IMMUNOCAT—A Data Management System for Epitope Mapping Studies

To enable rationale vaccine design, studies of molecular and cellular mechanisms of immune recognition need to be linked with clinical studies in humans. A major challenge in conducting such translational research studies lies in the management and integration of large amounts and various types of data collected from multiple sources. For this purpose, we have established “IMMUNOCAT”, an interactive data management system for the epitope discovery research projects conducted by our group. The system provides functions to store, query, and analyze clinical and experimental data, enabling efficient, systematic, and integrative data management. We demonstrate how IMMUNOCAT is utilized in a large-scale research contract that aims to identify epitopes in common allergens recognized by T cells from human donors, in order to facilitate the rational design of allergy vaccines. At clinical sites, demographic information and disease history of each enrolled donor are captured, followed by results of an allergen skin test and blood draw. At the laboratory site, T cells derived from blood samples are tested for reactivity against a panel of peptides derived from common human allergens. IMMUNOCAT stores results from these T cell assays along with MHC:peptide binding data, results from RAST tests for antibody titers in donor serum, and the respective donor HLA typing results. Through this system, we are able to perform queries and integrated analyses of the various types of data. This provides a case study for the use of bioinformatics and information management techniques to track and analyze data produced in a translational research study aimed at epitope identification

Carotid artery plaque in women with rheumatoid arthritis and low estimated cardiovascular disease risk: a cross-sectional study

INTRODUCTION: We previously reported that most patients with rheumatoid arthritis (RA) and moderate cardiovascular disease (CVD) risk according to the Systematic COronary Evaluation score (SCORE) experience carotid artery plaque. In this study, we aimed to identify patient characteristics that can potentially predict carotid plaque presence in women with RA and a concurrent low CVD risk according to the SCORE. METHODS: A cohort of 144 women with an evaluated low risk of CVD (SCORE value of zero) was assembled amongst 550 consecutive patients with RA that underwent CVD risk factor recording and carotid artery ultrasound. Participants had no established CVD, moderate or severe chronic kidney disease, or diabetes. We assessed carotid plaque(s) presence and its associated patient characteristics. RESULTS: Carotid artery plaque was present in 35 (24.3%) of women with RA. Age, the number of synthetic disease-modifying agents (DMARDs) and total cholesterol concentrations were independently associated with plaque in multivariable stepwise backward regression analysis (odds ratio (95% confidence interval)=1.15 (1.07 to 1.24), P49.5 years or/and total cholesterol concentration of >5.4 mmol/l, respectively, compared to only 7.8% in those (n=64; 44.4%) with age≤49.5 years or/and total cholesterol concentration of ≤5.4 mmol/l, respectively. CONCLUSIONS: Approximately one-third of women with RA who experience a low SCORE value and are aged >49.5 years or/and have a total cholesterol concentration of >5.4 mmol/l, experience high-risk atherosclerosis, which requires intensive CVD risk management

AIMD - A validated, simplified framework of interventions to promote and integrate evidence into health practices, systems, and policies

Background: Proliferation of terms describing the science of effectively promoting and supporting the use of research evidence in healthcare policy and practice has hampered understanding and development of the field. To address this, an international Terminology Working Group developed and published a simplified framework of interventions to promote and integrate evidence into health practices, systems, and policies. This paper presents results of validation work and a second international workgroup meeting, culminating in the updated AIMD framework [Aims, Ingredients, Mechanism, Delivery]. Methods: Framework validity was evaluated against terminology schemas (n = 51); primary studies (n = 37); and reporting guidelines (n = 10). Framework components were independently categorized as fully represented, partly represented, or absent by two researchers. Opportunities to refine the framework were systematically recorded. A meeting of the expanded international Terminology Working Group updated the framework by reviewing and deliberating upon validation findings and refinement proposals. Results: There was variation in representativeness of the components across the three types of literature, in particular for the component 'causal mechanisms'. Analysis of primary studies revealed that representativeness of this concept lowered from 92 to 68% if only explicit, rather than explicit and non-explicit references to causal mechanisms were included. All components were very well represented in reporting guidelines, however the level of description of these was lower than in other types of literature. Twelve opportunities were identified to improve the framework, 9 of which were operationalized at the meeting. The updated AIMD framework comprises four components: (1) Aims: what do you want your intervention to achieve and for whom? (2) Ingredients: what comprises the intervention? (3) Mechanisms: how do you propose the intervention will work? and (4) Delivery: how will you deliver the intervention? Conclusions: The draft simplified framework was validated with reference to a wide range of relevant literature and improvements have enhanced useability. The AIMD framework could aid in the promotion of evidence into practice, remove barriers to understanding how interventions work, enhance communication of interventions and support knowledge synthesis. Future work needs to focus on developing and testing resources and educational initiatives to optimize use of the AIMD framework in collaboration with relevant end-user groups

