bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functioning and disability levels in primary care out-patients with one or more anxiety disorders
Authors: Sherbourne C. D. , Sullivan G. , Craske M. G. , Roy-Byrne P. , Golinelli D. , Rose R. D. , Chavira D. A. , Bystritsky A. , Stein M. B. 
Published: February 2010

BackgroundAnxiety disorders are the most prevalent mental health disorders and are associated with substantial disability and reduced well-being. It is unknown whether the relative impact of different anxiety disorders is due to the anxiety disorder itself or to the co-occurrence with other anxiety disorders. This study compared the functional impact of combinations of anxiety disorders in primary care out-patients.MethodA total of 1004 patients with panic disorder (PD), generalized anxiety disorder (GAD), social anxiety disorder (SAD) or post-traumatic stress disorder (PTSD) provided data on their mental and physical functioning, and disability. Multivariate regressions compared functional levels for patients with different numbers and combinations of disorders.ResultsOf the patients, 42% had one anxiety disorder only, 38% two, 16% three and 3% all four. There were few relative differences in functioning among patients with only one anxiety disorder, although those with SAD were most restricted in their work, social and home activities and those with GAD were the least impaired. Functioning levels tended to deteriorate as co-morbidity increased.ConclusionsOf the four anxiety disorders examined, GAD appears to be the least disabling, although they all have more in common than in distinction when it comes to functional impairment. A focus on unique effects of specific anxiety disorders is inadequate, as it fails to address the more pervasive impairment associated with multiple anxiety disorders, which is the modal presentation in primary care.
A class of simpleC*-algebras arising from certain non-sofic subshifts
Authors: MATSUMOTO KENGO 
Published: February 2010

AbstractWe present a class of subshiftsZN,N=1,2,…, whose associatedC*-algebras 𝒪ZNare simple, purely infinite and not stably isomorphic to any Cuntz–Krieger algebra nor to the Cuntz algebra 𝒪∞. The class of the subshifts is the first example whose associatedC*-algebras are not stably isomorphic to any Cuntz–Krieger algebra nor to the Cuntz algebra 𝒪∞. The subshiftsZNare coded systems whose languages are context free. We compute the topological entropy for the subshifts and show that a KMS-state (a state satisfying the Kubo–Martin–Schwinger condition) for gauge action on the associatedC*-algebra 𝒪ZNexists if and only if the logarithm of the inverse temperature is the topological entropy for the subshiftZN, and the corresponding KMS-state is unique.
Spatial models of Boolean actions and groups of isometries
Authors: KWIATKOWSKA ALEKSANDRA , SOLECKI SŁAWOMIR 
Published: February 2010

AbstractGiven a Polish group G of isometries of a locally compact separable metric space, we prove that each measure-preserving Boolean action by G has a spatial model or, in other words, has a point realization. This result extends both a classical theorem of Mackey and a recent theorem of Glasner and Weiss, and it covers interesting new examples. In order to prove our result, we give a characterization of Polish groups of isometries of locally compact separable metric spaces which may be of independent interest. The solution to Hilbert’s fifth problem plays an important role in establishing this characterization.
Characterization of antimicrobial resistance, molecular and phage types ofSalmonella entericaserovar Typhi isolations
Authors: DEMCZUK W. H. B. , FINLEY R. , NADON C. , SPENCER A. , GILMOUR M. , NG L.-K. ,   PulseNet Canada,   the Canadian Integrated Program for Antimicrobial Resistance Surveillance Public Health Partnership,   the Canadian Public Health Laboratory Network
Published: February 2010

