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The objective of this study was to identify the prevalence and correlates of phosphatidylethanol (PEth) levels suggestive of unhealthy alcohol use among women living with and without HIV who self-reported no or low-risk drinking. We analyzed data from a cross-sectional study among women enrolled in the San Francisco Bay Area site of the Womens Interagency HIV Study (WIHS). Between October 2017 and March 2018, PEth was tested from dried blood spots in 192 women enrolled in the San Francisco site of the WIHS. Using multivariable logistic regression, we identified the correlates of PEth levels suggestive of unhealthy alcohol use (>50 ng/ml) among the 168 women who reported no or low-risk drinking ( 1 (aOR = 3.10, 95% CI = 1.18-8.13), higher high-density lipoprotein levels (aOR = 1.31 per 10 mg/dL increase, 95% CI = 1.01-1.70), and consuming a greater number of drinks per week in the past six months (aOR = 1.40, 95% CI = 1.10-1.78). Nearly a third of women in this study had PEth levels suggestive of unhealthy alcohol use and potentially under-reported their use. To optimize alcohol related health care, there is a need to consider approaches to improve ascertainment of unhealthy alcohol use, especially among Black/African American women and those living with liver disease, so that interventions can be initiated.

BACKGROUND: Almost half of all women in the US experience intimate partner violence (IPV) in their lifetime. The US Preventive Services Task Force recommends IPV screening paired with intervention for women of reproductive age. We aim to understand clinical practices and policies that are beneficial, detrimental, or insufficient to support survivors of IPV in a safety-net healthcare system. METHODS: We sampled 45 women who were 18-64 years old, had experienced IPV within the prior year and were patients in the San Francisco Health Network. We conducted in-depth, semi-structured interviews to elicit their perspectives on disclosing IPV and obtaining support within the healthcare system. We analyzed our data using thematic analysis and grounded theory practices informed by ecological systems theory. FINDINGS: We identified four themes regarding factors that impeded or facilitated discussing and addressing IPV across interpersonal and systemic levels relating to relationship-building, respect, autonomy and resources. (1) Interpersonal barriers included insufficient attention to relationship-building, lack of respect or concern for survivor circumstances, and feeling pressured to disclose IPV or to comply with clinicians recommended interventions. (2) Interpersonal facilitators consisted of patient-centered IPV inquiry, attentive listening, strength-based counseling and transparency regarding confidentiality. (3) Systemic barriers such as visit time limitations, clinician turn-over and feared loss of autonomy from involvement of governmental systems leading to separation from children or harm to partners, negatively affected interpersonal dynamics. (4) Systemic facilitators involved provision of resources through IPV universal education, on-site access to IPV services, and community partnerships. CONCLUSIONS: Women experiencing IPV in our study reported that relationship-building, respect, autonomy, and IPV-related resources were essential components to providing support, promoting safety, and enabling healing in the healthcare setting. Successful trauma-informed transformation of healthcare systems must optimize interpersonal and systemic factors that improve survivor wellbeing while eliminating barriers.

Mobile crisis services for people experiencing distress related to mental health or substance use are expanding rapidly across the US, yet there is little evidence to support these specific models of care. These new programs present a unique opportunity to expand the literature by utilizing implementation science methods to inform the future design of crisis systems. This mixed methods study will examine the effectiveness and acceptability of the Street Crisis Response Team (SCRT), a new 911-dispatched multidisciplinary mobile crisis intervention piloted in San Francisco, California. First, using quantitative data from electronic health records, we will conduct an interrupted time series analysis to quantitatively examine the impacts of the SCRT on people experiencing homelessness who utilized public behavioral health crisis services in San Francisco between November 2019 and August 2022, across four main outcomes within 30 days of the crisis episode: routine care utilization, crisis care reutilization, assessment for housing services, and jail entry. Second, to understand its impact on health equity, we will analyze racial and ethnic disparities in these outcomes prior to and after implementation of the SCRT. For the qualitative component, we will conduct semi-structured interviews with recipients of the SCRTs services to understand their experiences of the intervention and to identify how the SCRT influenced their health-related trajectories after the crisis encounter. Once complete, the quantitative and qualitative findings will be further analyzed in tandem to assist with more nuanced understanding of the effectiveness of the SCRT program. This evaluation of a novel mobile crisis response program will advance the field, while also providing a model for how real-world program implementation can be achieved in crisis service settings.

