bluuebunny/crossref_metadata_2025_split huggingface dataset:
AGOUTI: improving genome assembly and annotation using transcriptome data
Authors: Zhang Simo V. , Zhuo Luting , Hahn Matthew W. 
Published: November 2015

AbstractSummaryCurrent genome assemblies consist of thousands of contigs. These incomplete and fragmented assemblies lead to errors in gene identification, such that single genes spread across multiple contigs are annotated as separate gene models. We present AGOUTI (Annotated Genome Optimization Using Transcriptome Information), a tool that uses RNA-seq data to simultaneously combine contigs into scaffolds and fragmented gene models into single models. We show that AGOUTI improves both the contiguity of genome assemblies and the accuracy of gene annotation, providing updated versions of each as output.AvailabilityThe software is implemented in python and is available from github.com/svm-zhang/AGOUTI.Contactsimozhan@indiana.eduSupplementary informationSupplementary data are available atBioinformaticsonline.
Bedside healthcare rationing dilemmas: a survey from Portugal
Authors: Pinho Micaela , Borges Ana 
Published: November 2015

Purpose– The purpose of this paper is to seek to elicit, in a context of economic crisis, the social preferences for the microallocation of scarce healthcare resources.Design/methodology/approach– Data were collected from an online questionnaire which includes a hypothetical rationing choice scenario with four patients differentiated by their personal characteristics and health states competing for treatments and a set of statements that embodies: distributive criteria for prioritizing patients; the authorship of these types of decisions; and the likelihood of these decisions to be taken. Descriptive statistics, factor analysis and non-parametric test were used for describing and validating the data.Findings– Findings suggest that respondents: support a pluralism of distributive principles in prioritizing patients with an incident in utilitarianism and the reducing of inequalities in health, translated in the fair-inning and in emotional arguments of fragility; trust in the health professional to make prioritization decisions; and are conscious that rationing decisions will be real in the short term.Practical implications– The pursuit of efficiency and the equalizing of a lifetime health seem to be the criteria that should guide any rationing policy at the micro level.Originality/value– This study addresses simultaneously several ethical principles inherent to microallocation healthcare resources in a suitable context in which Portugal is facing an economic crisis and where, consequently, rationing healthcare policies gain prominence on the political agenda.
Re-positioning library technology support on Campus-Wilson Library’s journey
Authors: Jiang Amy , Beavers Karen , Cady Jennifer Esteron , McCoy Liberty 
Published: November 2015

Purpose
– The purpose of this paper is to discuss the changing role of the academic library, in relation to technology support services. It proposes that library technology services should expand to take a central role in developing student academic technology skills, and shows how moving into non-traditional areas of technology support can expand a library’s operation capabilities to include entrepreneurship and innovation for faculty, staff and students.

Design/methodology/approach
– The paper outlines how our library expanded its technology services to include course management support, technical literacy training and three-dimensional (3D) printing, and details future developments into robotics and software development. It details the authors initial objectives, the issues encountered, the improvements made in response and what the authors hope to do in the future.

Findings
– We are at a time when technology has made innovation and creation available to many. Academic libraries should take on this opportunity of repositioning technology services to provide and promote technical applications, becoming a central point for library users to share ideas and collaborate on projects. As a result of the interdisciplinary nature of academic libraries, the authors are in the best position to make this happen on campus.

Originality/value
– Even though continual change has been a theme in the development of libraries, very little has been written on the role of technology support services. This paper sets the foundation for further exploration in how taking on academic technology support services, 3D printing and makerspaces could be a part of library services.
Motivating language as a mediator between servant leadership and employee outcomes
Authors: Gutierrez-Wirsching Sandra , Mayfield Jacqueline , Mayfield Milton , Wang Wei 
Published: November 2015

