FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download.

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations

The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its significance in transplantation, disease association studies and diversity in populations led to the development of this electronic resource. At present, the system contains data from 1133 populations in 608 813 individuals on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms. The project was designed to create a central source for the storage of frequency data and provide individuals with a set of bioinformatics tools to analyze the occurrence of these variants in worldwide populations. The resource has been used in a wide variety of contexts, including clinical applications (histocompatibility, immunology, epidemiology and pharmacogenetics) and population genetics. Demographic information, frequency data and searching tools can be freely accessed through the website.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments

XGAP, a software platform for the integration and analysis of genotype and phenotype data.

We present an extensible software model for the genotype and phenotype community, XGAP. Readers can download a standard XGAP (http://www.xgap.org) or auto-generate a custom version using MOLGENIS with programming interfaces to R-software and web-services or user interfaces for biologists. XGAP has simple load formats for any type of genotype, epigenotype, transcript, protein, metabolite or other phenotype data. Current functionality includes tools ranging from eQTL analysis in mouse to genome-wide association studies in humans.

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.

Managing experimental data using FuGE

Data management and sharing in omics science is highly challenging due to the constant evolution of experimental techniques, the range of instrument types and software used for analysis, and the high volumes of data produced. The Functional Genomics Experiment (FuGE) Model was created to provide a model for capturing descriptions of sample processing, experimental protocols and multidimensional data for any kind of omics experiment. FuGE has two modes of action: (a) as a storage architecture for experimental workflows and (b) as a framework for building new technology-specific data standards.FuGE is an object model that is converted into an XML implementation for data exchange. Software toolkits have been developed for data handling and for bridging between XML data files and relational database implementations. FuGE has been adopted by the Proteomics Standards Initiative (PSI, http://www.psidev.info ) for building several new data formats, and it is being used in a variety of other experimental contexts, thus allowing data to be integrated across a range of experimental types to support Systems Biology approaches. This chapter provides a practical guide for laboratories or groups wishing to manage their data, and for developers wishing to create new data formats using FuGE.

Modeling and managing experimental data using FuGE

The Functional Genomics Experiment data model (FuGE) has been developed to increase the consistency and efficiency of experimental data modeling in the life sciences, and it has been adopted by a number of high-profile standardization organizations. FuGE can be used: (1) directly, whereby generic modeling constructs are used to represent concepts from specific experimental activities; or (2) as a framework within which method-specific models can be developed. FuGE is both rich and flexible, providing a considerable number of modeling constructs, which can be used in a range of different ways. However, such richness and flexibility also mean that modelers and application developers have choices to make when applying FuGE in a given context. This paper captures emerging best practice in the use of FuGE in the light of the experience of several groups by: (1) proposing guidelines for the use and extension of the FuGE data model; (2) presenting design patterns that reflect recurring requirements in experimental data modeling; and (3) describing a community software tool kit (STK) that supports application development using FuGE. We anticipate that these guidelines will encourage consistent usage of FuGE, and as such, will contribute to the development of convergent data standards in omics research.

FuGEFlow: data model and markup language for flow cytometry

Background

Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata.

Methods

We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description.

Results

The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project.

Conclusion

We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

LC-MS experiments can generate large quantities of data, for which a variety of database search engines are available to make peptide and protein identifications. Decoy databases are becoming widely used to place statistical confidence in result sets, allowing the false discovery rate (FDR) to be estimated. Different search engines produce different identification sets so employing more than one search engine could result in an increased number of peptides (and proteins) being identified, if an appropriate mechanism for combining data can be defined. We have developed a search engine independent score, based on FDR, which allows peptide identifications from different search engines to be combined, called the FDR Score. The results demonstrate that the observed FDR is significantly different when analysing the set of identifications made by all three search engines, by each pair of search engines or by a single search engine. Our algorithm assigns identifications to groups according to the set of search engines that have made the identification, and re-assigns the score (combined FDR Score). The combined FDR Score can differentiate between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine.

Effect of annealing temperatures on the secondary re-crystallization of extruded PM2000 steel bar

The ferritic oxide dispersion-strengthened alloy PM2000 is an ideal candidate for high-temperature applications as it contains uniform nano-oxide dispersoids, which act as pinning points to obstruct dislocation and grain boundary motion and therefore impart excellent creep resistance. The development of the microstructure during re-crystallization of oxide dispersion-strengthened alloys has been discussed by a number of authors, but the precise mechanism of secondary re-crystallization still remains uncertain. Hence, this work is aimed at investigating the re-crystallization behaviour of extruded PM2000 bar for different annealing temperatures, using electron backscatter diffraction, in particular, to determine grain orientations, grain boundary misorientation angles, etc. The results show that the as-extruded bar microstructure comprises both low-angle grain boundaries pinned by oxide particles and high-angle boundaries that will have inherent boundary mobility to allow boundary migration. In addition, dynamical re-crystallization was found in the outer region of the non-heat-treated PM2000 bar, which suggested that deformation heterogeneities can be introduced during thermo-mechanical processing that enhance the nucleation of re-crystallization. Subsequent heat treatments promote and stimulate secondary re-crystallization, giving rise to large grains with few sub-grain boundaries.

