bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pulsars & Magnetars
Authors: Kramer Michael 
Published: April 2009

AbstractThe largest magnetic field encountered in the observable Universe can be found in neutron stars, in particular in radio pulsars and magnetars. While recent discoveries have slowly started to blur the distinction between these two classes of highly magnetized neutron stars, it is possible that both types of sources are linked via an evolutionary sequence. Indications for this to be the case are obtained from observations of the spin-evolution of pulsars. It is found that most young pulsars are heading across the top of the main distribution of radio pulsars in the P–Ṗ-diagram, suggesting that at least a sub-class of young pulsars may evolve into objects with magnetar-like magnetic field strengths. Part of this evolutionary sequence could be represented by RRATs which appear to share at least in parts properties with both pulsars and magnetars.
Why we need to measure turbulent magnetic fields in HII regions
Authors: Beckman John E. , Relaño Mónica 
Published: April 2009

AbstractWe have measured the emission line profiles in Hα from populations of HII regions in nearby spiral galaxies, and extracted their non-thermal line widths. These are supersonic for the more luminous regions. We infer from plots of line width, σ, against Hα luminosity, a set of regions in virial equilibrium, and derive their masses summing all known components. The virial masses are considerably larger. If this discrepancy, and the supersonic line widths, are due to the presence of magnetic fields, we can estimate their strengths at a few microgauss. Observational confirmation is clearly required.
The integrated polarization of spiral galaxies
Authors: Stil Jeroen M. , Krause Marita , Mitchell Lydia , Beck Rainer , Taylor A. Russell 
Published: April 2009

AbstractWe present deep observations of polarized radio emission of distant spiral galaxies with the Effelsberg 100-m telescope† at 4.8 GHz. These cross scans with sensitivity of 50 μJy or better open the possibility of a statistical study of magnetic field properties and internal Faraday rotation as a function of inclination for a large sample of unresolved galaxies. The Square Kilometre Array (SKA) will be able to detect polarization of spiral galaxies to high redshift, probing the evolution of magnetic fields in disk galaxies over cosmic time.
DRAO deep polarization study at 1.4 GHz
Authors: Grant Julie K. , Taylor A. R. , Stil J. M. , Ricci R. , O'Sullivan S. P. , Landecker T. L. , Kothes R. , Ransom R. R. 
Published: April 2009

AbstractThe Dominion Radio Astrophysical Observatory synthesis telescope (DRAO-ST) was used to produce a deep polarization mosaic at 1.4 GHz to a noise level of 45 microJy beam−1 for both Stokes Q and U at 1′ resolution. The DRAO deep field covers 8.6 sq. degrees in polarization centered on the ELAIS N1 field. We identified over 1700 total intensity (Stokes I) radio sources of which 197 are linearly polarized down to a flux density level of 203 microJy. The fractional polarization of faint polarized sources are flat down to a polarized flux density of about 4 mJy, at which point the numbers increase, until the counts drop for polarized flux densities below 1 mJy. These faint polarized radio sources are mostly AGNs with luminosities below the traditional FRI/FRII boundary. Follow-up observations with the VLA show that the origin of the polarization of the radio sources down to a polarized flux of 1 mJy comes from both the lobes and central region of these objects.
Deriving AGN properties from circular and linear radio polarimetry
Authors: Cenacchi Elena , Kraus A. , Mack K.-H. 
Published: April 2009

AbstractWe report multi-frequency circular polarization measurements for the radio source 0056-00 taken at the Effelsberg 100-m radio telescope. The data reduction is based on a new calibration procedure that allows the contemporary measurement of the four Stokes parameters with single-dish radio telescopes.
Cosmic magnetism with the Square Kilometre Array and its pathfinders
Authors: Gaensler Bryan M. 
Published: April 2009

AbstractOne of the five key science projects for the Square Kilometre Array (SKA) is “The Origin and Evolution of Cosmic Magnetism”, in which radio polarimetry will be used to reveal what cosmic magnets look like and what role they have played in the evolving Universe. Many of the SKA prototypes now being built are also targeting magnetic fields and polarimetry as key science areas. Here I review the prospects for innovative new polarimetry and Faraday rotation experiments with forthcoming facilities such as ASKAP, LOFAR, the ATA, the EVLA, and ultimately the SKA. Sensitive wide-field polarisation surveys with these telescopes will provide a dramatic new view of magnetic fields in the Milky Way, in nearby galaxies and clusters, and in the high-redshift Universe.
Testing the cosmological evolution of magnetic fields in galaxies with the SKA
Authors: Arshakian Tigran G. , Beck Rainer , Krause Marita , Sokoloff Dimitry 
Published: April 2009

