bluuebunny/crossref_metadata_2025_split huggingface dataset:
Curation and annotation for BioModels Database, a resource of published quantitative kinetic models
Authors: Vijayalakshmi Chelliah , Endler Lukas , Laibe Camille , Li Chen , Le Novère Nicolas 
Published: April 2009

AbstractBioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations. Furthermore reproduction of results in the reference publication is checked.The different elements of the models are extensively annotated with references to controlled vocabularies and links to other databases, to allow for identification and search. Those references and links are provided in the exported SBML files as a URN (Uniform Resource Name), identifying the data-type and the data-set, and a qualifier, indicating the relation between the element and the referenced data-set. The URNs follow the MIRIAM scheme and are resolved, for instance to URLs, using the Web Services of MIRIAM Resources ("http://www.ebi.ac.uk/miriam/":http://www.ebi.ac.uk/miriam/).
Terminizer - Assisting Mark-Up of Text Using Ontological Terms
Authors: Hancock David , Morrison Norman , Velarde Giles , Field Dawn 
Published: April 2009

AbstractWe present a tool that automatically detects ontological terms in free text. Once candidate terms have been identified the results are displayed either overlaid on the original text or in a list organised by the ontology and frequency. The user can interactively accept or reject each match, or try to find a more appropriate match by exploring the network of ontology concepts themselves. In typical ontological resources, the parent(s) of a term represent broader concepts whilst the children of a term represent more specific concepts. In this way, the suggested match can used as a starting point for the user to find a more suitable term. The ontology browser interface incorporates a graphical visualisation which uses Flash to present an interactive view of the ontology.The "Terminizer services":http://terminizer.org/ offers the full set of ontologies are obtained from the OBO Foundry, a collection of over 40 biological ontologies in a common format. Any ontology available in the standard OBO format can easily be added to the database. In addition to the interactive mode, the software is also available as a Web service. Both the term detection service and the interactive presentation layer can be incorporated within other Web sites or programs.
The SOL Genomics Network Model: Making Community Annotation Work
Authors: Menda Naama , Tecle Isaak , Pujar Anuradha , Bombarely Aureliano , York Tom , Mills Adri , Gosselin Joseph , Buels Robert , Mueller Lukas 
Published: April 2009

AbstractThe concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.The Solanaceae Genomics Network ("SGN":http://sgn.cornell.edu/) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database ("SolCyc":http://solcyc.sgn.cornell.edu). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.This framework is easily adaptable for other projects working on other taxa (for example see "http://chlamybase.org":http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at "sgn‐feedback[at]sgn.cornell.edu":mailto:sgn-feedback@sgn.cornell.edu for more information.
Text Mining in Full Text Articles -- Methodical and Represenation Issues
Authors: Klinger Roman , Pesch Robert , Mevissen Theo , Fluck Juliane 
Published: April 2009

AbstractIn many cases, information from abstracts of biomedical publications is not sufficient for annotation of database entries. Therefore, text mining systems supporting curators of biodatabases should be able to process full text articles. Beside the technical problems arising from full text parsing, the representation of the annotated full text is an important issue. Journal articles are mostly electronically available in PDF or HTML format. Also with more easily manageable XML formats, readers would like to have a visualisation of annotations and semantic enrichment directly in the PDF or HTML. We summarize the technical problems arising from parsing of HTML and PDF journal full texts and show first results of visualisation in both formats.
Increasing Access To Bioinformatics Resources: Increase Community Curation by Increasing Your Community
Authors: Williams Jennifer 
Published: April 2009

AbstractThe amount of biological data has risen exponentially over the last decade. Along with this rise, the number and types of bioinformatics resources has risen such that the sheer number of bioinformatics resources is overwhelming. For these resources to attain their full potential, they must be efficiently and extensively utilized. But in such a plethora of resources, how does a researcher new to a field find the resources that will meet their needs. Once a resource is found, how does the researcher quickly learn to utilize that resource fully? There are resource lists such as those provided by the journal Nucleic Acid Research (NAR), BioMed Central and the Univ. of Pittsburgh Health Sciences Library, and most resources include their own documentation. But lists and site documentation don’t always cast a wide enough net to catch all users. For a resource to truly maximize their user community, it often takes multiple different outreach approaches. OpenHelix specializes in providing customized outreach services to bioinformatics resources, including those featured on this poster. Based on the conclusions from our Phase I SBIR grant, which tested the efficiency of several methods for training researchers on the use of genomic resources, OpenHelix ("www.openhelix.com":http://www.openhelix.com) has developed, and currently provides up-to-date online training materials on a large number of bioinformatics resources, covering major providers and research areas. Through a Phase II SBIR grant from NHGRI and other funding, we are developing a search portal for online bioinformatics resources. With the search portal, researchers will be able to find the bioinformatics and genomics online databases and resources most relevant to their needs. The search portal will contain an index of hundreds of the most popular and powerful resources, as well as the content of over 100 OpenHelix tutorials. Using various ranking techniques, the portal will be able to provide more relevant results than a simple keyword search. Additionally, as part of an extension of our Phase II grant, we are providing a sponsored suite of Model Organism Database trainings that include GBrowse, FlyBase, MGI, RGD, SGD, WormBase and ZFIN. We are also developing, and will be offering, sponsored live trainings on resources at NCBI as a way of filling the void left by the demise of the NCBI Field Guide outreach programs. Conclusion: OpenHelix aims to increase community curation by helping resources increase their user community
Self‐modelling as a relapse intervention following speech‐restructuring treatment for stuttering
Authors: Cream Angela , O'Brian Sue , Onslow Mark , Packman Ann , Menzies Ross 
Published: April 2009

