bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of RF micro‐discharge regimes in performance of evanescent‐mode cavity resonators
Authors: Semnani A. , Peroulis D. 
Published: August 2014

RF gas breakdown in small gaps is a primary limiting factor in the power handling of heavily loaded cavity‐based resonators. The effects of different RF micro‐discharge regimes in the performance of these resonators are studied. Specifically, two resonators at 1 and 50 GHz with the same critical gap size of 19 μm which are, respectively, working in the RF boundary and diffusion‐controlled regimes are considered. By combining plasma and electromagnetic simulations, the effects of high power gas breakdown in the performance of these resonators are compared. A sensitivity analysis on the effects of microscopic plasma parameters is also performed.
100 Gbit/s optical wireless communication system link throughput
Authors: Boucouvalas A.C. , Yiannopoulos K. , Ghassemlooy Z. 
Published: August 2014

Novel results on the link layer protocol performance of future infrared personal communication links at a line rate of 100 Gbit/s are presented. The discussion aims to demonstrate the shortcomings of the currently standardised half‐duplex mode of communications in the physical layer and details its negative impact on the link layer efficiency. Results of a non‐standardised full‐duplex mode of operation that is however suitable for application in future high capacity infrared links are also presented. The results predict that the migration to this full‐duplex mode can prove advantageous for the link layer performance, as it not only yields a higher efficiency, but also requires significantly smaller frame and window sizes.
The map, the group and language ideology
Authors: Wright Sue 
Published: August 2014

Abstract
This article chronicles the history of mapmaking, showing how the way maps develop is in tandem with the development of patterns of group identity. The central question concerns our ways of conceptualising the physical world and whether these feed into language ideology, that set of beliefs, values and attitudes drawn from our socio-political environment, which directs, constrains and moulds our language behaviour. Benedict Anderson noted the parallel development of mapping, identity and language practices in nation building. My argument here is that it is also possible to see this association in the European medieval world and that there are some indicators that such co-occurrence is discernible in mapmaking, identity formation and language practices in post-national settings. As ever in the social sciences, it would be inappropriate to claim clear cause and effect. However, it is possible to demonstrate that changes in world view co-occur with changes in language behaviour. It may, therefore, be legitimate to hypothesise that the view of ourselves that maps give us and the identities we assume as part of groups thus constructed play some part in the choice of languages we willingly acquire and speak.
A support vector machine to search for metal-poor galaxies
Authors: Shi Fei , Liu Yu-Yan , Kong Xu , Chen Yang , Li Zhong-Hua , Zhi Shu-Teng 
Published: August 2014

Abstract
To develop a fast and reliable method for selecting metal-poor galaxies (MPGs), especially in large surveys and huge data bases, a support vector machine (svm) supervized learning algorithms is applied to a sample of star-forming galaxies from the Sloan Digital Sky Survey data release 9 provided by the Max Planck Institute and the Johns Hopkins University (http://www.sdss3.org/dr9/spectro/spectroaccess.php). A two-step approach is adopted: (i) the svm must be trained with a subset of objects that are known to be either MPGs or metal-rich galaxies (MRGs), treating the strong emission line flux measurements as input feature vectors in n-dimensional space, where n is the number of strong emission line flux ratios. (ii) After training on a sample of star-forming galaxies, the remaining galaxies are classified in the automatic test analysis as either MPGs or MRGs using a 10-fold cross-validation technique. For target selection, we have achieved an acquisition accuracy for MPGs of ∼96 and ∼95 per cent for an MPG threshold of 12 + log(O/H) = 8.00 and 12 + log(O/H) = 8.39, respectively. Running the code takes minutes in most cases under the matlab 2013a software environment. The code in the Letter is available on the web (http://fshi5388.blog.163.com). The svm method can easily be extended to any MPGs target selection task and can be regarded as an efficient classification method particularly suitable for modern large surveys.
On the high-frequency spectrum of a classical accretion disc
Authors: Balbus Steven A. 
Published: August 2014