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

The role of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) is to produce and release community-accepted reporting requirements, interchange formats and controlled vocabularies for mass spectrometry proteomics and related technologies such as gel electrophoresis, column chromatography and molecular interactions. A number of significant advances were made at this workshop, with the new MS standard, mzML, being finalised prior to release on 1(st) June 2008 and analysisXML, which will allow protein and peptide identifications and post-translational modifications to be captured, being prepared to enter the review process this summer. The accompanying controlled vocabularies are continuing to evolve and a number of standards papers are now being finalised prior to publication.

A toolkit for capturing and sharing FuGE experiments

MOTIVATION

The Functional Genomics Experiment Object Model (FuGE) supports modelling of experimental processes either directly or through extensions that specialize FuGE for use in specific contexts. FuGE applications commonly include components that capture, store and search experiment descriptions, where the requirements of different applications have much in common.

RESULTS

We describe a toolkit that supports data capture, storage and web-based search of FuGE experiment models; the toolkit can be used directly on FuGE compliant models or configured for use with FuGE extensions. The toolkit is illustrated using a FuGE extension standardized by the proteomics standards initiative, namely GelML.

AVAILABILITY

The toolkit and a demonstration are available at http://code.google.com/p/fugetoolkit

Initial treatment with fixed-dose combination rosiglitazone/glimepiride in patients with previously untreated type 2 diabetes

AIM

This study assessed the efficacy and safety of two different dosing regimens of fixed-dose combination (FDC) rosiglitazone (RSG) plus glimepiride (GLIM) compared with RSG or GLIM monotherapy in drug-naive subjects with type 2 diabetes mellitus (T2DM).

METHODS

Drug-naive subjects (n = 901) were enrolled into this 28-week, double-blind, parallel-group study if their glycosylated haemoglobin A(1c) (HbA(1c)) was >7.5% but <or=12%. Subjects were randomized to receive either GLIM [4 mg once daily (OD) maximal], RSG (8 mg OD maximal) or RSG/GLIM FDC regimen A (4 mg/4 mg OD maximal) or RSG/GLIM FDC regimen B (8 mg/4 mg OD maximal). Patients were assessed for efficacy and safety every 4 weeks for the first 12 weeks of the study, and at weeks 20 and 28. The primary efficacy endpoint was change in HbA(1c) from baseline. Key secondary endpoints included the proportion of patients achieving recommended HbA(1c) and fasting plasma glucose (FPG) targets; change from baseline in FPG, insulin, C-reactive protein (CRP), adiponectin, free fatty acids and lipids; and percentage change in homeostasis model assessment-estimated insulin sensitivity and beta-cell function. Safety evaluations included adverse-event (AE) monitoring and clinical laboratory evaluations.

RESULTS

At week 28, both RSG/GLIM FDC regimens significantly reduced HbA(1c) (mean +/- s.d.: -2.4 +/- 1.4% FDC regimen A; -2.5 +/- 1.4% FDC regimen B) to a greater extent than RSG (-1.8 +/- 1.5%) or GLIM (-1.7 +/- 1.4%) monotherapy (model-adjusted mean treatment difference, p < 0.0001 vs. both RSG and GLIM). Significantly more subjects achieved HbA(1c) target levels of <or=6.5 and <7% with either RSG/GLIM FDC regimen compared with RSG or GLIM alone (model-adjusted odds ratio, p < 0.0001 for both comparisons). Similarly, a significantly greater reduction in FPG levels was observed in subjects treated with the RSG/GLIM FDC [mean +/- s.d. (mg/dl): -69.5 +/- 57.5 FDC regimen A; -79.9 +/- 56.8 FDC regimen B) compared with RSG (-56.6 +/- 58.1) or GLIM (-42.2 +/- 66.1) monotherapy (model-adjusted mean treatment difference, p < 0.0001 for both comparisons). Improvement in CRP was also observed in subjects who were treated with a RSG/GLIM FDC or RSG monotherapy compared with GLIM monotherapy. RSG/GLIM FDC was generally well tolerated, with no new safety or tolerability issues identified from its monotherapy components, and a similar AE profile was observed across FDC regimens. The most commonly reported AE was hypoglycaemia, and the incidence of confirmed symptomatic hypoglycaemia (3.6-5.5%) was comparable among subjects treated with an RSG/GLIM FDC and GLIM monotherapy.