Background: Speech restructuring is an efficacious method for the alleviation of stuttered speech. However, post‐treatment relapse is common.Aims: To investigate whether the use of video self‐modelling using restructured stutter‐free speech reduces stuttering in adults who had learnt a speech‐restructuring technique and subsequently relapsed.Methods & Procedures: Participants were twelve adults who had previously had speech‐restructuring treatment for stuttering and relapsed. They were video recorded for 1 hour within the clinic, practising their speech‐restructuring technique. The videos were then edited to remove all observable stuttering. Participants then viewed the resulting video of themselves using restructured stutter‐free speech each day for 1 month and were instructed to speak as they did on the video. Beyond‐clinic speech samples and self‐report severity data were collected before and after the intervention.Outcomes & Results: Very large effect sizes were found. The mean per cent syllables stuttered was 7.7 pre‐intervention and 2.3 post‐intervention. For all but one participant there was a reduction in stuttering from pre‐intervention to post‐intervention. These results were verified with self‐report data. Speech naturalness was not compromised by the video self‐modelling procedure.Conclusion & Implications: Video self‐modelling as a relapse management tool does not involve excessive time expenditure by the clinician or the client. The study indicates video self‐modelling is potentially useful for managing relapse after speech‐restructuring treatment for stuttering, and in some cases may be a stand‐alone procedure to manage relapse. Phase II and III trials are warranted to determine the size and duration of the effect. It is suggested video self‐modelling could also be included in a relapse management plan.
Cognitive predictors of language development in children with specific language impairment (SLI)
Authors: van Daal John , Verhoeven Ludo , van Balkom Hans 
Published: April 2009

Background: Language development is generally viewed as a multifactorial process. There are increasing indications that this similarly holds for the problematic language development process.Aims: A population of 97 young Dutch children with specific language impairment (SLI) was followed over a 2‐year period to provide additional evidence for the existence of underlying language factors. Furthermore, the children's language development was related to their non‐verbal intellectual reasoning capacity.Methods & Procedures: The language abilities were assessed via the administration of an extensive battery of language tests. Cognition was assessed via administration of the Raven progressive matrices, short‐term memory capacity via administration of the Digit Span task.Outcomes & Results: The results provide empirical support for distinct language factors for children with language problems. The detected factors were labelled: phonology, lexical–semantics, syntax, and speech production, and were found to be stable and interrelated. Short‐term memory showed strong relations with the language factor syntax and medium relations with the other language factors. Intellectual capacity showed weak to medium relations with three language factors but no relation with the factor speech.Conclusions & implications: The language development of 5‐ and 6‐year‐old Dutch children with SLI appears to be divided into four language factors. The language factors are very stable in this sample and correspond with language factors found in recent studies on language development in children with SLI. Short‐term auditory memory turns out to play an important role in the problematic language acquisition of children with SLI. It is recommended that children with SLI should be assessed on possible deficits in information processing and/or short‐term memory. The existence of such deficits calls for specific neuropsychological intervention.
Systematic analysis of synchronized oscillatory neuronal networks reveals an enrichment for coupled direct and indirect feedback motifs
Authors: Dong Chao-Yi , Lim Jisoon , Nam Yoonkey , Cho Kwang-Hyun 
Published: April 2009