Purpose– The purpose of this paper is to propose motivating language as a mediator to increase the positive effects of servant leadership on subordinates’ outcomes. The authors propose that motivating language acts as a mediator to transmit servant leadership traits and enhances the positive impact that servant leadership verbal behavior has on employees’ performance.Design/methodology/approach– By developing a conceptual model, the authors propose a connection between servant leadership and motivating language.Findings– In the proposed model, motivating language acts as a full and a partial mediator. The authors further categorize three distinct outcome sets that should be improved from this relationship. The first set includes improved worker performance, job satisfaction, absenteeism and worker innovation. The second set is composed of self-efficacy, organizational citizenship behavior and employee commitment. Finally, the third set includes trust, satisfaction with the leader and inspiration to become servant leaders.Research limitations/implications– Empirical research needs to be conducted to test this model.Practical implications– The positive effects of servant leadership through the use of motivating language could be operationalized in multiple ways. First, potential servant leaders could take the well-established, reliable and valid motivating language scale to diagnostically identify their leader-member communication strengths and weaknesses. Then, tailored motivating language trainings could be implemented which target motivating language weaknesses and key strategic outcomes in the proposed model. Furthermore, motivating language training would be a valuable instrument for transmission of a servant leadership culture.Social implications– Servant leadership style responds to the demand for positive ethical behavior that is much needed during these times when emphasis is given to profitability and lack of concern for people is the norm rather than the exception. It is also synchronized with the current benefits of organizational citizenship behaviors that have recently emerged in the field of managerial research.Originality/value– This paper aims at addressing a gap in the literature by developing a model of how leader strategic language, namely, motivating language, mediates between servant leadership and worker outcomes.
Effects of mountaintop removal mining and valley filling on the occupancy and abundance of stream salamanders
Authors: Price Steven J. , Muncy Brenee' L. , Bonner Simon J. , Drayer Andrea N. , Barton Christopher D. 
Published: November 2015

Summary

Human‐induced land‐use changes are among the primary causes of ecosystem degradation and biodiversity loss. Across central Appalachia (USA), mountaintop removal mining and valley filling (MTR/VF) is the prevailing form of land‐use change and represents a stressor to stream ecosystems. Salamanders are the dominant vertebrate in Appalachian headwater streams. Thus, we addressed the question: Is salamander occupancy and conditional abundance reduced in streams impacted by MTR/VF?

We conducted repeated counts of adult and larval salamanders within 10‐m reaches in 11 valley‐filled streams and 12 reference streams in south‐eastern Kentucky. Relationships between occupancy, conditional abundance, and site type (MTR/VF vs. reference) were modelled using the hurdle model (Ecology, 94, 2013 and 1472), where occupancy is modelled separately from abundance while accounting for differences in per‐individual detection probabilities among groups.

We found mean occupancy probabilities were >0·85 for all groups in reference reaches, whereas mean occupancy probabilities were relatively lower in MTR/VF reaches (ranging from 0·23 to 0·66). Posterior means of the difference in occupancy between site types were negative across all groups, although MTR/VF stream reaches were at least 95% less likely to be occupied by spring salamander Gyrinophilus porphyriticus, adult southern two‐lined salamander Eurycea cirrigera and larval dusky salamanders Desmognathus compared to reference reaches.

Posterior means of the difference in conditional abundance between MTR/VF and reference stream reaches were negative across all groups; 95% credible interval for difference in conditional abundance covered zero for only one species (red salamander Pseudotriton ruber). After adjusting for goodness‐of‐fit, point estimates of differences in occupancy and conditional abundance still remained below zero for most species. Additionally, MTR/VF reaches had higher ion concentrations, total organic carbon and specific conductance compared to reference reaches.

Synthesis and applications. Our study concludes that mountaintop removal mining and valley filling (MTR/VF) reduces salamander occupancy and conditional abundance. Although the potential mechanisms responsible for reduction are numerous, our findings suggest a change in the current regulatory framework is needed to offset the impacts of MTR/VF on stream ecosystems and biota. Reclamation techniques that enhance conditions for vegetative succession within catchments may improve habitat on reclaimed surface mines.
When does intraspecific trait variation contribute to functional beta‐diversity?
Authors: Spasojevic Marko J. , Turner Benjamin L. , Myers Jonathan A. 
Published: November 2015

Summary

Intraspecific trait variation (ITV) is hypothesized to play an important role in community assembly and the maintenance of biodiversity. However, fundamental gaps remain in our understanding of how ITV contributes to mechanisms that create spatial variation in the functional‐trait composition of communities (functional β‐diversity). Importantly, ITV may influence the perceived importance of environmental filtering across spatial scales.

We examined how ITV contributes to functional β‐diversity and environmental filtering in woody plant communities in a temperate forest in the Ozark ecoregion, Missouri, USA. To test the hypothesis that ITV contributes to changes in the perceived importance of environmental filtering across scales, we compared patterns of functional β‐diversity across soil‐resource and topographic gradients at three spatial grains and three spatial extents. To quantify the contribution of ITV to functional β‐diversity, we compared patterns that included ITV in five traits (leaf area, specific leaf area, leaf water content, leaf toughness and chlorophyll content) to patterns based on species‐mean trait values.

Functional β‐diversity that included ITV increased with spatial extent and decreased with spatial grain, suggesting stronger environmental filtering within spatially extensive landscapes that contain populations locally adapted to different habitats. In contrast, functional β‐diversity based on species‐mean trait values increased with spatial extent but did not change with spatial grain, suggesting weaker environmental filtering among larger communities which each contain a variety of habitats and locally adapted populations.