SUMMARYIsolation rates in Canada ofSalmonella entericaserovar Typhi increased from 0·29 to 0·55 isolations/100 000 population during 2000–2006. Although no ciprofloxacin resistance was detected, nalidixic acid resistance increased from 41% to 80%. Multidrug-resistantS. Typhi represented 18% of the strains tested. Pulsed-field gel electrophoresis (PFGE) analysis of 222 isolates resulted in 91 distinct patterns clustering into four major genetic similarity groups. The five most frequently occurring PFGE patterns accounted for 46% of the isolates. Drug-resistant isolates predominantly occurred in one PFGE similarity group. There were 39 phage types identified in 826 isolates analysed with 60% described by five phage types; 134 were untypable. The phage types associated with multidrug resistance were phage types 53, B1, D1, E1, E9, G3 and M1. Improved integration of epidemiological and laboratory case data will facilitate the protection of public health in Canada during an era of increasing travel and globalization.
Distributions of putative aerobic methanotrophs in diverse pelagic marine environments
Authors: Tavormina Patricia L , Ussler William , Joye Samantha B , Harrison Benjamin K , Orphan Victoria J 
Published: February 2010

Abstract
Aerobic methane oxidization in the pelagic ocean serves an important role in limiting methane release to the atmosphere, yet little is known about the identity and distribution of bacteria that mediate this process. The distribution of putative methane-oxidizing marine groups, OPU1, OPU3 and Group X, was assessed in different ocean provinces using a newly developed fingerprinting method (monooxygenase intergenic spacer analysis (MISA)) in combination with pmoA clone library analysis and quantitative PCR (qPCR). The distribution of these three distinct monooxygenase groups, previously reported from pelagic marine environments, was examined in 39 samples including active methane seeps in the Gulf of Mexico and Santa Monica Bay, submarine canyon heads along the California continental margin, an oligotrophic subtropical gyre and areas proximal to a hydrothermal vent in the North Fiji back-arc basin. OPU1 and OPU3 were widely and similarly distributed within the meso- and bathypelagic zone (110 to ∼2000 m water depth) and showed a &gt;50-fold greater abundance near methane seeps relative to non-seep sites. In contrast, Group X was predominantly recovered from samples along the California margin, at both seep and non-seep sites. All three phylotypes were below detection in the epipelagic zone to depths of 100 m. Several additional deeply branching monooxygenase sequences were also identified in this study, indicating the presence of uncharacterized groups of microorganisms potentially involved in the cycling of methane or ammonium.
Viral and microbial community dynamics in four aquatic environments
Authors: Rodriguez-Brito Beltran , Li LinLin , Wegley Linda , Furlan Mike , Angly Florent , Breitbart Mya , Buchanan John , Desnues Christelle , Dinsdale Elizabeth , Edwards Robert , Felts Ben , Haynes Matthew , Liu Hong , Lipson David , Mahaffy Joseph , Martin-Cuadrado Anna Belen , Mira Alex , Nulton Jim , Pašić Lejla , Rayhawk Steve , Rodriguez-Mueller Jennifer , Rodriguez-Valera Francisco , Salamon Peter , Srinagesh Shailaja , Thingstad Tron Frede , Tran Tuong , Thurber Rebecca Vega , Willner Dana , Youle Merry , Rohwer Forest 
Published: February 2010

Abstract
The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral–microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to &gt;1 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.
Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi
Authors: Scheublin Tanja R , Sanders Ian R , Keel Christoph , van der Meer Jan Roelof 
Published: February 2010

Abstract
Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that are intimately associated with the roots of the majority of land plants. They colonise the interior of the roots and the hyphae extend into the soil. It is well known that bacterial colonisation of the rhizosphere can be crucial for many pathogenic as well as symbiotic plant–microbe interactions. However, although bacteria colonising the extraradical AMF hyphae (the hyphosphere) might be equally important for AMF symbiosis, little is known regarding which bacterial species would colonise AMF hyphae. In this study, we investigated which bacterial communities might be associated with AMF hyphae. As bacterial-hyphal attachment is extremely difficult to study in situ, we designed a system to grow AMF hyphae of Glomus intraradices and Glomus proliferum and studied which bacteria separated from an agricultural soil specifically attach to the hyphae. Characterisation of attached and non-attached bacterial communities was performed using terminal restriction fragment length polymorphism and clone library sequencing of 16S ribosomal RNA (rRNA) gene fragments. For all experiments, the composition of hyphal attached bacterial communities was different from the non-attached communities, and was also different from bacterial communities that had attached to glass wool (a non-living substratum). Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi.
Phonological Acquisition in Bilingual Spanish–English Speaking Children
Authors: Fabiano-Smith Leah , Goldstein Brian A. 
Published: February 2010

Purpose
In this study, the authors aimed to determine how between-language interaction contributes to phonological acquisition in bilingual Spanish–English speaking children.