Abstract
Motivation: Synchronized bursting behavior is a remarkable phenomenon in neural dynamics. So, identification of the underlying functional structure is crucial to understand its regulatory mechanism at a system level. On the other hand, we noted that feedback loops (FBLs) are commonly used basic building blocks in engineering circuit design, especially for synchronization, and they have also been considered as important regulatory network motifs in systems biology. From these motivations, we have investigated the relationship between synchronized bursting behavior and feedback motifs in neural networks.
Results: Through extensive simulations of synthetic spike oscillation models, we found that a particular structure of FBLs, coupled direct and indirect positive feedback loops (PFLs), can induce robust synchronized bursting behaviors. To further investigate this, we have developed a novel FBL identification method based on sampled time-series data and applied it to synchronized spiking records measured from cultured neural networks of rat by using multi-electrode array. As a result, we have identified coupled direct and indirect PFLs.
Conclusion: We therefore conclude that coupled direct and indirect PFLs might be an important design principle that causes the synchronized bursting behavior in neuronal networks although an extrapolation of this result to in vivo brain dynamics still remains an unanswered question.
Contact: ckh@kaist.ac.kr; ynam@kaist.ac.kr
Supplementary Material: Supplementary data are available at Bioinformatics online.
Patterns of late gadolinium enhancement are associated with ventricular stiffness in patients with advanced non‐ischaemic dilated cardiomyopathy†
Authors: Choi Eui‐Young , Choi Byoung Wook , Kim Sung‐Ai , Rhee Sang Jae , Shim Chi Young , Kim Young Jin , Kang Seok‐Min , Ha Jong‐Won , Chung Namsik 
Published: April 2009

AimsDespite the prognostic importance of ventricular filling and ventricular–arterial interaction in patients with advanced systolic heart failure, the structural determinants of these parameters have not been fully studied. We aimed to investigate whether patterns of late gadolinium enhancement (LGE) on cardiac magnetic resonance affect ventricular elastic properties or performance in patients with non‐ischaemic dilated cardiomyopathy (DCM).Methods and resultsPatients (n = 49) with markedly reduced systolic function (left ventricular (LV) ejection fraction <35%) due to longstanding non‐ischaemic DCM underwent contrast‐enhanced cardiac magnetic resonance after comprehensive echo‐Doppler evaluations. The single beat‐derived end‐diastolic elastance, end‐systolic elastance, arterial elastance, and dyssynchrony indices were measured by echo. On the basis of LGE patterns, patients could be divided into three groups: non‐LGE (n = 18), non‐midwall LGE (n = 13), and midwall LGE (n = 18). The midwall LGE group had lower LV systolic longitudinal velocity (4.6 ± 1.7 for non‐LGE vs. 4.3 ± 1.2 for non‐midwall LGE vs. 3.5 ± 1.0 cm/s for midwall LGE, P = 0.025), higher end‐diastolic elastance index (0.41 ± 0.21 vs. 0.46 ± 0.31 vs. 0.85 ± 0.51 respectively, P = 0.008), and a more impaired ventriculoarterial coupling index (3.14 ± 1.53 vs. 2.88 ± 1.94 vs. 5.52 ± 3.18, P = 0.006) than other subgroups.ConclusionPatients with midwall LGE had a higher ventricular stiffness index and more impaired ventriculoarterial coupling when compared with other non‐ischaemic DCM patients.
Turnover in flightless invertebrate species composition over different spatial scales in Afrotemperate forest in the Drakensberg, South Africa
Authors: Uys Charmaine , Hamer Michelle , Slotow Rob 
Published: April 2009

AbstractAn understanding of species turnover at different spatial scales and the influence of environmental variables including distance are important for conservation planning and management. Ground dwelling, flightless invertebrates have poor dispersal abilities and other taxa may not be effective as surrogates. This is an important consideration for biodiversity conservation in Afrotemperate forests of the Drakensberg Mountains, South Africa, where flightless invertebrates are geographically isolated by the naturally fragmented state of forests. Seventeen Afrotemperate forests in four reserves across the Drakensberg were sampled using soil and leaf litter sampling, pitfall traps, active search quadrats and tree beats. Seventy‐two species were recorded, comprising 31 mollusc, nine earthworm, one onychophoran, six centipede, twelve millipede and thirteen ant species. Canonical correspondence analysis indicated that latitude (distance); fire history (disturbance) and mean annual precipitation were the most important factors governing invertebrate assemblage composition. βsim measurements detected change in species at all spatial scales investigated, but no clear trends were evident. Distance or spatial scale alone does not explain species turnover and community composition. Effective selection of target areas, therefore, requires species level information to identify species of special concern.
In vitro three‐dimensional modelling of human ovarian surface epithelial cells
Authors: Lawrenson K. , Benjamin E. , Turmaine M. , Jacobs I. , Gayther S. , Dafou D. 
Published: April 2009

