bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activities of key enzymes involved in starch synthesis in grains of wheat under different irrigation patterns
Authors: DAI Z. , YIN Y. , WANG Z. 
Published: April 2009

SUMMARYIt is generally accepted that sucrose phosphate synthase (SPS), sucrose synthase (SuSy), ADP-glucose pyrophosphorylase (AGPase), soluble starch synthase (SSS), granule-bound starch synthase (GBSS) and starch branching enzyme (SBE) play a key role in starch synthesis in wheat grains. Starch synthesis in wheat grains is influenced by genotype and environment. However, what is not known is the degree of variation in enzyme activities during starch accumulation of wheat cultivars field-grown in different water regimes. The present study was undertaken to determine whether irrigation patterns could cause differences in starch accumulation and activities of key enzymes involved in starch synthesis. Starch accumulation and related enzyme activities were investigated in two winter wheat varieties, JM20 and BY535, differing in grain starch content, under two irrigation patterns. Results showed that soil water deficit led to an increase at early grain filling and decrease during late grain filling in starch accumulation rate (SAR) and activities of key enzymes involved in starch synthesis, especially AGPase, SSS and SBE. Water deficit enhanced grain starch accumulation in two wheat cultivars, suggesting that rainfed treatments increase physiological activities during early grain filling and promote starch accumulation. Furthermore, the change of SAR is consistent with SuSy, AGPase, SSS and GBSS. The results suggest that these enzymes play a key role in starch synthesis, and the decrease of photosynthate produced in the source organ is not the factor inhibiting starch accumulation.
Genetic parameters of selection and stability and identification of divergent parents for hybridization in rice bean (Vigna umbellata Thunb. (Ohwi and Ohashi)) in India
Authors: GUPTA S. , KOZAK M. , SAHAY G. , DURRAI A. A. , MITRA J. , VERMA M. R. , PATTANAYAK A. , THONGBAM P. D. , DAS A. 
Published: April 2009

SUMMARYFifty-two genotypes of rice bean (Vigna umbellata Thunb. (Ohwi and Ohashi)), an under-cultivated crop, were evaluated in the rainy (kharif) seasons of 2001, 2002 and 2003 in the North Eastern Hill Region, India to select suitable genotypes for cultivation in the North Eastern Hill region and to identify promising parents for hybridization programmes. The germplasm studied comprised 44 Indian and eight foreign genotypes. A wide range of variability was observed for eight characters studied (plant height, number of branches/plant, stem thickness, pod length, number of seeds/pod, 100-seed weight, pod weight/plant and seed yield/plant). Number of days to mid-flowering and number of days to maturity showed little variation. High heritability (0·58) and high genetic advance (0·53) were observed for 100-seed weight, high heritability (0·93) and moderate genetic advance (0·37) for seed yield/plant, and high heritability (0·60) and low genetic advance (0·13) for number of days to mid-flowering. Since the main aim in rice bean breeding is to develop high yielding, early maturing genotypes with low plants, selection was based mainly on the mean performance of these three traits over the 3 years, as well as their stability. One of the genotypes, RBL 1, was very high yielding, although the yield was not stable across years. Another genotype, RBS 24, was very early maturing and had very short plants compared with the other genotypes studied. These two, along with several other genotypes selected, may be promising for a hybridization programme aiming to develop dwarf, early maturing genotypes with high yield. The best yielding genotypes, namely RBL 1, RCRB1-3 and IC 187911, may be recommended for cultivation in the shifting cultivation areas (Jhum) regions of North Eastern India.
Not just old and sick – the ‘will to health’ in later life
Authors: HIGGS PAUL , LEONTOWITSCH MIRANDA , STEVENSON FIONA , JONES IAN REES 
Published: April 2009

