bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anchor negatively regulates BMP signaling to control Drosophila wing development
Authors: Wang Xiaochun , Liu Ziguang , Jin Li hua 
Published: May 2016

ABSTRACTSummary statementThe novel geneanchoris the ortholog of vertebrate GPR155, which contributes to preventing wing disc tissue overgrowth and limiting the phosphorylation of Mad in presumptive veins during the pupal stage.G protein-coupled receptors play a particularly important function in many organisms. The novelDrosophilageneanchoris the ortholog of vertebrate GPR155, and its molecular function and biological process are not yet known, especially in wing development. Knocking downanchorresulted in increased wing size and extra and thickened veins. These abnormal wing phenotypes are similar to those observed in gain-of-function of BMP signaling experiments. We observed that the BMP signaling indicator p-Mad was significantly increased inanchorRNAi-induced wing discs in larvae and that it also abnormally accumulated in intervein regions in pupae. Furthermore, the expression of BMP signaling pathway target genes were examined using alacZreporter, and the results indicated thatombandsalwere substantially increased inanchorknockdown wing discs. In a study of genetic interactions between Anchor and BMP signaling pathway, the broadened and ectopic vein tissues were rescued by knocking down BMP levels. The results suggested that the function of Anchor is to negatively regulate BMP signaling during wing development and vein formation, and that Anchor targets or works upstream of Dpp.
Entropy and codon bias in HIV-1
Authors: Pandey Aakash 
Published: May 2016

AbstractFor the heterologous gene expression systems, the codon bias has to be optimized according to the host for efficient expression. Although DNA viruses show a correlation on codon bias with their hosts, HIV genes show low correlation for both nucleotide composition and codon usage bias with its human host which limits the efficient expression of HIV genes. Despite this variation, HIV is efficient at infecting hosts and multiplying in large number. In this study, first, the degree of codon adaptation is calculated as codon adaptation index (CAI) and compared with the expected threshold value (eCAI) determined from the sequences with the same nucleotide composition as that of the HIV-1 genome. Then, information theoretic analysis of nine genes of HIV-1 based on codon statistics of the HIV-1 genome, individual genes and codon usage of human genes is done. Comparison of codon adaptation indices with their respective threshold values shows that the CAI lies very close to the threshold values. Despite not being well adapted to the codon usage bias of human hosts, it was found that the Shannon entropies of the nine genes based on overall codon statistics of HIV-1 genome are very similar to the entropies calculated from codon usage of human genes. Similarly, for the HIV-1 genome sequence analyzed, the codon statistics of the third reading frame has the highest bias representing minimum entropy and hence the maximum information.
Unraveling K63 Polyubiquitination Networks by Sensor-Based Proteomics
Authors: Johnson Alexander , Vert Grégory 
Published: May 2016

Abstract
The polybiquitination of proteins can take on different topologies depending on the residue from ubiquitin involved in the chain formation. Although the role of lysine-48 (K48) polyubiquitination in proteasome-mediated degradation is fairly well characterized, much less is understood about the other types of ubiquitin chains and proteasome-independent functions. To overcome this, we developed a K63 polyubiquitin-specific sensor-based approach to track and isolate K63 polyubiquitinated proteins in plants. Proteins carrying K63 polyubiquitin chains were found to be enriched in diverse membrane compartments as well as in nuclear foci. Using liquid chromatography-tandem mass spectrometry, we identified over 100 proteins from Arabidopsis (Arabidopsis thaliana) that are modified with K63 polyubiquitin chains. The K63 ubiquitinome contains critical factors involved in a wide variety of biological processes, including transport, metabolism, protein trafficking, and protein translation. Comparison of the proteins found in this study with previously published nonresolutive ubiquitinomes identified about 70 proteins as ubiquitinated and specifically modified with K63-linked chains. To extend our knowledge about K63 polyubiquitination, we compared the K63 ubiquitinome with K63 ubiquitination networks based on the Arabidopsis interactome. Altogether, this work increases our resolution of the cellular and biological roles associated with this poorly characterized posttranslational modification and provides a unique insight into the networks of K63 polyubiquitination in plants.
The role of demographic factors of international students on teaching preferences
Authors: Rao Pramila 
Published: May 2016