Abstract
We derive simple and explicit expressions for the high-frequency spectrum of a classical accretion disc. Both stress-free and finite stress inner boundaries are considered. A classical accretion disc spectrum with a stress-free inner boundary departs from a Wien spectrum at large ν, scaling as ν2.5 (as opposed to ν3) times the usual exponential cut-off. If there is finite stress at the inner disc boundary, the maximum disc temperature generally occurs at this edge, even at relatively modest values of the stress. In this case, the high-frequency spectrum is proportional to ν2 times the exponential cut-off. If the temperature maximum is a local hotspot, instead of an axisymmetric ring, then an interior maximum produces a ν2 prefactor while an edge maximum yields ν1.5. Because of beaming effects, these latter findings should pertain to a classical relativistic disc. The asymptotics are in general robust and independent of the detailed temperature profile, provided only that the liberated free energy of differential rotation is dissipated locally, and may prove useful beyond the strict domain of classical disc theory. As observations continue to improve with time, our findings suggest the possibility of using the high-energy spectral component of black hole candidates as a signature prediction of classical theory, as well as a diagnostic of the stress at the inner regions of an accretion disc.
Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network
Authors: Kaboli Saeed , Yamakawa Takuya , Sunada Keisuke , Takagaki Tao , Sasano Yu , Sugiyama Minetaka , Kaneko Yoshinobu , Harashima Satoshi 
Published: August 2014

AbstractDespite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.
Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei
Authors: Reynolds David , Cliffe Laura , Förstner Konrad U. , Hon Chung-Chau , Siegel T. Nicolai , Sabatini Robert 
Published: August 2014

Abstract
Base J, β-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase (RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters.
Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis
Authors: Köster Tino , Meyer Katja , Weinholdt Claus , Smith Lisa M. , Lummer Martina , Speth Corinna , Grosse Ivo , Weigel Detlef , Staiger Dorothee 
Published: August 2014

Abstract
The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log2 fold change of ±0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing.
Inflammatory Bowel Disease in Children of Manitoba
Authors: El‐Matary Wael , Moroz Stan P. , Bernstein Charles N. 
Published: August 2014

ABSTRACTObjectives:The aim of this study was to describe the incidence and prevalence of inflammatory bowel disease (IBD) in children <17 years of age in 30 years from 1978 to 2007.Methods:From January 1, 1978, to December 31, 2007, the sex‐ and age‐adjusted annual incidence and prevalence of pediatric IBD per 100,000 population were calculated based on the pediatric IBD database of the only pediatric tertiary center in the province. The annual health statistics records for the Province of Manitoba were used to calculate population estimates for the participants. To ensure validity of data, the University of Manitoba IBD Epidemiology Database was analyzed for patients <17 years of age from 1989 to 2000.Results:The sex‐ and age‐adjusted incidence of pediatric Crohn disease has increased from 1.2/100,000 in 1978 to 4.68/100,000 in 2007 (P < 0.001). For ulcerative colitis, the incidence has increased from 0.47/100,000 in 1978 to 1.64/100,000 in 2007 (P < 0.001). During the same time period, the prevalence of Crohn disease has increased from 3.1 to 18.9/100,000 (P < 0.001) and from 0.7 to 12.7/100,000 for ulcerative colitis (P < 0.001). During the last 5 years of the study the average annual incidence of IBD in urban patients was 8.69/100,000 as compared with 4.75/100,000 for rural patients (P < 0.001).Conclusions:The incidence and prevalence of pediatric IBD are increasing. The majority of patients were residents of urban Manitoba, confirming the important role of environmental factors in the etiopathogenesis of IBD.
Psychometric Properties of PedsQL Generic Core Scales for Children With Functional Constipation in The Netherlands
Authors: Hartman Esther E. , Pawaskar Manjiri , Williams Valerie , McLeod Lori , Dubois Dominique , Benninga Marc A. , Joseph Alain 
Published: August 2014