e-MIR2: a public online inventory of medical informatics resources

Background. Over the last years, the number of available informatics resources in medicine has grown exponentially. While specific inventories of such resources have already begun to be developed for Bioinformatics (BI), comparable inventories are as yet not available for Medical Informatics (MI) field, so that locating and accessing them currently remains a hard and time-consuming task. Description. We have created a repository of MI resources from the scientific literature, providing free access to its contents through a web-based service. Relevant information describing the resources is automatically extracted from manuscripts published in top-ranked MI journals. We used a pattern matching approach to detect the resources? names and their main features. Detected resources are classified according to three different criteria: functionality, resource type and domain. To facilitate these tasks, we have built three different taxonomies by following a novel approach based on folksonomies and social tagging. We adopted the terminology most frequently used by MI researchers in their publications to create the concepts and hierarchical relationships belonging to the taxonomies. The classification algorithm identifies the categories associated to resources and annotates them accordingly. The database is then populated with this data after manual curation and validation. Conclusions. We have created an online repository of MI resources to assist researchers in locating and accessing the most suitable resources to perform specific tasks. The database contained 282 resources at the time of writing. We are continuing to expand the number of available resources by taking into account further publications as well as suggestions from users and resource developers

A demographic and epidemiological study of a Mexican chiropractic college public clinic

<p>Abstract</p> <p>Background</p> <p>Descriptive studies of chiropractic patients are not new, several have been performed in the U.S., Australia, Canada, and Europe. None have been performed in a Latin American country. The purpose of this study is to describe the patients who visited a Mexican chiropractic college public clinic with respect to demographics and clinical characteristics.</p> <p>Methods</p> <p>This study was reviewed and approved by the IRB of Parker College of Chiropractic and the Universidad Estatal del Valle de Ecatepec (UNEVE). Five hundred patient files from the UNEVE public clinic from May 2005 to May 2007 were selected from an approximate total number of 3,700. Information was collected for demographics, chief complaints, associated complaints, and previous care sought.</p> <p>Results</p> <p>The sample comprised 306 (61.2%) female. Most files (44.2%) were in the age range of 40–59 years (mean of 43.4 years). The most frequent complaints were lumbar pain (29.2%) and extremity pain (28.0%), most commonly the knee. Most (62.0%) described their complaints as greater than one year. Trauma (46.6%) was indicated as the initial cause. Mean VAS score was 6.26/10 with 20% rated at 8/10.</p> <p>Conclusion</p> <p>Demographic results compared closer to studies conducted with private clinicians (females within the ages of 40–59). The primary complaint and duration was similar to previous studies (low back pain and chronic), except in this population the cause was usually initiated by trauma. The most striking features were the higher number of extremity complaints and the marked increased level of VAS score (20% rated as 8/10).</p

Global nuclear energy partnership fuels transient testing at the Sandia National Laboratories nuclear facilities : planning and facility infrastructure options.

The Global Nuclear Energy Partnership fuels development program is currently developing metallic, oxide, and nitride fuel forms as candidate fuels for an Advanced Burner Reactor. The Advance Burner Reactor is being designed to fission actinides efficiently, thereby reducing the long-term storage requirements for spent fuel repositories. Small fuel samples are being fabricated and evaluated with different transuranic loadings and with extensive burnup using the Advanced Test Reactor. During the next several years, numerous fuel samples will be fabricated, evaluated, and tested, with the eventual goal of developing a transmuter fuel database that supports the down selection to the most suitable fuel type. To provide a comparative database of safety margins for the range of potential transmuter fuels, this report describes a plan to conduct a set of early transient tests in the Annular Core Research Reactor at Sandia National Laboratories. The Annular Core Research Reactor is uniquely qualified to perform these types of tests because of its wide range of operating capabilities and large dry central cavity which extents through the center of the core. The goal of the fuels testing program is to demonstrate that the design and fabrication processes are of sufficient quality that the fuel will not fail at its design limit--up to a specified burnup, power density, and operating temperature. Transient testing is required to determine the fuel pin failure thresholds and to demonstrate that adequate fuel failure margins exist during the postulated design basis accidents

Vector Transmission of Leishmania Abrogates Vaccine-Induced Protective Immunity

Numerous experimental vaccines have been developed to protect against the cutaneous and visceral forms of leishmaniasis caused by infection with the obligate intracellular protozoan Leishmania, but a human vaccine still does not exist. Remarkably, the efficacy of anti-Leishmania vaccines has never been fully evaluated under experimental conditions following natural vector transmission by infected sand fly bite. The only immunization strategy known to protect humans against natural exposure is “leishmanization,” in which viable L. major parasites are intentionally inoculated into a selected site in the skin. We employed mice with healed L. major infections to mimic leishmanization, and found tissue-seeking, cytokine-producing CD4+ T cells specific for Leishmania at the site of challenge by infected sand fly bite within 24 hours, and these mice were highly resistant to sand fly transmitted infection. In contrast, mice vaccinated with a killed vaccine comprised of autoclaved L. major antigen (ALM)+CpG oligodeoxynucleotides that protected against needle inoculation of parasites, showed delayed expression of protective immunity and failed to protect against infected sand fly challenge. Two-photon intra-vital microscopy and flow cytometric analysis revealed that sand fly, but not needle challenge, resulted in the maintenance of a localized neutrophilic response at the inoculation site, and removal of neutrophils following vector transmission led to increased parasite-specific immune responses and promoted the efficacy of the killed vaccine. These observations identify the critical immunological factors influencing vaccine efficacy following natural transmission of Leishmania