bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do Golden-cheeked Warblers Select Nest Locations on the Basis of Patch Vegetation?
Authors: Dearborn Donald C. , Sanchez Laura L. , Moore F. 
Published: September 2019

Abstract
Proper management of endangered species requires an understanding of habitat use at a variety of spatial scales, and information on nesting habitat is especially important in that regard. We examined vegetation features associated with nest patches of the Golden-cheeked Warbler (Dendroica chrysoparia), a federally endangered migrant songbird that breeds only in central Texas. We used a spatially paired design to measure 13 vegetation variables at 43 nests and at an equal number of randomly chosen nonuse patches, one located near each nest. Canopy closure was greater at nest patches than at nonuse patches. However, none of the other vegetation variables differed between a nest patch and its paired non-use patch on the same territory, despite high power to detect such differences. In contrast, 8 of the 13 variables exhibited significant variation among territories. For all 13 variables, effect size was substantially greater for variation between territories than for variation between nest patches and their paired nonuse patches. Lack of within-territory variation may reflect the scale at which vegetation varies in that habitat. Such a result suggests that territory selection may be more important than nest-patch selection in this species.
Nocturnal Heterothermy and Torpor in the Malachite Sunbird (Nectarinia Famosa)
Authors: Downs Colleen T. , Brown Mark 
Published: September 2019

Abstract
Heterothermy in birds occurs in species that are generally small and whose diet fluctuates. This study of thermoregulation of Malachite Sunbirds (Nectarina famosa) showed that they have circadian fluctuations in Tb and VO2, as in most birds. Of special importance was the high degree of rest-phase hypothermy and exhibition of torpor at ambient temperatures of 10°C and lower. These patterns are significant because they have not been described in detail for a passerine species. Surgically implanted minimitters were used to measure Tb continuously and without disturbing the birds. Minimum VO2 during rest phase was 1.70 (mL O2 g–1 h–1) at 25°C. As ambient temperature decreased, VO2 minimum during the rest phase did not increase to maintain Tb. No birds remained normothermic during scotophase. At 5°C, that resulted in torpor in Malachite Sunbirds with a decrease of 15°C in Tb. Birds increased Tb to active-phase levels with the onset of light. It was difficult to define limits and ranges of physiological parameters associated with observed heterothermy. Individuals showed similar responses; however, those differed with ambient temperature. Malachite Sunbirds conserved energy nocturnally by reducing metabolic rate and, concomitantly, Tb. This plasticity in Tb shows that daily variations in Tb of homeotherms are biologically important. Furthermore, this heterothermy (particularly nocturnal hypothermia and torpor) in a small avian species would be important in an unpredictable environment where food resources fluctuate to prevent an energy deficit.
Rediscovery of a Cryptic Species and Description of a New Subspecies in The Myrmeciza Hemimelaena Complex (Thamnophilidae) of the Neotropics
Authors: Isler Morton L. , Alonso José Alvarez , Isler Phyllis R. , Valqui Thomas , Begazo Alfredo , Whitney Bret M. 
Published: September 2019

AbstractThe recording in 1992 of an unknown antbird loudsong initiated a journey of discovery that led to the resolution of the conflict between John Zimmer (1932) and Melvin Carriker (1934) regarding the taxonomic standing of the population of Myrmeciza hemimelaena, a widespread southern Amazonian antbird, that occurs in lower Andean elevations in San Martín, Peru. Zimmer had described a new subspecies, M. h. castanea, from the Moyobamba Valley, but Carriker, on the basis of specimens he collected at the same elevation in an adjoining valley, could not find morphological differences between his specimens and the widespread nominate form of M. hemimelaena. Both authors were correct. Two cryptic sister taxa coexist in the foothills of San Martín. Diagnostic vocal and morphological characters and syntopy confirm their status as distinct species. Myrmeciza hemimelaena castanea Zimmer is revived and raised to species status. Concurrently, analysis of the vocalizations and morphology of the lowland population north of the Río Marañón in Peru, the loudsong recording of which initiated the project, revealed that this population was closely related to M. castanea of which it is described as a subspecies, M. c. centunculorum, under the biological species concept. The discovery that there are two cryptic species in the Myrmeciza hemimelaena complex exemplifies the continuing need to pursue field knowledge and analysis of avian species limits in the Neotropics required for the development of conservation strategies as well as phylogenetic understanding.
hypeR: an R package for geneset enrichment workflows
Authors: Federico Anthony , Monti Stefano 
Published: September 2019

Abstract

Summary
Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases.

