Miracle-dz/UniFAR-FTUs huggingface dataset:
High‐throughput sequencing and graph‐based cluster analysis facilitate microsatellite development from a highly complex genome

Abstract Despite recent advances in high‐throughput sequencing, difficulties are often encountered when developing microsatellites for species with large and complex genomes. This probably reflects the close association in many species of microsatellites with cryptic repetitive elements. We therefore developed a novel approach for isolating polymorphic microsatellites from the club‐legged grasshopper (Gomphocerus sibiricus), an emerging quantitative genetic and behavioral model system. Whole genome shotgun Illumina MiSeq sequencing was used to generate over three million 300 bp paired‐end reads, of which 67.75% were grouped into 40,548 clusters within RepeatExplorer. Annotations of the top 468 clusters, which represent 60.5% of the reads, revealed homology to satellite DNA and a variety of transposable elements. Evaluating 96 primer pairs in eight wild‐caught individuals, we found that primers mined from singleton reads were six times more likely to amplify a single polymorphic microsatellite locus than primers mined from clusters. Our study provides experimental evidence in support of the notion that microsatellites associated with repetitive elements are less likely to successfully amplify. It also reveals how advances in high‐throughput sequencing and graph‐based repetitive DNA analysis can be leveraged to isolate polymorphic microsatellites from complex genomes.
A HIGH-PERFORMANCE PARALLEL INCOMPRESSIBLE NAVIER-STOKES TWO-PHASE FLOW SOLVER USING THE LEVEL SET METHOD FOR HYDRODYNAMICS DESIGN

Recent developments in robustness and accuracy of computational methods to predict flow of immiscible fluids separated by an interface made possible their application to hydrodynamics design. The main challenge of those methods is to predict: accurately, the global loads exerted by the water on marine structures (ships, offshore platforms, .), and reliably local informations on the flow field making possible the optimization of the appendages and propulsive systems. Two important features of the computational method are required: a flexible unstructured discretization applied to locally-refined grids and highperformance parallelization of the CFD solvers able to run large 3D test cases (> 10 millions elements). In this paper, we propose the application of a massively parallel incompressible NavierStokes Eulerian two-phase flow solver to ship design process. The incompressible NavierStokes solver introduced in [8] is based on a parallel fractional predictor-corrector scheme implemented at the algebraic level, a Finite Element Method in space and implicit Finite Differences in time. It captures the interface motion on a fixed mesh using a Level Set method [24] discretized with the same features. The turbulence is modelled by the SpalartAllmaras one-equation closure [27]. A Reichardt wall function permits to approximate the velocity field behavior in the boundary layer [20]. Our numerical method was tested against forces and wake shape experimental data on a benchmark widely used in the ship hydrodynamics community : the bare hull David Taylor Model Basin (DTMB) model 5512 at steady state [9, 12]. Our proposed scheme shows a very high scalability tested on a large number of processors ( up to thousands ).
Legionella spp. in acute exacerbations of chronic obstructive pulmonary disease: what is the evidence?

Acute exacerbations are a frequent complication during the clinical course of chronic obstructive pulmonary disease (COPD). A recent monograph dealing with COPD exacerbations demonstrated that virtually all issues related to the management of acute exacerbations remain unsettled and controversial, including the definition, aetiology, microbial patterns, and antimicrobial treatment of this condition 1. This is of particular concern in view of the high burden of this complication on public health resources. With regards to microbial patterns and their possible involvement in the aetiology of acute exacerbations, it is a common view that Haemophilus influenzae , Streptococcus pneumoniae , and Moraxella catarrhali s are the leading pathogens. Viruses have also been shown to cause acute exacerbations, frequently working as copathogens together with bacterial pathogens 2–4. Only recently, important extensions of this concept have been provided. Firstly, evidence has grown that microbial patterns may move towards an increasing incidence of Gram-negative enterobacteriaceae and Pseudomonas aeruginosa in more advanced stages of COPD 5. Similar observations were made in severe exacerbations requiring ventilatory support 6, 7. Secondly, several studies found evidence of Chlamydia pneumoniae playing a role as a pathogen or copathogen in acute exacerbations 7–10. Finally, new challenges emerge from drug-resistant micro-organisms 11. Overall, bacterial pathogens were found to be present in approximately 50%, and atypical bacterial and viral pathogens in an additional 25% of cases. The presumptive aetiology in the remaining 25% of cases remained unclear 12. In this issue of the European Respiratory Journal , …
A Survey on Modeling Techniques for Formal Behavioral Verification of Software Product Lines

