bluuebunny/crossref_metadata_2025_split huggingface dataset:
exonsampler: a computer program for genome‐wide and candidate gene exon sampling for targeted next‐generation sequencing
Authors: Cosart Ted , Beja‐Pereira Albano , Luikart Gordon 
Published: April 2014

AbstractThe computer program exonsampler automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next‐generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User‐adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of exonsampler to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon‐capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16 000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection.
DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus)
Authors: Hyde John R. , Underkoffler Karen E. , Sundberg Meagan A. 
Published: April 2014

AbstractThe cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well‐supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes.
Seasonal and interannual variation in vegetation composition: Implications for survey design and data interpretation
Authors: Schultz Nick L. , Reid Nick , Lodge Greg , Hunter John T. 
Published: April 2014

AbstractUnderstanding how vegetation composition varies with season and interannual climate variability is important for any ecological research that uses vegetation data derived from surveys for the basis of inference. Misunderstanding this variation can influence land management and planning decisions, leading to poor implementation of biodiversity offsetting mechanisms, for example. We monitored plots (400 m2) grazed by livestock paired with adjacent ungrazed plots in derived native pastures four times a year over 2.5 years on the North‐West Slopes of New South Wales. Species density in plots varied greatly with season and interannual rainfall. Highest species density was recorded in spring, though species density in summer was not significantly lower, nor was a spring–summer peak in species density evident in the 2009 drought. Surveys in spring 2008 had the highest species density, and recorded only 60–72% of the total species recorded at each site over 2.5 years. Variation in the proportion of total site diversity represented in combinations of two or three surveys was large, though the best combinations comprised surveys from spring and summer in years of above‐average rainfall, either from the same spring‐summer, or from different years. Compositional differences among sites were much greater than within sites, showing that differences among sites related to broad environmental gradients were not overwhelmed by seasonal and interannual variability in site composition. When grazing was excluded, there was no evidence of competitive exclusion by the dominant grasses, and no directional shift in composition. The implications of these findings for ecological research depend on the question being addressed: if capturing a large proportion of site diversity is important, then surveys must be carefully timed, or repeat surveys must be conducted. Single surveys did not effectively capture site diversity for use in biodiversity offsetting, and the timing of repeat surveys was critical.
New gall midges (Diptera: Cecidomyiidae) from Papua New Guinea
Authors: Kolesik Peter , Butterill Philip T 
Published: April 2014

AbstractTwo new species of gall midges that feed on trees in Papua New Guinea are described. The larvae of Schizomyia novoguineensis Kolesik sp. nov. transform the flowers of Macaranga aleuritoides (Euphorbiaceae) into spherical galls preventing sexual reproduction of the host tree. The larvae of Rhopalomyia psychotriae Kolesik sp. nov. induce pustulate leaf galls on Psychotria ramuensis (Rubiaceae). Descriptions of adults and immature stages, and DNA sequences of the cytochrome oxidase unit I mitochondrial gene segment, are given for each of the new species.
Assessment of children's digital courseware in light of developmentally appropriate courseware criteria
Authors: Ihmeideh Fathi Mahmoud 
Published: April 2014

AbstractDevelopmentally appropriate courseware can play a crucial role in enhancing children's learning and development. Research studies have demonstrated that early childhood educators face major challenges in selecting and updating developmental courseware that supports young children's development. The primary purpose of this study was to assess children's digital courseware employed in Jordanian kindergartens in accordance with developmentally appropriate courseware criteria. A random sample of 57 courseware programs employed in both public and private kindergartens was assessed using 10 criteria for developmentally appropriate courseware. The findings suggest that the courseware implemented in Jordanian kindergartens exhibited a moderate degree of appropriateness. The courseware was the most developmentally appropriate in the areas of “technical features” and “clear instruction,” while the real‐work model and transformations were the least appropriate. Moreover, the findings revealed that children's courseware implemented in public kindergartens was more developmentally appropriate than those in private kindergartens. These findings and their implications were discussed.
Crucial role of androgen receptor in vascular H2S biosynthesis induced by testosterone
Authors: Brancaleone V , Vellecco V , Matassa D S , d'Emmanuele di Villa Bianca R , Sorrentino R , Ianaro A , Bucci M , Esposito F , Cirino G 
Published: April 2014

