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Biomedical subjects

Chris Taylor

Publications and source records attributed to Chris Taylor.

At least 19 recordsLinked to original sources
PubMed2006

An acoustical bubble counter for superheated drop detectors.

A new bubble counter has been developed based on the well-established approach of detecting vaporization events acoustically in superheated drop detectors (SDDs). This counter is called the Framework Scientific ABC 1260, and it represents a major improvement over prior versions of this technology. By utilizing advanced acoustic pattern recognition software, the bubble formation event can be differentiated from ambient background noise, as well as from other acoustic signatures. Additional structural design enhancements include a relocation of the electronic components to the bottom of the device; thus allowing for greater stability, easier access to vial SDDs without exposure to system electronics. Upgrades in the electronics permit an increase in the speed of bubble detection by almost 50%, compared with earlier versions of the counters. By positioning the vial on top of the device, temperature and sound insulation can be accommodated for extreme environments. Lead shells can also be utilized for an enhanced response to high-energy neutrons.

Acoustics↗
PubMed2006

The use of concept maps during knowledge elicitation in ontology development processes--the nutrigenomics use case.

BACKGROUND: Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies. RESULTS: Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer. CONCLUSION: The contributions of this paper are the thorough description of the steps we suggest when building an ontology, example use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process.

Algorithms↗
PubMed2006

The MGED Ontology: a resource for semantics-based description of microarray experiments.

MOTIVATION: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT: Stoeckrt@pcbi.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computational Biology↗
PubMed2006

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4-6, 2005.

The autumn workshop of the Proteomics Standards Initiative of the Human Proteomics Organisation met to further advance the development of the existing standards in the fields of molecular interactions and mass spectrometry. In addition, new areas were addressed, in particular developing standards for the description and exchange of data from gel electrophoresis experiments. The General Proteomics Standards group is now working closely with the FuGE (Functional Genomics Experiment) efforts to define a general standard in which to encode data that will enable a systems biology approach to data analysis. Common to all these efforts is the field of protein modifications, and work has been initiated to establish an ontology in this field that can be used by both workers in the field of proteomics and the wider scientific community.

Databases, Protein↗
PubMed2006

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase.

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well-defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false-positive rate.

Algorithms↗
PubMed2006

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

The theme of the third annual Spring workshop of the HUPO-PSI was "proteomics and beyond" and its underlying goal was to reach beyond the boundaries of the proteomics community to interact with groups working on the similar issues of developing interchange standards and minimal reporting requirements. Significant developments in many of the HUPO-PSI XML interchange formats, minimal reporting requirements and accompanying controlled vocabularies were reported, with many of these now feeding into the broader efforts of the Functional Genomics Experiment (FuGE) data model and Functional Genomics Ontology (FuGO) ontologies.

Animals↗
PubMed2006

Establishing reporting standards for metabolomic and metabonomic studies: a call for participation.

Metabolite concentrations in cellular systems are very much dependent on the physiological, environmental, and genetic status of an organism and are regarded as the ultimate result of cellular regulation, resulting in the visible phenotypes. Therefore, the comprehensive analysis of metabolite levels and fluxes renders a suitable tool for assessing the degree of perturbation in biological systems. Lessons derived from development of other OMICS areas (genomics, proteomics, and transcriptomics) have shown that large-scale comparisons and interpretations will require the re-use of data over long periods of time and by multiple laboratories with different expertise and backgrounds. Reaching this goal will require standardization of reporting structures of metabolomic studies for journal publication purposes, for regulatory deposition, and for database dissemination. An initiative by the Metabolomics Society is presented that aims to define important aspects of metabolomic workflows. These include biological study designs, chemical analysis, and data processing, as well as the ontologies that are necessary in this framework.

Animals↗
PubMed2006

Development of FuGO: an ontology for functional genomics investigations.

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the "semantic glue" to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans.

Biomedical Research↗
PubMed2006

Herpes simplex virus type 2 (HSV-2) seroprevalence at the time of HIV-1 diagnosis and seroincidence after HIV-1 diagnosis in an ethnically diverse cohort of HIV-1-infected persons.

OBJECTIVE: The objective of this study was to determine herpes simplex virus type 2 (HSV-2) seroprevalence at HIV-1 diagnosis and seroincidence > or =1 year after HIV-1 diagnosis. METHODS: HSV type-specific antibodies were detected by enzyme immunoassay. RESULTS: The cohort comprised 850 adults diagnosed HIV-positive in 1986-2001 and followed for a median of 3 years. HSV-2 seroprevalence was 63% (95% confidence interval [CI], 60-66%) and was associated with female gender, heterosexual risk group, black ethnicity, and older age. HSV-2 seroincidence was 1.8 per 100 person-years (95% CI, 0.8-2.8) and was associated with other sexually transmitted diseases, including human papilloma virus infection (P = 0.005) and gonorrhea (P = 0.05). A diagnosis of genital herpes was made in 21% HSV-2-seropositive persons and was more likely in those who tested HIV-positive before 1997 (adjusted odds ratio, 5.11; 95% CI, 3.28-7.98; P = 0.0001). CONCLUSIONS: Results confirm the epidemiologic association between HIV-1 and HSV-2. HSV-2 seroconversion was a marker of high-risk sexual behavior. The likelihood of developing symptoms of genital herpes declined from 1997 onward.