AbstractWe investigate the cosmological evolution of large- and small-scale magnetic fields in galaxies at high redshifts. Results from simulations of hierarchical structure formation cosmology provide a tool to develop an evolutionary model of regular magnetic fields coupled to galaxy formation and evolution. Turbulence in protogalactic halos generated by thermal virialization can drive an efficient turbulent dynamo. The mean-field dynamo theory is used to derive the timescales of amplification and ordering of regular magnetic fields in disk and dwarf galaxies. For future observations with the SKA, we predict an anticorrelation at fixed redshift between galaxy size and the ratio between ordering scale and galaxy size. Undisturbed dwarf galaxies should host fully coherent fields at z < 1, spiral galaxies at z < 0.5.
Reduction of nitrate in Shewanella oneidensis depends on atypical NAP and NRF systems with NapB as a preferred electron transport protein from CymA to NapA
Authors: Gao Haichun , Yang Zamin K , Barua Soumitra , Reed Samantha B , Romine Margaret F , Nealson Kenneth H , Fredrickson James K , Tiedje James M , Zhou Jizhong 
Published: April 2009

Abstract
In the genome of Shewanella oneidensis, a napDAGHB gene cluster encoding periplasmic nitrate reductase (NapA) and accessory proteins and an nrfA gene encoding periplasmic nitrite reductase (NrfA) have been identified. These two systems seem to be atypical because the genome lacks genes encoding cytoplasmic membrane electron transport proteins, NapC for NAP and NrfBCD/NrfH for NRF, respectively. Here, we present evidence that reduction of nitrate to ammonium in S. oneidensis is carried out by these atypical systems in a two-step manner. Transcriptional and mutational analyses suggest that CymA, a cytoplasmic membrane electron transport protein, is likely to be the functional replacement of both NapC and NrfH in S. oneidensis. Surprisingly, a strain devoid of napB encoding the small subunit of nitrate reductase exhibited the maximum cell density sooner than the wild type. Further characterization of this strain showed that nitrite was not detected as a free intermediate in its culture and NapB provides a fitness gain for S. oneidensis to compete for nitrate in the environments. On the basis results from mutational analyses of napA, napB, nrfA and napBnrfA in-frame deletion mutants, we propose that NapB is able to favor nitrate reduction by routing electrons to NapA exclusively.
IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR
Authors: Folch Géraldine , Jabado-Michaloud Joumana , Bellahcene Fatena , Regnier Laetitia , Giudicelli Véronique , Lefranc Marie-Paule 
Published: April 2009

AbstractThe cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the IMGT^®^ nucleotide database IMGT/LIGM-DB^1^ and 75% of them are from human and mouse. A few cDNA are germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have been studied extensively in IMGT^®^ ("http://www.imgt.org":http://www.imgt.org) ^2^, which allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts^3^ are the key elements indispensable to perform the annotation of IG and TR cDNA sequences. A Java program, IMGT/Automat^4^, was developed by IMGT^®^, to automatically annotate the IG and TR cDNA sequences and to produce a totally automatic and complete annotation. More than 9,000 human and mouse cDNA have already been successfully automatically annotated. The quality of the cDNA automatic annotation is equivalent to the quality of the annotation achieved by a human expert. The IMGT^®^ strategy is currently the only way, in the field of immunogenetics, to guarantee the annotation quality and the management of an always increasing number of IG and TR cDNA nucleotide sequences.
The development of skill and tactical competencies during a season of badminton
Authors: Hastie Peter A. , Sinelnikov Oleg A. , Guarino A. J. 
Published: April 2009

AbstractIn this study, we examined the development of skill competence and tactical knowledge of 41 eighth‐grade students (mean age 13.6 years) as they completed a season of badminton conducted following the features of Sport Education. Using data from students’ performance on badminton skills tests, their competence in game play, and their tactical knowledge, it was determined that these students made significant improvements in their ability to not only control the shuttle, but also to hit it more aggressively. This resulted in improvements in both the selection (what shot to make) and execution (ability to produce the desired shot) dimensions of their game play. In addition, the students demonstrated significant improvements in their ability to select tactical solutions and make arguments for those decisions when watching videotaped performances of badminton games. The key explanation for the development of competence in this setting was that the structure of the Sport Education season allowed for significant practice opportunities, and that the authenticity and consequential nature of the game play helped move all but weak novice students from a more cooperative version of net‐game play to one where tactical decision making and execution was valued.
A motivational model of performance in the sport domain
Authors: Gillet Nicolas , Berjot Sophie , Gobancé Lucie 
Published: April 2009

