bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organic enrichment and structure of macrobenthic communities in the glacial Baker Fjord, Northern Patagonia, Chile
Authors: Quiroga Eduardo , Ortiz Paula , Gerdes Dieter , Reid Brian , Villagran Soraya , Quiñones Renato 
Published: April 2011

In this study we describe community parameters such as densities, biomasses, species composition, feeding modes and normalized biomass size-spectra (NBSS) of macrobenthic invertebrate communities from three stations located in the Baker Fjord obtained on four seasonal campaigns in 2008 and 2009. The macrobenthic communities were dominated by small-bodied polychaetes (Paraonidae, Capitellidae and Cirratulidae) characterized by continuous year-round breeding, short life-spans, and fast turnover rates, which in turn regulated the standing stock in the communities. Principal component analysis and multiple-regression analysis demonstrate the distribution of macrobenthic communities in the study area to be mainly controlled by few local environmental conditions. Macrofaunal densities, diversity and feeding modes were significantly correlated with the total organic carbon (TOC; R2 = 0.74; P < 0.001) and chlorophyll-a (Chl-a; R2 = 0.55; P < 0.05) content in the sediments. This study also suggests that feeding modes and NBSS can be used to detect and follow possible changes caused by natural perturbations such as glacial lake outburst floods or anthropogenic stressors associated with ecological impacts generated by the construction and operation of hydroelectric power stations in the Baker River.
Cognitive correlates of vocabulary growth in English language learners
Authors: FARNIA FATANEH , GEVA ESTHER 
Published: April 2011

ABSTRACTThis study modeled vocabulary trajectories in 91 English language learners (ELLs) with Punjabi, Tamil, or Portuguese home languages, and 50 English monolinguals (EL1) from Grades 1 to 6. The concurrent and longitudinal relationships between phonological awareness and phonological short-term memory and vocabulary were examined. ELLs underperformed EL1s on vocabulary across all grades. Although vocabulary grew faster in ELLs than in EL1s in the primary grades, they did not close the gap after 6 years of English schooling. Mutual facilitation was found between phonological awareness, English-like nonwords, and vocabulary. A unidirectional relationship was found between Hebrew-like nonwords and vocabulary suggesting that the relationship between phonological short-term memory and vocabulary can be more accurately captured when using nonwords based on a remote, unfamiliar language.
Use of “um” in the deceptive speech of a convicted murderer
Authors: VILLAR GINA , ARCIULI JOANNE , MALLARD DAVID 
Published: April 2011

ABSTRACTPrevious studies have demonstrated a link between language behaviors and deception; however, questions remain about the role of specific linguistic cues, especially in real-life high-stakes lies. This study investigated use of the so-called filler, “um,” in externally verifiable truthful versus deceptive speech of a convicted murderer. The data revealed significantly fewer instances of “um” in deceptive speech. These results are in line with our recent study of “um” in laboratory elicited low-stakes lies. Rather than constituting a filled pause or speech disfluency, “um” may have a lexical status similar to other English words and may be under the strategic control of the speaker. In an attempt to successfully deceive, humans may alter their speech, perhaps in order to avoid certain language behaviors that they think might give them away.
Attitudes et perception de contrôle des personnes âgées envers la prise de médicaments à action anxiolytique, sédative et hypnotique (ASH)
Authors: Guindon Marilyn , Cappeliez Philippe 
Published: April 2011

ABSTRACTThis study examines the importance of variables from the Theory of Planned Behaviour (i.e.,attitudes toward behaviour, subjective norms, and perceived control) for the prediction of consumption of anxiolytic and sedative-hypnotic (ASH) medications in a sample of older persons, aged 69 years on average, 62 consumers and 92 non-consumers. A favourable attitude toward ASH and a sense of having less control regarding these drugs predict both current usage and intention to continue. Perceived control predicts intention to start consumption of ASH in current non-consumers. This study underlines the importance of considering the role of the older person’s decisional power in the consumption of these medications.
Burden of acute gastrointestinal illness in Denmark 2009: a population-based telephone survey
Authors: MÜLLER L. , KORSGAARD H. , ETHELBERG S. 
Published: April 2011