Background and PurposeHydrogen sulphide (H2S) is a gaseous mediator strongly involved in cardiovascular homeostasis, where it provokes vasodilatation. Having previously shown that H2S contributes to testosterone‐induced vasorelaxation, here we aim to uncover the mechanisms underlying this effect.Experimental ApproachH2S biosynthesis was evaluated in rat isolated aortic rings following androgen receptor (NR3C4) stimulation. Co‐immunoprecipitation and surface plasmon resonance analysis were performed to investigate mechanisms involved in NR3C4 activation.Key ResultsPretreatment with NR3C4 antagonist nilutamide prevented testosterone‐induced increase in H2S and reduced its vasodilator effect. Androgen agonist mesterolone also increased H2S and induced vasodilatation; effects attenuated by the selective cystathionine‐γ lyase (CSE) inhibitor propargylglycine. The NR3C4‐multicomplex‐derived heat shock protein 90 (hsp90) was also involved in this effect; its specific inhibitor geldanamycin strongly reduced testosterone‐induced H2S production. Neither progesterone nor 17‐β‐oestradiol induced H2S release. Furthermore, we demonstrated that CSE, the main vascular H2S‐synthesizing enzyme, is physically associated with the NR3C4/hsp90 complex and the generation of such a ternary system represents a key event leading to CSE activation. Finally, H2S levels in human blood collected from male healthy volunteers were higher than those in female samples.Conclusions and ImplicationsWe demonstrated that selective activation of the NR3C4 is essential for H2S biosynthesis within vascular tissue, and this event is based on the formation of a ternary complex between cystathionine‐γ lyase, NR3C4and hsp90. This novel molecular mechanism operating in the vasculature, corroborated by higher H2S levels in males, suggests that the L‐cysteine/CSE/H2S pathway may be preferentially activated in males leading to gender‐specific H2S biosynthesis.Linked ArticlesThis article is part of a themed section on Pharmacology of the Gasotransmitters. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2015.172.issue-6
Foster care assessment: an exploratory study of the placement assessment process in Flanders and the Netherlands
Authors: Vanderfaeillie Johan , Damen Harm , Pijnenburg Huub , van den Bergh Peter , Van Holen Frank 
Published: April 2014

AbstractFamily foster care placement decision‐making has a weak scientific underpinning. The identification of clusters of foster children (groups of foster children with similar characteristics) can help improve decision quality. In this study, we investigated if foster children could indeed be clustered, which problems were identified at the time of placement and what might be the influence of placement history. Two clusters of foster children were found: (i) young children with coinciding parental child‐rearing incapacity and familial problems, and (ii) older children with child problems. At the time of placement, familial problems were more often identified in younger children with a placement history. These findings stress the importance of approaching foster care assessment as part of a dynamic decision‐making process. It is key to finding the most appropriate situation for the child. At the same time, it must be decided how the desired situation can be realized, wherein placement decisions are based on an appraisal of whether or not a foster placement is an appropriate solution. In conjunction with this, it needs to be decided how the parents can be supported towards reunification, or whether or not long‐term foster care is the best option for the child, and if so what conditions need to be met.
Cost‐of‐illness of patients with contact dermatitis in Denmark
Authors: Sætterstrøm Bjørn , Olsen Jens , Johansen Jeanne Duus 
Published: April 2014

SummaryBackgroundContact dermatitis is a frequent occupational and non‐occupational skin disease.ObjectivesTo investigate the effects of contact dermatitis on labour market affiliation and societal costs in terms of healthcare costs and production loss.MethodsA total of 21 441 patients patch tested either in hospital departments or at dermatological clinics in the period 2004–2009 were included in the study. The analyses were stratified by children (age 0–15 years), occupational contact dermatitis (age 16–65 years), and non‐occupational dermatitis (age ≥ 16 years). Controls were selected from a 30% random sample of the population. Individual encrypted data were retrieved on healthcare utilization, socio‐demographics, education, labour market affiliation and transfer payments from public registers in Denmark for cases and controls.ResultsAttributable healthcare costs for 4 years prior to patch testing (1 year for children) and the year after patch testing were €959 for children, €724 for occupational contact dermatitis, and €1794 for non‐occupational dermatitis. Productivity costs for the same period were €10 722 for occupational contact dermatitis and €3074 for non‐occupational contact dermatitis.ConclusionsThe main findings of this study were that there were statistically significant attributable healthcare costs for both children and adults, and statistically significant productivity loss for adults.
NEW MEASURES OF THE COSTS OF UNEMPLOYMENT: EVIDENCE FROM THE SUBJECTIVE WELL‐BEING OF 3.3 MILLION AMERICANS
Authors: HELLIWELL JOHN F. , HUANG HAIFANG 
Published: April 2014