As software product lines are increasingly used for safety-critical systems, researchers have adapted formal verification techniques such as model checking and theorem proving to cope with compiletime variability. While the focus of the ongoing debate lies on the verification mechanisms itself, it becomes increasingly difficult for researchers to maintain an overview about the various accompanying modeling techniques. We survey existing approaches as a first step towards a unifying view on variability mechanisms in formal modeling techniques for product lines. We illustrate the approaches by means of a running example to illustrate their commonalities and differences.
Distributed source coding of correlated Gaussian observations

We consider a distributed source coding problem of L correlated Gaussian observations Yi, i = 1, 2,hellip, L. We consider the case where Yi, i = 1, 2,hellip, L satisfy Yi = Xi + Ni, i = 1, 2,hellip, L. Here Xi, i = 1, 2,hellip, L are L correlated Gaussian random variables and Ni, i = 1, 2,hellip, L are independent additive Gaussian noises also independent of Xi, i = 1, 2,hellip, L. The estimation error on the L correlated sources are measured by the distortion covariance matrix. The rate distortion region is defined by a set of all rate vectors for which the estimation error is upper bounded by an arbitrarily prescribed covariance matrix in the meaning of positive semi definite. In this paper we derive explicit outer and inner bounds of the rate distortion region. Our result may provide a useful tool to study two other open problems on this Gaussian distributed source coding system.
Standardization of ROC curve areas for diagnostic evaluation of liver fibrosis markers based on prevalences of fibrosis stages.

BACKGROUND The area under the ROC curve (AUC) is widely used as an estimate of the diagnostic value for fibrosis markers. Whether there is variability in the AUC related to the prevalence of fibrosis stages defining advanced and nonadvanced fibrosis is unknown. The aim of this study was to assess the relationships between the AUC and the prevalence of each fibrosis stage and to elaborate simple methods of standardization. METHODS The AUCs of FibroTest (FT) for the diagnosis of advanced fibrosis were estimated in patients with chronic hepatitis C using an integrated database including 1312 patients with FT and biopsy, and in an overview of 18 diagnostic studies. RESULTS In the integrated database considering stage prevalence, the FT AUC for advanced fibrosis varied (P <0.001) from 0.67 (only stage F2 as advanced fibrosis and only F1 as nonadvanced fibrosis) to 0.98 (only F4 as advanced fibrosis and only F0 as nonadvanced fibrosis). The same results were observed in the overview, in which the FT AUC varied (P <0.001) from 0.65 to 0.89 according to fibrosis stage prevalence. Two approaches for expressing standardized AUCs were developed: one approach assumed a uniform prevalence distribution of each fibrosis stage; the other approach used the prevalence distribution of fibrosis stages observed in the population. CONCLUSIONS The expressions of the AUCs of fibrosis markers should be standardized according to the prevalence of fibrosis stages defining advanced and nonadvanced fibrosis.
Patient satisfaction with oral implant rehabilitation: evaluation of responses to a questionnaire.