SUMMARYA cross-sectional telephone survey was conducted in Denmark throughout 2009 to determine the incidence of acute gastrointestinal illness (AGI). Using the Danish population register, a random population sample stratified by gender and age groups was selected and mobile or landline phone numbers found. Representative numbers of interviews were performed by gender, age group and month. A recently proposed international case definition of AGI, including cases with diarrhoea and/or vomiting in a 4-week recall period, was used. A total of 1853 individuals were included and 206 (11·1%) fulfilled the case definition; 78% reported diarrhoea. This corresponds to an overall standardized incidence rate of 1·4 (95% CI 1·2–1·6) episodes of AGI per person-year. The incidence rate was generally higher in the younger age groups; only being 2·3, 1·9 and 0·80 per person-year in the 0–9, 10–39 and ⩾40 years age groups, respectively. The incidence rate estimates were considerably higher when calculated from shorter recall periods.
Herpes simplex encephalitis and management of acyclovir in encephalitis patients in France
Authors: STAHL J. P. , MAILLES A. , De BROUCKER T. ,   the Steering Committee and Investigators Group
Published: April 2011

SUMMARYThis study reports on the clinical profiles of herpes simplex encephalitis (HSE) case-patients and the management of acyclovir prescriptions. We designed a study on the causes of encephalitis in France in 2007. Case-patients fulfilling the inclusion criteria were enrolled in all the hospitals that volunteered to participate. Fifty-five of 253 enrolled case-patients were diagnosed with HSE. Three (5%) HSE patients died and 48 (89%) were discharged with persistent neurological symptoms. All HSE patients were prescribed acyclovir, 10 of whom had a 2-week course; 42 a 3-week course; two received incomplete courses; and one received two courses of 21 days each due to relapse. The acyclovir dosage was reported for 45 adult HSE patients, 25 (53%) of whom received 10 mg/kg t.i.d. and 22 (47%) received 15 mg/kg t.i.d. The mortality rate was low despite 49% of patients being admitted to intensive-care units. A high dose of acyclovir was not associated with a better outcome in HSE patients. Most patients had persisting symptoms on discharge suggesting neuropsychological rehabilitation is an important issue for survivors.
Query-focused multi-document summarization: automatic data annotations and supervised learning approaches
Authors: CHALI YLLIAS , HASAN SADID A. 
Published: April 2011

AbstractIn this paper, we apply different supervised learning techniques to build query-focused multi-document summarization systems, where the task is to produce automatic summaries in response to a given query or specific information request stated by the user. A huge amount of labeled data is a prerequisite for supervised training. It is expensive and time-consuming when humans perform the labeling task manually. Automatic labeling can be a good remedy to this problem. We employ five different automatic annotation techniques to build extracts from human abstracts using ROUGE, Basic Element overlap, syntactic similarity measure, semantic similarity measure, and Extended String Subsequence Kernel. The supervised methods we use are Support Vector Machines, Conditional Random Fields, Hidden Markov Models, Maximum Entropy, and two ensemble-based approaches. During different experiments, we analyze the impact of automatic labeling methods on the performance of the applied supervised methods. To our knowledge, no other study has deeply investigated and compared the effects of using different automatic annotation techniques on different supervised learning approaches in the domain of query-focused multi-document summarization.
Evidence for a core gut microbiota in the zebrafish
Authors: Roeselers Guus , Mittge Erika K , Stephens W Zac , Parichy David M , Cavanaugh Colleen M , Guillemin Karen , Rawls John F 
Published: April 2011

Abstract
Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
Authors: Herlemann Daniel P R , Labrenz Matthias , Jürgens Klaus , Bertilsson Stefan , Waniek Joanna J , Andersson Anders F 
Published: April 2011

