pool sampling was relatively short. However, the more realistic case of asymmetrical mixing is not prohibitive if additional genetic data (e.g., 400 loci) are available. Notwithstanding some simplifying assumptions of our simulations and the knowledge gaps that remain about the circumstances under which lineage fusion is potentially detectable, we suggest that the recent release from data limitation allows phylogeographers to expand the scope of inferences about long‐term population history.
Underestimated and cryptic diversification patterns across Afro‐tropical lowland forests
Authors: Huntley Jerry W. , Keith Katrina D. , Castellanos Adrian A. , Musher Lukas J. , Voelker Gary 
Published: January 2019

AbstractAimVertebrate diversity in the Guineo‐Congolian forests (GCF) of Africa is high, yet mechanisms responsible for generating that diversity remain remarkably understudied. These forests have alternatively been viewed as centres of diversification (“cradles”) or more recently, as the opposite (“museums”). Here, we use a comparative dataset of avian and mammalian species to examine genetic diversification patterns across these forests and use these results to explain observed patterns in light of Plio‐Pleistocene climatic change and life‐history.LocationAfrica.MethodsWe analysed patterns of diversification across the GCF using a dataset composed of 629 and 1,048 mitochondrial sequences from 60 avian and 36 mammalian species, respectively. Uncorrected pairwise genetic distances were compared at three distinct geographical levels: west versus east of the Dahomey Gap, among the three major forest blocks, and among seven historical refugial areas. The timing of diversification was assessed for passerines, Rodentia, and Chiroptera.ResultsWe found substantial signatures of diversification in all three levels of our geographical comparisons. We recovered substantial disparity in the amount and depth of structure of diversification patterns between low dispersers (understorey birds and rodents) and more capable dispersers (other bird species and bats). Additionally, our chronogram recovered recent speciation and intraspecific diversification across songbird and mammalian lineages.Main conclusionsThe discrete, and often deep, structuring of genetic diversification for both birds and mammals across the GCF revealed strong correlations between historic landscape fragmentation and dispersal ability. Our results revealed a striking amount of unrecognized genetic diversity, which may be suggestive of cryptic species. Given the rate at which these forests are being negatively impacted by human intervention, our general lack of knowledge concerning vertebrate diversity across these forests may very well impact our ability to identify evolutionary processes underlying diversity and enact meaningful conservation efforts in the future.
Molecular biomarkers in cardiac hypertrophy
Authors: Zhu Liu , Li Chao , Liu Qiang , Xu Weiting , Zhou Xiang 
Published: January 2019

AbstractCardiac hypertrophy is characterized by an increase in myocyte size in the absence of cell division. This condition is thought to be an adaptive response to cardiac wall stress resulting from the enhanced cardiac afterload. The pathogenesis of heart dysfunction, which is one of the primary causes of morbidity and mortality in elderly people, is often associated with myocardial remodelling caused by cardiac hypertrophy. In order to well understand the potential mechanisms, we described the molecules involved in the development and progression of myocardial hypertrophy. Increasing evidence has indicated that micro‐RNAs are involved in the pathogenesis of cardiac hypertrophy. In addition, molecular biomarkers including vascular endothelial growth factor B, NAD‐dependent deacetylase sirtuin‐3, growth/differentiation factor 15 and glycoprotein 130, also play important roles in the development of myocardial hypertrophy. Knowing the regulatory mechanisms of these biomarkers in the heart may help identify new molecular targets for the treatment of cardiac hypertrophy.
Usefulness of newly modified fully covered metallic stent of 12 mm in diameter and anti‐migration feature for periampullary malignant biliary strictures: Comparison with conventional standard metal stent
Authors: Lee Hyun Woo , Moon Jong Ho , Lee Yun Nah , Lee Tae Hoon , Choi Moon Han , Cha Sang‐Woo , Cho Young Deok , Park Sang‐Heum 
Published: January 2019