PurposeThis empirical research was conducted in a medium-sized private university located in the north-eastern region of the USA. The purpose of this paper was to understand whether demographic attributes (age, gender, country of origin and years of stay in the USA) of international students will predict any preferences for specific teaching methods. This study was conducted with international students from October 2012 through May 2013 (fall and spring semesters).Design/methodology/approachThis research paper provides hypotheses to explore whether there is any relationship between demographic factors and preferences for various teaching methods. This study analyzes the results using both Pearson’s correlations and one-way ANOVA to reject or accept the hypotheses.FindingsThe results demonstrated that there were no significant correlations between the demographic variables of international students and teaching methods. However, the one-way ANOVA analyses suggested that there are differences among age groups and their preferences for group projects, years of studying in the USA and their preferences for classroom discussions, and gender and their preferences for textbook assignments.Practical implicationsThis study suggests that scholars provide orientation or training on the host country’s pedagogies so that international students can assimilate better into their academic communities.Originality/valueThis pioneering paper examines the role between demographic variables of international students and teaching pedagogies. This specific concept has not been examined in this literature before. This understanding could contribute to a richer understanding of this population of students.
Effects of a multicultural perspectives course on teacher candidates’ intercultural competence
Authors: Xu Yaoying , Hao Chenfang , Ellen Huennekens Mary 
Published: May 2016

Purpose
The purpose of this study was to investigate the intercultural competence of pre-service special education teacher candidates through the contents of a graduate-level multicultural perspectives course.

Design/methodology/approach
This study used a graduate-level multicultural perspectives course to examine the intercultural competence of special education teacher candidates. A paired-samples t-test of significance was performed to investigate the pre- and post-growth of participants’s cultural sensitivity using the intercultural development inventory (IDI).

Findings
Participants’ intercultural sensitivity mean score suggested that their intercultural competence needs to be improved. The results showed no significant difference in the overall mean developmental scores between pre- and post-tests. However, significant differences were found between the pre- and post-test scores in perceived orientation and acceptance cluster.

Originality/value
A significantly higher perceived score was identified suggesting that participants might overestimate their level of intercultural sensitivity. Different from the existing literature, this study suggested that gender and education level were significant predictors of post-test developmental scores.
Mental health, human rights and social inclusion for adults and children
Authors: Holttum Sue 
Published: May 2016

Purpose– The purpose of this paper is to consider three recent papers relating to human rights and applicable to adults or children given mental health diagnoses.Design/methodology/approach– The first paper discussed how to measure progress in different countries in their policy changes to abide by the UN Convention on rights of persons with disabilities, and discussed how all relevant groups could be involved. The second paper considered the problem of children’s rights being eroded by overuse of the mental health diagnosis of attention deficit hyperactivity disorder (ADHD) when they are restless. The third paper reported on an evaluation of how well advocacy services are enabling people who are sectioned to have a say in their care.Findings– When assessing how well countries are doing in ensuring the rights of people with disabilities, the first paper’s authors concluded that all groups must participate in the evaluation, even though there are many different agendas. The second paper reported on how professionals and parents could come to a shared understanding of how children might be wrongly given a diagnosis of ADHD and jointly suggested some solutions. The third paper illustrated how important advocacy is, and the difference it can make to the lives of people who are sectioned.Originality/value– The first paper’s authors are engaged in ground-breaking research to assess whether disabled people’s rights under the UN Convention are being honoured. The second paper raised vital questions about the misuse of diagnosis, contravening the UN Convention on the rights of the child, and illustrated how parents and professionals can come together in support of these rights. The third paper reported on the first systematic national study on the implementation of advocacy services to defend the rights of people who are sectioned to have a say in their care.
Bat communities respond positively to large‐scale thinning of forest regrowth
Authors: Blakey Rachel V. , Law Brad S. , Kingsford Richard T. , Stoklosa Jakub , Tap Patrick , Williamson Kelly 
Published: May 2016

Summary

Over half of the world's forests are secondary regrowth and support considerable biodiversity. Thinning of these forests is a widespread management practice that can affect forest species, including echolocating bats and their prey.