ABSTRACTObjectives:The aim of the study was to evaluate the psychometric properties of the Dutch translation of the Pediatric Quality of Life Inventory version 4.0 Generic Core Scales (PedsQL) in children with functional constipation (FC).Methods:The PedsQL was completed by children with FC ages 5 to 18 years and by the parents of children ages 2 to 18 years. To assess construct validity, all of the parents and children completed the PedsQL Gastrointestinal Symptoms Module (GI module) and children ages 8 to 18 years completed the defecation disorder list. Item response distributions, internal consistency reliability, patient–parent agreement, and discriminating ability were evaluated.Results:Overall, 269 children were enrolled. The PedsQL showed minimal missing responses (self‐report: 5.3% with >50% missing, parent report: 2.6% with >50% missing) and achieved satisfactory internal consistency for the total (self‐report: α = 0.86, parent report: α = 0.88), physical health (self‐report: α = 0.75, parent report α = 0.83), and psychosocial health (self‐report: α = 0.80; parent report: α = 0.85) scores. Internal consistency was less convincing for those ages 5 to 7 years (α = 0.53–0.77) than for older individuals. Self‐reported health‐related quality of life was lower than parent reported, with the exception of children ages 5 to 7 years. Interrater reliability intraclass correlations were 0.52 to 0.61 for the overall population. Correlations among the PedsQL, GI module, and defecation disorder list were consistent with a priori hypotheses and generally supported construct validity. The PedsQL distinguished between a previously published healthy reference sample and children with FC, and between those with mild and severe symptoms (P < 0.05).Conclusions:The self‐reported and proxy reported PedsQL demonstrated satisfactory measurement properties in Dutch children with FC ages 8 to 18 years. Further research is needed to establish internal consistency and validity in those ages 5 to 7 years.
Benchmarking undedicated cloud computing providers for analysis of genomic datasets
Authors: Yazar Seyhan , Gooden George E C , Mackey David A , Hewitt Alex W 
Published: August 2014

ABSTRACTA major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coliCC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95%CI: 27.5-78.2) forE.coliand 53.5% (95%CI: 34.4-72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95%CI: 211.5-303.1) and 173.9% (95%CI: 134.6-213.1) more expensive forE.coliand human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE.
Spatial distribution and seasonal fluctuations ofDrosophilaon Santa Catalina Island with an emphasis on the repleta species group
Authors: Kao JY , Nuzhdin SV 
Published: August 2014

AbstractSanta Catalina Island is a small island off the coast of southern California and for its modest size harbors several species of flies from theDrosophilagenus. We performed an island-wide survey ofDrosophilaspecies to ascertain which species were endemic to the island and where they were most abundant. In doing so, we have assembled useful sampling information for researchers who wish to conduct field studies on Santa Catalina Island. From this survey, we determined thatDrosophila hamatofila, Drosophila mainlandi,andDrosophila mettleriwere the prominent repleta species on the island. Other repleta species encountered includedDrosophila mojavensisandDrosophila wheeleri.Non-repleta species sighted on the island includeDrosophila melanogaster, Drosophila pseudoobscura, Drosophila simulans,and an unknown species not seen before on the island. Additionally, we performed seasonal collections at two locations on the island and observed that species abundance and composition at these two sites vary between seasons. One of the seasonal sites was sampled in two consecutive summer seasons, which revealed that species composition had shifted between years, but relative species abundances were approximately the same.
Postmating reproductive barriers contribute to the incipient sexual isolation of US and CaribbeanDrosophila melanogaster
Authors: Kao Joyce Y. , Lymer Seana , Hwang Sea H. , Sung Albert , Nuzhdin Sergey V. 
Published: August 2014

AbstractThe nascent stages of speciation start with the emergence of sexual isolation. Understanding the influence of reproductive barriers in this evolutionary process is an ongoing effort. We present a study ofDrosophila melanogasterpopulations from the southeast United States and Caribbean islands undergoing incipient sexual isolation. The existence of premating reproductive barriers have been previously established, but these types of barriers are not the only source shaping sexual isolation. To assess the influence of postmating barriers, we investigated putative postmating barriers of female remating and egg laying behavior, as well as hatchability of eggs laid and female longevity after mating. In the central region of our putative hybrid zone of American and Caribbean populations, we observed lower hatchability of eggs laid accompanied by increased resistance to harm after mating to less related males. These results illustrate that postmating reproductive barriers acting alongside premating barriers in a complex secondary contact zone. Furthermore, our findings suggest hybrid incompatibilities, likely due to the nature of genomic admixture of populations in the area, are influential even at the early phases of sexual isolation.
Carbon isotopic signatures of soil organic matter correlate with leaf area index across woody biomes
Authors: Ladd Brenton , Peri Pablo L. , Pepper David A. , Silva Lucas C. R. , Sheil Douglas , Bonser Stephen P. , Laffan Shawn W. , Amelung Wulf , Ekblad Alf , Eliasson Peter , Bahamonde Hector , Duarte‐Guardia Sandra , Bird Michael 
Published: August 2014