Synthesis. Although studies typically infer community assembly mechanisms from species‐mean trait values, our study suggests that mean trait values may mask the strength of assembly mechanisms such as environmental filtering, especially in landscape‐scale studies that encompass strong environmental gradients and locally adapted populations. Our study highlights the utility of integrating ITV into studies of functional β‐diversity to better understand the ecological conditions under which trait variation within and among species contributes most strongly to patterns of biodiversity across spatial scales.
Soil nutrients influence growth response of temperate tree species to drought
Authors: Lévesque Mathieu , Walthert Lorenz , Weber Pascale 
Published: November 2015

SummarySoil properties can buffer forest response to global climate change. However, it is unclear how soil characteristics, water availability and their interactions can affect drought response of trees. The aim of this study was to assess the influence of soil nutrients and physical soil properties on the growth sensitivity ofFagus sylvatica,Quercusspp.,Fraxinus excelsior,Abies alba, Picea abiesandPinus sylvestristo drought in Central Europe.Yearly growth data from increment cores were obtained from 538 trees and combined with forest inventory and soil data at 52 sites covering a large gradient of water availability and C/N ratios in soil. Linear mixed‐effects models were used to assess the species‐specific growth responses to climate and soil properties for the period 1957–2006. The growth of the species was further projected across the full range of C/N and water availability observed at 1029 sites where soil and species cover‐abundance data were available.Temperature, water and nutrient availability (C/N) were the most important factors for tree growth. Drought and low nutrient availability significantly reduced the growth of beech, ash, fir and spruce along the gradient. In contrast, the growth of pine and oak was little reduced on poor and dry sites, hence showing their competitive advantage over nutrient‐demanding species under such conditions. The growth of ash and pine was enhanced at sites with high species abundance, whereas an opposite response was found for spruce. No clear relationships between growth and species abundance were found for beech, oak and fir.Synthesis. Our results suggest that assessing tree responses to climate change without considering simultaneously soil properties and climate may be misleading since soil nutrients can influence growth response of trees to drought. A detailed analysis of the influence of the soil characteristics on growth responses of trees is necessary to understand the sensitivity of tree species to global climate change.
International patterns of the public awareness of aphasia
Authors: Code Chris , Papathanasiou Ilias , Rubio‐Bruno Silvia , de la Paz Cabana María , Villanueva Maria Marta , Haaland‐Johansen Line , Prizl‐Jakovac Tatjana , Leko Ana , Zemva Nada , Patterson Ruth , Berry Richard , Rochon Elizabeth , Leonard Carol , Robert Amelie 
Published: November 2015

AbstractBackground: It has been suggested that public awareness of aphasia is vital for extending services, research support, social inclusion and targeted raising of awareness. Earlier studies show that knowledge of aphasia varies across a range of variables, but is very low compared with other conditions.Aims: To report a series of surveys of public awareness of aphasia from six countries, the largest study conducted this far.Methods & Procedures: Surveys were conducted in Argentina (N = 800), Canada (N = 831), Croatia (N = 400), Greece (N = 800), Norway (N = 251) and Slovenia (N = 400) using the same methodology requesting information on age, sex and occupation, asking whether respondents had heard of aphasia and where they had heard of it. Respondents were tested on their levels of knowledge of aphasia.Outcomes & Results: Results revealed low levels of awareness of aphasia in countries surveyed with marked variability that appeared to interact with occupation, country, age and sex. We surveyed 3483 respondents (mean age = 43.16; SD = 17.68). Between 60% (Croatia) and 16% (Slovenia) said they had heard of aphasia (37.1% overall), but those with actual knowledge ranged from 13.9% (Norway) to 1.0% (Argentina). The combined mean of those with basic knowledge was 9.2%. Those who had heard of aphasia were younger; and females had higher levels of awareness. We also found associations between socio‐economic status and awareness. Those working in health, social and educational spheres had the highest levels. Respondents mainly heard about aphasia through the media and work or personal contact with aphasia.Conclusions & Implications: Levels of awareness are low everywhere in absolute terms, and relative to the awareness of other conditions, with significant variability between countries, sex and socio‐economic status. We examine how surveys can be utilized to plan ways to increase understanding and discuss the comparison of awareness of aphasia with other conditions.
Evidence of Place: Becoming a Region in Rural Canada
Authors: Markey Sean , Breen Sarah‐Patricia , Vodden Kelly , Daniels Jen 
Published: November 2015