Method

A total of 24 typically developing children, ages 3;0 (years;months) to 4;0, were included in this study: 8 bilingual Spanish–English speaking children, 8 monolingual Spanish speakers, and 8 monolingual English speakers. Single word and connected speech samples were obtained for each child. This study examined interaction between the two languages of bilingual children during phonological acquisition through the measurement of (a)
transfer
(the frequency and types of phonological transfer present in the speech of bilingual children); (b)
deceleration
(a slower rate of acquisition for bilinguals as compared with monolinguals); and (c)
acceleration
(a faster rate of acquisition for bilinguals as compared with monolinguals.

Results
Findings demonstrated that (a) transfer was evident in the productions of bilingual children, (b) differences were found in accuracy between monolingual and bilingual children, and (c) sound frequency did not predict differential accuracy of either phonetically similar sounds between languages or phonetically dissimilar sounds specific to Spanish or English.

Implications
The results from this study indicate that transfer, deceleration, and a possible variation of the acceleration hypothesis occur in bilingual phonological acquisition. Evidence was found for separation and interaction between the bilingual children’s 2 languages (J. Paradis & F. Genesee, 1996).
Initial Acquisition of Mental Graphemic Representations in Children with Language Impairment
Authors: Wolter Julie A. , Apel Kenn 
Published: February 2010

Purpose
The authors examined initial acquisition of mental graphemic representations (MGRs) for a set of pseudowords in children with language impairment (LI). They also determined whether the linguistic properties of the words (i.e., phonotactic and orthotactic probabilities) influenced MGR learning and whether the ability to acquire initial MGRs was related to performance on reading and spelling measures. The authors compared these children’s initial acquisition of MGRs to a group of children with typical language (TL) skills.

Method
A written fast mapping procedure was administered to 25 kindergarten children with LI and 31 with TL. During the procedure, the children were exposed to novel pseudowords varying in phonotactic and orthotactic probabilities in a computer-based, storybook reading task and then were asked to generate and identify those pseudoword spellings. Additionally, reading and spelling tasks were administered.

Results
Children with LI acquired some initial MGRs as evidenced by their ability to identify some pseudowords; however, their ability to identify and generate pseudowords was significantly poorer than that of the comparison group. Similar to their TL peers, the ability to identify pseudoword spellings by children with LI was affected by the linguistic properties of words, and written fast mapping performance was related to spelling performance. However, unlike the comparison group, written fast mapping performance of children with LI was not related to performance on a reading composite measure.

Conclusions
The authors propose that children with LI are less robust at developing initial MGRs than are children with TL and that this poor ability to acquire initial MGRs likely places them at risk for later literacy deficits.
Conversational Language Use as a Predictor of Early Reading Development: Language History as a Moderating Variable
Authors: DeThorne Laura Segebart , Petrill Stephen A. , Schatschneider Chris , Cutting Laurie 
Published: February 2010

Purpose
The present study examined the nature of concurrent and predictive associations between conversational language use and reading development during early school-age years.

Method
Language and reading data from 380 twins in the Western Reserve Reading Project were examined via phenotypic correlations and multilevel modeling on exploratory latent factors.

Results
In the concurrent prediction of children’s early reading abilities, a significant interaction emerged between children’s conversational language abilities and their history of reported language difficulties. Specifically, conversational language concurrently predicted reading development above and beyond variance accounted for by formal vocabulary scores, but only in children with a history of reported language difficulties. A similar trend was noted in predicting reading skills 1 year later, but the interaction was not statistically significant.

