bluuebunny/crossref_metadata_2025_split huggingface dataset:
gEVAL – A web based browser for evaluating genome assemblies
Authors: Chow William , Brugger Kim , Caccamo Mario , Sealy Ian , Torrance James , Howe Kerstin 
Published: February 2016

AbstractMotivationFor most research approaches, genome analyses are dependent on the existence of a high quality genome reference assembly. However, the local accuracy of an assembly remains difficult to assess and improve. The gEVAL browser allows the user to interrogate an assembly in any region of the genome by comparing it to different datasets and evaluating the concordance. These analyses include: a wide variety of sequence alignments, comparative analyses of multiple genome assemblies, and consistency with optical and other physical maps. gEVAL highlights allelic variations, regions of low complexity, abnormal coverage, and potential sequence and assembly errors, and offers strategies for improvement. While gEVAL focuses primarily on sequence integrity, it can also display arbitrary annotation including Ensembl or TrackHub sources. We provide gEVAL web sites for many human, mouse, zebrafish and chicken assemblies to support the Genome Reference Consortium, and gEVAL is also downloadable to enable its use for any organism and assembly.AvailabilityWeb Browser:http://geval.sanger.ac.uk, Plugin:http://wchow.github.io/wtsi-geval-plugin.Contactkj2@sanger.ac.ukSupplementary informationSupplementary data are available atBioinformaticsonline.
Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns
Authors: Shao Zhu-Qing , Xue Jia-Yu , Wu Ping , Zhang Yan-Mei , Wu Yue , Hang Yue-Yu , Wang Bin , Chen Jian-Qun 
Published: February 2016

Abstract
Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.
On ethnicity of idiosyncratic risk and stock returns puzzle
Authors: Al Rahahleh Naseem , Adeinat Iman , Bhatti Ishaq 
Published: February 2016

Purpose
– The purpose of this paper is to understand the controversial issue of whether stock returns and idiosyncratic risks are related positively or negatively in case of Singaporean ethically poor screened stocks.

Design/methodology/approach
– To achieve the major objectives of this paper, it uses a multiple regression to explore the relationship between expected stock returns and idiosyncratic risk. The paper replicates the Lee and Faff’s (2009) three-factor capital asset-pricing model (CAPM) model in creating the six size/book-to-market portfolios from which it constructs the small minus big (SMB) and high minus low (HML) portfolios that capture the size and book-to-market equity factors, respectively.

Findings
– The basic finding of the paper is that there is a strong relation between idiosyncratic risk and the expected stock returns. In more details, we observe that the portfolio of stocks with the highest idiosyncratic volatility generates higher average returns (4.36 per cent) than the portfolio of stocks with the lowest idiosyncratic volatility (0.79 per cent) over the sample period. The paper observes that the stock’s idiosyncratic volatility is inversely correlated with the size of the underlying firm. Moreover, there is a pattern of relationships nearer the periods of financial crises: Asian and global financial crises.

Research limitations/implications
– This paper uses only a three-factor model on a single country. So it cannot be generalized to a multi-country level in the Association of Southeast Asian Nations (ASEAN) region, as the structure of each member country is different.

Practical implications
– This paper provides guidelines for policymakers and foreign investors in Singapore about the relationship. This research can also be extended to other ASEAN countries to understand this puzzle.

Social implications
– Ethically sensitive and faithful investors with small investment can benefit from the findings of this paper.

Originality/value
– The work reported in this paper is original, unpublished and is also not under consideration for publication elsewhere.
Do sport tourists’ perceived risks affect their involvement and intention to (re)visit? An empirical study for risk-reduction strategies
Authors: Choo Ho Keun , Choo Yunjeong (Clara) , Kang Hyun Min 
Published: February 2016

Purpose
– The purpose of this paper is to investigate what factors have a significant effect on equestrians’ participation in equestrian tourism.

Design/methodology/approach
– The methodology was quantitative research data analysis. Survey questionnaires (perceived risk, involvement, and intention to (re)visit questions) were developed based on pertinent previous studies. A main study was conducted in West Texas in the USA with college students.

Findings
– This study found that the perceived risk factors significantly affected involvement factors and, in turn, affected intention to (re)visit in equestrian tourism.

Originality/value
– Although equestrian tourism has many positive effects on tourists such as health benefits as well as local economies, equestrian tourism in the USA is considered one of the least favorite leisure sports compared to other sports activities. Consequentially, there are few studies related to equestrian tourists, this paper adds to a currently niche area of study.
What makes an effective CSR program? An analysis of the constructs of a cause-related participant sport sponsorship event
Authors: Sung Minjung , Lee Woo-Young 
Published: February 2016

Purpose
– The purpose of this paper is to explain the benefits of charitable sport events and examines how consumer involvement in the cause, attitude toward the event, and event-sponsor fit influence corporate image (CI) and corresponding purchase intention (PI).