AbstractBackgroundsFully covered self‐expandable metal stent (FCSEMS) are preferred for distal malignant biliary stricture (MBS). However, stent migration is a major adverse event of FCSEMS, especially for far distal MBS. We evaluated the usefulness of newly modified FCSEMS (M‐FCSEMS) having 12 mm in diameter and anti‐migration feature to minimize stent migration compared with the conventional FCSEMS (C‐FCSEMS).MethodsTotal 102 patients were enrolled between January 2015 and September 2017 in this prospective comparative study; 50 were allocated to the M‐FCSEMS group and 52 to the C‐FCSEMS group. The primary outcome was stent migration, and the secondary outcomes were other adverse events, stent occlusion rate, and stent patency during the follow‐up period.ResultsThe baseline characteristics of the two groups did not significantly differ. Endoscopic stent placement was technically successful in all patients. Stent migration occurred in 8.0% (4/50) of the patients in the M‐FCSEMS group and 23.1% (12/52) of those in the C‐FCSEMS group (P = 0.036). The other adverse events, including stent‐related pancreatitis and cholecystitis did not significantly differ between the two groups (P = 0.415). Stent occlusion occurred in 23.9% (11/46) of the patients in the M‐FCSEMS group and 37.5% (15/40) in the C‐FCSEMS group (P = 0.171). Stent patency was significantly longer in the M‐FCSEMS group than in the C‐FCSEMS group (228 vs 157 days, P = 0.048).ConclusionsModified FCSEMS with 12‐mm diameter and anti‐migration feature significantly decreased the risk of stent migration and had longer patency compared with C‐FCSEMS in patients with periampullary MBS.
Feasibility and effectiveness of pre‐emptive rehabilitation in persons approaching dialysis (PREHAB)
Authors: Willingham Fiona C. , Speelman Irene , Hamilton Joanne , von Fragstein Gillian , Shaw Susan , Taal Maarten W. 
Published: January 2019

SUMMARYIntroductionEnd‐stage kidney disease (ESKD) is characterised by several complications, leading to reduced functional ability and quality of life during transition to dialysis. This study aimed to establish the feasibility and effectiveness of a patient‐centred programme of exercise, nutritional intervention and multidisciplinary education for persons approaching dialysis.MethodsPatients with eGFR <15 ml/min/1.73 m2 and anticipated to start dialysis within 6–12 months were invited to participate. The 10‐week pre‐dialysis intervention included a weekly 1‐hour gym‐based exercise circuit and an education programme. Feasibility and acceptability were assessed through recruitment and retention rates, adherence to the intervention, and from patient feedback following the intervention. Physical function, nutritional status, and anxiety and depression, were assessed at baseline, after intervention, and as dialysis commenced.ResultsThirty patients agreed to participate, with 22 completing the pre‐dialysis intervention. Thirteen (59%) participants achieved 100% attendance at the exercise and education sessions, with only two participants attending less than 8/10 sessions. The intervention also led to improved physical function, demonstrated by significant increase in both incremental shuttle walk distance (330 vs. 385 m, p = 0.006) and quadriceps one repetition maximum (p = 0.007), and a trend towards increased sit‐to‐stand repetitions (20–23, p = 0.11). There was a trend for improved patient perception of activity (Duke Activity Status Index score 31.55 vs. 33.75, p = 0.09). Hand grip strength (29.1 vs. 29.8 kg), body mass index (30.4 vs. 30.5 kg/m2) and nutritional status assessed by subjective global assessment (73% well‐nourished) were maintained.ConclusionThis study demonstrated the feasibility and effectiveness of a patient‐centred exercise and education programme in those approaching dialysis. Further research is therefore required to evaluate the impact of this programme on clinical outcomes.
The Contributions of Conversation Analysis and Interactional Linguistics to a Usage‐Based Understanding of Language: Expanding the Transdisciplinary Framework
Authors: HALL JOAN KELLY 
Published: January 2019

