bluuebunny/crossref_metadata_2025_split huggingface dataset:
Curation, integration and visualization of bacterial virulence factors in PATRIC
Authors: Mao Chunhong , Abraham David , Wattam Alice R. , Wilson Meredith J.C. , Shukla Maulik , Yoo Hyun Seung , Sobral Bruno W. 
Published: October 2014

Abstract
Motivation: We’ve developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org ) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity.
Results: We have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A–C bacterial pathogen genera, Mycobacterium , Salmonella , Escherichia , Shigella , Listeria and Bartonella , using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein–protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC.
Availability and implementation: All tools and data are freely available at PATRIC ( http://patricbrc.org ).
Contact: cmao@vbi.vt.edu .
Supplementary information: Supplementary data are available at Bioinformatics online.
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring
Authors: Tian Ye , Zhang Bai , Hoffman Eric P. , Clarke Robert , Zhang Zhen , Shih Ie-Ming , Xuan Jianhua , Herrington David M. , Wang Yue 
Published: October 2014

Abstract
Summary: We have developed an integrated molecular network learning method, within a well-grounded mathematical framework, to construct differential dependency networks with significant rewiring. This knowledge-fused differential dependency networks (KDDN) method, implemented as a Java Cytoscape app, can be used to optimally integrate prior biological knowledge with measured data to simultaneously construct both common and differential networks, to quantitatively assign model parameters and significant rewiring p-values and to provide user-friendly graphical results. The KDDN algorithm is computationally efficient and provides users with parallel computing capability using ubiquitous multi-core machines. We demonstrate the performance of KDDN on various simulations and real gene expression datasets, and further compare the results with those obtained by the most relevant peer methods. The acquired biologically plausible results provide new insights into network rewiring as a mechanistic principle and illustrate KDDN’s ability to detect them efficiently and correctly. Although the principal application here involves microarray gene expressions, our methodology can be readily applied to other types of quantitative molecular profiling data.
Availability: Source code and compiled package are freely available for download at http://apps.cytoscape.org/apps/kddn
Contact: yuewang@vt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
WhopGenome: high-speed access to whole-genome variation and sequence data in R
Authors: Wittelsbürger Ulrich , Pfeifer Bastian , Lercher Martin J. 
Published: October 2014

Abstract
Summary: The statistical programming language R has become a de facto standard for the analysis of many types of biological data, and is well suited for the rapid development of new algorithms. However, variant call data from population-scale resequencing projects are typically too large to be read and processed efficiently with R’s built-in I/O capabilities. WhopGenome can efficiently read whole-genome variation data stored in the widely used variant call format (VCF) file format into several R data types. VCF files can be accessed either on local hard drives or on remote servers. WhopGenome can associate variants with annotations such as those available from the UCSC genome browser, and can accelerate the reading process by filtering loci according to user-defined criteria. WhopGenome can also read other Tabix-indexed files and create indices to allow fast selective access to FASTA-formatted sequence files.
Availability and implementation: The WhopGenome R package is available on CRAN at http://cran.r-project.org/web/packages/WhopGenome/ . A Bioconductor package has been submitted.
Contact: lercher@cs.uni-duesseldorf.de
The RNA shapes studio
Authors: Janssen Stefan , Giegerich Robert 
Published: October 2014

Abstract
Motivation : Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach.
Results : We have rebuilt the original RNA shapes as a repository of components that allows us to integrate several established tools for RNA structure analysis: RNA shapes , RNA alishapes and pknots RG, including its recent extension p K iss . As a spin-off, we obtain heretofore unavailable functionality: e. g. with p K iss , we can now perform abstract shape analysis for structures holding pseudoknots up to the complexity of kissing hairpin motifs. The new tool p A li K iss can predict kissing hairpin motifs from aligned sequences. Along with the integration, the functionality of the tools was also extended in manifold ways.
Availability and implementation : As before, the tool is available on the Bielefeld Bioinformatics server at http://bibiserv.cebitec.uni-bielefeld.de/rnashapesstudio .
Contact : bibi-help@cebitec.uni-bielefeld.de
Starch Characteristics Influencing Resistant Starch Content of Cooked Buckwheat Groats
Authors: Lu Lu , Baik Byung‐Kee 
Published: October 2014