Design/methodology/approach
– The conceptual model developed in this research consolidates various constructs related to sponsors and events into a single comprehensive framework, thus offering an integrated view of the factors that determine consumers’ perceptions of a sponsorship and their attitudes toward a sponsor. Data were collected from participants in the Pink Ribbon Love Marathons (PRLM) held in Seoul, South Korea. A total of 650 female subjects (mean age=41.2, SD=12.5) participated in this investigation.

Findings
– The findings indicate that CI plays a significant role as a partial mediator within a reciprocal relationship between participants’ event perception and patronage intention. Sponsoring a well-targeted event might have a positive impact on CI and PI.

Originality/value
– What makes this study unique is the application of previous research examining cause-related sport sponsorship from a sport participant’s perspective. From a practical standpoint, the findings of this study reveal the importance of corporate communication in CSR.
Factors influencing the discovery and use of wildlife passages for small fauna
Authors: Martinig April Robin , Bélanger‐Smith Katrina 
Published: February 2016

Summary

While many studies have looked at how large mammals respond to road mitigation measures, few have examined the effects on smaller mammals.

We investigated the effectiveness of three different types of wildlife passages along Highway 175 in Quebec, Canada, for small‐ and medium‐sized mammals (<30 kg) using infrared cameras. Wildlife passages (n = 17) were monitored 24 h a day 7 days a week from 2012 to 2015. Two research questions were addressed: (i) What influences passage discovery and use? and (ii) does it differ between species? Global and species‐specific models were produced for both discovery and use. A linear mixed‐effects model was used for the discovery data (log‐transformed counts), and a generalized linear mixed model was used for the crossing data (binary response).

Species' responded to the passages differently, with discoveries increasing overall and in particular for marmots Marmota monax as latitude increased. Pipe culverts were significantly more likely to be discovered by micromammals and wooden ledge culverts by red squirrels Tamiasciurus hudsonicus. Older passages were discovered less in general, with the exception of marmots. Marmots were also the only species to show a difference in crossings by passage type, favouring pipe culverts. Passage use was less likely with a median present for all models, except squirrels. More open passages had higher use overall and particularly for marmots and weasels Mustela spp.

Synthesis and applications. By separating animal responses to wildlife passages into two types (discovery and use), we have shown it is possible to incorporate multiple dimensions into post‐mitigation evaluation. This study highlights how transportation agencies can engineer more effective wildlife passages by minimizing the barrier effect of the structures themselves and constructing more passages better suited to the needs of the species they are targeting. To benefit the most species, it is recommended that future projects contain a diversity of open, single segment passages requiring long‐term monitoring.
The application of a filter‐based assembly model to develop best practices for Pannonian sand grassland restoration
Authors: Halassy Melinda , Singh Anand Narain , Szabó Rebeka , Szili‐Kovács Tibor , Szitár Katalin , Török Katalin 
Published: February 2016

Summary

The application of a filter‐based assembly model is a promising concept to support ecological restoration. The filters illustrate dispersal, abiotic and biotic constraints that narrow down the species pool and determine the realized species composition. The aim of restoration interventions is the manipulation of filters to achieve a restoration target.

We tested the applicability of a filter‐based assembly model in the restoration of endemic Pannonian sandy grassland on old‐fields. We report the results of a six‐year experiment to identify key filters and find possible interactions. Treatments included the following: (i) seeding (dispersal filter), (ii) carbon amendment to lower nitrogen availability (abiotic filter) and (iii) mowing (biotic filter). Treatments were carried out in 1 m2 plots following the same Latin square design in three old‐fields.

Seeding was the most important treatment increasing species richness, vascular cover and enhancing target species composition. Mowing played a secondary role, acting primarily in interaction with the other treatments. Carbon amendment significantly reduced soil mineral nitrogen, but played a subordinate role in determining vegetation composition. Significant interactions were found between the biotic and dispersal and the biotic and abiotic filters determining primarily the structural characteristics of the vegetation in terms of vascular cover, moss cover, litter and bare ground. Regarding species composition, synergistic links between the dispersal and biotic filters for seeded species and long‐lived forbs, and antagonistic interaction between the dispersal and abiotic filters for seeded species were found.