AbstractA key insight of a transdisciplinary perspective on second language acquisition (SLA) as articulated by the Douglas Fir Group (2016) is its usage‐based understanding of language. Evidence on the fundamental role that usage plays in shaping individual language knowledge is no doubt compelling. However, while the force of social interaction in shaping language knowledge is acknowledged, missing are specifications of the jointly constructed actions and courses of action comprising social contexts of use. Also missing is a reconsideration of key SLA concepts engendered by a usage‐based understanding of language. The intent of this paper is to redress these limitations. First, I summarize the research programs of conversation analysis and interactional linguistics, which take as their central task the specifications of the jointly constructed actions and courses of action comprising social contexts and thus significantly enhance a usage‐based understanding of language. Then, arguing that more suitable conceptual tools are needed to better capture current understandings of language knowledge and objects of L2 learning, I offer repertoire, semiotic resources, and register as alternative terms to competence and grammar. I conclude with a proposal for a Conversation Analysis/Interactional Linguistics‐based research program for further advancing understandings of SLA and transforming understandings of L2 pedagogy.
Immigrants’ Wage Growth and Selective Out‐Migration
Authors: Bijwaard Govert E. , Wahba Jackline 
Published: January 2019

AbstractThis paper examines immigrant wage growth taking selective out‐migration into account using administrative data from the Netherlands. Addressing a limitation in the previous literature, we address the potential endogeneity of immigrants’ labour supply and out‐migration decisions on their earning profiles using a correlated competing risk model. We distinguish between labour and family migrants, given their different labour market and out‐migration behaviours. Our findings show that accounting for selective labour supply is as important as accounting for selective out‐migration. Controlling only for out‐migration selectivity would underestimate immigrants’ wage growth, whilst controlling only for labour market selectivity would overestimate their wage growth. This shows that different selections are important for different types of migrants.
Genetic analysis of gene‐specific resistance to mungbean yellow mosaic virus in mungbean (Vigna radiata)
Authors: Bhanu Akhouri Nishant , Singh Mahendra Narain , Srivastava Kartikeya 
Published: January 2019

AbstractSix intervarietal crosses involving two resistant and three susceptible genotypes of mungbean were attempted with the objectives to determine the mode of inheritance of gene‐specific Mungbean Yellow Mosaic Virus (MYMV) resistance. An infector row technique along with artificial inoculation was used for evaluating parents, F1, F2 and F3 plants for MYMV resistance. Disease scoring for MYMV indicated that F1s were highly susceptible as were the susceptible parents while resistant parent exhibited resistant reaction. The F2 progeny segregated in the ratio of 9 S:3 MS:3 MR:1 R suggesting that the resistance was governed by digenic recessive genes (rm1 and rm2). When one gene (rm1) was present in the homozygous recessive condition in different plants, it conferred moderately susceptible (MS) reaction, whereas when other gene (rm2) was in homozygous condition, moderately resistant (MR) reaction was obvious. When both genes (rm1 and rm2) were present together in the homozygous recessive condition, resistant reaction (R) was observed. The F2 segregation explained on the basis of phenotypic expression was further confirmed by F3 segregation.
The Influence of Feelings While Driving Regular Cars on the Perception and Acceptance of Self‐Driving Cars
Authors: Raue Martina , D'Ambrosio Lisa A. , Ward Carley , Lee Chaiwoo , Jacquillat Claire , Coughlin Joseph F. 
Published: January 2019