ABSTRACTCooked buckwheat groats are suggested to contain a greater amount of resistant starch (RS) than cereal grains. High RS content, in addition to dietary fibers present in groats, contributes to the low‐calorie, high‐fiber food status of buckwheat. Six buckwheat genotypes exhibiting high, medium, and low RS content of cooked groats were selected, and starches were isolated to determine their functional properties to explore the possible cause of high RS content of cooked buckwheat groats. Apparent and actual amylose contents were 27.4 and 31.6–34.5% in high, 27.4–28.6 and 32.5–33.7% in medium, and 21.4–25.6 and 24.5–32.0% in low RS genotypes, respectively. Genotypes of high RS content exhibited greater amylose leaching based on total starch content during cooking than genotypes of low RS content, mainly because of higher amylose content in the former than latter. Genotypes of low RS content exhibited a relatively high content of amylose‐lipid complexes, as determined with a differential scanning calorimeter (DSC). Gelatinization enthalpy and degree of amylopectin retrogradation determined with a DSC were not related to RS content. An evident relationship was observed between RS content of cooked groats and amylose retrogradation determined by gel hardness (r = 0.91, P < 0.05), cohesiveness (r = 0.89, P < 0.05), and syneresis (r = 0.88, P < 0.05). Increases in starch amylose content, amylose leaching capacity, and amylose retrogradation, as well as a decrease in the amount of amylose‐lipid complexes all appear to be related to high RS content of cooked buckwheat groats.
The Receptor Kinase IMPAIRED OOMYCETE SUSCEPTIBILITY1 Attenuates Abscisic Acid Responses in Arabidopsis
Authors: Hok Sophie , Allasia Valérie , Andrio Emilie , Naessens Elodie , Ribes Elsa , Panabières Franck , Attard Agnès , Ris Nicolas , Clément Mathilde , Barlet Xavier , Marco Yves , Grill Erwin , Eichmann Ruth , Weis Corina , Hückelhoven Ralph , Ammon Alexandra , Ludwig-Müller Jutta , Voll Lars M. , Keller Harald 
Published: October 2014

Abstract
In plants, membrane-bound receptor kinases are essential for developmental processes, immune responses to pathogens and the establishment of symbiosis. We previously identified the Arabidopsis (Arabidopsis thaliana) receptor kinase IMPAIRED OOMYCETE SUSCEPTIBILITY1 (IOS1) as required for successful infection with the downy mildew pathogen Hyaloperonospora arabidopsidis. We report here that IOS1 is also required for full susceptibility of Arabidopsis to unrelated (hemi)biotrophic filamentous oomycete and fungal pathogens. Impaired susceptibility in the absence of IOS1 appeared to be independent of plant defense mechanism. Instead, we found that ios1-1 plants were hypersensitive to the plant hormone abscisic acid (ABA), displaying enhanced ABA-mediated inhibition of seed germination, root elongation, and stomatal opening. These findings suggest that IOS1 negatively regulates ABA signaling in Arabidopsis. The expression of ABA-sensitive COLD REGULATED and RESISTANCE TO DESICCATION genes was diminished in Arabidopsis during infection. This effect on ABA signaling was alleviated in the ios1-1 mutant background. Accordingly, ABA-insensitive and ABA-hypersensitive mutants were more susceptible and resistant to oomycete infection, respectively, showing that the intensity of ABA signaling affects the outcome of downy mildew disease. Taken together, our findings suggest that filamentous (hemi)biotrophs attenuate ABA signaling in Arabidopsis during the infection process and that IOS1 participates in this pathogen-mediated reprogramming of the host.
Terroirin the media: the poetry of people, place and palate
Authors: Spielmann Nathalie , Jolly Sylvie , Parisot Fabrice 
Published: October 2014