Main objectiveSystematically review and synthesize preoperative and intraoperative factors associated with pain after total knee arthroplasty (TKA) in patients with osteoarthritis.MethodsBased on a peer-reviewed protocol, we searched Medline, Embase, CINAHL, Cochrane Library, and PEDro for prospective observational studies (January 2000 to February 2023) investigating factors associated with pain after TKA. The primary outcome was pain twelve months after TKA. Pain at three and six months were secondary outcomes. Multivariate random-effects meta-analyses were used to estimate mean correlation (95% CIs) between factors and pain. Sensitivity analysis was performed for each risk of bias domain and certainty of evidence was assessed.ResultsOf 13,640 studies, 29 reports of 10,360 patients and 61 factors were analysed. The mean correlation between preoperative factors and more severe pain at twelve months was estimated to be 0.36 (95% CI, 0.24, 0.47; P < .000; moderate-certainty evidence) for more catastrophizing, 0.15 (95% CI; 0.08, 0.23; P < .001; moderate-certainty evidence) for more symptomatic joints, 0.13 (95% CI, 0.06, 0.19; P < .001; very low-certainty evidence) for more preoperative pain. Mean correlation between more severe radiographic osteoarthritis and less pain was -0.15 (95% CI; -0.23, -0.08; P < .001; low-certainty evidence). In sensitivity analysis, the estimated correlation coefficient for pain catastrophizing factor increased to 0.38 (95% CI 0.04, 0.64). At six and three months, more severe preoperative pain was associated with more pain. Better preoperative mental health was associated with less pain at six months.Conclusion and relevanceMore pain catastrophizing, more symptomatic joints and more pain preoperatively were correlated with more pain, while more severe osteoarthritis was correlated with less pain one year after TKA. More preoperative pain was correlated with more pain, and better mental health with less pain at six and three months. These findings should be further tested in predictive models to gain knowledge which may improve TKA outcomes.

ObjectiveWe aimed to investigate whether anakinra, an interleukin-1receptor inhibitor, could improve outcome in moderate COVID-19 patients.MethodsIn this controlled, open-label trial, we enrolled adults with COVID-19 requiring oxygen. We randomly assigned patients to receive intravenous anakinra plus optimized standard of care (oSOC) vs. oSOC alone. The primary outcome was treatment success at day 14 defined as patient alive and not requiring mechanical ventilation or extracorporeal membrane oxygenation.ResultsBetween 27th April and 6th October 2020, we enrolled 71 patients (240 patients planned to been enrolled): 37 were assigned to the anakinra group and 34 to oSOC group. The study ended prematurely by recommendation of the data and safety monitoring board due to safety concerns. On day 14, the proportion of treatment success was significantly lower in the anakinra group 70% (n = 26) vs. 91% (n = 31) in the oSOC group: risk difference-21 percentage points (95% CI, -39 to -2), odds ratio 0.23 (95% CI, 0.06 to 0.91), p = 0.027. After a 28-day follow-up, 9 patients in the anakinra group and 3 in the oSOC group had died. Overall survival at day 28 was 75% (95% CI, 62% to 91%) in the anakinra group versus 91% (95% CI, 82% to 100%) (p = 0.06) in the oSOC group. Serious adverse events occurred in 19 (51%) patients in the anakinra group and 18 (53%) in the oSOC group (p = 0·89).ConclusionThis trial did not show efficacy of anakinra in patients with COVID-19. Furthermore, contrary to our hypothesis, we found that anakinra was inferior to oSOC in patients with moderate COVID-19 pneumonia.

The objective of this study was to identify the correlates of being at risk of clinical depression and examine the role of syndemic factors among marginally housed and homeless transitional age youth (TAY). From 2017-2018, 100 TAY between the ages of 18 and 24 in San Francisco were recruited from Larkin Street Youth Services into a cross-sectional study. Participants completed surveys on mental health, substance use, and HIV risk behaviors. A syndemic score ranging from 0-3 was calculated by summing dichotomous measures of moderate or severe anxiety in the past two weeks, PTSD symptoms in the past month and polysubstance use in the past three months. We used modified Poisson regression with robust error variances to identify the correlates of being at risk of clinical depression in the past week, all primary effects measures were modeled separately. Among 100 participants, the average age was 21 (SD = 1.7), 67% were male, 38% were Multiracial, 54% identified as gay, lesbian, bisexual or pansexual, 13% were unstably housed, 50% were homeless and 23% were living with HIV. The majority (74%) were at risk of clinical depression, 51% had symptoms of moderate or severe anxiety, 80% exhibited symptoms of PTSD and 33% reported polysubstance use. After controlling for age in years, gender, race/ethnicity and sexual orientation, factors independently associated with being at risk of clinical depression were; symptoms of moderate or severe anxiety (adjusted risk ratio [aRR] = 1.62, 95% confidence interval [CI] = 1.23-2.12, P

Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.