AbstractSelf‐driving vehicles will affect the future of transportation, but factors that underlie perception and acceptance of self‐driving cars are yet unclear. Research on feelings as information and the affect heuristic has suggested that feelings are an important source of information, especially in situations of complexity and uncertainty. In this study (N = 1,484), we investigated how feelings related to traditional driving affect risk perception, benefit perception, and trust related to self‐driving cars as well as people's acceptance of the technology. Due to limited experiences with and knowledge of self‐driving cars, we expected that feelings related to a similar experience, namely, driving regular cars, would influence judgments of self‐driving cars. Our results support this assumption. While positive feelings of enjoyment predicted higher benefit perception and trust, negative affect predicted higher risk and higher benefit perception of self‐driving cars. Feelings of control were inversely related to risk and benefit perception, which is in line with research on the affect heuristic. Furthermore, negative affect was an important source of information for judgments of use and acceptance. Interest in using a self‐driving car was also predicted by lower risk perception, higher benefit perception, and higher levels of trust in the technology. Although people's individual experiences with advanced vehicle technologies and knowledge were associated with perceptions and acceptance, many simply have never been exposed to the technology and know little about it. In the absence of this experience or knowledge, all that is left is the knowledge, experience, and feelings they have related to regular driving.
Explaining the effect of financial development on the quality of property rights
Authors: Banerjee Chandramouli , Bose Niloy , Rath Chitralekha 
Published: January 2019

AbstractEmpirical evidence suggests that financial development can catalyze property rights reforms. This paper offers a theory of financial markets to explain these facts defining the relationship. The explanation is based on a simple trade‐off between the costs and the benefits of securing property. Securing the right to property at a cost allows agents to post collateral against loans. However, the benefits of collateral vary according to the existing credit market conditions, which we take into account in the tradeoff between the costs and the benefits of securing property rights along the path of financial development to explain the conditions under which financial development can create incentives for better property rights institutions.
Visualizing Spatiotemporal Models with Virtual Reality: from Fully Immersive Environments to Applications in Stereoscopic View
Authors: Castruccio Stefano , Genton Marc G. , Sun Ying 
Published: January 2019

SummaryRecent advances in computing hardware and software present an unprecedented opportunity for statisticians who work with data indexed in space and time to visualize, explore and assess the structure of the data and to improve resulting statistical models. We present results of a 3-year collaboration with a team of visualization experts on the use of stereoscopic view and virtual reality (VR) to visualize spatiotemporal data with animations on non-trivial manifolds. We first present our experience with fully immersive VR with motion tracking devices that enable users to explore global three-dimensional time–temperature fields on a spherical shell interactively. We then introduce a suite of applications with VR mode, freely available for smartphones, to port a visualization experience to any interested people. We also discuss recent work with head-mounted devices such as a VR headset with motion tracking sensors.
Evaluation of art subjects implemented in the marquetry technique by the optical coherence microscopy method
Authors: Gurov Igor , Margaryants Nikita , Zhukova Ekaterina 
Published: January 2019

AbstractEvaluation of internal microstructure of decorative and applied art objects implemented in the intarsia and marquetry techniques by the optical coherence tomography method is considered. The high resolving optical coherence microscope with a radiation source with tunable wavelength in the range of 1305 ± 75 nm was applied. The ability to analyse layered microstructure of wood object surface layer in intarsia regions is demonstrated. The geometric features evaluation of the object's microstructure in the areas of interest was conducted. Systematisation of layers structure and typical defects inherent in intarsia regions was performed considering the structural features that may be important for restoration of such objects. Examples of experimentally obtained B‐scans and three‐dimensional representations of sample fragments of microstructure studied by the optical coherence microscopy method are given.
Photoacoustic spectroscopy telemetry of airport dangerous goods
Authors: Zhang Zhouqiang , Jia Shuhai , Xu Guangshen , Cao Yabin 
Published: January 2019

A novel photoacoustic spectroscopy telemetry method of detecting trace acetylene gas using a quartz tuning fork is reported. A 1532-nm CW-DFB, fiber-coupled diode laser with power of 12 mW was used as the excitation source while an astronomical telescope was used to collect laser light scattered on the surface of the detected object at a distance of 6 m and the photoacoustic spectroscopy of acetylene was performed. The detection results are consistent with the standard near-infrared absorption coefficient of acetylene. This study provides a new direction for research in photoacoustic spectroscopy telemetry. Future work will quantitatively analyze acetylene gas.
Deposition of ZnS thin films by electron beam evaporation technique, effect of thickness on the crystallographic and optical properties
Authors: Abdallah Bassam , Alnama Koutayba , Nasrallah Fareza 
Published: January 2019