CONCLUSIONS

Compared with RSG or GLIM monotherapy, the RSG/GLIM FDC improved glycaemic control with no significant increased risk of hypoglycaemia. RSG/GLIM FDC provides an effective and well-tolerated treatment option for drug-naive individuals with T2DM.

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

A proteomics analysis identifies one third of the predicted Toxoplasma gondii proteins and integrates proteomics and genomics data to refine genome annotation.

Background

Although the genomes of many of the most important human and animal pathogens have now been sequenced, our understanding of the actual proteins expressed by these genomes and how well they predict protein sequence and expression is still deficient. We have used three complementary approaches (two-dimensional electrophoresis, gel-liquid chromatography linked tandem mass spectrometry and MudPIT) to analyze the proteome of Toxoplasma gondii, a parasite of medical and veterinary significance, and have developed a public repository for these data within ToxoDB, making for the first time proteomics data an integral part of this key genome resource.

Results

The draft genome for Toxoplasma predicts around 8,000 genes with varying degrees of confidence. Our data demonstrate how proteomics can inform these predictions and help discover new genes. We have identified nearly one-third (2,252) of all the predicted proteins, with 2,477 intron-spanning peptides providing supporting evidence for correct splice site annotation. Functional predictions for each protein and key pathways were determined from the proteome. Importantly, we show evidence for many proteins that match alternative gene models, or previously unpredicted genes. For example, approximately 15% of peptides matched more convincingly to alternative gene models. We also compared our data with existing transcriptional data in which we highlight apparent discrepancies between gene transcription and protein expression.

Conclusion

Our data demonstrate the importance of protein data in expression profiling experiments and highlight the necessity of integrating proteomic with genomic data so that iterative refinements of both annotation and expression models are possible.

Protocol for evaluation of automated blood cell counters. International Committee for Standardization in Haematology (ICSH)

This protocol is proposed for the evaluation of automated blood cell counters to assess the performance, advantages and limitations of such instruments. It is based on the International Committee for Standardization in Haematology (ICSH) 'Protocol for type testing equipment and apparatus used for haematological analysis' (1978a) and the British Committee for Standardization in Haematology 'Guidelines for the evaluation of instruments used in haematology' (Shinton, England & Kennedy, 1982). The document has been prepared by the ICSH Panel on Cytometry after discussion with colleagues. This tentative protocol will be reviewed 1 year after publication, in accordance with the ICSH rules, before it is adopted as a definitive standard.

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France

Over the last five years, the Human Proteome Organisation Proteomics Standards Initiative (HUPO PSI) has produced and released community-accepted XML interchange formats in the fields of mass spectrometry, molecular interactions and gel electrophoresis, have led the field in the discussion of the minimum information with which such data should be annotated and are now in the process of publishing much of this information. At this 4(th) Spring workshop, the emphasis was on consolidating this effort, refining and improving the existing models and in pushing these forward to align with more broadly encompassing efforts such as FuGE (Jones, A.R., Pizarro, A., Spellman, P., Miller, M., FuGE Working Group FuGE: Functional Genomics Experiment Object Model. OMICS 2006, 10, 179-184) and the Ontology for Biomedical Investigation (OBI). The effort to merge the existing mass spectrometry XML interchange formats, mzData and mzXML, into one single standard mzML yielded significant progress. Also the preliminary design of AnalysisXML was extended to include several new use cases and better support for quantification information. Finally the Molecular Interaction group discussed the development of a molecular interaction scoring system with accompanying gold standard data test sets.

The minimum information about a proteomics experiment (MIAPE)

Both the generation and the analysis of proteomics data are now widespread, and high-throughput approaches are commonplace. Protocols continue to increase in complexity as methods and technologies evolve and diversify. To encourage the standardized collection, integration, storage and dissemination of proteomics data, the Human Proteome Organization's Proteomics Standards Initiative develops guidance modules for reporting the use of techniques such as gel electrophoresis and mass spectrometry. This paper describes the processes and principles underpinning the development of these modules; discusses the ramifications for various interest groups such as experimentalists, funders, publishers and the private sector; addresses the issue of overlap with other reporting guidelines; and highlights the criticality of appropriate tools and resources in enabling 'MIAPE-compliant' reporting.