Summary

Leaf area index (LAI), a measure of canopy density, is a key variable for modelling and understanding primary productivity, and also water use and energy exchange in forest ecosystems. However, LAI varies considerably with phenology and disturbance patterns, so alternative approaches to quantifying stand‐level processes should be considered. The carbon isotope composition of soil organic matter (δ13CSOM) provides a time‐integrated, productivity‐weighted measure of physiological and stand‐level processes, reflecting biomass deposition from seasonal to decadal time scales.

Our primary aim was to explore how well LAI correlates with δ13CSOM across biomes.

Using a global data set spanning large environmental gradients in tropical, temperate and boreal forest and woodland, we assess the strength of the correlation between LAI and δ13CSOM; we also assess climatic variables derived from the WorldClim database.

We found that LAI was strongly correlated with δ13CSOM, but was also correlated with Mean Temperature of the Wettest Quarter, Mean Precipitation of Warmest Quarter and Annual Solar Radiation across and within biomes.

Synthesis. Our results demonstrate that δ13CSOM values can provide spatially explicit estimates of leaf area index (LAI) and could therefore serve as a surrogate for productivity and water use. While δ13CSOM has traditionally been used to reconstruct the relative abundance of C3 versus C4 species, the results of this study demonstrate that within stable C3‐ or C4‐dominated biomes, δ13CSOM can provide additional insights. The fact that LAI is strongly correlated to δ13CSOM may allow for a more nuanced interpretation of ecosystem properties of palaeoecosystems based on palaeosol 13C values.
Incorporating family‐based therapy principles into a partial hospitalization programme for adolescents with anorexia nervosa: challenges and considerations
Authors: Hoste Renee Rienecke 
Published: August 2014

There is increasing research evidence that family‐based treatment (FBT) is the most effective form of treatment currently available for adolescents with anorexia nervosa, while preliminary evidence suggests that it may also be effective for adolescents with bulimia nervosa. Originally designed as a weekly outpatient treatment, FBT's efficacy has led to its adaptation for use in other treatment settings, such as partial hospitalization or intensive outpatient programmes. Although FBT cannot be replicated in these treatment settings, FBT principles can be borrowed and implemented. This article reviews challenges that arise when incorporating FBT into more intensive treatment settings while attempting to remain true to the intent of the original treatment approach.Practitioner points
FBT cannot be replicated in higher levels of care, but FBT principles can be effectively incorporated into a day treatment programme for eating disorders.
Challenges in incorporating FBT into higher levels of care include adequate parental involvement and empowerment.
Assessing Organizational Change in Multisector Community Health Alliances
Authors: Alexander Jeffrey A. , Hearld Larry R. , Shi Yunfeng 
Published: August 2014

ObjectiveThe purpose of this article was to identify some common organizational features of multisector health care alliances (MHCAs) and the analytic challenges presented by those characteristics in assessing organizational change.Data SourcesTwo rounds of an Internet‐based survey of participants in 14 MHCAs.Study DesignWe highlight three analytic challenges that can arise when quantitatively studying the organizational characteristics of MHCAs—assessing change in MHCA organization, assessment of construct reliability, and aggregation of individual responses to reflect organizational characteristics. We illustrate these issues using a leadership effectiveness scale (12 items) validated in previous research and data from 14 MHCAs participating in the Robert Wood Johnson Foundation's Aligning Forces for Quality (AF4Q) program.FindingsHigh levels of instability and turnover in MHCA membership create challenges in using survey data to study changes in key organizational characteristics of MHCAs. We offer several recommendations to diagnose the source and extent of these problems.