Deposition of Zinc sulfide (ZnS) thin films on Si (100) and glass substrates has been performed using electron beam evaporation (EBE) method without annealing. Film structure has been analyzed by XRD, while SEM and AFM have been used to explore the films morphology. Raman spectroscopy has been used to confirm film composition. The stoichiometry has been verified by EDX and XPS techniques. XRD patterns indicated that the films possess a polycrystalline cubic structure with orientations along (111) and (220) planes. The crystallinity has been better with film thickness in the 350–1700 nm range while the RMS roughness increases. Optical properties of the grown films were characterized by optical transmittance measurements (UV–Vis). The deduced energy band gap of the films shows a clear reduction from 3.45 eV to 3.36 eV with increasing film thickness. The evolution of refractive index, extinction coefficient, and dielectric constants with thickness has been investigated from transmittance spectra in the 500–1000 nm wavelength range.
Altered R-spondin 1/CART neurocircuit in the hypothalamus contributes to hyperphagia in diabetes
Authors: Li Ji-Yao , Wu Xiaoyin , Lee Allen , Zhou Shi-Yi , Owyang Chung 
Published: January 2019

Hyperphagia is common in diabetes and may worsen hyperglycemia and diabetic complications. The responsible mechanisms are not well understood. The hypothalamus is a key center for the control of appetite and energy homeostasis. The ventromedial nucleus (VMH) and arcuate nucleus (ARC) are two critical nuclei involved in these processes. We have reported that R-spondin 1 (Rspo1) and its receptor leucin-rich repeat and G protein-coupled receptor 4 (LGR4) in the VMH and ARC suppressed appetite, but the downstream neuronal pathways are unclear. Here we show that neurons containing cocaine and amphetamine-regulated transcript (CART) in ARC express both LGR4 and insulin receptor; intracerebroventricular injection of Rspo1 induced c-Fos expression in CART neurons of ARC; and silencing CART in ARC attenuated the anorexigenic actions of Rspo1. In diabetic and obese fa/fa rats, Rspo1 mRNA in VMH and CART mRNA in ARC were reduced; this was accompanied by increased food consumption. Insulin treatment restored Rspo1 and CART gene expressions and normalized eating behavior. Chronic intracerebroventricular injection of Rspo1 inhibited food intake and normalized diabetic hyperphagia; intracerebroventricular injection of Rspo1 or insulin increased CART mRNA in ARC. In the CART neuron cell line, Rspo1 and insulin potentiated each other on pERK and β-catenin, and in rats, they acted synergistically to inhibit food intake. Silencing Rspo1 in VMH reduced CART expression in ARC and attenuated the inhibitory effect of insulin on food intake. In conclusion, our data indicated that CART works downstream of Rspo1 and Rspo1 mediated the action of insulin centrally. The altered Rspo1/CART neurocircuit in the hypothalamus contributes to hyperphagia in diabetes. NEW & NOTEWORTHY This study reports that cocaine and amphetamine-regulated transcript (CART) neurons in the arcuate nucleus (ARC) of hypothalamus acted downstream of R-spondin 1 (Rspo1) to inhibit food intake. The Rspo1 mRNA level in ventromedial nucleus (VMH) and CART mRNA level in ARC were reduced in type 1 diabetic rat and obese fa/fa rat. Rspo1 and insulin acted synergistically on phospho-ERK and β-catenin signal pathways and in suppressing food intake. The current results proposed that altered Rspo1/CART neurocircuit in the hypothalamus contributes to hyperphagia in diabetes.