Availability and implementation
The most recent version of the package is available at https://github.com/montilab/hypeR.
EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements
Authors: Harmanci Arif , Harmanci Akdes Serin , Swaminathan Jyothishmathi , Gopalakrishnan Vidya 
Published: September 2019

Abstract

Motivation
Functional genomics experiments generate genomewide signal profiles that are dense information sources for annotating the regulatory elements. These profiles measure epigenetic activity at the nucleotide resolution and they exhibit distinctive patterns as they fluctuate along the genome. Most notable of these patterns are the valley patterns that are prevalently observed in assays such as ChIP Sequencing and bisulfite sequencing. The genomic positions of valleys pinpoint locations of cis-regulatory elements such as enhancers and insulators. Systematic identification of the valleys provides novel information for delineating the annotation of regulatory elements. Nevertheless, the valleys are not reported by majority of the analysis pipelines.

Results
We describe EpiSAFARI, a computational method for sensitive detection of valleys from diverse types of epigenetic profiles. EpiSAFARI employs a novel smoothing method for decreasing noise in signal profiles and accounts for technical factors such as sparse signals, mappability and nucleotide content. In performance comparisons, EpiSAFARI performs favorably in terms of accuracy. The histone modification valleys detected by EpiSAFARI exhibit high conservation, transcription factor binding and they are enriched in nascent transcription. In addition, the large clusters of histone valleys are found to be enriched at the promoters of the developmentally associated genes. Differential histone valleys exhibit concordance with differential DNase signal at cell line specific valleys. DNA methylation valleys exhibit elevated conservation and high transcription factor binding. Specifically, we observed enriched binding of transcription factors associated with chromatin structure around methyl-valleys.

Availability and implementation
EpiSAFARI is publicly available at https://github.com/harmancilab/EpiSAFARI.

Supplementary information
Supplementary data are available at Bioinformatics online.
Simple and Rapid Method by Ultra High-Performance Liquid Chromatography (UHPLC) with Ultraviolet Detection for Determination of Efavirenz in Plasma: Application in a Preclinical Pharmacokinetic Study
Authors: dos Santos Martins Evelin , Oliveira Jonata Augusto , Franchin Taísa Busaranho , Silva Bruna Cristina Ulian , Cândido Caroline Damico , Peccinini Rosângela Gonçalves 
Published: September 2019

Abstract
A simple and rapid ultra-high-performance liquid chromatography (UHPLC) method for determination of efavirenz (EFV) in plasma was developed and applied in a preclinical pharmacokinetic study. The method involves only addition of acetonitrile to precipitation of plasma proteins followed by solvent evaporation. The mobile phase consisted of methanol, acetonitrile and 0.1 M formic acid (20:50:30) at a flow rate of 0.3 mL/min with run time of 5 min. A CSH C18 column and a UHPLC-UV system operating at 245 nm were used. There was a linear response in the range of 0.078 to 10 μg/mL, and the equation was obtained by weighting (1/x2) with r2 = 0.9965. The pharmacokinetic disposition of EFV was investigated in rabbits (two groups, n = 7) following a single intravenous administration (IV group) at a dose of 2.7 mg/kg and a single oral administration (oral group) of EFV co-administered with lamivudine (3TC) and tenofovir (TNF) at a dose of 50, 25 and 25 mg, respectively. The study demonstrated the applicability of the method for determination of EFV in plasma without interference from other co-administered drugs, and the pharmacokinetic parameters were calculated. The method showed advantages over other methods in the literature, such as simplicity of sample processing and fast results.
Survival, Emigration, and Winter Population Structure of Harlequin Ducks
Authors: Cooke Fred , Robertson Gregory J. , Smith Cyndi M. , Ian Goudie R. , Sean Boyd W. 
Published: September 2019

AbstractA population of individually marked Harlequin Ducks (Histrionicus histrionicus) at White Rock, British Columbia, Canada was examined to measure the degree of population differentiation among birds which pair during the winter months. This required an understanding of the patterns of emigration among wintering sites in different segments of the population. Some juveniles arrived at the wintering grounds accompanied by their mothers, thus initially arriving into the same winter population as their parents. Young males were more likely than young females to disperse during the first two years of life. Adult males had higher local survival than adult females during the summer months, probably because of the greater mortality risks to nesting females. During the nonbreeding seasons, local survival was the same in both sexes. Paired males had a local survival of more than 90%, suggesting both high survival and strong philopatry. Unpaired males had a lower local survival rate, suggesting they have higher mortality and/or emigration rates. Young females had the same local survival rate as adult females, suggesting that they did not disperse during the winter. These winter philopatry patterns are similar to the general pattern of breeding philopatry in waterfowl, with females showing stronger philopatry than males, and paired adults stronger philopatry than unpaired and young birds. The dispersal of young males makes local population differentiation unlikely in this species.
Song Post and Foraging Site Characteristics of Breeding Varied Thrushes in Northwestern California
Authors: Beck Maurie J. , George T. Luke 
Published: September 2019