FuGE: Functional Genomics Experiment Object Model

This is an interim report on the Functional Genomics Experiment (FuGE) Object Model. FuGE is a framework for creating data standards for high-throughput biological experiments, developed by a consortium of researchers from academia and industry. FuGE supports rich annotation of samples, protocols, instruments, and software, as well as providing extension points for technology specific details. It has been adopted by microarray and proteomics standards bodies as a basis for forthcoming standards. It is hoped that standards developers for other omics techniques will join this collaborative effort; widespread adoption will allow uniform annotation of common parts of functional genomics workflows, reduce standard development and learning times through the sharing of consistent practice, and ease the construction of software for accessing and integrating functional genomics data.

A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group

In this article we present the Reporting Structure for Biological Investigation (RSBI), a working group under the Microarray Gene Expression Data (MGED) Society umbrella. RSBI brings together several communities to tackle the challenges associated with integrating data and representing complex biological investigations, employing multiple OMICS technologies. Currently, RSBI includes environmental genomics, nutrigenomics and toxicogenomics communities, where independent activities are underway to develop databases and establish data communication standards within their respective domains. The RSBI working group has been conceived as a "single point of focus" for these communities, conforming to general accepted view that duplication and incompatibility should be avoided where possible. This endeavour has aimed to synergize insular solutions into one common terminology between biologically driven standardisation efforts and has also resulted in strong collaborations and shared understanding between those in the technological domain. Through extensive liaisons with many standards efforts, several threads have been woven with the hope that ultimately technology-centered standards and their specific extensions into biological domains of interest will not only stand alone, but will also be able to function together, as interchangeable modules.

Control of glycolysis in mature boar spermatozoa: effect of pH in vitro

The glycolytic pathway in boar sperm is sensitive to pH, which decreases as lactate is produced from either glucose or fructose in vitro. The build up of lactate appears to be due to the saturation of mitochondrial lactate transporters, which causes the cytoplasmic pH to fall. Phosphofructokinase has been shown to be sensitive to this drop in pH rather than to the build up of lactate ions or ATP, thereby controlling the rate of glycolysis in vitro.

An Update on Data Standards for Gel Electrophoresis

The use of gel electrophoresis to separate and, in some instances, to quantify the abundance of large numbers of proteins from complex mixtures, has been well established for several decades. The quantity of publicly available data is still relatively modest due to a lack of community accepted data standards, tools to facilitate the data sharing process and controlled vocabularies to ensure that consistent terminology is used to describe the experimental methodology. It is becoming widely recognised that there are significant benefits in data sharing for proteomics, allowing results to be verified and new findings to be generated by re-analysis of published studies. We report on standards development by the Gel Analysis Workgroup of the Proteomics Standards Initiative. The workgroup develops reporting requirements, data formats and controlled vocabularies for experimental gel electrophoresis, and informatics performed on gel images. We present a tutorial on how such resources can be used and how the community should get involved with the on-going projects. Finally, we present a roadmap for future developments in this area.

Capture and analysis of quantitative proteomic data

Whilst the array of techniques available for quantitative proteomics continues to grow, the attendant bioinformatic software tools are similarly expanding in number. The data capture and analysis of such quantitative data is obviously crucial to the experiment and the methods used to process it will critically affect the quality of the data obtained. These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding MS scans in the experiment, construction of representative ion chromatograms, location of the true peptide ion chromatogram start and end, elimination of background signal in the mass spectrum and chromatogram and calculation of both peptide and protein ratios/abundances. A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. Currently, although there is no single consensus on precisely how to calculate protein and peptide abundances, many common themes have emerged which identify and reduce many of the key sources of error. These issues will be discussed, along with those relating to deposition of quantitative data. At present, mature data standards for quantitative proteomics are not yet available, although formats are beginning to emerge.

The HUPO Pre-Congress Proteomics Standards Initiative Workshop HUPO 5th Annual World Congress Long Beach, CA, USA 28 October–1 November 2006

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation provided an opportunity to update delegates on the progress of the work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI) to develop and implement standards in the field of proteomics. Significant advances have been made since the previous congress, with several of the interchange standards and minimal requirements documents being submitted for publication in the literature and being more widely adopted by both manufacturers and data repositories. An exciting development over the interim twelve months is the ongoing merger of the two existing mass spectrometry standards, the PSI mzData and Institute for Systems Biology mzXML, into a single product. This should be achieved by early in 2007.