Purpose– The purpose of this article is to review the use of the wordterroirby print media in France using a multi-method approach. The objective is to uncover whether and how the media framesterroir-marketed products as being qualitatively superior to non-terroirproducts.Design/methodology/approach– Every issue of five print magazines in France was analyzed over the period of one year. All references toterroirwere coded as well as all tasting notes with and withoutterroirreferences. > 6,500 tasting notes and 800 uses ofterroirin wine and food-related text from > 3,800 pages in 30 issues were identified and analyzed.Findings– The results show that although it is not a frequently used word,terroirin tasting notes leads to significantly higher scores and prices for wines than whenterroiris not included in the note. A further analysis reveals thatterroiris most often related to subjective experiences of taste.Practical implications– Wine managers should often use the wordterroirin their press releases and communication pieces. However, the dimension ofterroirthat brand managers put forward in their communication pieces will influence the way in which the media frame their product.Originality/value– Prior to this research there were no empirical results regarding how the media usesterroir. This research contributes to the growing body of research that seeks to understand the value ofterroiras a marketing attribute.
Organising cleaning in Norwegian public FM
Authors: Johanne Klungseth Nora 
Published: October 2014

Purpose– This paper aims to give an overview of the alternatives that Norwegian municipalities have regarding organisational models for their facility management (FM) and cleaning organisations, and to investigate what organisational models they apply, if building category or size of municipality influences their use of organisational models and whether their FM and cleaning organisations are organised similarly within identical municipalities.Design/methodology/approach– The research is based on a national survey conducted during year 2010. All Norwegian municipalities were invited to respond. The survey asked the head of the FM departments (or the chief executive officer [CEO] if the first could not answer) what organisational models they used for their FM and cleaning organisations and what changes they planned for the organisation in the future. All questions were asked according to different building categories to determine whether building category had any influence on their choices.Findings– Limited research has been published regarding the structure of the FM organisations in Norwegian municipalities and even less regarding their cleaning organisations. The results show that Norwegian municipalities prefer integrated models and also purchasing services from the private sector prior to applying decoupled models as inter-municipal alternatives and Municipal Limited Companies. The results do also indicate that Norwegian municipalities’ interest in such models is rising and that they seem to be moving away from traditional and integrated alternatives.Research limitations/implications– Although all municipalities were invited to the survey, only one-third responded.Originality/value– The article may represent a first thorough overview of what organisational models and what combinations of models Norwegian municipalities use for their FM and cleaning organisations. Compared to former studies, this article explores a greater variety in organisational models and a greater variety in researched building categories.
Determining finite difference weights for the acoustic wave equation by a new dispersion‐relationship‐preserving method
Authors: Liang Wenquan , Wang Yanfei , Yang Changchun 
Published: October 2014

ABSTRACTNumerical simulation of the acoustic wave equation is widely used to theoretically synthesize seismograms and constitutes the basis of reverse‐time migration. With finite‐difference methods, the discretization of temporal and spatial derivatives in wave equations introduces numerical grid dispersion. To reduce the grid dispersion effect, we propose to satisfy the dispersion relation for a number of uniformly distributed wavenumber points within a wavenumber range with the upper limit determined by the maximum source frequency, the grid spacing and the wave velocity. This new dispersion‐relationship‐preserving method relatively uniformly reduces the numerical dispersion over a large‐frequency range. Dispersion analysis and seismic numerical simulations demonstrate the effectiveness of the proposed method.
Size and Shape Differences in the Distal Femur and Proximal Tibia between Normal Weight and Obese American Whites
Authors: Harrington Katherine I. , Wescott Daniel J. 
Published: October 2014

