Updates on the web-based VIOLIN vaccine database and analysis system.

The integrative Vaccine Investigation and Online Information Network (VIOLIN) vaccine research database and analysis system (http://www.violinet.org) curates, stores, analyses and integrates various vaccine-associated research data. Since its first publication in NAR in 2008, significant updates have been made. Starting from 211 vaccines annotated at the end of 2007, VIOLIN now includes over 3240 vaccines for 192 infectious diseases and eight noninfectious diseases (e.g. cancers and allergies). Under the umbrella of VIOLIN, >10 relatively independent programs are developed. For example, Protegen stores over 800 protective antigens experimentally proven valid for vaccine development. VirmugenDB annotated over 200 'virmugens', a term coined by us to represent those virulence factor genes that can be mutated to generate successful live attenuated vaccines. Specific patterns were identified from the genes collected in Protegen and VirmugenDB. VIOLIN also includes Vaxign, the first web-based vaccine candidate prediction program based on reverse vaccinology. VIOLIN collects and analyzes different vaccine components including vaccine adjuvants (Vaxjo) and DNA vaccine plasmids (DNAVaxDB). VIOLIN includes licensed human vaccines (Huvax) and veterinary vaccines (Vevax). The Vaccine Ontology is applied to standardize and integrate various data in VIOLIN. VIOLIN also hosts the Ontology of Vaccine Adverse Events (OVAE) that logically represents adverse events associated with licensed human vaccines.

Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development.

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format.

Effect of air exposure and suction on blood cell activation and hemolysis in an in vitro cardiotomy suction model.

Cardiopulmonary bypass (CPB) elicits a systemic inflammatory response. The cause may include surface-induced leukocyte activation and hemolysis. A study was designed to describe the effects of both suction and an air-blood interface independently and in combination on leukocyte and platelet activation, and hemolysis in an in vitro model. Fresh human blood was drawn and tested in four different conditions including control (A), 10 minutes of -600 mm Hg suction (B), 10 minutes of blood exposure to room air at 100 ml/min (C), and 10 minutes of simultaneous suction and air flow (D). Samples were analyzed by flow cytometry (platelets and leukocytes) and plasma-free hemoglobin (PFHb). Leukocyte CD11b expression and platelet P-selectin (CD62P) were analyzed by flow cytometry. In comparison with baseline, granulocytes were significantly activated by air (group C, p = 0.0029) and combination (group D, p = 0.0123) but not by suction alone (group B). Monocytes and platelets were not significantly activated in any group. The PFHb increased significantly in group C (p < 0.001) and group D (p < 0.001). This study suggests that the inflammatory response and associated hemolysis during CPB may be related to air exposure, which could be reduced by minimizing the air exposure of air to blood during cardiotomy suction.