AbstractThe aim of the present study was to propose and test a motivational model of sport performance based on the hierarchical model of intrinsic and extrinsic motivation (Vallerand, 1997). Tennis players completed the French version of the Sport Motivation Scale (Brière et al., 1995) at the beginning of the season. Two years later, they completed the same instrument and also a questionnaire designed to assess their perceptions of competence, autonomy, and relatedness. Their performances during three seasons were obtained via the French Tennis Federation. First, the present results reveal that self‐determined motivation has a positive impact on sport performance both during one and two seasons. The results also provide support for the mediating role of psychological need satisfaction in the relationship between sport performance and athletes’ motivation. Results are discussed in light of self‐determination theory (Deci & Ryan, 1985).
The influence of instructions and body‐scaling as constraints on decision‐making processes in team sports
Authors: Cordovil Rita , Araújo Duarte , Davids Keith , Gouveia Luís , Barreiros João , Fernandes Orlando , Serpa Sidónio 
Published: April 2009

AbstractTeam games conceptualized as dynamical systems engender a view of emergent decision‐making behaviour under constraints, although specific effects of instructional and body‐scaling constraints have yet to be verified empirically. For this purpose, we studied the effects of task and individual constraints on decision‐making processes in basketball. Eleven experienced female players performed 350 trials in 1 vs. 1 sub‐phases of basketball in which an attacker tried to perturb the stable state of a dyad formed with a defender (i.e. break the symmetry). In Experiment 1, specific instructions (neutral, risk taking or conservative) were manipulated to observe effects on emergent behaviour of the dyadic system. When attacking players were given conservative instructions, time to cross court mid‐line and variability of the attacker's trajectory were significantly greater. In Experiment 2, body‐scaling of participants was manipulated by creating dyads with different height relations. When attackers were considerably taller than defenders, there were fewer occurrences of symmetry‐breaking. When attackers were considerably shorter than defenders, time to cross court mid‐line was significantly shorter than when dyads were composed of athletes of similar height or when attackers were considerably taller than defenders. The data exemplify how interacting task and individual constraints can influence emergent decision‐making processes in team ball games.
MeSH Up: effective MeSH text classification for improved document retrieval
Authors: Trieschnigg Dolf , Pezik Piotr , Lee Vivian , de Jong Franciska , Kraaij Wessel , Rebholz-Schuhmann Dietrich 
Published: April 2009

AbstractMotivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by reducing the ambiguity inherent to free-text data. Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation, but they are either limited to a small subset of MeSH or have only been compared with a limited number of other systems.Results: We compare the performance of six MeSH classification systems [MetaMap, EAGL, a language and a vector space model-based approach, a K-Nearest Neighbor (KNN) approach and MTI] in terms of reproducing and complementing manual MeSH annotations. A KNN system clearly outperforms the other published approaches and scales well with large amounts of text using the full MeSH thesaurus. Our measurements demonstrate to what extent manual MeSH annotations can be reproduced and how they can be complemented by automatic annotations. We also show that a statistically significant improvement can be obtained in information retrieval (IR) when the text of a user's query is automatically annotated with MeSH concepts, compared to using the original textual query alone.Conclusions: The annotation of biomedical texts using controlled vocabularies such as MeSH can be automated to improve text-only IR. Furthermore, the automatic MeSH annotation system we propose is highly scalable and it generates improvements in IR comparable with those observed for manual annotations.Contact: trieschn@ewi.utwente.nlSupplementary information: Supplementary data are available at Bioinformatics online.
Application and evaluation of automated semantic annotation of gene expression experiments
Authors: French Leon , Lane Suzanne , Law Tamryn , Xu Lydia , Pavlidis Paul 
Published: April 2009

Abstract
Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets.
Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma.
Availability: The source code, documentation and Supplementary Materials are available at http://www.chibi.ubc.ca/GEOMMTX. The results of the manual evaluations are provided as Supplementary Material. Both manual and predicted annotations can be viewed and searched via the Gemma website at http://www.chibi.ubc.ca/Gemma. The complete set of predicted annotations is available as a machine readable resource description framework graph.
Contact: paul@chibi.ubc.ca
A stochastic model for the evolution of metabolic networks with neighbor dependence
Authors: Mithani Aziz , Preston Gail M. , Hein Jotun 
Published: April 2009

