Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode

Timing of therapy for latent tuberculosis infection among immigrants presenting to a U.S. public health clinic: a retrospective study

<p>Abstract</p> <p>Background</p> <p>In the U.S. more than half of incident tuberculosis (TB) cases occur in immigrants. Current guidelines recommend screening and treatment for latent TB infection (LTBI) within 5 years of arrival to the U.S. This study evaluates the timing of LTBI therapy among immigrants presenting for care to a public health TB clinic.</p> <p>Methods</p> <p>Retrospective chart review of patients prescribed LTBI treatment based on medical records from Prince Georges County Health Department.</p> <p>Results</p> <p>1882 immigrants received LTBI therapy at Prince Georges County Health Department between 1999 and 2004. 417 of these patients were diagnosed with LTBI through contact investigations and were excluded from the analysis. Among the remaining 1465 individuals, median time from arrival to the U.S. until initiation of LTBI therapy was 5 months (range 0–42.4 years). 16% of all immigrants initiated therapy more than 5 years after arrival to the U.S. A logistic regression model using risks identified on univariate analysis revealed that referral for therapy by non-immigration proceedings was the strongest predictor of initiation of therapy more than 5 years after arrival to the U.S. Other factors associated with > 5 year U.S. residence prior to initiation of LTBI therapy included female gender (adjusted odds ratio (AOR) 1.8, 95% CI 1.2–2.6), age ≥ 35 (AOR = 4.1, 95% 2.5–6.6), and originating from Latin American and the Caribbean (AOR = 1.9, 95% CI 1.3–3.0).</p> <p>Conclusion</p> <p>Foreign-born individuals who are not referred for LTBI therapy through immigration proceedings are less likely to receive LTBI therapy within 5 years of arrival to the U.S. These data highlight the need to explore other mechanisms for timely LTBI screening beyond services provided by immigration.</p

Exploring the dynamics of the quality of HIV care experienced by female sex workers living in the Dominican Republic

Despite increased attention and efforts to improve HIV care among female sex workers (FSWs), they continue to have suboptimal HIV outcomes. Exploring the socio-structural dynamics related to the quality of HIV care received by FSWs is critical to further strengthen interventions to improve their HIV care continuum outcomes. In this study, we conducted two rounds of qualitative in-depth interviews with 20 FSWs living with HIV in the Dominican Republic to explore how healthcare experiences contributed to their quality of HIV care. Data was analyzed using a thematic analytic approach exploring diverse structural and relational aspects of the quality of HIV care affecting FSWs as they navigate the clinic environment. Results indicated that quality of HIV care was influenced by both structural and relational factors within clinics. At the structural level, insufficient stock of antiretroviral therapy and the financial burden created by HIV care related costs hindered FSWs’ satisfaction with their current HIV care and presented a barrier in FSWs’ ability to access HIV care services. Quality of care was also closely linked to relational aspects of the HIV care environment, including FSWs’ relationship and communication with their clinical providers, as FSWs often expressed their satisfaction with HIV care experiences based on these interpersonal factors. Lastly, personal agency emerged as an important factor contributing to the quality of HIV care, specifically as FSWs’ treatment literacy resulted in greater advocacy and demands for quality care. Programmatic efforts should be directed to improving the quality of HIV care experiences of FSWs in the clinic environment. These include addressing resource shortages, promoting positive and effective patient-provider relationships, and facilitating HIV treatment education opportunities for FSWs

A Crowdsourcing Open Contest to Design Pre-Exposure Prophylaxis Promotion Messages: Protocol for an Exploratory Mixed Methods Study.

BACKGROUND: In the United States, black men who have sex with men (BMSM) are disproportionately affected by HIV. Pre-exposure prophylaxis (PrEP) can reduce HIV incidence. However, real-world implementation of PrEP outside of clinical trials has identified racial disparities in PrEP awareness, uptake, and adherence. In the context of a long history of medical mistrust and power imbalances between scientists and community members, strategies to increase uptake of PrEP among BMSM should consider ways to ensure messages address the needs and priorities of the community. Crowdsourcing contests shift traditional individual tasks to a large group and may enhance community engagement. OBJECTIVE: This paper describes the research protocol of a contest approach to soliciting PrEP promotion messages among BMSM in Baltimore. METHODS: Open-contest implementation and evaluation will proceed as follows: (1) organize a community steering group; (2) develop platforms to solicit crowd input; (3) engage the community to contribute ideas through a Web-based forum and in-person events; (4) evaluate contest entries using both community panel judge assessment and crowd voting; (5) utilize mixed methods to evaluate feasibility, acceptability, and community engagement; and (6) disseminate contest results. RESULTS: This study was funded by the National Institutes of Health (National Institute of Mental Health: R34MH116725) in May 2018 and was approved by the institutional review board in April 2018. The open contest started in February 2019, and data analyses for the mixed method evaluation are expected to complete in December 2019. CONCLUSIONS: The contest will potentially bring new ideas in developing more impactful and locally defined PrEP promotion campaigns. We will determine whether an open-contest approach is acceptable among BMSM in Baltimore. If successful, this study can inform future projects using a similar approach on how to identify and implement programs and policies that are more responsive to community needs and that build up community assets. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/15590

Objectively measured physical activity and sedentary time in youth: the International children's accelerometry database (ICAD).