AbstractThe purpose of this article is to investigate whether place is emerging in practice as a critical dimension in the development of Canadian rural regions. Recently, Jones and Paasi set regional researchers the task of better understanding how regions ‘become'. In researching this question, we are particularly interested in the definition and expression of place‐based identity as a mobilizing force for regionalism. Our findings suggest that, while identity plays a critical role in fostering regional development processes, it is either too emergent or actively resisted within our research sites to be a significant force for place‐based regional development.
Effects of Expanded California Health Coverage on Hospitals: Implications for ACA Medicaid Expansions
Authors: Bazzoli Gloria J. 
Published: November 2015

ObjectiveTo assess the effects on hospitals of early California actions to expand insurance coverage for low‐income uninsured adults after passage of the Affordable Care Act.Data Sources/Study SettingData from the California Office of Statewide Health Planning and Development and the California Department of Health were merged with U.S. census data for 294 short‐term general hospitals during the period 2009–2012.Study DesignA difference‐in‐difference analysis was conducted with hospitals in counties that did not implement insurance expansions used as a comparison group. Variables examined included payer mix, costs of unreimbursed care, and hospital operating margin. Sensitivity analyses were conducted as well as a triple difference analysis. Effects were estimated for hospitals overall and by ownership type.Principal FindingsCalifornia insurance expansions primarily benefited for‐profit hospitals, with these facilities experiencing significant decreases in self‐pay patients, increases in county‐covered patients, and reductions in charity care. Most models yielded no significant change in payer mix and conflicting changes in unreimbursed care for nonprofit hospitals.ConclusionsCalifornia hospitals that treated the most uninsured prior to insurance expansions did not as a group experience substantial benefit in terms of reduced uninsured burden or better financial performance after program expansions occurred.
Trust and Reflection in Primary Care Practice Redesign
Authors: Lanham Holly Jordan , Palmer Raymond F. , Leykum Luci K. , McDaniel Reuben R. , Nutting Paul A. , Stange Kurt C. , Crabtree Benjamin F. , Miller William L. , Jaén Carlos Roberto 
Published: November 2015

ObjectiveTo test a conceptual model of relationships, reflection, sensemaking, and learning in primary care practices transitioning to patient‐centered medical homes (PCMH).Data Sources/Study SettingPrimary data were collected as part of the American Academy of Family Physicians' National Demonstration Project of the PCMH.Study DesignWe conducted a cross‐sectional survey of clinicians and staff from 36 family medicine practices across the United States. Surveys measured seven characteristics of practice relationships (trust, diversity, mindfulness, heedful interrelation, respectful interaction, social/task relatedness, and rich and lean communication) and three organizational attributes (reflection, sensemaking, and learning) of practices.Data Collection/Extraction MethodsWe surveyed 396 clinicians and practice staff. We performed a multigroup path analysis of the data. Parameter estimates were calculated using a Bayesian estimation method.Principal FindingsTrust and reflection were important in explaining the characteristics of practice relationships and their associations with sensemaking and learning. The strongest associations between relationships, sensemaking, and learning were found under conditions of high trust and reflection. The weakest associations were found under conditions of low trust and reflection.ConclusionsTrust and reflection appear to play a key role in moderating relationships, sensemaking, and learning in practices undergoing practice redesign.
Prebiotic Low Sugar Chocolate Dairy Desserts: Physical and Optical Characteristics and Performance of PARAFAC and PCA Preference Map
Authors: Morais E. C. , Esmerino E. A. , Monteiro R. A. , Pinheiro C. M. , Nunes C. A. , Cruz A.G. , Bolini Helena M.A. 
Published: November 2015

AbstractThe addition of prebiotic and sweeteners in chocolate dairy desserts opens up new opportunities to develop dairy desserts that besides having a lower calorie intake still has functional properties. In this study, prebiotic low sugar dairy desserts were evaluated by 120 consumers using a 9‐point hedonic scale, in relation to the attributes of appearance, aroma, flavor, texture, and overall liking. Internal preference map using parallel factor analysis (PARAFAC) and principal component analysis (PCA) was performed using the consumer data. In addition, physical (texture profile) and optical (instrumental color) analyses were also performed. Prebiotic dairy desserts containing sucrose and sucralose were equally liked by the consumers. These samples were characterized by firmness and gumminess, which can be considered drivers of liking by the consumers. Optimization of the prebiotic low sugar dessert formulation should take in account the choice of ingredients that contribute in a positive manner for these parameters. PARAFAC allowed the extraction of more relevant information in relation to PCA, demonstrating that consumer acceptance analysis can be evaluated by simultaneously considering several attributes. Multiple factor analysis reported Rv value of 0.964, suggesting excellent concordance for both methods.