ABSTRACTThe end of the ‘Golden Age’ of welfare capitalism in the 1970s was the prelude to a period of greater individualisation within societies and was accompanied by an increase in the importance of consumption as a way of organising social relations. During the same period there was also an expansion in the discourses aimed at enhancing the government of the autonomous self. One such discourse operates around what has been termed the ‘will to health’: it suggests that health has become a required goal for individual behaviour and has become synonymous with health itself. The generational groups whose lifecourses were most exposed to these changes are now approaching later life. We explore the extent to which social transformations related to risk, consumption and individualisation are reflected in the construction of later-life identities around health and ageing. We examine how the growth in health-related ‘technologies of the self’ have fostered a distinction between natural and normal ageing, wherein the former is associated with coming to terms with physical decline and the latter associated with maintaining norms of self-care aimed at delaying such decline. Finally, we consider anti-ageing medicine as a developing arena for the construction of later-life identities and discuss the implications of the social changes for researching later life.
A new measurement of stimulated Brillouin scattering phase conjugation fidelity for high pump energies
Authors: Wang Y.L. , Lu Z.W. , He W.M. , Zheng Z.X. , Zhao Y.H. 
Published: April 2009

AbstractIn order to measure the phase conjugation-fidelity of stimulated Brillouin scattering with high pump energy more accurately and conveniently, a new measurement is proposed. According to the definition of the fidelity with optical field correlated integral, the method of recording the far-field by array camera is analyzed theoretically. By the method, an experiment for high energy stimulated Brillouin scattering is arranged, and the maximum energy of 3.42 J is achieved in a single-cell stimulated Brillouin scattering generator. For small pump pulse, the fidelity maintains a high value of more than 0.9. However, the reflectivity fluctuation is significant when the pump energy is larger than 1.5 J. As a result, the fidelity decreases gradually to 0.5 at the pump energy of 3.42 J. The reflectivity shows the same character of great fluctuation as the fidelity at high pump energy.
X-ray Thomson scattering cross-section in strongly correlated plasmas
Authors: Fortmann C. , Bornath T. , Redmer R. , Reinholz H. , Röpke G. , Schwarz V. , Thiele R. 
Published: April 2009

AbstractWith the advent of intense, coherent light sources in the XUV and soft X-ray regime, X-ray Thomson scattering becomes a unique tool for the diagnostics of dense plasmas. The scattering spectrum gives direct access to plasma properties like density, temperature, and composition. In dense systems, collisions among constituents are of primary importance for the prediction and interpretation of the scattering signal. We present a systematic approach to the dynamical structure factor using the Born-Mermin ansatz to include collisions via the dynamical collision frequency. Calculations of the scattering spectrum are performed for X-ray scattering on solid and compressed beryllium targets as well as for XUV-photons scattering on hydrogen at near solid density.
Mono-energetic ions from collisionless expansion of spherical multi-species clusters
Authors: Popov K.I. , Bychenkov V.Yu. , Rozmus W. , Kovalev V.F. , Sydora R.D. 
Published: April 2009

AbstractKinetic collisionless expansion of a spherical cluster composed of light and heavy cold ions and hot electrons is studied for arbitrary electron temperature. A wide set of regimes of plasma expansion, from nearly quasi-neutral to Coulomb explosion, is described from a unified description. The time evolution of the velocity, density, and energy spectra for accelerated ions is studied. The study demonstrates that an optimum light ion concentration from few percent to few tens percent, depending on the electron temperature, leads to a quasi-monoenergetic spectra with numbers as high as 70–80% of the total number of light ions.
P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function
Authors: Livstone Michael , Oughtred Rose , Heinicke Sven , Kang Fan , Vernot Benjamin , Goldman Aiton , Durand Dannie , Botstein David , Dolinski Kara 
Published: April 2009

AbstractP-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms into families of homologs and provides curated evidence from the literature addressing these relationships. The web page for each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD, papers describing complementation experiments, and OMIM gene and disease information.As participants in the Gene Ontology Consortium’s Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins. We have expanded P-POD to include the protein complement of the twelve Reference Genomes. In addition, we have added new tools and search options to provide greater depth, breadth, and flexibility. Users may view families from multiple analyses generated by different methods and/or based on different sets of proteins. Using Notung, a software package that uses duplication-loss parsimony to resolve uncertainty in protein family trees, we have improved P-POD’s phylogenetic trees by fitting the protein trees to an established species phylogeny and annotating them with duplications and losses. A Notung applet on the P-POD web site identifies orthologous and paralogous relationships within each family and allows users to perform custom analyses on the phylogenies. These improvements and others make P-POD, in conjunction with the PANTHER database, an ideal tool for predicting the function of new, uncharacterized genes on the basis of their orthologous relationships to characterized ones.All the data in P-POD are freely and publicly available through the web and by downloading the entire database system via the URL "http://ortholog.princeton.edu/". This work is supported by supplemental funds (Kara Dolinski, subcontract PI) to NHGRI grant HG002273 (PIs Judith Blake, Michael Ashburner, J. Michael Cherry and Suzanna Lewis).
Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal Scanning
Authors: Browne Paul , Eberhardt Ruth 
Published: April 2009