AIM This pilot study evaluated patients' experience of oral surgical and prosthetic procedures as well as their opinions regarding function, aesthetics, comfort, and satisfaction with treatment outcomes. MATERIALS AND METHODS Forty-nine subjects treated with oral implants completed questionnaires comprising 44 questions. Three questionnaires were used related to implant-supported single-tooth, fixed implant-supported prostheses and implant-retained overdentures. The questions related to demographic data (age, sex, employment, marital status and educational level), the source of information, the reason they underwent implant treatment, the discomfort related to all phases of treatment, and their functional and aesthetic satisfaction. RESULTS Most of the patients (53.8%) were employed and had received a high school certificate or a university diploma. Patients heard about implants from various sources, including referring dentists (55.8%), relatives and friends (23.1%), and television, radio and the Internet (17.3%). The main reasons for choosing implant treatment were restoring lost teeth (35,5%), following dentist's advice (33,3%), improving stability of the removable denture (15.4%), eating habits (13.5%) and aesthetics (1.9%). Most patients considered that the procedure took a long time (44.2%) but was not traumatic (62.5%). Pain was almost absent in most cases (64.5%) and swelling, when present, was generally moderate (48.1%) and seldom was marked (17.3%). Patients were very satisfied about the aesthetics (82.7%) and function (94.2%), and considered the implant prosthesis to be part of themselves (84.6%). Most of the patients considered the implant prostheses to be easy to clean (73.1%), and would repeat the treatment if necessary (86.5%) and recommend it to other people (94.2%). CONCLUSIONS Although the present study is limited by the small sample, the outcomes suggest that oral implant rehabilitation meets patients' needs and aesthetic demands.
Meta-analysis of scientometric research of knowledge management: discovering the identity of the discipline

Purpose – The purpose of this study is to conduct a meta-analysis of prior scientometric research of the knowledge management (KM) field. Design/methodology/approach – A total of 108 scientometric studies of the KM discipline were subjected to meta-analysis techniques. Findings – The overall volume of scientometric KM works has been growing, reaching up to ten publications per year by 2012, but their key findings are somewhat inconsistent. Most scientometric KM research is published in non-KM-centric journals. The KM discipline has deep historical roots. It suffers from a high degree of over-differentiation and is represented by dissimilar research streams. The top six most productive countries for KM research are the USA, the UK, Canada, Germany, Australia, and Spain. KM exhibits attributes of a healthy academic domain with no apparent anomalies and is progressing towards academic maturity. Practical implications – Scientometric KM researchers should use advanced empirical methods, become aware of prior .
Protection of Spanish Ibex (Capra pyrenaica) against Bluetongue Virus Serotypes 1 and 8 in a Subclinical Experimental Infection

Many wild ruminants such as Spanish ibex (Capra pyrenaica) are susceptible to Bluetongue virus (BTV) infection, which causes disease mainly in domestic sheep and cattle. Outbreaks involving either BTV serotypes 1 (BTV-1) and 8 (BTV-8) are currently challenging Europe. Inclusion of wildlife vaccination among BTV control measures should be considered in certain species. In the present study, four out of fifteen seronegative Spanish ibexes were immunized with a single dose of inactivated vaccine against BTV-1, four against BTV-8 and seven ibexes were non vaccinated controls. Seven ibexes (four vaccinated and three controls) were inoculated with each BTV serotype. Antibody and IFN-gamma responses were evaluated until 28 days after inoculation (dpi). The vaccinated ibexes showed significant (P<0.05) neutralizing antibody levels after vaccination compared to non vaccinated ibexes. The non vaccinated ibexes remained seronegative until challenge and showed neutralizing antibodies from 7 dpi. BTV RNA was detected in the blood of non vaccinated ibexes from 2 to the end of the study (28 dpi) and in target tissue samples obtained at necropsy (8 and 28 dpi). BTV-1 was successfully isolated on cell culture from blood and target tissues of non vaccinated ibexes. Clinical signs were unapparent and no gross lesions were found at necropsy. Our results show for the first time that Spanish ibex is susceptible and asymptomatic to BTV infection and also that a single dose of vaccine prevents viraemia against BTV-1 and BTV-8 replication.
Accounting for unequal access to higher education: The role of social identity factors

Western societies stress the potential for anyone, irrespective of social background, to improve their position within society. However, disadvantaged students face barriers in gaining a good education. Two studies in secondary schools show how perceptions of identity compatibility and anticipated fit influence students’ university choices. It was found that relatively disadvantaged students scored lower on identity compatibility, and that low scores on identity compatibility were associated with lower anticipated fit at a local selective (Study 1) or highly selective (Study 2) university. Anticipated fit, in turn, predicted the type of university to which participants wanted to apply; those who anticipated fitting in more at selective universities were more likely to apply to higher status universities. These relations were significant while controlling for academic achievement. Together, these studies suggest that social identity factors play a relevant role in explaining higher education choices among low-status group members.
Mash-Up Approach for Web Video Category Recommendation