Adolescent↗
PubMed2006

Colonic and duodenal flat adenomas in children with classical familial adenomatous polyposis.

Flat adenomas of the colon and duodenum have been described as associating with familial adenomatous polyposis (FAP), its attenuated variant, and the so-called hereditary nonpolyposis colorectal cancer. There seem to be no report on the occurrence of flat adenomas in pediatric patients with family history of FAP. We are reporting 4 children from 2 cancer-prone families in whom colonic and duodenal moderately dysplastic flat adenomas were found. Gastrointestinal endoscopy and biopsies were performed in 3 female siblings (7, 9, and 11 years old) and 1 male (9 years old) when referred for screening owing to familial history of bowel cancer (family 1) or evidence of bilateral congenital hypertrophy of the retinal pigment epithelium (CHRPE), which is known to be associated with FAP (family 2). Endoscopic visualization of the mucosa was improved by use of 0.2% indigo carmine solution spray. Biopsies were routinely processed for H&E and immunohistochemistry staining. Present patients were asymptomatic, with the exception of 2 weeks rectal bleeding in 1 of them. The colonic videoendoscopy showed in 2/3 siblings hundreds of flat or slightly raised plaques less than 1 cm in diameter as well as some classic polyps throughout the colon. The other sibling showed 40 flat-topped lesions with minimal elevation and central umbilication in the cecum. Upper endoscopy demonstrated a few flat lesions in the nonperiampullary area of the duodenum in 2/4 patients. The colonic videoendoscopy performed on the 9-year-old boy revealed multiple small sessile polyps. Microscopic study demonstrated tubular adenomas with a few neoplastic crypts, slight disarray of the overall architecture, and moderate (low-grade) dysplasia of the epithelium. These features were more obvious at the center and superficial areas of the adenomas. The 4 children had multiple flat adenomas of the colon and duodenum (2/4) matching with those described in adult patients. Flat adenomas in the context of FAP probably represent early stages of the adenoma development. Careful endoscopic-histologic correlation may result in increasing recognition of these lesions at the pediatric age.

Adenoma↗
PubMed2005

Snapping knee: an unusual biceps femoris tendon injury.

We report a case of acute post-traumatic snapping of the biceps femoris tendon following a soccer injury. Surgical stabilisation, achieved by re-routing the tendon insertion through a tunnel in the fibular head, resolved the symptoms after conservative management failed. We believe this is the first report of a 'snapping knee' resulting from direct injury to the biceps femoris tendon insertion.

Adult↗
PubMed2005

PRIDE: the proteomics identifications database.

The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation.

Computational Biology↗
PubMed2005

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project.

The pilot phase of the HUPO Plasma Proteome Project (PPP) is an international collaboration to catalog the protein composition of human blood plasma and serum by analyzing standardized aliquots of reference serum and plasma specimens using a variety of experimental techniques. Data management for this project included collection, integration, analysis, and dissemination of findings from participating organizations world-wide. Accomplishing this task required a communication and coordination infrastructure specific enough to support meaningful integration of results from all participants, but flexible enough to react to changing requirements and new insights gained during the course of the project and to allow participants with varying informatics capabilities to contribute. Challenges included integrating heterogeneous data, reducing redundant information to minimal identification sets, and data annotation. Our data integration workflow assembles a minimal and representative set of protein identifications, which account for the contributed data. It accommodates incomplete concordance of results from different laboratories, ambiguity and redundancy in contributed identifications, and redundancy in the protein sequence databases. Recommendations of the PPP for future large-scale proteomics endeavors are described.

Algorithms↗
PubMed2005

5th HUPO BPP Bioinformatics Meeting at the European Bioinformatics Institute in Hinxton, UK--Setting the analysis frame.

The Bioinformatics Committee of the HUPO Brain Proteome Project (HUPO BPP) meets regularly to execute the post-lab analyses of the data produced in the HUPO BPP pilot studies. On July 7, 2005 the members came together for the 5th time at the European Bioinformatics Institute (EBI) in Hinxton, UK, hosted by Rolf Apweiler. As a main result, the parameter set of the semi-automated data re-analysis of MS/MS spectra has been elaborated and the subsequent work steps have been defined.

Computational Biology↗