AbstractMost sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool "SPIN":http://www.ebi.ac.uk/swissprot/Submissions/spin. Curators use a range of sequence analysis tools to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be kept confidential for a limited period at the submitter's request. UniProtKB submission is complemented by the journal scan project that monitors the scientific literature for papers containing directly sequenced proteins. UniProtKB entries are then created for those sequences that are not yet in the database and have not been submitted via SPIN.
Ontology-based Assisted Curation of Biomedical Data
Authors: Plake Conrad 
Published: April 2009

AbstractManual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering and summarizing long lists of genes. Through the integration of known gene annotations from UniProt and EntrezGene with text-mined annotations from all abstracts in PubMed, GoGene currently contains up to 4,000,000 associations between genes and concepts from GO and MeSH for ten model organisms. The quality of all associations can be verified by following the links to their origin, that is, literature or database entries.GoPubMed aims at reducing the limitations of classical keyword search. It handles inconsistent vocabulary such as synonyms and specialized terminology. It shows the most relevant concepts in GO and MeSH for a search and thus reveals information which otherwise remains buried in the masses of text. This feature as well as the entire bibliography of all authors in PubMed facilitate comprehensive literature search. GoWeb translates these ideas to the World Wide Web and is thus not only limited to PubMed abstracts. GoWeb uses a standard web-search service and organizes search results based on GO, MeSH, and other concepts such as companies and institutions.
PDBWiki
Authors: Stehr Henning , Duarte Jose , Lappe Michael , Bhak Jong , Bolser Dan 
Published: April 2009

Abstract
*Background:*
The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. However, there is currently no consensus about how best to achieve this goal.*Methodology/Principal Findings:* Here we present a community knowledge base for the annotation of biological molecular structures that addresses some of these issues. This Wiki-style database consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows users to attach categorised comments and discussions to the entries. The core data for each entry is shown as a summary and can be used for searching and navigation via categories. A user-editable list of database cross references is automatically included in each page. Like in a database, it is possible to produce tabular reports and 'structure galleries' based on user defined queries. PDBWiki runs in parallel to the PDB and is automatically synchronised every week.

*Conclusions/Significance:*
"PDBWiki":http://www.pdbwiki.org is a simple but usable system that serves as a bug-tracker, discussion forum and community annotation system for the structures in the PDB. We believe that PDBWiki can serve as a model for better understanding how to capture community knowledge in the biological sciences.
Evidence attribution in the UniProt Knowledgebase
Authors: Magrane Michele , Consortium UniProt 
Published: April 2009

AbstractUniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system and plans for its future development and enhancement will be presented.
Cardiovascular Gene Ontology Annotation Initiative
Authors: Khodiyar Varsha , Barrell Daniel , Scambler Peter , Hubank Mike , Apweiler Rolf , Talmud Philippa , Lovering Ruth 
Published: April 2009

AbstractGene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional annotation to proteins across a wide range of species ("www.geneontology.org":http://www.geneontology.org). The BHF-UCL team is funded by the British Heath Foundation to supply GO annotation specifically for human proteins involved in cardiovascular (CV) processes. This is the first time that a physiological process-centered approach has been used for human protein GO annotation. Experienced GO curators from the BHF-UCL team work alongside the bench scientists from the CV genetics group at University College London. By working in a CV dedicated environment the GO curators are able to build up their expertise in the CV field. Over 4000 proteins have been identified as being cardiovascular related and over the last 14 months, the BHF-UCL team has added 6840 Gene Ontology annotations to 603 human CV related proteins, including CDKN2A, CDKN2B, EDN2, GH1 and TERF1. In order to provide detailed annotations the BHF-UCL GO curators also initiate the development of new GO terms related to cardiovascular processes. The development of these terms, such as lipoprotein-mediated signalling, regulation of cardiac muscle hypertrophy and cardiac epithelial to mesenchymal transition, are made in collaboration with the GO editorial office and CV scientists. We will present details of the progress made in the first year of the BHF-UCL GO annotation project and the impact on microarray analysis.
Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Authors: Köhn Dagmar , Le Novère Nicolas , Knüpfer Christian 
Published: April 2009