Abstract
Salinity is a major factor controlling the distribution of biota in aquatic systems, and most aquatic multicellular organisms are either adapted to life in saltwater or freshwater conditions. Consequently, the saltwater–freshwater mixing zones in coastal or estuarine areas are characterized by limited faunal and floral diversity. Although changes in diversity and decline in species richness in brackish waters is well documented in aquatic ecology, it is unknown to what extent this applies to bacterial communities. Here, we report a first detailed bacterial inventory from vertical profiles of 60 sampling stations distributed along the salinity gradient of the Baltic Sea, one of world's largest brackish water environments, generated using 454 pyrosequencing of partial (400 bp) 16S rRNA genes. Within the salinity gradient, bacterial community composition altered at broad and finer-scale phylogenetic levels. Analogous to faunal communities within brackish conditions, we identified a bacterial brackish water community comprising a diverse combination of freshwater and marine groups, along with populations unique to this environment. As water residence times in the Baltic Sea exceed 3 years, the observed bacterial community cannot be the result of mixing of fresh water and saltwater, but our study represents the first detailed description of an autochthonous brackish microbiome. In contrast to the decline in the diversity of multicellular organisms, reduced bacterial diversity at brackish conditions could not be established. It is possible that the rapid adaptation rate of bacteria has enabled a variety of lineages to fill what for higher organisms remains a challenging and relatively unoccupied ecological niche.
Gender and Politics in the Henrician Court: The Douglas-Howard Lyrics in the Devonshire Manuscript (BL Add 17492)*
Authors: Irish Bradley J. 
Published: April 2011

AbstractBL Additional MS 17492, the so-called Devonshire Manuscript of Henrician courtly verse, is a prime example of how social and cultural phenomena contributed to early modern manuscript culture. Among the treasures of the Devonshire MS is a series of lyrics that chronicles a fascinating courtly intrigue of the 1530s: the illicit, clandestine marriage of Lord Thomas Howard and Lady Margaret Douglas, the headstrong niece of Henry VIII. After unpacking this historical drama, this essay advances the first substantial literary analysis of these poems by exploring the textual strategies through which Howard and Douglas attempted to negotiate the crown's insistent management of their erotic life. This treatment of the Douglas-Howard lyrics provides new opportunity to consider how the Devonshire MS reflects and refracts the gender dynamics of the contemporary Henrician court.
Nothing But the Truth? Hermeneutics and Morality in the Doctrines of Equivocation and Mental Reservation in Early Modern Europe
Authors: Tutino Stefania 
Published: April 2011

AbstractThis article examines certain aspects of the history of the doctrines of equivocation and mental reservation in early modern Catholic elaborations. It argues that the first Catholic theologians who engaged systematically with these doctrines, Domingo de Soto and Martin de Azpilcueta (Navarrus), used them as tools to investigate the potentialities and limitations of human language as a means to communicate meaning between a speaker and a listener. This article also shows that between the end of the sixteenth and the beginning of the seventeenth centuries Catholic theologians, both Jesuit and non-Jesuit, changed the debate over these doctrines into a debate over the moral quality of the speaker's intention. By analyzing the developments of the Catholic debate over equivocation and mental reservation, this article seeks to offer a fresh interpretation of the links between theology, morality, and hermeneutics.
DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models
Authors: Taslim Cenny , Huang Tim , Lin Shili 
Published: April 2011

Abstract
Summary: Differential Identification using Mixtures Ensemble (DIME) is a package for identification of biologically significant differential binding sites between two conditions using ChIP-seq data. It considers a collection of finite mixture models combined with a false discovery rate (FDR) criterion to find statistically significant regions. This leads to a more reliable assessment of differential binding sites based on a statistical approach. In addition to ChIP-seq, DIME is also applicable to data from other high-throughput platforms.
Availability and implementation: DIME is implemented as an R-package, which is available at http://www.stat.osu.edu/~statgen/SOFTWARE/DIME. It may also be downloaded from http://cran.r-project.org/web/packages/DIME/.
Contact: shili@stat.osu.edu
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards
Authors: Hemani Gibran , Theocharidis Athanasios , Wei Wenhua , Haley Chris 
Published: April 2011