AbstractThis study tests for differences in articular and diaphyseal size and shape of the distal femur and proximal tibia between normal weight and obese individuals, and discusses the effects of obesity on the patterns of sexual dimorphism and secular change in the skeletal morphology of the knee. Measurements of the femur and tibia were recorded for 143 American White adult males and females born in the 20th century. The sample was divided into normal and obese weight categories based on the body mass index. Results show differences between normal weight and obese individuals in the size and shape of the femoral shaft and the medial side of the knee joint, none of which affect the pattern of sexual dimorphism. While changes in skeletal morphology associated with obesity may be observed in recent secular changes, its role is still unclear because of the relatively recent increase in obesity prevalence.
Post‐release survival of captive‐reared Allegheny woodrats
Authors: Blythe R. M. , Smyser T. J. , Johnson S. A. , Swihart R. K. 
Published: October 2014

AbstractCaptive breeding to augment wild animal populations is an important tool in the recovery of imperiled species, but low post‐release survival and substantial program expenses require methodologies that maximize utility. We evaluated post‐release survival of captive‐reared Allegheny woodrats (Neotoma magister) introduced into a declining metapopulation in southern Indiana. We hard‐released 16 captive‐reared woodrats in 2011 and soft‐released 14 woodrats in 2012, while monitoring parallel samples of 16 and 17 wild‐born individuals in each year, respectively. We obtained Kaplan–Meier estimates of survivorship for both groups and used Cox proportional hazards regression to estimate the association between survival and rearing environment (wild or captive), release strategy, sex, body condition and age at release. We quantified movement patterns and related the results of survival models to behavioral tendencies. Survivorship of wild‐born individuals was consistently higher than captive‐reared individuals. Patterns of survival were best explained by rearing environment and its interaction with time, although disparities in survival between wild‐born and captive‐reared animals decreased over time. Higher mortality among captive‐reared individuals may have been due to more exploratory behavior, as captive‐reared woodrats used more dens and traveled farther among successive relocations than wild‐born conspecifics. Soft‐released individuals had higher initial survival rates and tended to choose dens similar to those of wild individuals, providing evidence that this strategy eased the transition to a wild environment. We recommend future programs use soft‐release techniques but also explore other pre‐release preparatory strategies such as anti‐predator conditioning and environmental enrichment to increase survival.
Senile scleral plaques imaged with enhanced depth optical coherence tomography
Authors: Beck Marco , Schlatter Bettina , Wolf Sebastian , Zinkernagel Martin S. 
Published: October 2014

AbstractPurposeSenile scleral plaques (SSP) are sharply demarcated greyish areas located just anterior to the insertions of the horizontal rectus muscles and thus are frequently encountered during transscleral intravitreal injections. The aim of this study was to characterize SSP using enhanced depth imaging spectral domain anterior segment optical coherence tomography (OCT) in a cohort of patients attending intravitreal injection clinics.MethodsProspective cross‐sectional study of 380 patients attending the clinic for intravitreal injections at the Department of Ophthalmology at the Bern University Hospital. Thirty‐two patients with SSP were identified and the anatomical features were assessed using anterior segment OCT.ResultsIn our patient cohort, we found a SSP prevalence of 8.2%. Senile scleral plaques were easily identifiable using anterior segment OCT and were found at the insertion sites of the horizontal recti muscles. The mean horizontal diameter was 2.2 mm (±760 μm SD), the mean vertical diameter was 3.3 mm (±144 μm SD), and the average surface area was 5.3 mm2 (±0.4 mm2 SD). The mean senile scleral plaque thickness was 0.6 mm (±149 μm SD). The mean distance from the limbus was 2.24 mm for nasally located SSP and 3.22 mm for temporally located SSP.ConclusionSSP are frequently encountered during intravitreal injections as they are located just anterior to the insertion sites of the horizontal recti muscles. Because the scleral stroma is rarefied and due to calcifications within SSP, these areas should be avoided when performing multiple intravitreal injections as this may result in rupture of the sclera.
Longitudinal study of thinness from birth to early childhood: the association with parental thinness
Authors: Kato Rena , Kubota Masaru , Higashiyama Yukie , Nagai Ayako 
Published: October 2014

