Access to Scientific Publications: The Scientist's Perspective

BACKGROUND: Scientific publishing is undergoing significant changes due to the growth of online publications, increases in the number of open access journals, and policies of funders and universities requiring authors to ensure that their publications become publicly accessible. Most studies of the impact of these changes have focused on the growth of articles available through open access or the number of open-access journals. Here, we investigated access to publications at a number of institutes and universities around the world, focusing on publications in HIV vaccine research--an area of biomedical research with special importance to the developing world. METHODS AND FINDINGS: We selected research papers in HIV vaccine research field, creating: 1) a first set of 50 most recently published papers with keywords "HIV vaccine" and 2) a second set of 200 articles randomly selected from those cited in the first set. Access to the majority (80%) of the recently published articles required subscription, while cited literature was much more accessible (67% freely available online). Subscriptions at a number of institutions around the world were assessed for providing access to subscription-only articles from the two sets. The access levels varied widely, ranging among institutions from 20% to 90%. Through the WHO-supported HINARI program, institutes in low-income countries had access comparable to that of institutes in the North. Finally, we examined the response rates for reprint requests sent to corresponding authors, a method commonly used before internet access became widespread. Contacting corresponding authors with requests for electronic copies of articles by email resulted in a 55-60% success rate, although in some cases it took up to 1.5 months to get a response. CONCLUSIONS: While research articles are increasingly available on the internet in open access format, institutional subscriptions continue to play an important role. However, subscriptions do not provide access to the full range of HIV vaccine research literature. Access to papers through subscriptions is complemented by a variety of other means, including emailing corresponding authors, joint affiliations, use of someone else's login information and posting requests on message boards. This complex picture makes it difficult to assess the real ability of scientists to access literature, but the observed differences in access levels between institutions suggest an unlevel playing field, in which some researchers have to spend more efforts than others to obtain the same information

AIDS Vaccine for Asia Network (AVAN): Expanding the Regional Role in Developing HIV Vaccines

Yiming Shao and colleagues describe the work of AVAN, the AIDS Vaccine for Asia Network, which aims to strengthen its regional efforts in finding an AIDS vaccine

Declining HIV-1 Prevalence and Incidence among Police Officers - A potential Cohort for HIV Vaccine Trials, in Dar es Salaam, Tanzania.

A safe effective and affordable HIV vaccine is the most cost effective way to prevent HIV infection worldwide. Current studies of HIV prevalence and incidence are needed to determine potentially suitable cohorts for vaccine studies. The prevalence and incidence of HIV-1 infection among the police in Dar es Salaam in 1996 were 13.8% and 19.6/1000 PYAR respectively. This study aimed at determining the current prevalence and incidence of HIV in a police cohort 10 years after a similar study was conducted. Police officers in Dar es Salaam, Tanzania were prospectively enrolled into the study from 2005 and followed-up in an incidence study three years later. HIV infection was determined by two sequential enzyme linked immunosorbent assays (ELISAs) in the prevalence study and discordant results between two ELISAs were resolved by a Western blot assay. Rapid HIV assays (SD Bioline and Determine) were used for the incidence study. A total of 1,240 police participated in the HIV prevalence study from August 2005 to November 2008. Of these, 1101 joined the study from August 2005-September 2007 and an additional 139 were recruited between October 2007 to November 2008 while conducting the incidence study. A total of 726 (70%) out of the 1043 eligible police participated in the incidence study.The overall HIV-1 prevalence was 65/1240 (5.2%). Females had a non-statistically significant higher prevalence of HIV infection compared to males 19/253, (7.5%) vs. 46/987 (4.7%) respectively (p = 0.07). The overall incidence of HIV-1 was 8.4 per 1000 PYAR (95% CI 4.68-14.03), and by gender was 8.8 and 6.9 per 1000 PYAR, among males and females respectively, (p = 0.82). The HIV prevalence and incidence among the studied police has declined over the past 10 years, and therefore this cohort is better suited for phase I/II HIV vaccine studies than for efficacy trials

A Qualitative Study of Perceived Risk for HIV Transmission among Police Officers in Dar es Salaam, Tanzania.

Understanding people's views about HIV transmission by investigating a specific population may help to design effective HIV prevention strategies. In addition, knowing the inherent sexual practices of such a population, as well as the risky circumstances that may facilitate HIV transmission, is crucial for the said strategies to become effective. In this article, we report how police officers in Dar es Salaam, Tanzania, perceived the problem of HIV and AIDS in their local context, particularly in relation to unsafe sexual practices. The study was done with the view to recommending ways by which HIV transmission could be minimised within the police force. The study was conducted among members of the police force in Dar es Salaam, Tanzania. Eight focus group discussions (FGDs) were conducted, with a total of 66 participants who were mixed in terms of age, gender, and marital status. Some of these were caregivers to patients with AIDS. Data were analysed using the interpretive description approach. The participants believed that both individual sexual behaviour and work-related circumstances were sources of HIV infection. They also admitted that they were being tempted to engage in risky sexual practices because of the institutional rules that prohibit officers from getting married during their training and for three years after. Nevertheless, as members of the Police Force, they stressed the fact that the risky sexual behaviour that exposes them to HIV is not limited to the force; it is rather a common problem that is faced by the general population. However, they complained, the nature of their job exposes them to road accident victims, subjecting them further to possible infection, especially when they have to handle these road accident casualties without proper protective gear. Individual sexual behaviour and job-related circumstances are worth investigating if proper advice is to be given to the police regarding HIV prevention strategies. In order to improve the lives of these police officers, there is a need to review the existing institutional rules and practices to accommodate individual sexual needs. In addition, improving their working environment may minimize the risk of HIV transmission from handling casualties in emergency situations