AbstractUsing two large U.S. surveys, we estimate the effects of unemployment on the subjective well‐being (SWB) of the unemployed and the rest of the population. For the unemployed, the nonpecuniary costs of unemployment are several times as large as those resulting from lower incomes, while the indirect effect at the population level is 15 times as large. For those who are still employed, a one percentage point increase in local unemployment has an impact on well‐being roughly equivalent to a 4% decline in household income. We also find evidence indicating that job security is an important channel for the indirect effects of unemployment. (JEL E24, H23, J64, J68)
Habituation in Frankliniella occidentalis to deterrent plant compounds and their blends
Authors: Egger Barbara , Spangl Bernhard , Koschier Elisabeth Helene 
Published: April 2014

AbstractFeeding and oviposition deterrence of three secondary plant compounds and their 1:1 blends to adult female Frankliniella occidentalis Pergande (Thysanoptera: Thripidae) and the potential for habituation of the thrips to the pure compounds and the 1:1 blends at various concentrations were investigated. In choice assays, we tested dose‐dependent feeding and oviposition deterrence of the two fatty acid derivatives methyl jasmonate and cis‐jasmone, the phenylpropanoid allylanisole, and their blends when directly applied to bean leaf discs. The concentration required to reduce the feeding damage by 50% relative to the control treatment (FDC50) was lowest for cis‐jasmone and highest for allylanisole. The feeding deterrent effect of both jasmonates was increased when blended with allylanisole. Feeding deterrence and oviposition deterrence were strongly correlated. In no‐choice assays conducted over four consecutive days, we discovered that dilutions at low concentrations (FDC15) applied to bean leaves resulted in habituation to the deterrents, whereas no habituation occurred at higher concentrations (FDC50). We observed a tendency that the 1:1 blends reduce the probability that thrips habituate to the deterrent compounds. Our results may be useful in the development of integrated crop protection strategies with the implementation of allelochemicals as pest behaviour‐modifying agents.
Responses of Thrips tabaci to odours of herbivore‐induced cotton seedlings
Authors: Silva Rehan , Walter Gimme H. , Wilson Lewis J. , Furlong Michael J. 
Published: April 2014

AbstractHerbivore‐induced changes in plants have been widely viewed as defensive responses against further insect attack. However, changes in plants as a consequence of herbivore feeding can elicit various responses in herbivores; these are variable, context dependent, and often unpredictable. In this laboratory study, the responses of Thrips tabaci Lindeman (Thysanoptera: Thripidae) to volatiles emitted by intact and herbivore‐damaged or mechanically damaged cotton seedlings [Gossypium hirsutum L. (Malvaceae)] were investigated in dual‐choice olfactometer assays. Thrips tabaci showed increased attraction to seedlings subject to foliar mechanical damage and those with foliar damage inflicted by conspecifics or Tetranychus urticae Koch (Acari: Tetranychidae), upon which it preys. However, T. tabaci did not discriminate between intact seedlings and those with foliar damage inflicted by Helicoverpa armigera Hübner (Lepidoptera: Noctuidae), two other species of thrips, Frankliniella schultzei Trybom and Frankliniella occidentalis Pergrande (Thysanoptera: Thripidae), or those with root damage inflicted by Tenebrio molitor L. (Coleoptera: Tenebrionidae). Attraction of T. tabaci was also affected by herbivore density on damaged plants. That is, seedlings damaged by higher densities of T. urticae or T. tabaci were more attractive than seedlings damaged by lower densities of the corresponding arthropod. Although attracted to plants damaged by conspecifics or T. urticae, T. tabaci showed greater attraction to seedlings damaged by T. urticae than to seedlings damaged by conspecifics. Results are discussed in the context of the responses of F. schultzei and F. occidentalis to herbivore‐induced cotton seedlings, highlighting the complexity, variability, and unpredictability of the responses of even closely related species of insects to plants under herbivore attack.
Historicism and Critique in Herder's Another Philosophy of History: Some Hermeneutic Reflections
Authors: Mertel Kurt C. M. 
Published: April 2014

AbstractIn Another Philosophy of History, J.G. Herder claims that his aim is not to compare and judge different cultures, but merely to describe and explain how each came into being and thus to adopt the standpoint of an impartial observer. I argue, however, that there is a tension between Herder's understanding of his own project—his stated doctrine of historicism and cultural relativism—and the way in which it is actually put into practice. That is, despite Herder's stated aims, he is nevertheless unable to avoid justifying premodern forms of life and making context‐transcending evaluative judgments in the process of trying to understand cultures on their own terms and holding them up as exemplars vis à vis the Enlightenment. This tension presents the challenge of accounting for it in the most charitable and illuminating way. I argue that this goal can be achieved by appealing to the resources of the philosophical hermeneutics of Hans‐Georg Gadamer, which enables us to disclose two enabling conditions for Herder's project of which he was not explicitly aware, viz., the internal connection between understanding and justification and the enabling character of prejudice as the condition for the possibility of understanding as such.
Why are some microbes more ubiquitous than others? Predicting the habitat breadth of soil bacteria
Authors: Barberán Albert , Ramirez Kelly S. , Leff Jonathan W. , Bradford Mark A. , Wall Diana H. , Fierer Noah 
Published: April 2014