Whole-grain intake of British young people aged 4–18 years

Inverse associations between whole-grain food consumption and risk of CVD, some cancers and type 2 diabetes have been reported. However, there are few reports of whole-grain intake, particularly among young people. The objective of the present study was to estimate whole-grain intake in a nationally representative sample of young people aged 4–18 years living in Great Britain. Whole-grain intake was estimated using 7d weighed dietary records from 1583 young people who participated in the cross-sectional National Diet and Nutrition Survey in 1997. Whole-grain intake was quantified from the consumption of all foods containing ≥10% whole-grain content. Median whole-grain intake was 7g/d (interquartile range 0–19g/d), with a corresponding mean of 13 (sd18) g/d. Intake was significantly lower among young people whose head of household had a manual occupation, but did not differ significantly by sex, age, region or season. There was no whole-grain intake for 27% of participants. The percentages for less than one and less than three 16g amounts of whole-grain intake per d were 70 and 94, respectively, while corresponding percentages based on 20g amounts were 76 and 97. Foods with <51% whole-grain content provided 28% of whole-grain intake overall, with a higher percentage in older adolescents. The main sources of whole-grain intake were breakfast cereals (56%) and bread (25%). The present study provides the first quantification of absolute whole-grain intake from all significant food sources in any representative age group in the UK. Although there is some debate regarding the quantity of whole grains required for good health, whole-grain intake among British young people is low.

Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25–27 September 2006, Washington DC, USA

Since its conception in April 2002, the Human Proteome Organisation Proteomics Standards Initiative has contributed to the development of community standards for proteomics in a collaborative and very dynamic manner, resulting in the publication and increasing adoption of a number of interchange formats and controlled vocabularies. Repositories supporting these formats are being established or are already operational. In parallel with this, minimum reporting requirement have been developed and are now maturing to the point where they have been submitted for journal publication after prolonged exposure to community-input via the PSI website.

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ

Background

Proteomics continues to play a critical role in post-genomic science as continued advances in mass spectrometry and analytical chemistry support the separation and identification of increasing numbers of peptides and proteins from their characteristic mass spectra. In order to facilitate the sharing of this data, various standard formats have been, and continue to be, developed. Still not fully mature however, these are not yet able to cope with the increasing number of quantitative proteomic technologies that are being developed.

Results

We propose an extension to the PRIDE and mzData XML schema to accommodate the concept of multiple samples per experiment, and in addition, capture the intensities of the iTRAQ^TM reporter ions in the entry. A simple Java-client has been developed to capture and convert the raw data from common spectral file formats, which also uses a third-party open source tool for the generation of iTRAQ^TM reported intensities from Mascot output, into a valid PRIDE XML entry.

Conclusion

We describe an extension to the PRIDE and mzData schemas to enable the capture of quantitative data. Currently this is limited to iTRAQ^TM data but is readily extensible for other quantitative proteomic technologies. Furthermore, a software tool has been developed which enables conversion from various mass spectrum file formats and corresponding Mascot peptide identifications to PRIDE formatted XML. The tool represents a simple approach to preparing quantitative and qualitative data for submission to repositories such as PRIDE, which is necessary to facilitate data deposition and sharing in public domain database. The software is freely available from .

Radioactive materials in biosolids: dose modeling

The Interagency Steering Committee on Radiation Standards (ISCORS) has recently completed a study of the occurrence within the United States of radioactive materials in sewage sludge and sewage incineration ash. One component of that effort was an examination of the possible transport of radioactivity from sludge into the local environment and the subsequent exposure of humans. A stochastic environmental pathway model was applied separately to seven hypothetical, generic sludge-release scenarios, leading to the creation of seven tables of Dose-to-Source Ratios (DSR), which can be used in translating from specific activity in sludge into dose to an individual. These DSR values were then combined with the results of an ISCORS survey of sludge and ash at more than 300 publicly owned treatment works, to explore the potential for radiation exposure of sludge workers and members of the public. This paper provides a brief overview of the pathway modeling methodology employed in the exposure and dose assessments and discusses technical aspects of the results obtained.

An analysis of extensible modelling for functional genomics data

Background

Several data formats have been developed for large scale biological experiments, using a variety of methodologies. Most data formats contain a mechanism for allowing extensions to encode unanticipated data types. Extensions to data formats are important because the experimental methodologies tend to be fairly diverse and rapidly evolving, which hinders the creation of formats that will be stable over time.

Results

In this paper we review the data formats that exist in functional genomics, some of which have become de facto or de jure standards, with a particular focus on how each domain has been modelled, and how each format allows extensions. We describe the tasks that are frequently performed over data formats and analyse how well each task is supported by a particular modelling structure.

Conclusion

From our analysis, we make recommendations as to the types of modelling structure that are most suitable for particular types of experimental annotation. There are several standards currently under development that we believe could benefit from systematically following a set of guidelines.

