The Phyre2 web portal for protein modeling, prediction and analysis

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission

History of malaria treatment as a predictor of subsequent subclinical parasitaemia: A cross-sectional survey and malaria case records from three villages in Pailin, western Cambodia

Background: Treatment of the sub-clinical reservoir of malaria, which may maintain transmission, could be an important component of elimination strategies. The reliable detection of asymptomatic infections with low levels of parasitaemia requires high-volume quantitative polymerase chain reaction (uPCR), which is impractical to conduct on a large scale. It is unknown to what extent sub-clinical parasitaemias originate from recent or older clinical episodes. This study explored the association between clinical history of malaria and subsequent sub-clinical parasitaemia. Methods: In June 2013 a cross-sectional survey was conducted in three villages in Pailin, western Cambodia. Demographic and epidemiological data and blood samples were collected. Blood was tested for malaria by high-volume qP

History of malaria treatment as a predictor of subsequent subclinical parasitaemia: a cross-sectional survey and malaria case records from three villages in Pailin, western Cambodia

Background Treatment of the sub-clinical reservoir of malaria, which may maintain transmission, could be an important component of elimination strategies. The reliable detection of asymptomatic infections with low levels of parasitaemia requires high-volume quantitative polymerase chain reaction (uPCR), which is impractical to conduct on a large scale. It is unknown to what extent sub-clinical parasitaemias originate from recent or older clinical episodes. This study explored the association between clinical history of malaria and subsequent sub-clinical parasitaemia. Methods In June 2013 a cross-sectional survey was conducted in three villages in Pailin, western Cambodia. Demographic and epidemiological data and blood samples were collected. Blood was tested for malaria by high-volume qPCR. Positive samples were analysed by nested PCR to determine the Plasmodium species. To identify previous episodes of malaria, case records were collected from village malaria workers and local health facilities and linked to study participants. Results Among 1343 participants, 40/122 (32.8 %) with a history of clinical malaria were parasitaemic during the cross-sectional survey, compared to 172/1221 (14.1 %) without this history (p Conclusions A clinical episode of vivax malaria was associated with subsequent sub-clinical parasitaemia. Treatment of P. vivax with artemisinin-based combination therapy without primaquine often resulted in recurrent episodes. Targeting individuals with a history of clinical malaria will be insufficient to eliminate the sub-clinical reservoir as they constitute a minority of parasitaemias.</p

Pharmacology, physiology and performance: occupational drug use and HIV risk among female entertainment and sex workers in Cambodia.

In Cambodia, HIV prevalence among female entertainment and sex workers (FESW) is up to twenty times higher than in the general population. Use of amphetamine-type stimulants (ATS) has been associated with increased risk of HIV and other sexually transmitt

Pharmacology, physiology and performance: occupational drug use and HIV risk among female entertainment and sex workers in Cambodia.

In Cambodia, HIV prevalence among female entertainment and sex workers (FESW) is up to twenty times higher than in the general population. Use of amphetamine-type stimulants (ATS) has been associated with increased risk of HIV and other sexually transmitt

HIV treatment cascade among female entertainment and sex workers in Cambodia: Impact of amphetamine use and an HIV prevention program

Background: HIV prevalence remains high in Cambodia among female entertainment and sex workers (FESW), and amphetamine-type stimulant (ATS) use significantly increases risk of infection. A successful continuum of care (CoC) is key to effective clinical care and prevention. This study aimed to describe the HIV CoC in HIV-positive FESW. We examined CoC outcomes among HIV-positive FESW participating in the Cambodia Integrated HIV and Drug Prevention Implementation (CIPI) study, being implemented in ten provinces. CIPI is a trial aimed at reducing ATS use concomitant with the SMARTgirl HIV prevention program. Methods: From 2013 to 2016, 1198 FESW ≥ 18 years old who reported multiple sex partners and/or transactional sex were recruited. We identified 88 HIV-positive women at baseline. We described linkage to care as 12-month retention and viral suppression (<1000 copies/mL). Logistic regression analyses were conducted to examine correlates of retention in care at 12 months, and viral suppression. Results: Median age of the 88 HIV-positive women was 32 years [interquartile range (IQR) 28, 35]; 50% were working in entertainment venues and 50% as freelance sex workers; 70% reported SMARTgirl membership. In the past 3 months, women reported a median of 15 sex partners, 38% reported unprotected sex, and 55% reported using ATS. Overall, 88% were receiving HIV care, 83% were on antiretroviral therapy, 39% were retained in care at 12 months, and 23% were virally suppressed. SMARTgirl membership was independently associated with fourfold greater odds of 12-month retention in care (AOR = 4.16, 95% CI 1.38, 12.56). Those at high risk for an ATS use disorder had 91% lower odds of 12-month retention in care (AOR = 0.09, 95% CI 0.01, 0.72). Viral suppression was independently associated with SMARTgirl membership, older age, reporting of STI symptoms, worse symptoms of psychological distress, and greater numbers of sex partners. Conclusions: This is the first study to characterize the HIV CoC in Cambodian FESW. While most women were successfully linked to HIV care, retention and viral suppression were low. Tailored programs like SMARTgirl, targeting the broader population of HIV-positive FESW as well as interventions to reduce ATS use could optimize the clinical and population health benefits of HIV treatment. Trial registration This work reports data collected as part of a trial: NCT01835574. This work does not present trial results

