A Model for a Chikungunya Outbreak in a Rural Cambodian Setting: Implications for Disease Control in Uninfected Areas

Following almost 30 years of relative silence, chikungunya fever reemerged in Kenya in 2004. It subsequently spread to the islands of the Indian Ocean, reaching Southeast Asia in 2006. The virus was first detected in Cambodia in 2011 and a large outbreak occurred in the village of Trapeang Roka Kampong Speu Province in March 2012, in which 44% of the villagers had a recent infection biologically confirmed. The epidemic curve was constructed from the number of biologically-confirmed CHIKV cases per day determined from the date of fever onset, which was self-reported during a data collection campaign conducted in the village after the outbreak. All individuals participating in the campaign had infections confirmed by laboratory analysis, allowing for the identification of asymptomatic cases and those with an unreported date of fever onset. We develop a stochastic model explicitly including such cases, all of whom do not appear on the epidemic curve. We estimate the basic reproduction number of the outbreak to be 6.46 (95% C.I. [6.24, 6.78]). We show that this estimate is particularly sensitive to changes in the biting rate and mosquito longevity. Our model also indicates that the infection was more widespread within the population on the reported epidemic start date. We show that the exclusion of asymptomatic cases and cases with undocumented onset dates can lead to an underestimation of the reproduction number which, in turn, could negatively impact control strategies implemented by public health authorities. We highlight the need for properly documenting newly emerging pathogens in immunologically naive populations and the importance of identifying the route of disease introduction.     

Molecular structure of the rhamsan-like exocellular polysaccharide RMDP17 from Sphingomonas paucimobilis.

X-Ray diffraction analysis of the sodium salt of the polysaccharide RMDP17, a 2-deoxy rhamsan analog, reveals that it adopts a gellan-like, half-staggered, threefold, left handed, double helix of pitch 57.4 A. The side chain of the branched polymer is hydrogen bonded to the main chain. Sodium ions, linked to the carboxylate groups, promote the association of helices via water molecules. Two helices of opposite polarity occupy a trigonal unit cell of dimensions a=17.6 and c=28.7 A. The packing arrangement displays a series of hydrogen bonds involving main chain and side chain atoms, as well as some water bridges, between the helices.     

Life cycle assessment of Australian sugarcane products with a focus on cane processing

Purpose  

This work generates attributional life cycle assessment (LCA) results for products produced from Australian sugarcane—raw sugar, molasses, electricity (from bagasse combustion), and ethanol (from molasses). It focuses on cane processing in sugar mills and is a companion to the work presented in (Renouf et al. 2010), where the focus is on cane growing. This work also examines the preferred approach for assigning impacts to the multiple products from cane processing, and the influence that variability in cane growing has on the results.     

Small mammal (rodents and lagomorphs) European biogeography from the Late Oligocene to the mid Pliocene

Aim To analyse the fossil species assemblages of rodents and lagomorphs from the European Neogene in order to assess what factors control small mammal biogeography at a deep‐time evolutionary time‐scale. Location Western Europe: 626 fossil‐bearing localities located within 31 regions and distributed among 18 successive biochronological units ranging from c. 27 Ma (million years ago; Late Oligocene) to c. 3 Ma (mid Pliocene). Methods Taxonomically homogenized pooled regional assemblages are compared using the Raup and Crick index of faunal similarity; then, the inferred similarity matrices are visualized as neighbour‐joining trees and by projecting the statistically significant interregional similarities and dissimilarities onto palaeogeographical maps. The inferred biogeographical patterns are analysed and discussed in the light of known palaeogeographical and palaeoclimatic events. Results Successive time intervals with distinct biogeographical contexts are identified. Prior to c. 18 Ma (Late Oligocene and Early Miocene), a relative faunal homogeneity (high interregional connectivity) is observed all over Europe, a time when major geographical barriers and a weak climatic gradient are known. Then, from the beginning of the Middle Miocene onwards, the biogeography is marked by a significant decrease in interregional faunal affinities which matches a drastic global climatic degradation and leads, in the Late Miocene (c. 11 Ma), to a marked latitudinal pattern of small mammal distribution. In spite of a short rehomogenization around the Miocene/Pliocene boundary (6–4 Ma), the biogeography of small mammals in the mid Pliocene (c. 3 Ma) finally closely reflects the extant situation. Main conclusions The resulting biogeographical evolutionary scheme indicates that the extant endemic situation has deep historical roots corresponding to global tectonic and climatic events acting as primary drivers of long‐term changes. The correlation of biogeographical events with climatic changes emphasizes the prevalent role of the climate over geography in generating heterogeneous biogeographical patterns at the continental scale.     

