An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities

BACKGROUND: Epitopes can be defined as the molecular structures bound by specific receptors, which are recognized during immune responses. The Immune Epitope Database and Analysis Resource (IEDB) project will catalog and organize information regarding antibody and T cell epitopes from infectious pathogens, experimental antigens and self-antigens, with a priority on NIAID Category A-C pathogens () and emerging/re-emerging infectious diseases. Both intrinsic structural and phylogenetic features, as well as information relating to the interactions of the epitopes with the host's immune system will be catalogued. DESCRIPTION: To effectively represent and communicate the information related to immune epitopes, a formal ontology was developed. The semantics of the epitope domain and related concepts were captured as a hierarchy of classes, which represent the general and specialized relationships between the various concepts. A complete listing of classes and their properties can be found at . CONCLUSION: The IEDB's ontology is the first ontology specifically designed to capture both intrinsic chemical and biochemical information relating to immune epitopes with information relating to the interaction of these structures with molecules derived from the host immune system. We anticipate that the development of this type of ontology and associated databases will facilitate rigorous description of data related to immune epitopes, and might ultimately lead to completely new methods for describing and modeling immune responses

The Immune Epitope Database and Analysis Resource: From Vision to Blueprint

A planned repository of immune epitope data with associated analysis tools should be a boon to vaccine developmen

Curation of complex, context-dependent immunological data

BACKGROUND: The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data . DESCRIPTION: To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation. CONCLUSION: Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise

Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data of the MHC molecule examined, but no specific peptide:MHC binding data. Moreover, these methods retain the ability to make predictions in a sufficiently short time scale to be useful in a real world application, such as screening a whole proteome for candidate binding peptides. A rigorous evaluation of each methods prediction performance showed that these are significantly better than random, but still substantially lower than the best performing sequence based class II prediction methods available. While the approaches presented here were developed independently, we have chosen to present our results together in order to support the notion that generating structure based predictions of peptide:MHC binding without using binding data is unlikely to give satisfactory results

Developing a mHealth intervention to promote uptake of HIV testing among African communities in the UK: a qualitative study

Background: HIV-related mHealth interventions have demonstrable efficacy in supporting treatment adherence, although the evidence base for promoting HIV testing is inconclusive. Progress is constrained by a limited understanding of processes used to develop interventions and weak theoretical underpinnings. This paper describes a research project that informed the development of a theory-based mHealth intervention to promote HIV testing amongst city-dwelling African communities in the UK. Methods: A community-based participatory social marketing design was adopted. Six focus groups (48 participants in total) were undertaken and analysed using a thematic framework approach, guided by constructs from the Health Belief Model. Key themes were incorporated into a set of text messages, which were pre-tested and refined. Results: The focus groups identified a relatively low perception of HIV risk, especially amongst men, and a range of social and structural barriers to HIV testing. In terms of self-efficacy around HIV testing, respondents highlighted a need for communities and professionals to work together to build a context of trust through co-location in, and co-involvement of, local communities which would in turn enhance confidence in, and support for, HIV testing activities of health professionals. Findings suggested that messages should: avoid an exclusive focus on HIV, be tailored and personalised, come from a trusted source, allay fears and focus on support and health benefits. Conclusions: HIV remains a stigmatized and de-prioritized issue within African migrant communities in the UK, posing barriers to HIV testing initiatives. A community-based participatory social marketing design can be successfully used to develop a culturally appropriate text messaging HIV intervention. Key challenges involved turning community research recommendations into brief text messages of only 160 characters. The intervention needs to be evaluated in a randomized control trial. Future research should explore the application of the processes and methodologies described in this paper within other communities

Technol Health Care

Thyroid metabolism involves iodine, which allows us to use radioactive iodine for diagnostic and therapy purposes. The efficiency of radioiodine therapy depends on several parameters; the ability of thyroid tissue to uptake radioactive iodine is one of them. The objective of this work is to quantify the radioactive iodine uptake on thyroid tissue. In this work, we developed a method to quantify the in vivo uptake of iodine-131 on sections of thyroid glands removed by thyroidectomies. We performed an analysis of histological sections of the thyroid tissue by beta imaging. We had the opportunity to quantify the fixed radioactivity and to analyze its distribution in the thyroid gland, thanks to the good spatial resolution available with the type of detector used. The results gave a high image resolution showing the heterogeneity of iodine-131 fixation by the thyroid tissue. We were able to quantify the tissue radioactivity in mega Becquerel (MBq) per volume unit. This work has shown that the direct quantification of the thyroid tissue uptake is possible using the beta imaging system