Abstract
We used a hierarchical approach to describe habitat characteristics of song posts and foraging sites used by Varied Thrushes (Ixoreus naevius) in coastal redwood (Sequoia sempervirens) forests of northwestern California. We measured mesohabitat (0.04-ha circular plots) and microhabitat (0.5-m radius) scale attributes centered on occupied and random song posts and foraging locations at four study sites during March–August of 1994 and 1995. Ninety-five percent of song posts were in trees or snags. Male thrushes used song posts with low foliage density near the top of large conifers (microhabitat scale), located on steeper slopes, surrounded by a high density of trees, and centered in drainages closer to water (mesohabitat scale) as compared to random locations. Varied Thrushes foraged predominantly on the ground early in the breeding season, then subsequently included fruit in their diet after the young had fledged. Although many variables were correlated with ground foraging locations, microhabitat foliage density had the greatest explanatory power, indicating thrushes selected foraging locations primarily at the microhabitat scale, and emphasizing the importance of measuring habitat characteristics at the appropriate spatial scale. Abrupt forest edges, such as those produced by clearcuts, may reduce habitat suitability for Varied Thrushes possibly explaining their absence from small forest fragments during the breeding season.
Breeding Bird Communities in Boreal Forest of Western Canada: Consequences of “Unmixing” the Mixedwoods
Authors: Hobson Keith A. , Bayne Erin 
Published: September 2019

Abstract
Silvicultural practices following clearcutting in boreal forest may encourage the creation of monospecific, single-aged stands having less vegetation heterogeneity and diversity than original stands. We conducted point counts in central Saskatchewan, Canada, 1993–1995, in pure and mixedwood stands dominated by black spruce (Picea mariana), jackpine (Pinus banksiana), trembling aspen (Populus tremuloides), or white spruce (Picea glauca). Mixedwood stands supported more individuals and more species than pure stands. Higher abundance in mixedwood stands relative to pure stands was consistent among nesting guilds and migration strategies. Rarefaction revealed similar patterns, although pure trembling aspen stands were predicted to support more species than aspen-dominated mixedwood stands. Increased avian diversity in mixedwood stands was not solely the result of the mixing of bird species associated with coniferous or deciduous forest types. Chipping Sparrow (Spizella passerina), Pine Siskin (Carduelis pinus), White-winged Crossbill (Loxia leucoptera), Red-breasted Nuthatch (Sitta canadensis), Swainson's Thrush (Catharus ustulatus), and Tennessee Warbler (Vermivora peregrina) were more abundant in mixedwood stands than pure stands. Black-throated Green Warbler (Dendroica virens), Magnolia Warbler (D. magnolia), and Blackburnian Warbler (D. fusca) were abundant in stands dominated by white spruce but were absent from jackpine or black spruce. Other species such as American Redstart (Setophaga ruticilla) and Chestnut-sided Warbler (D. pensylvanica) relied exclusively on pure trembling aspen, particularly stands with dense shrub cover. Several bird species in the boreal forest will be adversely affected by forestry practices that target mature to old aspen and white spruce mixedwoods and promote reduction in mixedwood compositions of regenerating stands.
Non-standard Schedules, Work–Family Conflict, and the Moderating Role of National Labour Context: Evidence from 32 European Countries
Authors: Taiji Riley , Mills Melinda C 
Published: September 2019

AbstractA wide body of research over the past 30 years links non-standard work schedules to increased work–family conflict (WFC), but often only within single country contexts. A relatively under-explored question is the extent to which the effects of non-standard schedules on family life might vary by country or be buffered by institutional context. Building on past research, this study uses multilevel modelling techniques on 2004 and 2010 European Social Survey data to explore whether the effects of non-standard schedules on WFC vary across 32 countries in Europe, and if so, whether this contextual variation can be explained by labour regulations and industrial relations characteristics measured at the country level. Findings show that while non-standard work hours and days are associated with increased WFC across the majority of sampled countries, the strength of this association varies significantly between countries. The strongest factor shaping the social consequences of non-standard schedules is the degree to which workers are covered under collective bargaining agreements in a country, which explains as much as 17% of the observed between-country variation in the effects of non-standard schedules on WFC. These findings highlight collective agreements as one of the central mechanisms through which family-friendly regulations on working times and conditions are generated for non-standard schedule workers across Europe. More broadly, findings suggest that when studying the social consequences of non-standard schedules, these arrangements must be contextualized in the broader institutional frameworks within which they are organized and regulated.
The organizational domain in HTA reports: towards a technology-oriented assessment
Authors: Cacciatore Pasquale , Specchia Maria Lucia , Solinas Maria Giuliana , Ricciardi Walter , Damiani Gianfranco 
Published: September 2019

Abstract

Background
Organizational aspects in Health Technology Assessment (HTA) reports play a significant role in managing policies and strategies to implement new health technologies. The organizational domain, however, is often under-represented in HTA reports. This study explored how organizational assessment is carried out in HTA reports and designed a new perspective through an empirical approach after the comparison with EUnetHTA's Core Model 3.0.