AbstractAimEpidemiological research on thinness, particularly in early childhood, is limited. This study tracked thin children aged 5 years back to birth, compared them with normal‐weight children and investigated the relationship with parental thinness.MethodsWe enrolled 2678 children (50.5% boys) aged 5 years and attending kindergarten or nursery in the Nara Prefecture of Japan. The children's height and weight at birth, 1.5 years and 3.5 years, were obtained from mother–child health records. Child thinness was defined as having a body mass index (BMI) of less than the fifth percentile of the reference values for Japanese children, and parental thinness was defined as a BMI of <18.5.ResultsThe overall prevalence of thinness at 5 years of age was 4%, with no significant difference between genders. At every age, weight z‐scores and BMI percentiles were significantly lower in thin children than normal‐weight children. The increment in weight z‐scores between birth and the age of 1.5 years was significantly lower in thin children. The only parental link was paternal thinness and thinness in boys.ConclusionCareful observation of body weight from birth is important to reduce thinness at 5 years of age. Paternal thinness may be a risk factor for thinness in boys.
Anti‐inflammatory cytokine therapy in dystrophinopathies
Authors: Suzumura Akio 
Published: October 2014

AbstractThe precise cause of dystrophinopathies is still elucidative. Some studies have suggested involvement of immune‐mediated mechanisms in the disease progression. Recently, it has been reported that anti‐inflammatory cytokine therapy improves muscle pathology as well as progression of muscle weakness in model mice. However, mechanisms of how blocking of anti‐inflammatory cytokines alleviates dystrophinopathy are yet to be clarified. In addition, there is another conflicting report against the efficacy of anti‐inflammatory cytokine therapy in dystrophinopathy.
Validation of the Chinese version of the Canadian Haemophilia Outcomes‐Kids' Life Assessment Tool (the CHO‐KLAT)
Authors: Wu R. , Zhang J. , Sun J. , Zhou M. , Wu J. S. , Li N. , Li X. , Luke K. H. , Poon M.‐C. , Blanchette V. S. , Young N. L. 
Published: October 2014

SummaryIt is important to assess the health‐related quality of life outcomes of boys in China, but there are no tools validated for this purpose. The objective of the study was to assess the validity of the Simplified Chinese version of the CHO‐KLAT2.0. We recruited 60 boys with either haemophilia A (HA) or haemophilia B (HB) and their parents from four regions in China, and assessed the validity of CHO‐KLAT compared to the PedsQL. All participants complete the CHO‐KLAT a second time 1–2 weeks later to assess reliability. The boys ranged in age from 7 to 18 (mean = 12.4; SD = 3.03) years. The severity distribution was: mild (9), moderate (10) and severe (41). On‐demand therapy was received by 26 boys, while 18 received low‐dose prophylaxis (HA: 10 IU kg−1 2–3 times week−1, and HB: 20 IU kg−1 1 time week−1). The mean CHO‐KLAT scores were 63.7 (SD = 10.6) for child‐report and 58.3 (SD = 11.4) for parent‐report. Validity was supported by a correlation of 0.67 (P < 0.0001) with the PedsQL for child‐report and 0.64 (P < 0.0001) for parent‐report. The test–retest reliability was 0.88 (95% CI: 0.82–0.94) for child‐report, and 0.90 (95% CI: 0.86–0.95) for parent‐report. Inter‐rater reliability was 0.46 (95% CI: 0.26–0.66). CHO‐KLAT scores were 11 points higher among patients who had been on prophylaxis 3 times per week for ≥24 weeks. These results confirm the reliability and validity of the Chinese version of the CHO‐KLAT. This measure is suitable for use in prospective clinical trials in boys with haemophilia in China.