Lack of antifertility properties of novel halogenated glycolytic inhibitors and the urinary excretion and metabolism of 1,6-dichloro-1,6-dideoxy-D-fructofuranose in the male rat

The antifertility action of (R,S)-alpha-chlorohydrin administered orally to male rats was compared with that of several novel chlorinated compounds known to inhibit glycolysis and the kinematics of rat sperm in vitro. Oral gavage of 1,6-dichloro-1,6-dideoxy-D-fructofuranose (dichlorodideoxyfructose, DCF), 1-chloro-3-hydroxypropanone, its dimethylketal and bromopyruvate did not reduce the fertility of male rats below that of controls at the equivalent antifertility dose of (R,S)-alpha-chlorohydrin (5 mg/kg/day) or higher. As anticipated for a compound cleaved to products of (S)-chirality even high doses of DCF (200 mg/kg) showed no effect on renal function. 36Cl-Labelled DCF administered orally to male rats was eliminated only slowly in the urine (16% of the ingested dose excreted in 96 h). In the first 8 h, approximately 50% of DCF was excreted unchanged, 30% was excreted as 3-chlorolactate (BCLA), the oxidation product 3-chlorolactaldehyde and 25% as Cl-. By 24 h little DCF remained and the major metabolite (70%) was BCLA and 20% Cl-. The high rate of dechlorination is most likely responsible for the low antifertility action of DCF.

MRI susceptibility artefacts related to scaphoid screws: the effect of screw type, screw orientation and imaging parameters

Metal implants produce susceptibility artefacts in magnetic resonance imaging. We have explored the effects of scaphoid screw characteristics and orientation on MR susceptibility artefact. Titanium alloy, smallness and longitudinal alignment with the z-axis of the main magnetic field reduce the size of the susceptibility artefact.

The effect of (R,S)-ornidazole on the fertility of male mice and the excretion and metabolism of 36Cl-(R,S)-ornidazole and 36Cl-(R,S)-alpha-chlorohydrin in male mice and rats

(R,S)-Ornidazole, an effective antifertility agent for male rats at 400 mg/kg/day, was ineffective at this dose in male mice and at 1000 mg/kg/day caused neural effects. The compound was not excreted unchanged and more polar metabolites and Cl- were detected in 0-8 h urine following a single injection (400 mg/kg). In 8-24 h urine even these metabolites and most Cl ion were absent, indicating rapid metabolism of ornidazole. There was no organ specific accumulation of 36Cl-(R,S)-ornidazole in murine tissues. After injection of 36Cl-(R,S)-alpha-chlorohydrin, another antifertility agent in the rat but not the mouse, there was also no tissue-specific accumulation of radioactivity in the reproductive tract of either species. Urinary excretion rates of alpha-chlorohydrin were twice as rapid in mice as in rats. In mice, alpha-chlorohydrin was the major urinary metabolite, but in the rat metabolites included Cl-, 3-chlorolactate (BCLA) at 5 and 10 h and BCLA only at 24 h. BCLA was the major metabolite detected in most tissues at 10 and 24 h. In the rat cauda (but not caput) epididymidis the glycolytic inhibitor 3-chlorolactaldehyde was present at 5 h (but not 10 h), indicative of early metabolism. These results demonstrate a greater metabolism and excretion of putative antifertility agents in the mouse than the rat, lowering the amount of effective inhibitor circulating in the animal, which may explain why (R,S)-alpha-chlorohydrin and (R,S)-ornidazole are ineffective in this species at the dosages and injection times used, despite their spermatozoa being sensitive to inhibition by (R,S)-alpha-chlorohydrin in vitro.

Fructose metabolism by mature boar spermatozoa

In 1945, Mann showed fructose to be the principal sugar in semen. For over half a century the means by which fructose is metabolized by sperm has been assumed to be by an initial phosphorylation catalysed by hexokinase, but this has never been substantiated. In the present study, by comparing the metabolism of glucose and fructose by both whole boar sperm and hypotonically treated cells, it is confirmed that fructose is phosphorylated by hexokinase to produce fructose 6-phosphate.

Smoke alarm ownership and installation: a comparison of a rural and a suburban community in Georgia

As part of a smoke alarm giveaway and installation program (The Get-Alarmed Campaign), a total of 454 households were surveyed in two counties in Georgia, one metropolitan and one nonmetropolitan. The targeted communities in these counties had a high prevalence of low-income and minority populations and thus were at high risk of house fire-related morbidity and mortality. The objectives of the program were to determine the prevalence of and predictors for installed, functioning smoke alarms, and to install at least one smoke alarm and/or smoke alarm batteries in 100% of participating homes in need. Characteristics associated with smoke alarm ownership included home ownership, having a higher income, and having a central heating source, factors which should be considered in targeting future intervention strategies. At onset, 159/454 households (35.0%) had no smoke alarms installed and 56/275 households with existing smoke alarms (20.4%) had none that were functional. Regardless of ownership status, a free smoke alarm was installed in the household of 93.8% of participants and new batteries were installed in existing smoke alarms for 31.7% of participants. This project illustrates the usefulness of a door-to-door campaign in increasing smoke alarm ownership in both a rural and a suburban community with a high concentration of residents at high risk of house fire-related morbidity and mortality.