Abstract
Motivation: Hundreds of genome-wide association studies have been performed over the last decade, but as single nucleotide polymorphism (SNP) chip density has increased so has the computational burden to search for epistasis [for n SNPs the computational time resource is O(n(n−1)/2)]. While the theoretical contribution of epistasis toward phenotypes of medical and economic importance is widely discussed, empirical evidence is conspicuously absent because its analysis is often computationally prohibitive. To facilitate resolution in this field, tools must be made available that can render the search for epistasis universally viable in terms of hardware availability, cost and computational time.
Results: By partitioning the 2D search grid across the multicore architecture of a modern consumer graphics processing unit (GPU), we report a 92× increase in the speed of an exhaustive pairwise epistasis scan for a quantitative phenotype, and we expect the speed to increase as graphics cards continue to improve. To achieve a comparable computational improvement without a graphics card would require a large compute-cluster, an option that is often financially non-viable. The implementation presented uses OpenCL—an open-source library designed to run on any commercially available GPU and on any operating system.
Availability: The software is free, open-source, platform-independent and GPU-vendor independent. It can be downloaded from http://sourceforge.net/projects/epigpu/.
Contact: gib.hemani@roslin.ed.ac.uk
First Report of Pantoea agglomerans Causing Brown Apical Necrosis of Walnut in China
Authors: Yang K. Q. , Qu W. W. , Liu X. , Liu H. X. , Hou L. Q. 
Published: April 2011

Brown apical necrosis (BAN) of walnut (Juglans regia L.) causes premature fruit drop and yield losses and has been reported to be an important walnut production problem in Spain, Italy, France, and Turkey (1,2). A number of organisms have been associated with BAN on walnut: Xanthomonas arboricola pv. juglandis, Fusarium spp., and Alternaria spp. (3). Since the spring of 2007, BAN was observed in 50 to 60% of the trees in walnut orchards in Taian City and Laiwu City, Shandong Province, China. Surface-disinfested tissue from premature walnut fruits was placed onto potato dextrose agar. Alternaria spp., X. arboricola pv. juglandis, and Pantoea agglomerans (formerly Enterobacter agglomerans) were isolated 76, 35, and 45% of the time, respectively. The P. agglomerans cultures formed a yellow lawn and were rod shaped with the body length of 1.5 to 3.0 μm, width of 0.5 to 1.0 μm, and four to six flagella. In biochemical tests, these bacteria were gram negative, lactose positive, and indole negative. Genomic DNA was extracted from one HXJ isolate and the 16S rRNA gene sequence (GenBank Accession No. HM016799) was obtained using universal primers 27F and 1492R. HM016799 had 99% sequence identity with P. agglomerans accessions in GenBank (GU477762, GQ494018, FJ756355, and AB004757). To confirm pathogenicity, HXJ isolate (108 CFU·ml–1) was inoculated at the bottom of the stigma within 5 days after florescence (DAF) and in premature fruit wounded with a needle within 30 DAF in 2008 to 2010. Stigmas injected with only sterile water served as controls. The bacteria were inoculated into three replicate 9-year-old plants of the walnut cv. Xiangling. Forty nuts on each plant were inoculated. The plants were grown in Shandong Province, China (36°09′59″N, 117°13′30″E). Ten days after inoculation, typical internal BAN symptoms were observed on all treated nuts and the controls were still healthy. In the inoculated stigmas, necrosis of stigma and style spread to internal tissues and reached the kernel. In treated premature fruit, internal tissues became necrotic and blackish and eventually led to nut drop. The same bacterium was reisolated from the inoculated tissue. On the basis of morphological, physiological, and biochemical characteristics and sequencing of the 16S rRNA gene, the bacterium was identified as P. agglomerans. To our knowledge, this is the first report of P. agglomerans causing internal type BAN of walnut in China or worldwide. References: (1) A. Belisario et al. Plant Dis. 6:599, 2002. (2) G. Bouvet. Acta Hortic. 705:447, 2005. (3) C. Moragrega and H. Özaktan. J. Plant Pathol. 92:S1.67, 2010.
First Report of a 16SrII-D Subgroup Phytoplasma Associated with Pale Purple Coneflower Witches'-Broom Disease in Australia
Authors: Pearce T. L. , Scott J. B. , Pethybridge S. J. 
Published: April 2011