BackgroundFirearm violence remains a persistent public health threat. Comparing the impact of targeted high-risk versus population-based approaches to prevention may point to efficient and efficacious interventions. We used agent-based modeling to conduct a hypothetical experiment contrasting the impact of high-risk (disqualification) and population-based (price increase) approaches on firearm homicide in New York City (NYC).MethodsWe simulated 800,000 agents reflecting a 15% sample of the adult population of NYC. Three groups were considered and disqualified from all firearm ownership for five years, grouped based on prevalence: low prevalence (psychiatric hospitalization, alcohol-related misdemeanor and felony convictions, 0.23%); moderate prevalence (drug misdemeanor convictions, domestic violence restraining orders, 1.03%); and high prevalence (all other felony/misdemeanor convictions, 2.30%). Population-level firearm ownership was impacted by increasing the price of firearms, assuming 1% price elasticity.ResultsIn this hypothetical scenario, to reduce firearm homicide by 5% in NYC, 25% of the moderate prevalence group, or 12% of the high prevalence group needed to be effectively disqualified; even when all of the low prevalence group was disqualified, homicide did not decrease by 5%. An 18% increase in price similarly reduced firearm homicide by 5.37% (95% CI 4.43-6.31%). Firearm homicide declined monotonically as the proportion of disqualified individuals increased and/or price increased. A combined intervention that both increased price and effectively disqualified "high-risk" groups achieved approximately double the reduction in homicide as any one intervention alone. Increasing illegal firearm ownership by 20%, a hypothetical response to price increases, did not meaningfully change results.ConclusionA key takeaway of our study is that adopting high-risk versus population-based approaches should not be an "either-or" question. When individual risk is variable and diffuse in the population, "high-risk approaches" to firearm violence need to focus on relatively prevalent groups and be highly efficacious in disarming people at elevated risk to achieve meaningful reductions in firearm homicide, though countering issues of social justice and stigma should be carefully considered. Similar reductions can be achieved with population-based approaches, such as price increases, albeit with fewer such countering issues.

California's vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California's vernal pool branchiopods: The Vernal Pool Fairy Shrimp Branchinecta lynchi (BRLY), the Midvalley Fairy Shrimp Branchinecta mesovallensis (BRME), and the Conservancy Fairy Shrimp Branchinecta conservatio (BRCO), and the Vernal Pool Tadpole Shrimp Lepidurus packardi (LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.

Youth homelessness has been demonstrated to disproportionately affect sexual and gender minority (SGM) youth compared to heterosexual cisgender peers. In this context, we aimed to compare health risks between service-seeking SGM and heterosexual cisgender youth experiencing homelessness, including harmful risks stemming from substance use and severity of symptoms of mental health disorders. We recruited 100 racially diverse, unstably housed participants aged 18-24 who access services at an urban non-profit organization in San Francisco, CA. Data analysis included 56 SGM participants who identified as gay, lesbian, bisexual, pansexual, unsure, transgender, and nongender, and 44 heterosexual cisgender participants. In contrast to previous studies reporting significantly higher frequency of substance use and more severe symptoms of depression, generalized anxiety, and post-traumatic stress disorder among SGM youth compared to heterosexual cisgender peers, many of these health disparities were not observed in our diverse study population of service-seeking youth. Furthermore, with the exception of methamphetamine, SGM participants did not exhibit greater harmful risks resulting from substance use, such as health, social, financial, and legal complications. We discuss the reduced burden of health disparities between SGM and heterosexual cisgender youth in our service-seeking study population within the context of gender- and sexuality-affirming programming offered at the partnering community organization. We conclude that longitudinal data on these tailored community-level interventions are needed to further explore the reduced burden of health disparities observed among service-seeking SGM youth experiencing homelessness in San Francisco in order to continue supporting pathways out of homelessness for youth of all sexual and gender identities nationwide.

Clinical and surveillance testing for the SARS-CoV-2 virus relies overwhelmingly on RT-qPCR-based diagnostics, yet several popular assays require 2-3 separate reactions or rely on detection of a single viral target, which adds significant time, cost, and risk of false-negative results. Furthermore, multiplexed RT-qPCR tests that detect at least two SARS-CoV-2 genes in a single reaction are typically not affordable for large scale clinical surveillance or adaptable to multiple PCR machines and plate layouts. We developed a RT-qPCR assay using the Luna Probe Universal One-Step RT-qPCR master mix with publicly available primers and probes to detect SARS-CoV-2 N gene, E gene, and human RNase P (LuNER) to address these shortcomings and meet the testing demands of a university campus and the local community. This cost-effective test is compatible with BioRad or Applied Biosystems qPCR machines, in 96 and 384-well formats, with or without sample pooling, and has a detection sensitivity suitable for both clinical reporting and wastewater surveillance efforts.

BackgroundIn Mozambique, HIV counseling and testing (HCT) rates are low and the cascade (or continuum) of care is poor. Perhaps more importantly, low disclosure rates and low uptake of joint testing are also related to both (1) limitations on access to services and (2) the availability of trained staff. We describe the implementation and impact of a disclosure support implemented by peer educators (PE).MethodsTen PEs, previously trained in basic HIV and post-test counseling, completed additional training on providing disclosure support for newly-diagnosed persons living with HIV (PLH).ResultsOf the 6,092 persons who received HCT, 677 (11.1%) tested positive. Any newly-diagnosed PLH who was tested when PEs were present (606 / 677) was approached about participating in the disclosure program; of these, 94.2% of PLH (n = 574) agreed to participate. Of these, at follow-up (between 1 day and 3 months later, depending on client inclination and availability) 91.9% (n = 528) said that they had disclosed their HIV infection, of whom 66.9% (n = 384) were female and 24.1% (n = 144) male. In turn, 92.7% of partners (n = 508) who had received HIV-related exposure information were tested; of these, 78.7% (n = 400) were found to be HIV-positive. Of the latter, 96.3% (n = 385) were then seen by health care providers and referred for further diagnosis and treatment.ConclusionsSupporting newly-diagnosed PLH is important both for their own health and that of others. For the newly-diagnosed, there are extensive challenges related to understanding the implications of their illness; social support from clinical care teams can be vital in planning and coping. Our study has shown that such support of PLH is also crucial to disclosure, in part via improving awareness of positive health implications for (and from) family, friends and other support networks.