Willingness to participate in future HIV prevention studies among gay and bisexual men in Scotland, UK: a challenge for intervention trials

This article examines willingness to participate in future HIV prevention research among gay and bisexual men in Scotland, UK. Anonymous, self-complete questionnaires and Orasure Gäó oral fluid samples were collected in commercial gay venues. 1,320 men were eligible for inclusion. 78.2% reported willingness to participate in future HIV prevention research; 64.6% for an HIV vaccine, 57.4% for a behaviour change study, and 53.0% for a rectal microbicide. In multivariate analysis, for HIV vaccine research, greater age, minority ethnicity, and not providing an oral fluid sample were associated with lower willingness; heterosexual orientation and not providing an oral fluid sample were for microbicides; higher education and greater HIV treatment optimism were for behaviour change. STI testing remained associated with being more willing to participate in microbicide research and frequent gay scene use remained associated with being more willing to participate in behaviour change research. Having an STI in the past 12 months remained significantly associated with being willing to participate in all three study types. There were no associations between sexual risk behaviour and willingness. Although most men expressed willingness to participate in future research, recruitment of high-risk men, who have the potential to benefit most, is likely to be more challenging

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software

Pregnancy Incidence and Correlates during the HVTN 503 Phambili HIV Vaccine Trial Conducted among South African Women

HIV prevention trials are increasingly being conducted in sub-Saharan Africa. Women at risk for HIV are also at risk of pregnancy. To maximize safety, women agree to avoid pregnancy during trials, yet pregnancies occur. Using data from the HVTN 503/"Phambili" vaccine trial, we report pregnancy incidence during and after the vaccination period and identify factors, measured at screening, associated with incident pregnancy.To enrol in the trial, women agreed and were supported to avoid pregnancy until 1 month after their third and final vaccination ("vaccination period"), corresponding to the first 7 months of follow-up. Unsterilized women, pooled across study arms, were analyzed. Poisson regression compared pregnancy rates during and after the vaccination period. Cox proportional hazards regression identified associations with first pregnancy.Among 352 women (median age 23 yrs; median follow-up 1.5 yrs), pregnancy incidence was 9.6/100 women-years overall and 6.8/100 w-yrs and 11.3/100 w-yrs during and after the vaccination period, respectively [Rate Ratio = 0.60 (0.32-1.14), p = 0.10]. In multivariable analysis, pregnancy was reduced among women who: enrolled at sites providing contraception on-site [HR = 0.43, 95% CI (0.22-0.86)]; entered the trial as injectable contraceptive users [HR = 0.37 (0.21-0.67)] or as consistent condom users (trend) [HR = 0.54 (0.28-1.04)]. Compared with women with a single partner of HIV-unknown status, pregnancy rates were increased among women with: a single partner whose status was HIV-negative [HR = 2.34(1.16-4.73)] and; 2 partners both of HIV-unknown status [HR = 4.42(1.59-12.29)]. Women with 2 more of these risk factors: marijuana use, heavy drinking, or use of either during sex, had increased pregnancy incidence [HR = 2.66 (1.24-5.72)].It is possible to screen South African women for pregnancy risk at trial entry. Providing injectable contraception for free on-site and supporting consistent condom use may reduce incident pregnancy. Screening should determine the substance use, partnering, and HIV status of both members of the couple for both pregnancy and HIV prevention.SA National Health Research Database DOH-27-0207-1539; Clinicaltrials.gov NCT00413725

Altering an Artificial Gagpolnef Polyprotein and Mode of ENV Co-Administration Affects the Immunogenicity of a Clade C HIV DNA Vaccine

HIV-1 candidate vaccines expressing an artificial polyprotein comprising Gag, Pol and Nef (GPN) and a secreted envelope protein (Env) were shown in recent Phase I/II clinical trials to induce high levels of polyfunctional T cell responses; however, Env-specific responses clearly exceeded those against Gag. Here, we assess the impact of the GPN immunogen design and variations in the formulation and vaccination regimen of a combined GPN/Env DNA vaccine on the T cell responses against the various HIV proteins. Subtle modifications were introduced into the GPN gene to increase Gag expression, modify the expression ratio of Gag to PolNef and support budding of virus-like particles. I.m. administration of the various DNA constructs into BALB/c mice resulted in an up to 10-fold increase in Gag- and Pol-specific IFNγ+ CD8+ T cells compared to GPN. Co-administering Env with Gag or GPN derivatives largely abrogated Gag-specific responses. Alterations in the molar ratio of the DNA vaccines and spatially or temporally separated administration induced more balanced T cell responses. Whereas forced co-expression of Gag and Env from one plasmid induced predominantly Env-specific T cells responses, deletion of the only H-2d T cell epitope in Env allowed increased levels of Gag-specific T cells, suggesting competition at an epitope level. Our data demonstrate that the biochemical properties of an artificial polyprotein clearly influence the levels of antigen-specific T cells, and variations in formulation and schedule can overcome competition for the induction of these responses. These results are guiding the design of ongoing pre-clinical and clinical trials