Synthesis and applications. Based on the impact and interactions of filters uncovered in this experiment, we propose a scheme for Pannonian grassland restoration, which can be validated and also used for other oligotrophic systems. In the proposed conceptual model, the dispersal filter plays a key role in determining the outcome of restoration measures followed by the biotic filter if manipulated by mowing, while the abiotic filter altered by nitrogen immobilization proved to have a weak effect. Based on our results, targeting several filters in parallel would improve restoration outcome. We propose that filter interactions should form an integral part of filter‐based assembly models and should be taken into account in restoration decisions.
The Effect of Clinical Chorioamnionitis on Cesarean Delivery in the United States
Authors: Bommarito Kerry M. , Gross Gilad A. , Willers Denise M. , Fraser Victoria J. , Olsen Margaret A. 
Published: February 2016

ObjectiveTo examine the association of clinical chorioamnionitis on cesarean delivery in a national sample of hospital discharges.Data SourceHospital discharge data from the 1998–2010 Nationwide Inpatient Sample.Study DesignWe performed a cross‐sectional study and general linear modeling was used to determine the association of clinical chorioamnionitis on risk of cesarean delivery.Principal FindingsA total of 10,843,682 deliveries and 51,799,431 nationally weighted deliveries were identified. Clinical chorioamnionitis was present in 2.9 percent of cesarean and 1.3 percent of vaginal deliveries (p < .001). In multivariate analysis, clinical chorioamnionitis was associated with a 1.39‐fold increased risk of cesarean delivery. Compared with women without clinical chorioamnionitis at an urban/teaching hospital, women with clinical chorioamnionitis at an urban/teaching, urban/nonteaching, and rural hospital were 1.4–1.5 times more likely to have cesarean delivery. Compared with women without clinical chorioamnionitis in the Midwest, the relative risk for cesarean in women with clinical chorioamnionitis was 1.54 for women in the South, 1.47 in the Northeast, 1.39 in the Midwest, and 1.34 in the West.ConclusionsWomen with clinical chorioamnionitis were more likely to have cesarean delivery than those without clinical chorioamnionitis, and the risk of cesarean delivery varied significantly by hospital location, teaching status, and U.S. region.
The Comparison of Matching Methods Using Different Measures of Balance: Benefits and Risks Exemplified within a Study to Evaluate the Effects of German Disease Management Programs on Long‐Term Outcomes of Patients with Type 2 Diabetes
Authors: Fullerton Birgit , Pöhlmann Boris , Krohn Robert , Adams John L. , Gerlach Ferdinand M. , Erler Antje 
Published: February 2016

ObjectiveTo present a case study on how to compare various matching methods applying different measures of balance and to point out some pitfalls involved in relying on such measures.Data SourcesAdministrative claims data from a German statutory health insurance fund covering the years 2004–2008.Study DesignWe applied three different covariance balance diagnostics to a choice of 12 different matching methods used to evaluate the effectiveness of the German disease management program for type 2 diabetes (DMPDM2). We further compared the effect estimates resulting from applying these different matching techniques in the evaluation of the DMPDM2.Principal FindingsThe choice of balance measure leads to different results on the performance of the applied matching methods. Exact matching methods performed well across all measures of balance, but resulted in the exclusion of many observations, leading to a change of the baseline characteristics of the study sample and also the effect estimate of the DMPDM2. All PS‐based methods showed similar effect estimates. Applying a higher matching ratio and using a larger variable set generally resulted in better balance. Using a generalized boosted instead of a logistic regression model showed slightly better performance for balance diagnostics taking into account imbalances at higher moments.ConclusionBest practice should include the application of several matching methods and thorough balance diagnostics. Applying matching techniques can provide a useful preprocessing step to reveal areas of the data that lack common support. The use of different balance diagnostics can be helpful for the interpretation of different effect estimates found with different matching methods.
Risk Adjustment Tools for Learning Health Systems: A Comparison of DxCG and CMS‐HCC V21
Authors: Wagner Todd H. , Upadhyay Anjali , Cowgill Elizabeth , Stefos Theodore , Moran Eileen , Asch Steven M. , Almenoff Peter 
Published: February 2016

ObjectiveTo compare risk scores computed by DxCG (Verisk) and Centers for Medicare and Medicaid Services (CMS) V21.Research DesignAnalysis of administrative data from the Department of Veterans Affairs (VA) for fiscal years 2010 and 2011.Study DesignWe regressed total annual VA costs on predicted risk scores. Model fit was judged by R‐squared, root mean squared error, mean absolute error, and Hosmer–Lemeshow goodness‐of‐fit tests. Recalibrated models were tested using split samples with pharmacy data.Data CollectionWe created six analytical files: a random sample (n = 2 million), high cost users (n = 261,487), users over age 75 (n = 644,524), mental health and substance use users (n = 830,832), multimorbid users (n = 817,951), and low‐risk users (n = 78,032).Principal FindingsThe DxCG Medicaid with pharmacy risk score yielded substantial gains in fit over the V21 model. Recalibrating the V21 model using VA pharmacy data‐generated risk scores with similar fit statistics to the DxCG risk scores.ConclusionsAlthough the CMS V21 and DxCG prospective risk scores were similar, the DxCG model with pharmacy data offered improved fit over V21. However, health care systems, such as the VA, can recalibrate the V21 model with additional variables to develop a tailored risk score that compares favorably to the DxCG models.
Sudden Death Caused by Anomalous Origin of the Coronary Artery During Exercise
Authors: Kurosu Akira , Kuroyanagi Kazumi , Yamauchi Shinobu , Omura Kazunobu , Saito Kazuyuki 
Published: February 2016