Smoking is a potentially causal behavioral risk factor for type 2 diabetes (T2D), but not all smokers develop T2D. It is unknown whether genetic factors partially explain this variation. We performed genome-environment-wide interaction studies to identify loci exhibiting potential interaction with baseline smoking status (ever vs. never) on incident T2D and fasting glucose (FG). Analyses were performed in participants of European (EA) and African ancestry (AA) separately. Discovery analyses were conducted using genotype data from the 50,000-single-nucleotide polymorphism (SNP) ITMAT-Broad-CARe (IBC) array in 5 cohorts from from the Candidate Gene Association Resource Consortium (n = 23,189). Replication was performed in up to 16 studies from the Cohorts for Heart Aging Research in Genomic Epidemiology Consortium (n = 74,584). In meta-analysis of discovery and replication estimates, 5 SNPs met at least one criterion for potential interaction with smoking on incident T2D at p

Our intuitive understanding of adaptation by natural selection is dominated by the power of selection at early ages in large populations. Yet, as the forces of natural selection fall with adult age, we expect adaptation to be attenuated with age. Explicit simulations of age-dependent adaptation suggest that populations adapt to a novel environment quickly at early ages, but only slowly and incompletely at later adult ages. Experimental tests for age-dependent adaptation to a novel diet were performed on populations of Drosophila melanogaster. The results support the prediction that populations should perform better on an ancestral, long-abandoned diet, compared to an evolutionarily recent diet, only at later ages. D. melanogaster populations also perform poorly on a novel diet compared to an evolutionarily recent diet that has been sustained for hundreds of generations, particularly at earlier ages. Additional experiments demonstrate that the timing of the shift to better performance in our populations on the long-abandoned diet is dependent on when the forces of natural selection weaken in the evolutionary history of experimental populations. Taken together, these experimental findings suggest that the forces of natural selection scale the rate of adaptation to novel environments.

Ocean acidification (OA) represents a serious challenge to marine ecosystems. Laboratory studies addressing OA indicate broadly negative effects for marine organisms, particularly those relying on calcification processes. Growing evidence also suggests OA combined with other environmental stressors may be even more deleterious. Scaling these laboratory studies to ecological performance in the field, where environmental heterogeneity may mediate responses, is a critical next step toward understanding OA impacts on natural communities. We leveraged an upwelling-driven pH mosaic along the California Current System to deconstruct the relative influences of pH, ocean temperature, and food availability on seasonal growth, condition and shell thickness of the ecologically dominant intertidal mussel Mytilus californianus. In 2011 and 2012, ecological performance of adult mussels from local and commonly sourced populations was measured at 8 rocky intertidal sites between central Oregon and southern California. Sites coincided with a large-scale network of intertidal pH sensors, allowing comparisons among pH and other environmental stressors. Adult California mussel growth and size varied latitudinally among sites and inter-annually, and mean shell thickness index and shell weight growth were reduced with low pH. Surprisingly, shell length growth and the ratio of tissue to shell weight were enhanced, not diminished as expected, by low pH. In contrast, and as expected, shell weight growth and shell thickness were both diminished by low pH, consistent with the idea that OA exposure can compromise shell-dependent defenses against predators or wave forces. We also found that adult mussel shell weight growth and relative tissue mass were negatively associated with increased pH variability. Including local pH conditions with previously documented influences of ocean temperature, food availability, aerial exposure, and origin site enhanced the explanatory power of models describing observed performance differences. Responses of local mussel populations differed from those of a common source population suggesting mussel performance partially depended on genetic or persistent phenotypic differences. In light of prior research showing deleterious effects of low pH on larval mussels, our results suggest a life history transition leading to greater resilience in at least some performance metrics to ocean acidification by adult California mussels. Our data also demonstrate "hot" (more extreme) and "cold" (less extreme) spots in both mussel responses and environmental conditions, a pattern that may enable mitigation approaches in response to future changes in climate.