Methods
Full HTA reports were extracted from the websites of members of International Network of Agencies for HTA and the aspects relating to the organizational assessment were analysed. HTA reports were classified into 4 typologies of technologies (device, diagnosis/screening, intervention and organizational procedures) and organizational aspects described were explored through a framework of 5 domains and 15 subdomains from Core Model. Specific Multiple Correspondence Analyses were carried out to identify technology-related domains for organizational assessment in reports.

Results
The analysis showed that domains and subdomains of Core Model were not covered homogeneously by the organizational assessments in the HTA reports. Through Multiple Correspondence Analyses, four new technology-related dimensions were identified and named according to the Core Model’s subdomains in the four new clusters.

Conclusions
This study analyzed the significance of organizational assessments in current literature and the challenges of improving this domain in HTA reports. Through an empirical analysis, we proposed a new methodology to cover the most relevant aspects of organizational appraisal according to new domains to promote support to the assessment of organizational issues in reports and fulfil the needs of future HTA research.
Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life
Authors: Saito Motofumi , Sato Asako , Nagata Shohei , Tamaki Satoshi , Tomita Masaru , Suzuki Haruo , Kanai Akio 
Published: September 2019

AbstractClp1, a polyribonucleotide 5′-hydroxyl kinase in eukaryotes, is involved in pretRNA splicing and mRNA 3′-end formation. Enzymes similar in amino acid sequence to Clp1, Nol9, and Grc3, are present in some eukaryotes and are involved in prerRNA processing. However, our knowledge of how these Clp1 family proteins evolved and diversified is limited. We conducted a large-scale molecular evolutionary analysis of the Clp1 family proteins in all living organisms for which protein sequences are available in public databases. The phylogenetic distribution and frequencies of the Clp1 family proteins were investigated in complete genomes of Bacteria, Archaea and Eukarya. In total, 3,557 Clp1 family proteins were detected in the three domains of life, Bacteria, Archaea, and Eukarya. Many were from Archaea and Eukarya, but a few were found in restricted, phylogenetically diverse bacterial species. The domain structures of the Clp1 family proteins also differed among the three domains of life. Although the proteins were, on average, 555 amino acids long (range, 196–2,728), 122 large proteins with >1,000 amino acids were detected in eukaryotes. These novel proteins contain the conserved Clp1 polynucleotide kinase domain and various other functional domains. Of these proteins, >80% were from Fungi or Protostomia. The polyribonucleotide kinase activity of Thermus scotoductus Clp1 (Ts-Clp1) was characterized experimentally. Ts-Clp1 preferentially phosphorylates single-stranded RNA oligonucleotides (Km value for ATP, 2.5 µM), or single-stranded DNA at higher enzyme concentrations. We propose a comprehensive assessment of the diversification of the Clp1 family proteins and the molecular evolution of their functional domains.
Health Care Access and Utilization for American Indian Elders: A Concept-Mapping Study
Authors: Sommerfeld David H , Jaramillo Elise Trott , Lujan Erik , Haozous Emily , Willging Cathleen E 
Published: September 2019

Abstract

Objectives
Inequities in access to and utilization of health care greatly influence the health and quality of life of American Indian elders (AIEs). This study explores the importance and perceived prevalence of factors affecting health care use within this population and assesses the changeability of these factors to produce a list of action items that are timely and relevant to improving health care access and utilization.

Method
Concept mapping was conducted with AIEs (n = 65) and professional stakeholders (n = 50), including tribal leaders, administrators of public-sector health systems, outreach workers, and health care providers. Data were analyzed using multidimensional scaling and cluster analyses.

Results
The final concept-map model comprised nine thematic clusters related to factors affecting elder health care: Difficulties Obtaining and Using Insurance; Insecurity from Lack of Knowledge; Limited Availability of Services; Scheduling Challenges; Provider Issues and Relationships; Family and Emotional Challenges; Health-Related Self-Efficacy and Knowledge; Accessibility and Transportation Barriers; and Tribal/National Policy.

Discussion
Findings suggest that improvements in access to and utilization of health care among AIEs will require actions across multiple domains, including health system navigation services, workforce improvements, and tribal, state, and federal policy. A multilevel socioecological approach is necessary to organize and undertake these actions.