With the advent of web 2.0, billions of videos are now freely available online. Meanwhile, rich user generated information for these videos such as tags and online encyclopedia offer us a chance to enhance the existing video analysis technologies. In this paper, we propose a mash-up framework to realize video category recommendation by leveraging web information from different sources. Under this framework, we build a web video dataset from the You Tube API, and construct a concept collection for web video category recommendation (CCWV-CR) from this dataset, which consists of the web video concepts with small semantic gap and high categorization distinguish ability. Besides, Wikipedia Propagation is proposed to optimize the video similarity measurement. The experiments on the large-scale dataset with 80,031 web videos demonstrate that: (1) the mash-up category recommendation framework has a great improvement than the existing state-of-art methods. (2) CCWV-CR is an efficient feature space for video category recommendation. (3) Wikipedia Propagation could boost the performance of video category recommendation.
HeadacheCoach: Towards Headache Prevention by Sensing and Making Sense of Personal Lifestyle Data

Estimates are that almost half of the world’s population has an active primary headache disorder, i.e. with no illness as an underlying cause. These can start manifesting in early adulthood and can last until the rest of the sufferer’s life. Most specialists concur that sudden changes in daily lifestyle, such are sleep rhythm, nutrition behavior or stress experience, can be valid triggers for headache sufferers. Health care professionals recommend leading a diary to self-monitor personal headache triggers in order to learn to avoid headache attacks. However, making sense out of this data is difficult. Despite existing smartphone approaches in literature that have evaluated behavior change support systems for headaches, they have failed to provide appropriate feedback on the collected daily data to showcase what causes or prevents an individual’s headache attacks. In this paper, we present HeadacheCoach, a smartphone app that tracks headache-triggering lifestyle data and headache attacks on a daily basis and propose a mixed-method approach to examine which feedback method( s) can strive the behavior change most in order to prevent future headache attacks.
A New Technique for Load-Flow Analysis of Radial Distribution Networks

A simple method to solve the load-flow problem of radial distribution networks is reported in this paper. This algorithm easily computes the power flow through any branch exploiting the radial feature of the distribution networks. The proposed method also reduces the data preparation and can handle arbitrary node numbering scheme very easily. The proposed method is compared with the other methods proposed by Das et al. (15), Ghosh et al . (16) and Ranjan et al. (19) to demonstrate its effectiveness. The detailed load-flow results for three examples with different kinds of load -modelling along with conclusion are presented in this paper.
Warrant Valuation and Strategic Exercise in Continuous Time and Imperfect Competition

This paper focuses on the valuation of warrants using a game-theoretic approach, incorporating strategic exercise of the warrants. Unlike previous work on strategic exercise of warrants, this paper employs a continuous time framework for the case of an oligopolistic holding structure of the warrants and also allows the firm to apply a combination of uses for the exercise proceeds. The results suggest that American warrants might be worth less than European warrants, in much broader sets of parameters than previously shown in the literature. * The Eitan Berglas School of Economics, Tel Aviv University, Israel. I would like to thank the following people for their useful comments during the preparation of this paper: Simon Benninga, Iddo Eliazar, David Frankel and Avner Kalay.
Dust depletion and abundance pattern in damped Lyα systems: A sample of Mn and Ti abundances at z < 2.2

