Laura Cowen

Global Proteome Analysis of Leptospira interrogans

Comparative global proteome analyses were performed on Leptospira interrogans serovar Copenhageni grown under conventional in vitro conditions and those mimicking in vivo conditions (iron limitation and serum presence). Proteomic analyses were conducted using iTRAQ and LC-ESI-tandem mass spectrometry complemented with two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry. A total of 563 proteins were identified in this study. Altered expression of 65 proteins, including upregulation of the L. interrogans virulence factor Loa22 and 5 novel proteins with homology to virulence factors found in other pathogens, was observed between the comparative conditions. Immunoblot analyses confirmed upregulation of 5 of the known or putative virulence factors in L. interrogans exposed to the in vivo-like environmental conditions. Further, ELISA analyses using serum from patients with leptospirosis and immunofluorescence studies performed on liver sections derived from L. interrogans-infected hamsters verified expression of all but one of the identified proteins during infection. These studies, which represent the first documented comparative global proteome analysis of Leptospira, demonstrated proteome alterations under conditions that mimic in vivo infection and allowed for the identification of novel putative L. interrogans virulence factors.

Peer Review on Open-Source Software Projects: Parameters, Statistical Models, and Theory

Peer review is seen as an important quality-assurance mechanism in both industrial development and the open-source software (OSS) community. The techniques for performing inspections have been well studied in industry; in OSS development, software peer reviews are not as well understood. To develop an empirical understanding of OSS peer review, we examine the review policies of 25 OSS projects and study the archival records of six large, mature, successful OSS projects. We extract a series of measures based on those used in traditional inspection experiments. We measure the frequency of review, the size of the contribution under review, the level of participation during review, the experience and expertise of the individuals involved in the review, the review interval, and the number of issues discussed during review. We create statistical models of the review efficiency, review interval, and effectiveness, the issues discussed during review, to determine which measures have the largest impact on review efficacy. We find that OSS peer reviews are conducted asynchronously by empowered experts who focus on changes that are in their area of expertise. Reviewers provide timely, regular feedback on small changes. The descriptive statistics clearly show that OSS review is drastically different from traditional inspection.

New Proteins for a New Perspective on Syphilis Diagnosis

ABSTRACT Syphilis is a sexually transmitted disease caused by Treponema pallidum subsp. pallidum; it can be effectively treated with penicillin yet remains prevalent worldwide, due in part to the shortcomings of current diagnostic tests. Here we report the production of soluble recombinant versions of three novel diagnostic candidate proteins, Tp0326, Tp0453, and a Tp0453-Tp0326 chimera. The sensitivities of these recombinant proteins were assessed by screening characterized serum samples from primary, secondary, and latent stages of infection (n = 169). The specificities were assessed by screening false positives identified with the standard diagnostic testing algorithm (n = 21), samples from patients with potentially cross-reactive infections (Leptospira spp., Borrelia burgdorferi, Helicobacter pylori, Epstein-Barr virus, hepatitis B virus, hepatitis C virus, or cytomegalovirus) (n = 38), and samples from uninfected individuals (n = 11). The sensitivities of Tp0326, Tp0453, and the Tp0453-Tp0326 chimera were found to be 86%, 98%, and 98%, respectively, and the specificities were 99%, 100%, and 99%. In a direct comparison, the Captia syphilis (T. pallidum)-G enzyme immunoassay (Trinity Biotech) was used to screen the same serum samples and was found to have a sensitivity of 98% and a specificity of 90%. In particular, Tp0453 and the chimera exhibited superior accuracy in classifying analytical false-positive samples (100%, compared to 43% for the Captia assay). These findings identify Tp0453 and the Tp0453-Tp0326 chimera as novel syphilis-specific diagnostic candidates that surpass the performance of a currently available diagnostic enzyme immunoassay test for syphilis and that allow accurate detection of all stages of infection.

A mixed methods approach to delineating and understanding injection practices among clientele of a Victoria, British Columbia needle exchange program

INTRODUCTION AND AIMS Systematic reviews and meta-analyses show that needle exchange programs reduce HIV and HCV transmission for injection drug users (IDUs) but far less is known about the injection practices of IDUs enrolled in these programs. This study adopts a mixed methods approach to quantify high-risk injection practice patterns among IDUs enrolled in a needle exchange program in Victoria, British Columbia, Canada and gather qualitative data to understand underlying injection behaviour rationales and patterns. DESIGN AND METHODS Survey data collected in 2008 from 105 IDUs registered as clientele of the AIDS Vancouver Island-Street Outreach Services (AVI-SOS) Needle Exchange were analysed via univariate and multivariate statistical methods. Presentation of this analysis to an AVI-SOS needle exchange clientele group generated qualitative data offering an explanation for quantitative results. RESULTS . Univariate analysis showed all respondents reporting at least one high-risk practice within the past month. Multivariate logistic regression analysis using input from AVI-SOS clientele confirmed the importance of housing status as a determinant of injection practices. DISCUSSION AND CONCLUSIONS The importance of housing status points to the need to combine harm reduction services, for example needle exchange and appropriate housing and highlights the benefits of including IDUs in data interpretation.