Pale purple coneflower, Echinacea pallida (Nutt.) Nutt., is an herbaceous perennial cultivated for its ornamental and medicinal properties. In 2005, phytoplasma-like symptoms, including virescence, phyllody, and chlorotic leaves, were first observed in coneflower fields in northern Tasmania, Australia. During the 2010–2011 growing season, the incidence of affected plants was estimated to be 12% within a single field. Total DNA was extracted from symptomatic plants with a DNeasy Plant Mini Kit (QIAGEN Inc., Valencia, CA) according to the manufacturer's instructions. DNA was also extracted, as described above, from asymptomatic coneflower seedlings obtained by germinating surface-sterilized seed on water agar. DNA was amplified via a nested PCR using universal primer pairs P1/P7 followed by R16F2n/R16R2 to detect putative phytoplasmas (2). Amplifications yielded expected products of 1.8 and 1.2 kb, respectively, only from symptomatic samples. Subsequently, PCR products from six arbitrarily selected samples were used for sequencing (Genome Lab Dye Terminator Cycling Sequence with Quick Start Chemistry) and read in a CEQ8000 sequencer (Beckman Coulter Inc., Brea, CA). Sequence homology indicated 100% similarity between isolates designated EWB1 to EWB4 (GenBank Accession Nos. JF340075 and JF340077 to JF340079) and between EWB5 and EWB6 (JF340076 and JF40080). Sequence homology between the two observed groups was 99.7%, resulting from a 4-bp difference in the R16F2n primer region. Blast search revealed isolates EWB1 to EWB4 were 100% homologous with Catharanthus roseus phytoplasma (EU096500.1), Tomato big bud phytoplasma (EF193359.1), Scaevola witches'-broom phytoplasma (AB257291.1), and Mollicutes sp. (Y10097.1 and Y10096.1). Moreover, isolates EWB5 and EWB6 shared 99% sequence identity with the above isolates. iPhyClassifier (4) was used to perform sequence similarity and generate virtual restriction fragment length polymorphism (RFLP) profiles. The 16S rDNA sequence of isolates EWB1 to EWB4 and EWB5 to EWB6 shared 100 and 99.7% similarity, respectively, to the ‘Candidatus Phytoplasma australasiae’ reference strain (Y10097). RFLP profiles from all isolates suggested that they belonged to the 16SrII-D subgroup. To our knowledge, this is the first report of a 16SrII-D subgroup phytoplasma infecting E. pallida in Australia. Aster yellow phytoplasmas (16SrI-C subgroup) infections of E. purpurea have been recorded in Slovenia (3) and southern Bohemia (1). References: (1) J. Franova et al. Eur. J. Plant Pathol. 123:85, 2009. (2) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998. (3) S. Radišek et al. Plant Pathol. 58:392, 2009. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.
Duplicate Maize Wrinkled1 Transcription Factors Activate Target Genes Involved in Seed Oil Biosynthesis
Authors: Pouvreau Benjamin , Baud Sébastien , Vernoud Vanessa , Morin Valérie , Py Cyrille , Gendrot Ghislaine , Pichon Jean-Philippe , Rouster Jacques , Paul Wyatt , Rogowsky Peter M. 
Published: April 2011

Abstract
WRINKLED1 (WRI1), a key regulator of seed oil biosynthesis in Arabidopsis (Arabidopsis thaliana), was duplicated during the genome amplification of the cereal ancestor genome 90 million years ago. Both maize (Zea mays) coorthologs ZmWri1a and ZmWri1b show a strong transcriptional induction during the early filling stage of the embryo and complement the reduced fatty acid content of Arabidopsis wri1-4 seeds, suggesting conservation of molecular function. Overexpression of ZmWri1a not only increases the fatty acid content of the mature maize grain but also the content of certain amino acids, of several compounds involved in amino acid biosynthesis, and of two intermediates of the tricarboxylic acid cycle. Transcriptomic experiments identified 18 putative target genes of this transcription factor, 12 of which contain in their upstream regions an AW box, the cis-element bound by AtWRI1. In addition to functions related to late glycolysis and fatty acid biosynthesis in plastids, the target genes also have functions related to coenzyme A biosynthesis in mitochondria and the production of glycerol backbones for triacylglycerol biosynthesis in the cytoplasm. Interestingly, the higher seed oil content in ZmWri1a overexpression lines is not accompanied by a reduction in starch, thus opening possibilities for the use of the transgenic maize lines in breeding programs.