We analyse a sample of 24 damped Lyman- α (DLA)/moderate DLA systems at intermediate redshifts, $0.3<z_{\rm abs}<2.2$, all with measurement of the weak Mn ii absorption lines, to investigate which elemental ratios could possibly be used as tracers of either dust depletion or nucleosynthesis effects. We applied a component-by-component analysis to the five systems of the sample with new observations and, using this procedure, re-analyzed data gathered from the literature whenever possible. We show that the standard method which uses column densities integrated over the whole absorption profiles could substantially underestimate the abundance of rare elements relative to Fe. We find a correlation between the observed [Si/Fe] and [Zn/Fe] ratios, present in our sample at the $2.9\sigma$ significance level. This correlation is fully consistent with a dust depletion sequence only for a Galactic warm disk cloud or halo cloud depletion pattern. The correlation between [Mn/Fe] and [Zn/Fe], detected at the $3.2\sigma$ significance level, cannot be accounted for by any dust depletion sequence: it implies either variations of the intrinsic Mn abundance relative to Fe from -0.3 to +0.1 dex and/or a relation between depletion level and metallicity. The correlation between [Mn/Fe] and metallicity ($2.6\sigma$ significance level) strengthens the assumption of intrinsic variations of [Mn/Fe] although some marginal correlation between [Zn or Si/Fe] and [Zn/H] is present as well. Extension of the sample toward low metallicity is needed to confirm the correlation between depletion level and metallicity. The variations of [Ti/Fe] vs. [Zn/Fe] cannot be fitted by a single dust depletion sequence either. We then adopt a warm disk cloud or halo cloud depletion pattern and compare the resulting dust-corrected abundance ratios to those observed in Galactic and SMC stars. At high metallicity, [ Fe/H$]_{\rm dc}\ga -0.5$, the intrinsic abundance pattern of Si, Ti, Cr and Mn in DLA absorbers closely follows the trends observed in Galactic stars and these absorbers should thus have a chemical evolution similar to that of our Galaxy. At lower metallicity, some absorbers do follow the trends present in Galactic stars but a substantial fraction of them have elemental ratios (in particular [ Si/Fe$]_{\rm dc}$ and [ Mn/Fe$]_{\rm dc}$) closer to the solar values than Galactic stars. This could be explained by a larger contribution of type Ia supernovae to the chemical enrichment of these DLA absorbers than in Galactic stars of similar metallicity. This metal-poor DLA absorber population could trace H i-rich dwarf galaxies.
The Prevalence of Scabies and Impetigo in the Solomon Islands: A Population-Based Survey

Background Scabies and impetigo are common, important and treatable skin conditions. Reports from several Pacific island countries show extremely high prevalence of these two conditions, but for many countries, including the Solomon Islands, there is a paucity of epidemiological data. Methodology Ten rural villages in the Western Province of the Solomon Islands were included in the study, chosen so that data collection could be integrated with an existing project investigating clinical and serological markers of yaws. All residents were eligible to participate, and 1908 people were enrolled. Participants were interviewed and examined by a paediatric registrar, who recorded relevant demographic information, and made a clinical diagnosis of scabies and/or impetigo, severity and distribution. Principal Findings The total unweighted prevalence of scabies was 19.2% (95% confidence interval [CI] 17.5–21.0), and age and gender weighted prevalence 19.2% (95%CI 16.7–21.9). The adult prevalence of scabies was 10.4% (95%CI 8.2–13.2), and the highest prevalence was found in infants < 1 year of age (34.1%, adjusted odds ratio [AOR] compared with adults: 3.6, 95%CI 2.2–6.0) and children aged 1–4 years (25.7%, AOR 2.6, 95%CI 1.7–3.9). Scabies affected two or more body regions in 80.9% of participants, and 4.4% of scabies cases were classified as severe. The total unweighted prevalence of active impetigo was 32.7% (95%CI 30.6–34.8), and age and gender weighted prevalence 26.7% (95%CI 24.2–29.5). The highest prevalence was found in children aged 1–4 years (42.6%, AOR compared with adults: 4.1, 95%CI 2.9–5.8). Scabies infestation was associated with active impetigo infection (AOR 2.0, 95%CI 1.6–2.6); with 41.1% of active impetigo cases also having scabies. Conclusions and Significance Scabies and impetigo are very common in the rural Western Province of the Solomon Islands. Scabies infestation is strongly associated with impetigo. Community control strategies for scabies may reduce the burden of both conditions and their downstream complications.