Many high-risk conditions of pregnancy are undetected until the time of delivery in low-income countries. We developed a point-of-care ultrasound training protocol for providers in rural Uganda to detect fetal distress or demise, malpresentation, multiple gestation, placenta previa, oligohydramnios and preterm delivery. This was a mixed-methods study to evaluate the 2-week training curriculum and trainees' ability to perform a standard scanning protocol and interpret ultrasound images. Surveys to assess provider confidence were administered pre-training, immediately after, and at 3-month follow up. Following lecture and practical demonstrations, each trainee conducted 25 proctored scans and were required to pass an observed structured clinical exam (OSCE). All images produced 8 weeks post course underwent blinded review by two ultrasound experts to assess image quality and to identify common errors. Key informant interviews further assessed perceptions of the training program and utility of point-of-care ultrasound. All interviews were audio recorded, transcribed, and reviewed by multiple readers using a content analysis approach. Twenty-three nurse/nurse midwives and two physicians from one district hospital and three health centers participated in the training curriculum. Confidence levels increased from an average of 1 point pre-course to over 6 points post-course for all measures (maximum of 7 points). Of 25 participants, 22 passed the OSCE on the first attempt (average score 89.4%). Image quality improved over time; the final error rate at week 8 was less than 5%, with an overall kappa of 0.8-1 for all measures between the two reviewers. Among the 12 key informant interviews conducted, key themes included a desire for more hands-on training and longer duration of training and challenges in balancing clinical duties with ability to attend training sessions. This study demonstrates that providers without previous ultrasound experience can detect high-risk conditions during labor with a high rate of quality and accuracy after training.

Over half of all children with autism spectrum disorders (ASD) have gastrointestinal (GI) co-morbidities including chronic constipation, diarrhea, and irritable bowel syndrome. The severity of these symptoms has been correlated with the degree of GI microbial dysbiosis. The study objective was to assess tolerability of a probiotic (Bifidobacterium infantis) in combination with a bovine colostrum product (BCP) as a source of prebiotic oligosaccharides and to evaluate GI, microbiome and immune factors in children with ASD and GI co-morbidities. This pilot study is a randomized, double blind, controlled trial of combination treatment (BCP + B. infantis) vs. BCP alone in a cross-over study in children ages 2-11 with ASD and GI co-morbidities (n = 8). This 12-week study included 5 weeks of probiotic-prebiotic supplementation, followed by a two-week washout period, and 5 weeks of prebiotic only supplementation. The primary outcome of tolerability was assessed using validated questionnaires of GI function and atypical behaviors, along with side effects. Results suggest that the combination treatment is well-tolerated in this cohort. The most common side effect was mild gassiness. Some participants on both treatments saw a reduction in the frequency of certain GI symptoms, as well as reduced occurrence of particular aberrant behaviors. Improvement may be explained by a reduction in IL-13 and TNF-α production in some participants. Although limited conclusions can be drawn from this small pilot study, the results support the need for further research into the efficacy of these treatments.

Maize farmers in sub-Saharan Africa recently experienced unusual damage in their farms, attributed to the fall armyworm (FAW) Spodoptera frugiperda (J. E. Smith). This pest was first recorded in Africa in 2016, but detailed information on its distribution and damage and farmer's response in invaded areas are largely lacking. In this study, we determined FAW distribution, genetic diversity, host plants, crop damage, and farmers' responses. S. frugiperda was recorded in the 10 regions of Cameroon. Average percentage of infested plants and damage severity (on a scale of 1 to 5) were lowest-20.7 ± 7.4% and 2.1 ± 0.1 respectively-in the Sahelian regions and greatest-69.0 ± 4.3% and 3.1 ± 0.1 respectively-in the Western Highlands. Altitude did not influence FAW incidence and severity and its larvae infrequently co-occurred with maize stemborers on the same plants, suggesting possible direct and/or indirect competition between the two groups of maize pests. In response to this new threat to maize production, farmers have opted for the application of synthetic pesticides. Although our experiments were not designed to determine pesticide efficacy, as parameters such as time since application were not considered, our observations suggest lack of a drastic effect on S. frugiperda infestations on maize. There were two haplotypes of FAW co-occurring in Cameroon corresponding to the rice and corn strains and separated by 1.7% sequence divergence, which does not support the existence of cryptic species. S. frugiperda larvae were also recorded on Sorghum bicolor (L.) Moench (10.6%), Solanum tuberosum L. (2.8%), Ipomoea batatas (L.) Lam. (1.9%), Saccharum officinarum L (0.8%), Phaseolus vulgaris L. (0.4%) and Gossypium hirsutum L. (1.9%). This study show that two strains are present in all agroecological zones in Cameroon, and probably in neighboring countries of central Africa sharing the same agroecologies. Management options should therefore consider the use of specific natural enemies and an informed decision of intervention based on strain capture and damage threshold, to avoid pesticide resistance that may arise from inadequate use of chemicals. Further studies should also be undertaken to assess the response of the two S. frugiperda strains to biopesticides and botanical insecticides.

[This corrects the article DOI: 10.1371/journal.pone.0215749.].

Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to California, USA, and we compared the efficacy of eDNA and aquatic trapping. We tested 3-9 water samples each from 30 sites near the known range of N. fasciata, and 61 sites near the known range of N. sipedon. We also deployed aquatic funnel traps at a subset of sites for each species. We detected N. fasciata eDNA in three of nine water samples from just one site, but captured N. fasciata in traps at three of ten sites. We detected N. sipedon eDNA in five of six water samples from one site, which was also the only site of nine at which this species was captured in traps. Traditional trapping surveys had a higher probability of detecting watersnakes than eDNA surveys, and both survey methods had higher detection probability for N. sipedon than N. fasciata. Occupancy models that integrated both trapping and eDNA surveys estimated that 5 sites (95% Credible Interval: 4-10) of 91 were occupied by watersnakes (both species combined), although snakes were only detected at four sites (three for N. fasciata, one for N. sipedon). Our study shows that despite the many successes of eDNA surveys, traditional sampling methods can have higher detection probability for some species. We recommend those tasked with managing species invasions explicitly compare eDNA and traditional survey methods in an occupancy framework to inform their choice of the best method for detecting nascent populations.

This study estimates the effect of data sharing on the citations of academic articles, using journal policies as a natural experiment. We begin by examining 17 high-impact journals that have adopted the requirement that data from published articles be publicly posted. We match these 17 journals to 13 journals without policy changes and find that empirical articles published just before their change in editorial policy have citation rates with no statistically significant difference from those published shortly after the shift. We then ask whether this null result stems from poor compliance with data sharing policies, and use the data sharing policy changes as instrumental variables to examine more closely two leading journals in economics and political science with relatively strong enforcement of new data policies. We find that articles that make their data available receive 97 additional citations (estimate standard error of 34). We conclude that: a) authors who share data may be rewarded eventually with additional scholarly citations, and b) data-posting policies alone do not increase the impact of articles published in a journal unless those policies are enforced.

The size and complexity of 3D macromolecular structures available in the Protein Data Bank is constantly growing. Current tools and file formats have reached limits of scalability. New compression approaches are required to support the visualization of large molecular complexes and enable new and scalable means for data analysis. We evaluated a series of compression techniques for coordinates of 3D macromolecular structures and identified the best performing approaches. By balancing compression efficiency in terms of the decompression speed and compression ratio, and code complexity, our results provide the foundation for a novel standard to represent macromolecular coordinates in a compact and useful file format.

The centrosome serves as the main microtubule-organizing center in metazoan cells, yet despite its functional importance, little is known mechanistically about the structure and organizational principles that dictate protein organization in the centrosome. In particular, the protein-protein interactions that allow for the massive structural transition between the tightly organized interphase centrosome and the highly expanded matrix-like arrangement of the mitotic centrosome have been largely uncharacterized. Among the proteins that undergo a major transition is the Drosophila melanogaster protein centrosomin that contains a conserved carboxyl terminus motif, CM2. Recent crystal structures have shown this motif to be dimeric and capable of forming an intramolecular interaction with a central region of centrosomin. Here we use a combination of in-cell microscopy and in vitro oligomer assessment to show that dimerization is not necessary for CM2 recruitment to the centrosome and that CM2 alone undergoes significant cell cycle dependent rearrangement. We use NMR binding assays to confirm this intramolecular interaction and show that residues involved in solution are consistent with the published crystal structure and identify L1137 as critical for binding. Additionally, we show for the first time an in vitro interaction of CM2 with the Drosophila pericentrin-like-protein that exploits the same set of residues as the intramolecular interaction. Furthermore, NMR experiments reveal a calcium sensitive interaction between CM2 and calmodulin. Although unexpected because of sequence divergence, this suggests that centrosomin-mediated assemblies, like the mammalian pericentrin, may be calcium regulated. From these results, we suggest an expanded model where during interphase CM2 interacts with pericentrin-like-protein to form a layer of centrosomin around the centriole wall and that at the onset of mitosis this population acts as a nucleation site of intramolecular centrosomin interactions that support the expansion into the metaphase matrix.

The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).

The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation.

BACKGROUND: In 2013, Uganda updated its prevention of maternal-to-child transmission of HIV program to Option B+, which requires that all HIV-infected pregnant and breastfeeding women be started on lifelong antiretroviral therapy (ART) regardless of CD4 count. We describe retention in care and factors associated with loss to follow-up (LTFU) among women initiated on Option B+ as part of an evaluation of the effectiveness of the national program. METHODS: We conducted a retrospective cohort analysis of data abstracted from records of 2,169 women enrolled on Option B+ between January and March 2013 from a representative sample of 145 health facilities in all 24 districts of the Central region of Uganda. We defined retention as being alive and receiving ART at the last clinic visit. We used Kaplan-Meier analysis to estimate retention in care and compared differences between women retained in care and those LTFU using the chi-squared test for dichotomized or categorical variables. RESULTS: The median follow-up time was 20.2 months (IQR 4.2-22.5). The proportion of women retained in HIV care at 6, 12 and 18 months post-ART initiation was 74.2%, 66.7% and 62.0%, respectively. Retention at 18 months varied significantly by level of health facility and ranged from 70.0% among those seen at hospitals to 56.6% among those seen at lower level health facilities. LTFU was higher among women aged less than 25 years, 59.3% compared to those aged 25 years and above, 40.7% (p = 0.02); among those attending care at lower level facilities, 44.0% compared to those attending care at hospitals, 34.1% (p = 0.01), and among those who were not tested for CD4 cell count at ART initiation, 69.4% compared to those who were tested, 30.9% (p = 0.002). CONCLUSION: Retention of women who were initiated on Option B+ during the early phases of roll-out was only moderate, and could undermine the effectiveness of the program. Identifying reasons why women drop out and designing targeted interventions for improved retention should be a priority.