We compared total activity of 11 bat taxa, foraging activity of six bat guilds and biomass of 11 insect orders across four forest thinning categories in managed remnant eucalypt forests in south‐eastern Australia: unthinned regrowth, forest thinned recently (0–4 years) and in the medium term (5–10 years) and reference (mature open forest). Thinning had been carried out at large (˜350 ha) spatial scales.

Total bat activity was 60% less and foraging activity was 80% less in unthinned regrowth, compared to reference sites, but activity levels were similar among thinned and reference sites. Insect biomass was greatest in unthinned sites, and while bat activity was related to prey biomass, this relationship was weak in unthinned sites. Together, this suggests that forest structure was more important than prey availability or time since thinning in influencing bat activity patterns.

Synthesizing our findings with the broader literature on bats and thinning, we found support for a clutter threshold of 1100 stems ha−1, above which bat activity was markedly lower, across two continents (the USA and Australia) and four broad vegetation types (eucalypt, conifer, deciduous and mixed forests).

While elsewhere bats with adaptive traits for open habitats generally respond positively to thinning, in our study, species with traits consistent with clutter tolerance (high call frequency and low wing aspect ratio) had lowest activity levels (up to 22 times) in unthinned regrowth compared to all other forest types.

Synthesis and applications. Widespread dense regrowth forest can restrict movement and foraging of bats, even those adapted to clutter. We recommend thinning dense regrowth or plantations to below 1100 stems ha−1 when targeting bat foraging habitat, but effects of thinning on roost habitat and other forest biota require further investigation.
A before‐and‐after assessment of patch‐burn grazing and riparian fencing along headwater streams
Authors: Larson Danelle M. , Dodds Walter K. , Whiles Matt R. , Fulgoni Jessica N. , Thompson Thomas R. 
Published: May 2016

Summary

Fire and grazing are common in grasslands world‐wide to maintain grass cover and cattle production. The effects of fire, cattle grazing and riparian fencing efficacy on prairie stream ecology are not well characterized at catchment scales.

We examined alterations to stream water quality and biology from patch‐burn grazing (PBG) in tallgrass prairie during a five‐year, replicated, catchment scale experiment that used a Before‐After/Control‐Impact (BACI) design and was analysed by mixed‐effects models. Treatments included two patch‐burned control catchments (fire but no grazers) and PBG in two riparian‐fenced and two unfenced catchments. We assessed the effectiveness of riparian fencing for mitigating potential water quality impacts by monitoring water quality and riparian usage by cattle via Global Positioning System.

Riparian fences effectively excluded cattle; however, in unfenced pastures, cattle aggregated along streams 10–20% of the grazing season.

After initiation of PBG, we detected large increases in some nutrients, Escherichia coli, algal biomass, primary productivity and community respiration in all catchments with PBG. Some water quality variables, such as E. coli concentrations, recovered quickly after cattle were removed from pasture, which indicated resiliency.

Riparian fencing moderately reduced the impacts to stream variables, indicating either overland flow and/or subsurface flow allowed nutrients and bacteria to enter the streams.