BACKGROUND: Physical activity and sedentary behaviour in youth have been reported to vary by sex, age, weight status and country. However, supporting data are often self-reported and/or do not encompass a wide range of ages or geographical locations. This study aimed to describe objectively-measured physical activity and sedentary time patterns in youth. METHODS: The International Children's Accelerometry Database (ICAD) consists of ActiGraph accelerometer data from 20 studies in ten countries, processed using common data reduction procedures. Analyses were conducted on 27,637 participants (2.8-18.4 years) who provided at least three days of valid accelerometer data. Linear regression was used to examine associations between age, sex, weight status, country and physical activity outcomes. RESULTS: Boys were less sedentary and more active than girls at all ages. After 5 years of age there was an average cross-sectional decrease of 4.2% in total physical activity with each additional year of age, due mainly to lower levels of light-intensity physical activity and greater time spent sedentary. Physical activity did not differ by weight status in the youngest children, but from age seven onwards, overweight/obese participants were less active than their normal weight counterparts. Physical activity varied between samples from different countries, with a 15-20% difference between the highest and lowest countries at age 9-10 and a 26-28% difference at age 12-13. CONCLUSIONS: Physical activity differed between samples from different countries, but the associations between demographic characteristics and physical activity were consistently observed. Further research is needed to explore environmental and sociocultural explanations for these differences

Association between maternal education and objectively measured physical activity and sedentary time in adolescents

Investigating socioeconomic variation in physical activity (PA) and sedentary time is important as it may represent a pathway by which socioeconomic position (SEP) leads to ill health. Findings on the association between children's SEP and objectively assessed PA and/or sedentary time are mixed, and few studies have included international samples.Examine the associations between maternal education and adolescent's objectively assessed PA and sedentary time.This is an observational study of 12 770 adolescents (10-18 years) pooled from 10 studies from Europe, Australia, Brazil and the USA. Original PA data were collected between 1997 and 2009. The associations between maternal education and accelerometer variables were examined using robust multivariable regression, adjusted for a priori confounders (ie, body mass index, monitor wear time, season, age and sex) and regression coefficients combined across studies using random effects meta-analyses. Analyses were conducted in March 2014.Adolescents of university educated mothers spent more time sedentary (9.5 min/day, p=0.005) and less time in light activity (10 min/day, p<0.001) compared with adolescents of high school educated mothers. Pooled analysis across two studies from Brazil and Portugal (analysed separately because of the different coding of maternal education) showed that children of higher educated mothers (tertiary vs primary/secondary) spent less time in moderate to vigorous PA (MVPA) (6.6 min/day, p=0.001) and in light PA (39.2 min/day: p<0.001), and more time sedentary (45.9 min/day, p<0.001).Across a number of international samples, adolescents of mothers with lower education may not be at a disadvantage in terms of overall objectively measured PA

The Democratic Biopolitics of PrEP

PrEP (Pre-Exposure Prophylaxis) is a relatively new drug-based HIV prevention technique and an important means to lower the HIV risk of gay men who are especially vulnerable to HIV. From the perspective of biopolitics, PrEP inscribes itself in a larger trend of medicalization and the rise of pharmapower. This article reconstructs and evaluates contemporary literature on biopolitical theory as it applies to PrEP, by bringing it in a dialogue with a mapping of the political debate on PrEP. As PrEP changes sexual norms and subjectification, for example condom use and its meaning for gay subjectivity, it is highly contested. The article shows that the debate on PrEP can be best described with the concepts ‘sexual-somatic ethics’ and ‘democratic biopolitics’, which I develop based on the biopolitical approach of Nikolas Rose and Paul Rabinow. In contrast, interpretations of PrEP which are following governmentality studies or Italian Theory amount to either farfetched or trivial positions on PrEP, when seen in light of the political debate. Furthermore, the article is a contribution to the scholarship on gay subjectivity, highlighting how homophobia and homonormativity haunts gay sex even in liberal environments, and how PrEP can serve as an entry point for the destigmatization of gay sexuality and transformation of gay subjectivity. ‘Biopolitical democratization’ entails making explicit how medical technology and health care relates to sexual subjectification and ethics, to strengthen the voice of (potential) PrEP users in health politics, and to renegotiate the profit and power of Big Pharma

Harmonising data on the correlates of physical activity and sedentary behaviour in young people: Methods and lessons learnt from the international Children's Accelerometry database (ICAD).

BACKGROUND: Large, heterogeneous datasets are required to enhance understanding of the multi-level influences on children's physical activity and sedentary behaviour. One route to achieving this is through the pooling and co-analysis of data from multiple studies. Where this approach is used, transparency of the methodology for data collation and harmonisation is essential to enable appropriate analysis and interpretation of the derived data. In this paper, we describe the acquisition, management and harmonisation of non-accelerometer data in a project to expand the International Children's Accelerometry Database (ICAD). METHOD: Following a consultation process, ICAD partners were requested to share accelerometer data and information on selected behavioural, social, environmental and health-related constructs. All data were collated into a single repository for cataloguing and harmonisation. Harmonised variables were derived iteratively, with input from the ICAD investigators and a panel of invited experts. Extensive documentation, describing the source data and harmonisation procedure, was prepared and made available through the ICAD website. RESULTS: Work to expand ICAD has increased the number of studies with longitudinal accelerometer data, and expanded the breadth of behavioural, social and environmental characteristics that can be used as exposure variables. A set of core harmonised variables, including parent education, ethnicity, school travel mode/duration and car ownership, were derived for use by the research community. Guidance documents and facilities to enable the creation of new harmonised variables were also devised and made available to ICAD users. An expanded ICAD database was made available in May 2017. CONCLUSION: The project to expand ICAD further demonstrates the feasibility of pooling data on physical activity, sedentary behaviour and potential determinants from multiple studies. Key to this process is the rigorous conduct and reporting of retrospective data harmonisation, which is essential to the appropriate analysis and interpretation of derived data. These documents, made available through the ICAD website, may also serve as a guide to others undertaking similar projects