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

BackgroundRegular fish and omega-3 consumption may have several health benefits and are recommended by major dietary guidelines. Yet, their intakes remain remarkably variable both within and across populations, which could partly owe to genetic influences.ObjectiveTo identify common genetic variants that influence fish and dietary eicosapentaenoic acid plus docosahexaenoic acid (EPA+DHA) consumption.DesignWe conducted genome-wide association (GWA) meta-analysis of fish (n = 86,467) and EPA+DHA (n = 62,265) consumption in 17 cohorts of European descent from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium Nutrition Working Group. Results from cohort-specific GWA analyses (additive model) for fish and EPA+DHA consumption were adjusted for age, sex, energy intake, and population stratification, and meta-analyzed separately using fixed-effect meta-analysis with inverse variance weights (METAL software). Additionally, heritability was estimated in 2 cohorts.ResultsHeritability estimates for fish and EPA+DHA consumption ranged from 0.13-0.24 and 0.12-0.22, respectively. A significant GWA for fish intake was observed for rs9502823 on chromosome 6: each copy of the minor allele (FreqA = 0.015) was associated with 0.029 servings/day (~1 serving/month) lower fish consumption (P = 1.96x10-8). No significant association was observed for EPA+DHA, although rs7206790 in the obesity-associated FTO gene was among top hits (P = 8.18x10-7). Post-hoc calculations demonstrated 95% statistical power to detect a genetic variant associated with effect size of 0.05% for fish and 0.08% for EPA+DHA.ConclusionsThese novel findings suggest that non-genetic personal and environmental factors are principal determinants of the remarkable variation in fish consumption, representing modifiable targets for increasing intakes among all individuals. Genes underlying the signal at rs72838923 and mechanisms for the association warrant further investigation.

Conflict settings and refugee camps can be chaotic places, with large and rapid population movements, exacerbated public health problems, and ad hoc health services. Reproductive health care that includes family planning is of heightened importance in such settings, however, funding and resources tend to be constrained and geared towards acute health services such as trauma management and infectious disease containment. Here we report on the complexities and challenges of providing family planning in a post-emergency refugee setting, using the example of the largest refugee camp on the Thai-Myanmar border, in existence now for over 30 years. Data from 2009 demonstrates an upward trend in uptake of all contraceptives, especially long acting reversible contraception (LARC) and permanent methods (e.g. sterilization) over time. Increased uptake occurred during periods of time when there were boosts in funding or when barriers to access were alleviated. For example a surgeon fluent in local languages is correlated with increased uptake of tubal ligation in females. These data indicate that funding directed toward contraceptives in this refugee setting led to increases in contraceptives use. However, contraceptive uptake estimates depend on the baseline population which is difficult to measure in this setting. As far as we are aware, this is the longest reported review of family planning services for a refugee camp setting to date. The lessons learned from this setting may be valuable given the current global refugee crisis.

Our objective was to explore the association between weight status and behavioral problems in children before school age. We examined whether the association between weight status and behavioral problems varied by age and sex.

BackgroundData are limited on genome-wide association studies (GWAS) for incident coronary heart disease (CHD). Moreover, it is not known whether genetic variants identified to date also associate with risk of CHD in a prospective setting.MethodsWe performed a two-stage GWAS analysis of incident myocardial infarction (MI) and CHD in a total of 64,297 individuals (including 3898 MI cases, 5465 CHD cases). SNPs that passed an arbitrary threshold of 5×10-6 in Stage I were taken to Stage II for further discovery. Furthermore, in an analysis of prognosis, we studied whether known SNPs from former GWAS were associated with total mortality in individuals who experienced MI during follow-up.ResultsIn Stage I 15 loci passed the threshold of 5×10-6; 8 loci for MI and 8 loci for CHD, for which one locus overlapped and none were reported in previous GWAS meta-analyses. We took 60 SNPs representing these 15 loci to Stage II of discovery. Four SNPs near QKI showed nominally significant association with MI (p-value