Abstract
Motivation: Most current research in network evolution focuses on networks that follow a Duplication Attachment model where the network is only allowed to grow. The evolution of metabolic networks, however, is characterized by gain as well as loss of reactions. It would be desirable to have a biologically relevant model of network evolution that could be used to calculate the likelihood of homologous metabolic networks.
Results: We describe metabolic network evolution as a discrete space continuous time Markov process and introduce a neighbor-dependent model for the evolution of metabolic networks where the rates with which reactions are added or removed depend on the fraction of neighboring reactions present in the network. We also present a Gibbs sampler for estimating the parameters of evolution without exploring the whole search space by iteratively sampling from the conditional distributions of the paths and parameters. A Metropolis–Hastings algorithm for sampling paths between two networks and calculating the likelihood of evolution is also presented. The sampler is used to estimate the parameters of evolution of metabolic networks in the genus Pseudomonas.
Availability: An implementation of the Gibbs sampler in Java is available at http://www.stats.ox.ac.uk/∼mithani/networkGibbs/
Contact: mithani@stats.ox.ac.uk
Supplementary information: Supplementary data are available at the Bioinformatics online.
Domain Interaction Footprint: a multi-classification approach to predict domain–peptide interactions
Authors: Schillinger Christian , Boisguerin Prisca , Krause Gerd 
Published: April 2009

Abstract
Motivation: The flow of information within cellular pathways largely relies on specific protein–protein interactions. Discovering such interactions that are mostly mediated by peptide recognition modules (PRM) is therefore a fundamental step towards unravelling the complexity of varying pathways. Since peptides can be recognized by more than one PRM and high-throughput experiments are both time consuming and expensive, it would be preferable to narrow down all potential peptide ligands for one specific PRM by a computational method. We at first present Domain Interaction Footprint (DIF) a new approach to predict binding peptides to PRMs merely based on the sequence of the peptides. Second, we show that our method is able to create a multi-classification model that assesses the binding specificity of a given peptide to all examined PRMs at once.
Results: We first applied our approach to a previously investigated dataset of different SH3 domains and predicted their appropriate peptide ligands with an exceptionally high accuracy. This result outperforms all recent methods trained on the same dataset. Furthermore, we used our technique to build two multi-classification models (SH3 and PDZ domains) to predict the interaction preference between a peptide and every single domain in the corresponding domain family at once. Predicting the domain specificity most reliably, our proposed approach can be seen as a first step towards a complete multi-domain classification model comprised of all domains of one family. Such a comprehensive domain specificity model would benefit the quest for highly specific peptide ligands interacting solely with the domain of choice.
Contact: gkrause@fmp-berlin.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Decadal changes in surface carbon dioxide and related variables in the Mediterranean Sea as inferred from a coupled data-diagnostic model approach
Authors: Louanchi Ferial , Boudjakdji Meriem , Nacef Lamri 
Published: April 2009

Abstract
Louanchi, F., Boudjakdji, M, and Nacef, L. 2009. Decadal changes in surface carbon dioxide and related variables in the Mediterranean Sea as inferred from a coupled data-diagnostic model approach. – ICES Journal of Marine Science, 66: 1538–1546. A coupled approach based on available datasets of temperature, salinity, oxygen, nutrients, and chlorophyll, and a surface layer box model previously developed and modified for the present study, allowed us to reconstruct dissolved inorganic carbon (DIC), total alkalinity, and carbon dioxide fugacity (fCO2) mixed-layer fields for the Mediterranean Sea, from the 1960s to the 1990s. The approach used in this study resulted in a 7% relative error on reconstructed surface fCO2 fields. The Mediterranean Sea transformed from a source of 0.62 Tg C year−1 for atmospheric CO2 in the 1960s, to a net sink of −1.98 Tg C year−1 in the 1990s. The annual cycle in surface fCO2 was driven mainly by temperature variations in the Mediterranean Sea, whereas its decadal variations resulted from a balance between primary production and the thermal effect. According to our model results, the atmospheric CO2 increase of ∼40 µatm over the period of our investigation induced an increase in DIC of ∼30 µmol l−1 in surface waters. A 50% reduction in the magnitude of seasonal variations in surface temperature occurred during the 1990s relative to the earlier decades. Therefore, surface fCO2 only increased by 24 µatm from the 1960s to the 1990s. Changes in pH were not significant over this period.