Facilitating the analysis of immunological data with visual analytic techniques.

Visual analytics (VA) has emerged as a new way to analyze large dataset through interactive visual display. We demonstrated the utility and the flexibility of a VA approach in the analysis of biological datasets. Examples of these datasets in immunology include flow cytometry, Luminex data, and genotyping (e.g., single nucleotide polymorphism) data. Contrary to the traditional information visualization approach, VA restores the analysis power in the hands of analyst by allowing the analyst to engage in real-time data exploration process. We selected the VA software called Tableau after evaluating several VA tools. Two types of analysis tasks analysis within and between datasets were demonstrated in the video presentation using an approach called paired analysis. Paired analysis, as defined in VA, is an analysis approach in which a VA tool expert works side-by-side with a domain expert during the analysis. The domain expert is the one who understands the significance of the data, and asks the questions that the collected data might address. The tool expert then creates visualizations to help find patterns in the data that might answer these questions. The short lag-time between the hypothesis generation and the rapid visual display of the data is the main advantage of a VA approach.

Ontogeny of Toll-like receptor mediated cytokine responses of human blood mononuclear cells.

Newborns and young infants suffer increased infectious morbidity and mortality as compared to older children and adults. Morbidity and mortality due to infection are highest during the first weeks of life, decreasing over several years. Furthermore, most vaccines are not administered around birth, but over the first few years of life. A more complete understanding of the ontogeny of the immune system over the first years of life is thus urgently needed. Here, we applied the most comprehensive analysis focused on the innate immune response following TLR stimulation over the first 2 years of life in the largest such longitudinal cohort studied to-date (35 subjects). We found that innate TLR responses (i) known to support Th17 adaptive immune responses (IL-23, IL-6) peaked around birth and declined over the following 2 years only to increase again by adulthood; (ii) potentially supporting antiviral defense (IFN-α) reached adult level function by 1 year of age; (iii) known to support Th1 type immunity (IL-12p70, IFN-γ) slowly rose from a low at birth but remained far below adult responses even at 2 years of age; (iv) inducing IL-10 production steadily declined from a high around birth to adult levels by 1 or 2 years of age, and; (v) leading to production of TNF-α or IL-1ß varied by stimuli. Our data contradict the notion of a linear progression from an 'immature' neonatal to a 'mature' adult pattern, but instead indicate the existence of qualitative and quantitative age-specific changes in innate immune reactivity in response to TLR stimulation.

Surveillance of mosquito-borne viruses in Alberta using reverse transcription polymerase chain reaction with generic primers.

Mosquitoes collected during 2003, 2004, and 2005 in Alberta, Canada, were screened for the presence of a wide range of arboviruses by reverse transcription-polymerase chain reaction (RT-PCR). Nucleic acid extracts from mosquito slurries were amplified using universal primers designed to detect viruses belonging to the Flavivirus genus of the Flaviviridae family and California and Bunyamwera serogroups of the Bunyavirus genus within the Bunyaviridae family. Species-specific detection of Western equine encephalitis virus and Eastern equine encephalitis virus was also performed. Amplified products were analyzed, and the viral target was identified by sequencing. Of the 418 pools tested, 3 pools contained Cache Valley virus belonging to Bunyaviridae and 103 pools were positive for a previously undescribed flaviviral sequence that was most similar to Kamiti River virus. These data suggest that nucleic acid amplification using broadly reactive primers can be adopted for arbovirus surveillance in mosquito populations, and this approach has the potential to detect both previously recognized and novel viruses.

Adamantane resistance in circulating human influenza A viruses from Alberta, Canada (1970-2007).

Mutation in one of five key amino acid residues (positions 26, 27, 30, 31 and 34) within the M2 protein of influenza A viruses, leads to resistance against the adamantane class of anti-influenza drugs. To investigate the emergence and prevalence of adamantane resistance in Alberta, Canada (between 1970 and 2007), 381 influenza A positive samples (original patient specimens) or isolates (virus cultured from patient specimens) were analyzed for changes in these critical amino acid residues. Our results show a significant increase in adamantane resistance in circulating H3N2 viruses in Alberta from 2005 and 2006 when compared with those from 2004 (p<0.001). Adamantane resistance peaked at 74% in 2006 and then decreased (to 38%) in 2007 (p=0.001). All resistant H3N2 viruses contained the substitution Ser to Asn at amino acid position 31 of the M2 protein with two viruses having an additional Ala to Val substitution at position 30. Resistance was not observed in the H1N1 viruses tested. Results presented here are concordant with, and extend, previous reports of increased resistance to adamantanes in Asia and North America in recent years. It is important to continue studies to evaluate circulating influenza A viruses for antiviral resistance markers to ensure their optimal use for prophylaxis and treatment of influenza.