AbstractAnomalous origin of the coronary artery (AOCA) is a rare, but important cause of sudden cardiac death among young athletes. Nine autopsy cases (8 male, 1 female; mean age, 17.9 years; age range, 11–31 years) of sudden death during or just after exercise caused by AOCA were reviewed. The exercises performed at the time of death were running (4 cases), soccer (2 cases), and baseball, swimming and kendo (Japanese swordsmanship) (1 case each). In 6 cases, the left coronary artery arose from the right sinus of Valsalva, and in 3, the right coronary artery from the left sinus. The coronary arteries passed between the pulmonary artery and the aorta with an acute angle takeoff from the orifice. Three cases had cardiovascular manifestations prior to death. In cases with cardiovascular manifestations, novel imaging methods should be considered to prevent sudden death.
Clinical provision of improvised nasal naloxone without experimental testing and without regulatory approval: imaginative shortcut or dangerous bypass of essential safety procedures?
Authors: Strang John , McDonald Rebecca , Tas Basak , Day Ed 
Published: February 2016

AbstractContextTake‐home naloxone is increasingly provided to prevent heroin overdose deaths. Naloxone 0.4–2.0 mg is licensed for use by injection. Some clinicians supply improvised nasal naloxone kits (outside lisenced approval). Is this acceptable?Aims(1) To consider provision of improvised nasal naloxone in clinical practice and (2) to search for evidence for pharmacokinetics and effectiveness (versus injection).Methods(1) To document existing nasal naloxone schemes and published evidence of pharmacokinetics (systematic search of the CINAHL, Cochrane, EMBASE and MEDLINE databases and 18 records included in narrative synthesis). (2) To analyse ongoing studies investigating nasal naloxone (WHO International Clinical Trials Registry Platform and US NIH RePORT databases).Findings(1) Multiple studies report overdose reversals following administration of improvised intranasal naloxone. (2) Overdose reversal after nasal naloxone is frequent but may not always occur. (3) Until late 2015, the only commercially available naloxone concentrations were 0.4 mg/ml and 2 mg/2 ml. Nasal medications are typically 0.05–0.25 ml of fluid per nostril. The only published study of pharmacokinetics and bioavailability finds that nasal naloxone has poor bioavailability.Questions for debate(1) Why are pharmacokinetics and bioavailability data for nasal naloxone not available before incorporation into standard clinical practice? (2) Does nasal naloxone have the potential to become a reliable clinical formulation? (3) What pre‐clinical and clinical studies should precede utilization of novel naloxone formulations as standard emergency medications?ConclusionsThe addictions treatment field has rushed prematurely into the use of improvised nasal naloxone kits. Evidence of adequate bioavailability and acceptable pharmacokinetic curves are vital preliminary steps, especially when effective approved formulations exist.
Can a Welfarist Approach be Used to Justify a Moral Duty to Cognitively Enhance Children?
Authors: Krutzinna Jenny 
Published: February 2016

AbstractThe desire to self‐improve is probably as old as humanity: most of us want to be smarter, more athletic, more beautiful, or more talented. However, in the light of an ever increasing array of possibilities to enhance our capacities, clarity about the purpose and goal of such efforts becomes crucial. This is especially true when decisions are made for children, who are exposed to their parents’ plans and desires for them under a notion of increasing wellbeing. In recent years, cognitive enhancement has become a popular candidate for the promotion of wellbeing; welfarists even impose a moral duty on parents to cognitively enhance their children for the sake of their wellbeing. In this article, I aim to show that welfarists are mistaken in inferring such a moral obligation from the potential benefit of cognitive enhancement. In support of this, I offer three arguments: (a) the vagueness of wellbeing as a theoretical concept means it becomes impossible to apply in practice; (b) the link between cognition and wellbeing is far from unequivocal; and (c) quantification issues with regard to cognition make a duty impossible to discharge. In conclusion, I reject the welfarist approach as a justification for a parental moral obligation to cognitively enhance children.