Worry as a window into the lives of people who use injection drugs: a factor analysis approach

BackgroundThe concept of risk dominates the HIV/AIDS literature pertaining to People Who Use Injection Drugs (PWUID). In contrast the associated concept of worry is infrequently applied, even though it can produce important perspectives of PWUIDs lives. This study asked a sample (n = 105) of PWUID enrolled in a Victoria, British Columbia needle exchange program to evaluate their degree of worry about fourteen factors they may encounter in their daily lives.MethodsExploratory factor analysis was used to analyze their responses.ResultsFactor analysis delineated three factors: 1) overall personal security, 2) injection drug use-specific risks including overdosing and vein collapse and, 3) contracting infectious diseases associated with injection drug use (e.g. HIV/AIDS and hepatitis C).ConclusionPWUID in this study not only worry about HIV/AIDS but also about stressful factors in their daily life which have been linked to both increased HIV/AIDS risk behaviour and decreased anti-retroviral treatment adherence. The importance PWUID give to this broad range of worry/concerns emphasizes the need to place HIV/AIDS intervention, education, and treatment programs within a broader harm-reduction framework that incorporates their perspectives on both worry and risk.

Effects of Angling on Chinook Salmon for the Nicola River, British Columbia, 1996–2002

Abstract To sustain viable fish populations, protect stocks of wild salmon Oncorhynchus spp., and successfully manage the Pacific salmon fishery, all sources of fishing mortality need to be understood. The fishery targeting Chinook salmon O. tshawytscha is an important component of the commercial, recreational, and First Nations fisheries in British Columbia. A mark–recovery study was used to investigate the effect of angling on both the immediate hooking mortality and subsequent spawning success of Chinook salmon in the Nicola River, British Columbia, from 1996 to 2002. The immediate hooking mortality rate was lower than mortality rates reported for marine and other freshwater fisheries. Higher hooking mortality rates were found for fish hooked in critical locations, which were associated with heavy bleeding. However, increased bleeding did not translate into reduced spawning success for those fish that survived. Conclusions regarding hook size and its association with hooking mortality rate and spawning...

A comparison of abundance estimates from extended batch-marking and Jolly–Seber-type experiments

Little attention has been paid to the use of multi-sample batch-marking studies, as it is generally assumed that an individuals capture history is necessary for fully efficient estimates. However, recently, Huggins et al. (2010) present a pseudo-likelihood for a multi-sample batch-marking study where they used estimating equations to solve for survival and capture probabilities and then derived abundance estimates using a Horvitz–Thompson-type estimator. We have developed and maximized the likelihood for batch-marking studies. We use data simulated from a Jolly–Seber-type study and convert this to what would have been obtained from an extended batch-marking study. We compare our abundance estimates obtained from the Crosbie–Manly–Arnason–Schwarz (CMAS) model with those of the extended batch-marking model to determine the efficiency of collecting and analyzing batch-marking data. We found that estimates of abundance were similar for all three estimators: CMAS, Huggins, and our likelihood. Gains are made when using unique identifiers and employing the CMAS model in terms of precision; however, the likelihood typically had lower mean square error than the pseudo-likelihood method of Huggins et al. (2010). When faced with designing a batch-marking study, researchers can be confident in obtaining unbiased abundance estimators. Furthermore, they can design studies in order to reduce mean square error by manipulating capture probabilities and sample size.

Applying open population capture–recapture models to estimate the abundance of injection drug users in Victoria, Canada

Abstract Background: Injection drug users (IDUs) are considered a hidden, hard to reach population that is difficult to measure. Multi-list recapture methods are commonly used to estimate IDU population sizes but do not allow inference on population dynamics. In Victoria, Canada, closed population capture–recapture methods have been used to estimate the abundance of IDUs. In this study, we make use of a newer sample of a survey of IDUs to relax the closure assumption. Methods: The I-Track survey of IDUs was carried out in Victoria on three occasions (2003, 2005 and 2009). Data from the three samples were linked using unique subject identifiers. A Jolly-Seber model was used to estimate the number of IDUs. Results: The results were very similar to a two-sample closed population analysis. However, when using open-population models, it is possible to get estimates for each time period of abundance and survival. The estimate of the number of the IDUs in Greater Victoria was relatively stable with fewer than 3000 individuals over the six-year study. Discussion: Improved estimates of population size and dynamics will assist in improving access to harm reduction services, which may reduce higher risk drug use practices.

Hidden Markov Models for Extended Batch Data

Batch marking provides an important and efficient way to estimate the survival probabilities and population sizes of wild animals. It is particularly useful when dealing with animals that are difficult to mark individually. For the first time, we provide the likelihood for extended batch-marking experiments. It is often the case that samples contain individuals that remain unmarked, due to time and other constraints, and this information has not previously been analyzed. We provide ways of modeling such information, including an open N-mixture approach. We demonstrate that models for both marked and unmarked individuals are hidden Markov models; this provides a unified approach, and is the key to developing methods for fast likelihood computation and maximization. Likelihoods for marked and unmarked individuals can easily be combined using integrated population modeling. This allows the simultaneous estimation of population size and immigration, in addition to survival, as well as efficient estimation of standard errors and methods of model selection and evaluation, using standard likelihood techniques. Alternative methods for estimating population size are presented and compared. An illustration is provided by a weather-loach data set, previously analyzed by means of a complex procedure of constructing a pseudo likelihood, the formation of estimating equations, the use of sandwich estimates of variance, and piecemeal estimation of population size. Simulation provides general validation of the hidden Markov model methods developed and demonstrates their excellent performance and efficiency. This is especially notable due to the large numbers of hidden states that may be typically required.