Positive Impact of Increases in Condom Use among Female Sex Workers and Clients in a Medium HIV Prevalence Epidemic: Modelling Results from Project SIDA1/2/3 in Cotonou,Benin

Background

A comprehensive, HIV prevention programme (Projet Sida1/2/3) was implemented among female sex workers (FSWs) in Cotonou, Benin, in 1993 following which condom use among FSWs increased threefold between 1993 and 2008 while FSW HIV prevalence declined from 53.3% to 30.4%.

Objective

Estimate the potential impact of the intervention on HIV prevalence/incidence in FSWs, clients and the general population in Cotonou, Benin.

Methods and Findings

A transmission dynamics model parameterised with setting-specific bio-behavioural data was used within a Bayesian framework to fit the model and simulate HIV transmission in the high and low-risk population of Cotonou and to estimate HIV incidence and infections averted by SIDA1/2/3. Our model results suggest that prior to SIDA1/2/3 commercial sex had contributed directly or indirectly to 93% (84–98%) of all cumulative infections and that the observed decline in FSWs HIV prevalence was more consistent with the self-reported post-intervention increase in condom use by FSWs than a counterfactual assuming no change in condom use after 1993 (CF-1). Compared to the counterfactual (CF-1), the increase in condom use may have prevented 62% (52–71%) of new HIV infections among FSWs between 1993 and 2008 and 33% (20–46%) in the overall population.

Conclusions

Our analysis provides plausible evidence that the post-intervention increase in condom use during commercial sex significantly reduced HIV prevalence and incidence among FSWs and general population. Sex worker interventions can be effective even in medium HIV prevalence epidemics and need to be sustained over the long-term.     

Probiotics: from bench to market

"Probiotics: From Bench to Market" was a one-day conference convened by the New York Academy of Sciences on June 11, 2010, with the goal of stimulating discussion of the physiological effects of probiotics on the gastrointestinal, nervous, and immune systems. The program included speakers from academia, industry, and government to give conference participants a full understanding of the state of the field of probiotics. The overall goal of the program was to increase communication and collaboration among these groups to advance probiotic research and probiotic contributions to public health. The conference was divided into three sessions and included both oral and visual presentations as well as panel discussions.     

Heterologous Prime-Boost Regimens with a Recombinant Chimpanzee Adenoviral Vector and Adjuvanted F4 Protein Elicit Polyfunctional HIV-1-Specific T-Cell Responses in Macaques

HIV-1-specific CD4⁺ and CD8⁺ T lymphocytes are important for HIV-1 replication control. F4/AS01 consists of F4 recombinant fusion protein (containing clade B Gag/p24, Pol/RT, Nef and Gag/p17) formulated in AS01 Adjuvant System, and was shown to induce F4-specific polyfunctional CD4⁺ T-cell responses in humans. While replication-incompetent recombinant HIV-1/SIV antigen-expressing human adenoviral vectors can elicit high-frequency antigen-specific CD8⁺ T-cell responses, their use is hampered by widespread pre-existing immunity to human serotypes. Non-human adenovirus serotypes associated with lower prevalence may offer an alternative strategy. We evaluated the immunogenicity of AdC7-GRN (‘A’), a recombinant chimpanzee adenovirus type 7 vector expressing clade B Gag, RT and Nef, and F4/AS01 (‘P’), when delivered intramuscularly in homologous (PP or AA) and heterologous (AAPP or PPAA) prime-boost regimens, in macaques and mice. Vaccine-induced HIV-1-antigen-specific T cells in peripheral blood (macaques), liver, spleen, and intestinal and genital mucosa (mice) were characterized by intracellular cytokine staining. Vaccine-specific IgG antibodies (macaques) were detected using ELISA. In macaques, only the heterologous prime-boost regimens induced polyfunctional, persistent and balanced CD4⁺ and CD8⁺ T-cell responses specific to each HIV-1 vaccine antigen. AdC7-GRN priming increased the polyfunctionality of F4/AS01-induced CD4⁺ T cells. Approximately 50% of AdC7-GRN-induced memory CD8⁺ T cells exhibited an effector-memory phenotype. HIV-1-specific antibodies were detected with each regimen. In mice, antigen-specific CD4⁺ and CD8⁺ T-cell responses were detected in the mucosal and systemic anatomical compartments assessed. When administered in heterologous prime-boost regimens, AdC7-GRN and F4/AS01 candidate vaccines acted complementarily in inducing potent and persistent peripheral blood HIV-1-specific CD4⁺ and CD8⁺ T-cell responses and antibodies in macaques. Besides, adenoviral vector priming modulated the cytokine-expression profile of the protein-induced CD4⁺ T cells. Each regimen induced HIV-1-specific T-cell responses in systemic/local tissues in mice. This suggests that prime-boost regimens combining adjuvanted protein and low-seroprevalent chimpanzee adenoviral vectors represent an attractive vaccination strategy for clinical evaluation.