Synthesis and applications. Patch‐burn grazing is a measurable disturbance that can alter the ecological condition of streams. Riparian fencing lessened the degree of impact, yet some water quality variables still exceeded regional reference conditions. Managers will need to assess the costs of riparian fencing compared to the moderate benefits that fencing provides to water quality.
Soil and vegetation recovery following alien tree clearing in the Eastern Cape Province of South Africa
Authors: Ndou Esther , Ruwanza Sheunesu 
Published: May 2016

AbstractThe impact of alien tree clearing on soil and vegetation recovery remains largely understudied. This study focused on changes in soil and vegetation properties following Acacia removal. The aim was to quantify the long‐term consequences of alien clearing. Paired cleared (old – 15 years; medium – 11 years; recent – 6 years) and uncleared sites were selected along the Palmiet catchment in Eastern Cape Province, South Africa. Various soil physico‐chemical properties (soil moisture, pH, P, N, C, K, Na, Ca, Mg and soil repellency) and vegetation diversity measures were studied on 10 m × 10 m plots. Results indicate that measured soil nutrients are significantly (P < 0.05) lower in cleared than in uncleared sites. However, comparisons among cleared sites alone indicate that soil properties are recovering with older cleared sites having higher (P < 0.05) nutrients than recent cleared sites. Soils in uncleared sites are more repellent than soil in cleared sites. Vegetation recovery in cleared sites was taking place with older cleared sites having higher native species diversity than recently cleared site. We conclude that the removal of alien plants could have caused a reduction in soil nutrients. However, as native vegetation recovers on cleared sites, soil nutrients are gradually improving.
Land‐use history exerts long‐term effects on the clear‐cut flora in boreonemoral Sweden
Authors: Jonason Dennis , Bergman Karl‐Olof , Westerberg Lars , Milberg Per 
Published: May 2016

AbstractQuestionsCan signs of 19th century grassland management, which can be observed in the flora immediately (2–4 yrs) after clear‐cutting in boreonemoral Sweden, still remain 4 yrs later? Do the effects from the time since clear‐cutting differ between forest and grassland plant species?LocationProvince of Östergötland, southern Sweden.MethodsTwelve contemporary clear‐cut areas that were once meadows and 12 that were once forests were selected using land‐use maps from the 1870s. Grasses and herbaceous plants were surveyed twice, once in 2009 and once in 2013 (2–4 and 6–8 yrs after clear‐cutting, respectively). Plant presence was recorded within 100 circular sample plots (radius 1 m) placed evenly throughout each respective clear‐cut area along transects spaced 25‐m apart. The number of sample plots in which a species was present was taken as a measure of that species' frequency. Random effects meta‐analysis, odds ratios andANCOVAwere used to analyse species responses to clear‐cutting over time.ResultsA total of 170 plant species were found in the study, of which 33 were classified as grassland indicator species and 31 as plants primarily confined to forests. Clear‐cut areas with a history as meadowland had, on average, up to 64% higher total species richness and 110% more grassland indicator species than did clear‐cut areas with a history as forest. The time since clear‐cutting had no effect on total species richness. However, the odds of finding a grassland indicator species decreased with the time since clear‐cutting, whereas the odds of finding a forest species increased.ConclusionsWe concluded that land‐use history plays an important role in explaining the flora found in Swedish clear‐cuts, and that its effects on species richness remain for a minimum of 8 yrs after harvest (conservative estimate). This phenomenon highlights the importance of acknowledging land‐use legacies in ecological research and conservation. Future studies should investigate various options for the promotion of grassland plants in clear‐cuts with a history of grassland management while also acknowledging the potential conflicts between conservation and production. The results may pertain to other countries with similar land‐use histories.
Respiratory effect of beta‐blocker eye drops in asthma: population‐based study and meta‐analysis of clinical trials
Authors: Morales Daniel R. , Dreischulte Tobias , Lipworth Brian J. , Donnan Peter T. , Jackson Cathy , Guthrie Bruce 
Published: May 2016