AbstractComputational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of models.For this purpose we propose two ontologies: The Kinetic Simulation Algorithm Ontology (KiSAO) and the TErminology for the Description of DYnamics (TEDDY). KiSAO covers algorithms used for simulation of computational models. The ontology classifies and puts into context existing simulation algorithms. For the classification, it uses several criteria such as deterministic/stochastic or spatial/nonspatial. The aim of TEDDY is to provide terms for describing and characterising dynamical behaviours, observable dynamical phenomena, and control elements of biological models and biological systems in Systems Biology and Synthetic Biology.We demonstrate how these new ontologies can extend the formalisation of models beyond structure, using the well-known repressilator model as an example. The simulation results depend pragmatically on the used algorithm: We compare the simulation results of the deterministic Livermore solver for ordinary differential equations (KiSAO:0000071) to the simulation results of the stochastic Gibson and Bruck’s next reaction method (KiSAO:0000027). The simulation results depend dynamically on the parameter setting: While parameter * (maximum number of produced proteins per promotor) is increased the modelled dynamical system undergoes a Supercritical Hopf Bifurcation (TEDDY_0000074). Below the critical value of * the system exhibits _Damped Oscillation_ (TEDDY_0000063) converging to a Stable Spiral Point (TEDDY_0000126). Above the bifurcation the system possesses a Stable _Limit Cycle_ (TEDDY_0000114), i.e. it shows Sustained Oscillation. The Negative Feedback (TEDDY_0000034) of the system is a necessary precondition for the ability of the system to oscillate.For details on KiSAO see the "MIASE project page":http://sourceforge.net/projects/miase, for details on TEDDY see the "project page":http://sourceforge.net/projects/teddyontology.
Data submission and curation for caArray, a standard based microarray data repository system
Authors: Bian X , Klemm J , Basu A , Hadfield J , Srinivasa R , Parnell T , Miller S , Mason W , Kokotov D , Duncan M , Duvall P , Gurses L , Boal T , Misquitta L , Swan D , Wysong R , Klink A , Johnson A , Fontenay G , Liu J , Colbert M , Komatsoulis G 
Published: April 2009

AbstractcaArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG™), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG™. Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the MAGE-TAB, a spreadsheet-based format for annotating and communicating microarray data in a MIAME-compliant fashion ("http://www.mged.org/mage-tab":http://www.mged.org/mage-tab). MAGE-TAB is built on community standards – MAGE, MIAME, and Ontology. The components and work flow of MAGE-TAB files are organized in such a way which is already familiar to bench scientists and thus minimize the time and frustration of reorganizing their data before submission. The MAGE-TAB files are also structured to be machine readable so that they can be easily parsed into database. Users can control public access to experiment- and sample-level data and can create collaboration groups to support data exchange among a defined set of partners. All data submitted to caArray at NCI will go through strict curation by a group of scientists against these standards to make sure that the data are correctly annotated using proper controlled vocabulary terms and all required information are provided. Two of mostly used ontology sources are MGED ontology ("http://mged.sourceforge.net/ontologies/MGEDontology.php":http://mged.sourceforge.net/ontologies/MGEDontology.php) and NCI thesaurus ("http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do":http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). The purpose of data curation is to ensure easy comparison of results from different labs and unambiguous report of results. Data will also undergo automatic validation process before parsed into database, in which minimum information requirement and data consistency with the array designs are checked. Files with error found during validation are flagged with error message. Curators will re-examine those files and make necessary corrections before re-load the files. The iteration repeats until files are validated successfully. Data are then imported into the system and ready for access through the portal or through API. Interested parties are encouraged to review the installation package, documentation, and source code available from "http://caarray.nci.nih.gov":http://caarray.nci.nih.gov.