Qualitative research and implementation science: Informing the acceptability and implementation of a trial of a conditional cash transfer intervention designed to reduce drug use and HIV risk

HIV risk remains high among Cambodian female entertainment and sex workers, driven by amphetamine-type substance use and sexual risk. Conditional cash transfer is an evidence-based approach to reduce stimulant use and optimize HIV/AIDS prevention, but questions remain regarding implementation in resource-limited settings. We conducted formative qualitative research to enhance acceptability of a conditional cash transfer intervention aimed at reducing amphetamine-type substance use and HIV risk among female entertainment/sex workers and inform implementation as part of a large cluster randomized trial. We conducted in-depth interviews with 30 female entertainment/sex workers. Interviews were digitally recorded and conducted and transcribed in Khmer. English transcripts were read for emerging themes and an initial coding scheme was developed. Data were coded using open and axial coding to clarify and consolidate initial themes. While most participants expressed enthusiasm for the intervention, financial and transportation issues emerged as key barriers to participation. The proposed incentive of USD$1 per screen was regarded as unacceptable and participants identified a need for transportation assistance. Participants also expressed concerns about directly observed urine specimen collection. Finally, while most participants found the 4-week aftercare program acceptable, the need for enjoyable as well as educational content was emphasized. Revisions to the protocol taking these data into account were made to optimize the acceptability of the intervention and the implementation of the trial. Findings identified key concerns and preferences that were taken into account in the final trial protocol. In particular, financial and transportation issues were identified as critical barriers to participation, with the potential to impact both intervention uptake and trial feasibility. Results demonstrate the value of formative qualitative research for clinical trial planning and implementation, particularly in settings where little is known about acceptability of interventions or willingness to participate

Protocol of a cluster randomised stepped-wedge trial of behavioural interventions targeting amphetamine-type stimulant use and sexual risk among female entertainment and sex workers in Cambodia

Introduction: HIV risk among female entertainment and sex workers (FESW) remains high and use of amphetamine-type stimulants (ATS) significantly increases this risk. We designed a cluster randomised stepped wedge trial (The Cambodia Integrated HIV and Drug Prevention Implementation (CIPI) study) to test sequentially delivered behavioural interventions targeting ATS use. Methods and analysis: The trial combines a 12-week Conditional Cash Transfer (CCT) intervention with 4 weeks of cognitive-behavioural group aftercare (AC) among FESW who use ATS. The primary goal is to reduce ATS use and unprotected sex among FESW. The CCT+AC intervention is being implemented in 10 provinces where order of delivery was randomised. Outcome assessments (OEs) including biomarkers and self-reported measures of recent sexual and drug use behaviours are conducted prior to implementation, and at three 6-month intervals after completion. Consultation with multiple groups and stakeholders on implementation factors facilitated acceptance and operationalisation of the trial. Statistical power and sample size calculations were based on expected changes in ATS use and unprotected sex at the population level as well as within subjects. Ethics and dissemination: Ethical approvals were granted by the Cambodia National Ethics Committee; University of New Mexico; University of California, San Francisco; and FHI360. The trial is registered with ClinicalTrials.gov. Dissemination of process indicators during the multiyear trial is carried out through annual in-country Stakeholder Meetings. Provincial 'Close-Out' forums are held at the conclusion of data collection in each province. When analysis is completed, dissemination meetings will be held in Cambodia with stakeholders, including community-based discussion sessions, policy briefs and results published and presented in the HIV prevention scientific journals and conferences. Conclusions: CIPI is the first trial of an intervention to reduce ATS use and HIV risk among FESW in Cambodia. Results: Will inform both CCT+AC implementation in low and middle-income countries and programmes designed to reach FESW. Trial registration number: NCT01835574; Pre-results