AimsTo measure the prevalence of beta‐blocker eye drop prescribing and respiratory effect of ocular beta‐blocker administration in people with asthma.MethodsWe measured the prevalence of ocular beta‐blocker prescribing in people with asthma and ocular hypertension, and performed a nested case–control study (NCCS) measuring risk of moderate exacerbations (rescue steroids in primary care) and severe exacerbations (asthma hospitalization) using linked data from the UK Clinical Practice Research Datalink. We then performed a systematic review and meta‐analysis of clinical trials evaluating changes in lung function following ocular beta‐blocker administration in people with asthma.ResultsFrom 2000 to 2012, the prevalence of non‐selective and selective beta‐blocker eye drop prescribing in people with asthma and ocular hypertension fell from 23.0% to 13.4% and from 10.5% to 0.9% respectively. In the NCCS, the relative incidence (IRR) of moderate exacerbations increased significantly with acute non‐selective beta‐blocker eye drop exposure (IRR 4.83, 95% CI 1.56–14.94) but not with chronic exposure. In the meta‐analysis, acute non‐selective beta‐blocker eye drop exposure caused significant mean falls in FEV1 of −10.9% (95% CI −14.9 to −6.9), and falls in FEV1 of ≥20% affecting one in three. Corresponding values for selective beta‐blockers in people sensitive to ocular non‐selective beta‐blockers was −6.3% (95% CI −11.7 to −0.8), and a non‐significant increase in falls in FEV1 of ≥20%.ConclusionNon‐selective beta‐blocker eye drops significantly affect lung function and increase asthma morbidity but are still frequently prescribed to people with asthma and ocular hypertension despite safer agents being available.
Pronounced between‐subject and circadian variability in thymidylate synthase and dihydropyrimidine dehydrogenase enzyme activity in human volunteers
Authors: Jacobs Bart A. W. , Deenen Maarten J. , Pluim Dick , van Hasselt J. G. Coen , Krähenbühl Martin D. , van Geel Robin M. J. M. , de Vries Niels , Rosing Hilde , Meulendijks Didier , Burylo Artur M. , Cats Annemieke , Beijnen Jos H. , Huitema Alwin D. R. , Schellens Jan H. M. 
Published: May 2016

AbstractAimsThe enzymatic activity of dihydropyrimidine dehydrogenase (DPD) and thymidylate synthase (TS) are important for the tolerability and efficacy of the fluoropyrimidine drugs. In the present study, we explored between‐subject variability (BSV) and circadian rhythmicity in DPD and TS activity in human volunteers.MethodsThe BSVs in DPD activity (n = 20) in peripheral blood mononuclear cells (PBMCs) and in plasma, measured by means of the dihydrouracil (DHU) and uracil (U) plasma levels and DHU : U ratio (n = 40), and TS activity in PBMCs (n = 19), were examined. Samples were collected every 4 h throughout 1 day for assessment of circadian rhythmicity in DPD and TS activity in PBMCs (n = 12) and DHU : U plasma ratios (n = 23). In addition, the effects of genetic polymorphisms and gene expression on DPD and TS activity were explored.ResultsPopulation mean (± standard deviation) DPD activity in PBMCs and DHU : U plasma ratio were 9.2 (±2.1) nmol mg−1 h−1 and 10.6 (±2.4), respectively. Individual TS activity in PBMCs ranged from 0.024 nmol mg−1 h−1 to 0.596 nmol mg−1 h−1. Circadian rhythmicity was demonstrated for all phenotype markers. Between 00:30 h and 02:00 h, DPD activity in PBMCs peaked, while the DHU : U plasma ratio and TS activity in PBMCs showed trough activity. Peak‐to‐trough ratios for DPD and TS activity in PBMCs were 1.69 and 1.62, respectively. For the DHU : U plasma ratio, the peak‐to‐trough ratio was 1.43.ConclusionsBSV and circadian variability in DPD and TS activity were demonstrated. Circadian rhythmicity in DPD might be tissue dependent. The results suggested an influence of circadian rhythms on phenotype‐guided fluoropyrimidine dosing and supported implications for chronotherapy with high‐dose fluoropyrimidine administration during the night.