MRI assessment of the proximal pole of the scaphoid after internal fixation with a titanium alloy Herbert screw

We report a series of scaphoid fractures fixed with titanium alloy Herbert screws in which postoperative Magnetic Resonance Imaging (MRI) was used to assess the marrow signal in the proximal pole of the scaphoid and thus detect the presence of avascular necrosis. The artefact produced by the titanium alloy Herbert screw did not preclude this assessment.

Root mucilage from pea and its utilization by rhizosphere bacteria as a sole carbon source

Plant roots secrete a complex polysaccharide mucilage that may provide a significant source of carbon for microbes that colonize the rhizosphere. High molecular weight mucilage was separated by high-pressure liquid chromatography gel filtration from low molecular weight components of pea root exudate. Purified pea root mucilage generally was similar in sugar and glycosidic linkage composition to mucilage from cowpea, wheat, rice, and maize, but appeared to contain an unusually high amount of material that was similar to arabinogalactan protein. Purified pea mucilage was used as the sole carbon source for growth of several pea rhizosphere bacteria, including Rhizobium leguminosarum 8401 and 4292, Burkholderia cepacia AMMD, and Pseudomonas fluorescens PRA25. These species grew on mucilage to cell densities of three- to 25-fold higher than controls with no added carbon source, with cell densities of 1 to 15% of those obtained on an equal weight of glucose. Micromolar concentrations of nod gene-inducing flavonoids specifically stimulated mucilage-dependent growth of R. leguminosarum 8401 to levels almost equaling the glucose controls. R. leguminosarum 8401 was able to hydrolyze p-nitrophenyl glycosides of various sugars and partially utilize a number of purified plant polysaccharides as sole carbon sources, indicating that R. leguminosarum 8401 can make an unexpected variety of carbohydrases, in accordance with its ability to extensively utilize pea root mucilage.

Susceptibility of glycolytic enzyme activity and motility of spermatozoa from rat, mouse, and human to inhibition by proven and putative chlorinated antifertility compounds in vitro

Nonhormonal contraceptives that act by blocking energy metabolism within sperm have the advantage over spermatogenic inhibitors by their fast onset of infertility and their almost immediate restoration of fertility after withdrawal of the contraceptive agent. This study was done to test new chlorinated compounds for their contraceptive potency on rodent and human sperm in vitro. Cells were incubated in a medium containing glucose as the sole energy source with 1-chloro-3-hydroxypropanone (CHOP) and 1,6-dichloro-1,6-dideoxy-D-fructose (DCDF), chlorinated analogues of glycolytic substrates, as well as racemic (R,S)-alpha-chlorohydrin (ACH). After incubation, enzymatic activity and kinematic parameters were estimated. A dose-dependent inhibition of the glycolytic enzyme, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), of rat and mouse distal cauda epididymidal and human ejaculated sperm by ACH, CHOP, and DCDF was demonstrated. Triosephosphate isomerase (TPI) was inhibited by ACH, but not by CHOP and DCDF, irrespective of species. All compounds inhibited sperm motility and kinematic parameters with increasing concentration. The results confirm that inhibition of glycolytic enzymes of sperm, including those of human, can be effectively brought about by a variety of chloro-compounds that can be converted to (S)-3-chlorolactaldehyde, the stereospecific chloro-derivative of the enzyme's natural substrate, (R)-glyceraldehyde 3-phosphate, and could be developed into contraceptive agents for men.

Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.

Glycolytic enzyme activity in hypotonically treated boar spermatozoa

Treatment of washed boar sperm with hypotonic phosphate buffer disrupted the cytoplasmic membrane and released the soluble contents and phosphofructokinase, but the other glycolytic enzymes and lactate dehydrogenase were retained. Addition of the appropriate substrates and co-factor(s) to preparations of treated cells in phosphate-buffered saline showed that enzyme activity could be re-instated. This simple preparation should be of assistance in the investigation of specific sections of the glycolytic pathway without the use of chemical inhibitors.