Conclusions
Findings suggest a more nuanced view of the association between spoken language and early reading than is commonly proposed. One possibility is that children with and without a history of reported language difficulties rely on different skills, or the same skills to differing degrees, when completing early reading-related tasks. Future studies should examine the causal link between conversational language and early reading specifically in children with a history of reported language difficulties.
Assigning roles to DNA regulatory motifs using comparative genomics
Authors: Buske Fabian A. , Bodén Mikael , Bauer Denis C. , Bailey Timothy L. 
Published: February 2010

Abstract
Motivation: Transcription factors (TFs) are crucial during the lifetime of the cell. Their functional roles are defined by the genes they regulate. Uncovering these roles not only sheds light on the TF at hand but puts it into the context of the complete regulatory network.
Results: Here, we present an alignment- and threshold-free comparative genomics approach for assigning functional roles to DNA regulatory motifs. We incorporate our approach into the Gomo algorithm, a computational tool for detecting associations between a user-specified DNA regulatory motif [expressed as a position weight matrix (PWM)] and Gene Ontology (GO) terms. Incorporating multiple species into the analysis significantly improves Gomo's ability to identify GO terms associated with the regulatory targets of TFs. Including three comparative species in the process of predicting TF roles in Saccharomyces cerevisiae and Homo sapiens increases the number of significant predictions by 75 and 200%, respectively. The predicted GO terms are also more specific, yielding deeper biological insight into the role of the TF. Adjusting motif (binding) affinity scores for individual sequence composition proves to be essential for avoiding false positive associations. We describe a novel DNA sequence-scoring algorithm that compensates a thermodynamic measure of DNA-binding affinity for individual sequence base composition. Gomo's prediction accuracy proves to be relatively insensitive to how promoters are defined. Because Gomo uses a threshold-free form of gene set analysis, there are no free parameters to tune. Biologists can investigate the potential roles of DNA regulatory motifs of interest using Gomo via the web (http://meme.nbcr.net).
Contact: t.bailey@uq.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Authors: MacLean Brendan , Tomazela Daniela M. , Shulman Nicholas , Chambers Matthew , Finney Gregory L. , Frewen Barbara , Kern Randall , Tabb David L. , Liebler Daniel C. , MacCoss Michael J. 
Published: February 2010

Abstract
Summary: Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools.
Availability: Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
Contact: brendanx@u.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Crystal Structure and Functional Insights of Hemopexin Fold Protein from Grass Pea
Authors: Gaur Vineet , Qureshi Insaf A. , Singh Apekshita , Chanana Veenu , Salunke Dinakar M. 
Published: February 2010

Abstract
A regulatory protein from grass pea (Lathyrus sativus), LS-24, a close homolog of albumin 2 from garden pea (Pisum sativum) that is associated with polyamine biosynthesis, was characterized and the structure of a hemopexin-type fold among plant proteins illustrated. Crystal structure of LS-24 determined at 2.2 Å resolution by multiple isomorphous replacement phasing showed four-bladed β-propeller structure having a pseudo 4-fold molecular symmetry along a metal ion-binding central channel. The structure represents typical mammalian hemopexin fold with discernible features correlated with the possible functional variations. The protein was found to exist in the dimeric state. While LS-24 dimer binds to spermine in the crystal structure as well as in solution, binding of heme in solution resulted in the dissociation of the dimer into monomers with concomitant release of bound spermine. Interactions of heme and spermine with LS-24 bear physiological implications. While binding of spermine to LS-24 can be linked with polyamine biosynthesis that of heme correlates with oxidative stress. Mutually exclusive binding of heme and spermine in different oligomeric states suggest a role for LS-24 in sensing oxidative stress through a ligand-regulated monomer-dimer transition switch.
Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves
Authors: Rios-Estepa Rigoberto , Lange Iris , Lee James M. , Lange B. Markus 
Published: February 2010

Abstract
We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Mentha × piperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a χ 2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.
The cross-correlation function: main properties and first applications
Authors: Carrozzini Benedetta , Cascarano Giovanni Luca , Giacovazzo Carmelo 
Published: February 2010

When a model structure, and more generally a model electron density ρM(r), is available, its cross-correlation functionC(u) with the unknown true structure ρ(r) cannot be exactly calculated. A useful approximation ofC(u) is obtained by replacing exp[i(φh − φMh)] by its expected value. In this caseC′(u), a potentially useful approximation of the functionC(u), is obtained. In this paper the main crystallographic properties of the functionsC(u) andC′(u) are established. It is also shown that such functions may be useful for the success of the phasing process.