The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release ‘modules’ that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available through feature-rich web applications that provide search, data mining, and genome browser functionality, and also by bulk download and web services. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe. The site also hosts ‘science apps,’ developed as prototypes for community modules that use dynamic web pages to present data obtained on-demand from third-party servers via RESTful web services. Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages collaborative enhancement of the resource by its user community.

Natural hazards engineering plays an important role in minimizing the effects of natural hazards 9 on society through the design of resilient and sustainable infrastructure. The DesignSafe 10 cyberinfrastructure has been developed to enable and facilitate transformative research in natural 11 hazards engineering, which necessarily spans across multiple disciplines and can take advantage 12 of advancements in computation, experimentation, and data analysis. DesignSafe allows researchers to more effectively share and find data using cloud services, perform numerical 14 simulations using high performance computing, and integrate diverse datasets such that researchers can make discoveries that were previously unattainable. This paper describes the design principles used in the cyberinfrastructure development process, introduces the main components of the DesignSafe cyberinfrastructure, and illustrates the use of the DesignSafe cyberinfrastructure in research in natural hazards engineering through various examples.

Culture for Bordetella pertussis (B. pertussis) is the traditional gold standard for laboratory diagnosis of pertussis but is insensitive, especially later in the course of illness and in vaccinated persons. Interpretation of serology is limited by the lack of an appropriate reference standard. An outbreak of pertussis in a crowded boarding-school dormitory allowed evaluation of laboratory correlates of infection. Questionnaires, serum samples and throat swabs were collected from members of the exposed group. Serum samples from unexposed controls of a similar age group were used for comparison. B. pertussis PCR was performed on throat swabs, and sera were tested for IgA antibodies against whole-cell (WC) B. pertussis antigen and IgG antibodies to pertussis toxin (PT). The Centers for Disease Control and Prevention definition for pertussis was used to define clinical cases. We evaluated the use of a previously published cut-off for PT IgG of 125 EIA units (EU)/ml. Completed questionnaires were obtained from 115 students, of whom 85 (74%) reported coughing symptoms, including 32 (28%) who met the clinical case definition for pertussis. B. pertussis was detected by PCR in 17 (15%) and WC IgA in 22 (19%) students; neither correlated with symptoms, but dormitory of residence strongly predicted PCR status. The mean PT IgG geometric mean concentration, in this situation of high pertussis exposure, correlated with severity of symptoms and was significantly higher in both symptomatic and asymptomatic children exposed during the outbreak (P < 0.001) than in control children. A cut-off for PT IgG of 125 EU/ml was too high in an outbreak situation to be sensitive enough to identify pertussis cases. A case of pertussis in a crowded boarding-school dormitory resulted rapidly in an outbreak. Serology and PCR were useful in identifying the outbreak and commencing disease control measures. The use of serology has mostly been evaluated in community serosurveys, where it is not possible to determine if immunity reflects vaccination, asymptomatic disease or symptomatic disease. This outbreak gave us the opportunity to evaluate the value of serology and PCR in the presence of confirmed exposure to pertussis.

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A study over a 5-year period (1979-1983) of RSV infections in children in Sydney, Australia is reported. In common with findings made elsewhere in the world, annual epidemics of RSV infection commencing in autumn and lasting 4-6 months, with peak activity in mid-winter, were observed in 1979, 1980, and 1983. However, in 1981 and 1982 virus activity was first detected in midsummer, peaked in autumn, and was present throughout most months of the year. The alteration in virus activity in 1981 and 1982 was not associated with changes restricted to these 2 years in factors such as the age groups or sex ratio of patients affected or in the clinical categories predominantly affected. A study of climatic variables, however, indicated unusually low rainfall in 3 of 4 years encompassing this period. Study over a longer period is indicated to determine if these observed alterations in seasonal activity of RSV will be repeated in future years. Any possible relationship of such a change to rainfall could then also be better assessed.

In Australia, notification of pertussis cases in older children or adults has increased significantly in recent years. In most cases, laboratory diagnosis is based only on a positive serological test for IgA antibody against whole cell Bordetella pertussis. During a 3-month period, 318 consecutive sera submitted for diagnosis of pertussis were tested for IgA antibody against whole cell (WC) sonicated B. pertussis, pertussis toxin (PT), filamentous haemagglutinin (FHA) and pertactin (PRN). Results of one or more of these tests were positive in sera from 175 subjects and clinical information was obtained by telephone interview from 90 subjects. Using a clinical case definition as the reference standard, the sensitivities of the four IgA assays were variable but quite low (24-64%), but the specificities were high (93-98%). For diagnosis of pertussis in subjects with a compatible clinical illness, these and other findings support the use of serological testing for IgA antibody.

Objective To evaluate the effectiveness in older Australians of the current tetanus vaccination program. Design A cross‐sectional survey of tetanus immunity (enzyme immunoassay of serum samples) in an older population in New South Wales. Self‐reported history of tetanus vaccination was compared with serologically measured immunity. Participants: 430 randomly selected adults, 49 years of age and older, from the Blue Mountains Eye Study population. Results Fifty‐two per cent (95% confidence interval [Cl], 47%–57%) of adults 49 years of age and older had protective levels of tetanus antitoxin (>0.15IU/mL). There was a significant decline in the prevalence of immunity with increasing age (χ2 for linear trend, P=0.036), and women were less likely to be immune regardless of their age (Mantel–Haenszel weighted odds ratio, 0.65; CI, 0.43–0.92). Thirty‐five per cent (95% CI, 31%–40%) of all participants reported that they had been vaccinated in the preceding 10 years. Although self‐reported tetanus vaccination history was associated with tetanus immunity, it was neither sensitive nor specific as a test for immunity. Conclusions About half the adults 49 years of age and older in the Blue Mountains area of New South Wales do not have protective levels of tetanus antitoxin because of inadequate vaccination coverage in this age group. Vaccination history is not a reliable indicator of tetanus immunity and a system is needed for accurate recording of adult vaccination.