Influence of a rural primary care clerkship on medical students' intentions to practice in a rural community

The purpose of this study is to examine the relationship of a rural clerkship to medical students' interest in establishing careers in rural communities. The Association of American Medical Colleges Medical School Graduation Questionnaire (GQ) for years 1988 through 1997 was examined to compare the career plans of students graduating from Morehouse School of Medicine (MSM) with those of all students graduating from United States medical schools before the period 1988 through 1992 and after the period 1993 through 1997, after the inception of the rural clerkship at MSM. Select GQ data items examined include student demographics, medical school experiences, and career plans. Statistical analyses were used to compare pre- and post-clerkship responses for MSM students and to compare their responses with the national trends. Results indicate that, following a transition period, MSM students showed an increased preference for a future career in a rural community. A smaller upward trend in the national data was observed. There appears to be an association between the rural clerkship experience at MSM and the stated preferred career choices of the students.

Using benthic recruitment to assess the significance of contaminated sediments: the influence of taxonomic resolution

The use of small-scale experimental units as a means of evaluating the ecological effects of contaminated sediments was examined at the species, family, mixed and phylum levels of taxonomic resolution. Sediments were taken from various locations representing a range of contaminant loads. Containers with these sediments were placed in situ at a relatively uncontaminated location for 90 days. The containers were retrieved and the abundance of the macrofauna which recruited to the containers was estimated. The results showed that the composition of the benthic communities in the more highly contaminated sediments differed significantly from those in less contaminated sediments. Analyses at the different taxonomic levels showed that all but the phylum level data showed some differences in community structure among sediment types. The study showed that small-scale experiments are useful for examining the effects of contaminants and that higher levels of taxonomic resolution can be used to describe variations in the structure of benthic communities at this spatial scale.

Time to think: temporal considerations in nursing practice and research

AIMS OF THE STUDY/PAPER: To explore the meaning of nursing time, both as it is represented in the literature and interpreted within nursing practice. To explore how nursing time may be better conceptualized through exploring non-nursing literature and the use of theory derivation.

BACKGROUND/RATIONALE

The dynamic of time is one of the most important influences upon nursing behaviour, yet temporal issues have attracted very little attention in the literature regarding nursing practice, theory and research.

DESIGN/METHOD

In the course of this literature review an attempt is made, via the process of theory derivation, to clarify the meaning of 'nursing time', and how nursing time is valued and perceived by others.

RESULTS/FINDINGS

The literature reveals misconceptions and a lack of value of nursing time, possibly indicative of the dominance of linear models of time (such as clock and calendar time), and the historical ascendancy of medicine and the positivistic sciences over nursing. It is proposed here that nurses exist and practice within nonlinear, complex and parallel temporal worlds; these are considered by examining research data that illustrates a moment in nursing time. Exploring this moment gives an opportunity to introduce some terms and concepts that may be useful in the future conceptualization of nursing time.

CONCLUSIONS

It is recommended that attention to such factors as the complex temporal dynamics inherent within health care in general, and nursing in particular, should be considered within the domains of nursing practice and research. This may help in distinguishing the fundamental identity and nature of nursing within health care and health care professions.

Testicular microlithiasis in a UK population: its incidence, associations and follow-up

OBJECTIVES

To determine the incidence of testicular microlithiasis in men presenting for testicular ultrasonography, to identify any associated pathology (with particular reference to testicular neoplasia) and to report the follow-up of those patients in whom testicular microlithiasis was identified.

PATIENTS AND METHODS

In this retrospective study, the results of all testicular ultrasonography undertaken between July 1995 and March 1998 in a district general hospital were reviewed. The records of all patients diagnosed ultrasonographically to have testicular microlithiasis were retrieved and the pathology database was accessed for all testicular tumours diagnosed in the same period.

RESULTS

During the study period 2215 scans were taken; 34 cases of testicular microlithiasis were identified, giving an incidence of 1.4%. Thirty-one testicular tumours were removed during the same period. Of the 34 cases with testicular microlithiasis, five had histologically confirmed testicular tumours (15%). The incidence of testicular tumours in the scans showing no microlithiasis was 26 in 2181 (1.1%). The differential incidence of tumours in the two groups is statistically significant (P < 0.001, chi-square analysis). Patients with testicular microlithiasis but no tumour were followed up for a median (range) of 41 (19-54) months; no interval tumours have developed to date.

CONCLUSION

This study confirms an incidence of testicular microlithiasis comparable with that in other reported series, albeit in a selected population. There was a strong association between testicular microlithiasis and testicular tumours. Whether this is a causal relationship has yet to be determined. Careful clinical and ultrasonographic follow-up of these patients is therefore recommended until the significance of testicular microlithiasis is clear.