AbstractIdentifying the traits that determine spatial distributions can be challenging when studying organisms, like bacteria, for which phenotypic information is limited or non‐existent. However, genomic data provide another means to infer traits and determine the ecological attributes that account for differences in distributions. We determined the spatial distributions of ~124 000 soil bacterial taxa across a 3.41 km2 area to determine whether we could use phylogeny and/or genomic traits to explain differences in habitat breadth. We found that occupancy was strongly correlated with environmental range; taxa that were more ubiquitous were found across a broader range of soil conditions. Across the ~500 taxa for which genomic information was available, genomic traits were more useful than phylogeny alone in explaining the variation in habitat breadth; bacteria with larger genomes and more metabolic versatility were more likely to have larger environmental and geographical distributions. Just as trait‐based approaches have proven to be so useful for understanding the distributions of animals and plants, we demonstrate that we can use genomic information to infer microbial traits that are difficult to measure directly and build trait‐based predictions of the biogeographical patterns exhibited by microbes.
Flows for native fish in the Murray‐Darling Basin: lessons and considerations for future management
Authors: Koehn John D. , King Alison J. , Beesley Leah , Copeland Craig , Zampatti Brenton P. , Mallen‐Cooper Martin 
Published: April 2014

SummaryIncreased regulation and extraction of water from rivers has contributed to the decline of fishes, and the use of environmental water allocations (EWAs) is now a key rehabilitation measure. Major reform of water policy in the Murray‐Darling Basin (MDB), Australia, has recently provided significant EWAs to improve ecological outcomes. Conflict over water buybacks, the value of the water and the need to maximise environmental benefits and minimise risks of unwanted outcomes has increased the expectation for science to underpin and justify such actions. Recent research has focussed attention on the need to understand fish–flow relationships. The Native Fish Strategy for the Murray‐Darling Basin 2003–2013 (NFS), while not specifically targeted at water policy reform or water delivery, has provided fish ecology research and flow restoration experimentation and contributed considerable new scientific knowledge to support flow management. It has contributed to a substantial and positive change in environmental watering for fish, with native fish targets now regularly incorporated into watering objectives. This study documents changes to water management in the MDB, summarises current knowledge of flow‐related fish ecology in the MDB, highlights the benefits and risks of some water management practises and provides recommendations for future management and research. A major recommendation is the need for a coordinated, cross‐jurisdictional approach to flow restoration for native fish, ensuring that the best available science is being used in all watering allocations. We caution on the use of environmental works such as regulators to artificially inundate floodplains and suggest that such approaches should be viewed as large‐scale experiments with the significant risks posed to fish needing to be recognised, adequately monitored and adaptively managed.
Fish passage in the Murray‐Darling Basin, Australia: Not just an upstream battle
Authors: Baumgartner Lee , Zampatti Brenton , Jones Matthew , Stuart Ivor , Mallen‐Cooper Martin 
Published: April 2014

SummaryConstruction of instream barriers, preventing fish from accessing spawning, nursery and feeding habitat, is a major issue impacting fisheries sustainability throughout the world. Since European settlement, development in the Murray‐Darling Basin for irrigation and potable water supplies has led to the construction of over 10,000 barriers to fish movement. The Native Fish Strategy listed fish passage as a major driving action and was proactive in progressing cost‐effective solutions to help inform large‐scale rehabilitation programmes. The strategy identified a list of high‐priority barriers for mitigation works based on feedback from jurisdictional agencies. Research initiatives were then implemented, with measurable outcomes, to help address key knowledge gaps. Research demonstrated that a project to restore passage to the Murray River main channel was meeting all ecological and engineering objectives. Follow‐on work identified low‐cost mechanisms to improve the effectiveness of existing fishways without compromising ecological functionality. The Native Fish Strategy was also explicit in addressing fish passage issues at irrigation infrastructure and wetland regulators. Work to minimise these impacts included quantifying the scale of irrigation‐associated infrastructure and also optimising screen designs to be retrofitted to pump systems to prevent fish entrainment. Options to enhance lateral movement were also identified. The objective of this study is to summarise the fish passage issues progressed by the Native Fish Strategy to develop basin‐wide solutions to enhance fish passage over the long term.