AbstractObjectives:  Ninety percent of malignant ovarian cancers are epithelial and thought to arise from the ovarian surface epithelium (OSE). We hypothesized that biological characteristics of primary OSE cells would more closely resemble OSE in vivo if established as three‐dimensional (3D) cultures.Materials and methods:  OSE cells were cultured as multicellular spheroids (MCS) (i) in a rotary cell culture system (RCCS) and (ii) on polyHEMA‐coated plastics. The MCSs were examined by electron microscopy and compared to OSE from primary tissues and cells grown in 2D. Annexin V FACS analysis was used to evaluate apoptosis and expression of extracellular matrix (ECM) proteins was analysed by immunohistochemical staining.Results:  On polyHEMA‐coated plates, OSE spheroids had defined internal architecture. RCCS MCSs had disorganized structure and higher proportion of apoptotic cells than polyHEMA MCSs and the same cells grown in 2D culture. In 2D, widespread expression of AE1/AE3, laminin and vimentin were undetectable by immunohistochemistry, whereas strong expression of these proteins was observed in the same cells grown in 3D culture and in OSE on primary tissues.Conclusions:  Physiological and biological features of OSE cells grown in 3D culture more closely resemble characteristics of OSE cells in vivo than when grown by classical 2D approaches. It is likely that establishing in vitro 3D OSE models will lead to greater understanding of the mechanisms of neoplastic transformation in epithelial ovarian cancers.
Arsenic trioxide suppresses paclitaxel‐induced mitotic arrest
Authors: Duan Q. , Komissarova E. , Dai W. 
Published: April 2009

AbstractObjectives:  To understand if there exists a functional interaction between arsenic trioxide and paclitaxel in vitro.Materials and methods:  HeLa and HCT116 (ρ53+/+ and ρ53−/−) cells were treated with As2O3 and/or paclitaxel for various times. Treated cells were collected for analyses using a combination of flow cytometry, fluorescence microscopy and Western blotting.Results:  Because As2O3 is capable of inhibiting tubulin polymerization and inducing mitotic arrest, we examined whether there existed any functional interaction between As2O3 and paclitaxel, a well‐known microtubule poison. Flow cytometry and fluorescence microscopy revealed that although As2O3 alone caused a moderate level of mitotic arrest, it greatly attenuated paclitaxel‐induced mitotic arrest in cells with p53 deficiency. Western blot analysis showed that As2O3 significantly blocked phosphorylation of BubR1, Cdc20, and Cdc27 in cells treated with paclitaxel, suggesting that arsenic compromised the activation of the spindle checkpoint. Our further studies revealed that the attenuation of paclitaxel‐induced mitotic arrest by As2O3 resulted primarily from sluggish cell cycle progression at S phase but not enhanced mitotic exit.Conclusion:  The observations that As2O3 has a negative impact on the cell cycle checkpoint activation by taxol should have significant clinical implications because the efficacy of taxol in the clinics is associated with its ability to induce mitotic arrest and subsequent mitotic catastrophe.
Thalidomide has a therapeutic effect on interstitial lung fibrosis: evidence from in vitro and in vivo studies
Authors: Zhao L , Xiao K , Wang H , Wang Z , Sun L , Zhang F , Zhang X , Tang F , He W 
Published: April 2009

Summary
The objective of this study was to investigate the effects of thalidomide (THD) on interstitial lung fibrosis (ILF). In vitro, human fetal lung fibroblast (HFL-F) to myofibroblast (MF) trans-differentiation was induced by transforming growth factor (TGF)-β1. The effects of THD on trans-differentiation process or differentiated MF were evaluated by measuring hydroxyproline (HYP) content by alkaline hydrolysis colorimetry, α-smooth muscle actin (α-SMA) protein by Western blot and α-SMA and pro-collagen III mRNA expressions by semi-quantitative reverse transcription–polymerase chain reaction; in vivo, a mouse model of ILF was generated by daily subcutaneous injection of bleomycin (BLM) in female C3H mice. Gastric perfusion of THD began 1 week prior to injection and lasted for 8 weeks. Lung specimens were harvested at different time-points (1, 4, 6 and 8 weeks) for pathology and immunohistochemistry examination. The HYP content, α-SMA and pro-collagen III mRNA expressions were also assessed. THD inhibited the up-regulation of HYP protein, pro-collagen III mRNA and α-SMA protein induced by TGF-β1 in HFL-F cells, and additionally inhibited pro-collagen III mRNA expression on trans-differentiated MF. THD reduced HYP synthesis in the lung tissues of BLM-treated mice at week 4, and slightly reduced the numbers of α-SMA-positive cells. THD had an effect on ILF models both in vitro and in vivo.