The Protein Data Bank (PDB) is the worldwide repository of 3D structures of proteins, nucleic acids and complex assemblies. The PDB's large corpus of data (> 100,000 structures) and related citations provide a well-organized and extensive test set for developing and understanding data citation and access metrics. In this paper, we present a systematic investigation of how authors cite PDB as a data repository. We describe a novel metric based on information cascade constructed by exploring the citation network to measure influence between competing works and apply that to analyze different data citation practices to PDB. Based on this new metric, we found that the original publication of RCSB PDB in the year 2000 continues to attract most citations though many follow-up updates were published. None of these follow-up publications by members of the wwPDB organization can compete with the original publication in terms of citations and influence. Meanwhile, authors increasingly choose to use URLs of PDB in the text instead of citing PDB papers, leading to disruption of the growth of the literature citations. A comparison of data usage statistics and paper citations shows that PDB Web access is highly correlated with URL mentions in the text. The results reveal the trend of how authors cite a biomedical data repository and may provide useful insight of how to measure the impact of a data repository.

Prior to age four, children succeed in non-elicited-response false-belief tasks but fail elicited-response false-belief tasks. To explain this discrepancy, the processing-load account argues that the capacity to represent beliefs emerges in infancy, as indicated by early success on non-elicited-response tasks, but that children's ability to demonstrate this capacity depends on the processing demands of the task and children's processing skills. When processing demands exceed young children's processing abilities, such as in standard elicited-response tasks, children fail despite their capacity to represent beliefs. Support for this account comes from recent evidence that reducing processing demands improves young children's performance: when demands are sufficiently reduced, 2.5-year-olds succeed in elicited-response tasks. Here we sought complementary evidence for the processing-load account by examining whether increasing processing demands impeded children's performance in a non-elicited-response task. 3-year-olds were tested in a preferential-looking task in which they heard a change-of-location false-belief story accompanied by a picture book; across children, we manipulated the amount of linguistic ambiguity in the story. The final page of the book showed two images: one that was consistent with the main character's false belief and one that was consistent with reality. When the story was relatively unambiguous, children looked reliably longer at the false-belief-consistent image, successfully demonstrating their false-belief understanding. When the story was ambiguous, however, this undermined children's performance: looking times to the belief-consistent image were correlated with verbal ability, and only children with verbal skills in the upper quartile of the sample demonstrated a significant preference for the belief-consistent image. These results support the processing-load account by demonstrating that regardless of whether a task involves an elicited response, children's performance depends on the processing demands of the task and their processing skills. These findings also have implications for alternative, deflationary accounts of early false-belief understanding.

PURPOSE: Semi-automated diffusion tensor imaging (DTI) analysis of white matter (WM) microstructure offers a clinically feasible technique to assess neonatal brain development and provide early prognosis, but is limited by variable methods and insufficient evidence regarding optimal parameters. The purpose of this research was to investigate the influence of threshold values on semi-automated, atlas-based brain segmentation in very-low-birth-weight (VLBW) preterm infants at near-term age. MATERIALS AND METHODS: DTI scans were analyzed from 45 VLBW preterm neonates at near-term-age with no brain abnormalities evident on MRI. Brain regions were selected with a neonatal brain atlas and threshold values: trace 0.15, FA>0.20, and FA>0.25. Relative regional volumes, FA, axial diffusivity (AD), and radial diffusivity (RD) were compared for twelve WM regions. RESULTS: Near-term brain regions demonstrated differential effects from segmentation with the three FA thresholds. Regional DTI values and volumes selected in the PLIC, CereP, and RLC varied the least with the application of different FA thresholds. Overall, application of higher FA thresholds significantly reduced brain region volume selected, increased variability, and resulted in higher FA and lower RD values. The lower threshold FA>0.15 selected 78±21% of original volumes segmented by the atlas, compared to 38±12% using threshold FA>0.25. CONCLUSION: Results indicate substantial and differential effects of atlas-based DTI threshold parameters on regional volume and diffusion scalars. A lower, more inclusive FA threshold than typically applied for adults is suggested for consistent analysis of WM regions in neonates.

The roles of history, chance and selection have long been debated in evolutionary biology. Though uniform selection is expected to lead to convergent evolution between populations, contrasting histories and chance events might prevent them from attaining the same adaptive state, rendering evolution somewhat unpredictable. The predictability of evolution has been supported by several studies documenting repeatable adaptive radiations and convergence in both nature and laboratory. However, other studies suggest divergence among populations adapting to the same environment. Despite the relevance of this issue, empirical data is lacking for real-time adaptation of sexual populations with deeply divergent histories and ample standing genetic variation across fitness-related traits. Here we analyse the real-time evolutionary dynamics of Drosophila subobscura populations, previously differentiated along the European cline, when colonizing a new common environment. By analysing several life-history, physiological and morphological traits, we show that populations quickly converge to the same adaptive state through different evolutionary paths. In contrast with other studies, all analysed traits fully converged regardless of their association with fitness. Selection was able to erase the signature of history in highly differentiated populations after just a short number of generations, leading to consistent patterns of convergent evolution.

BackgroundIncreased rates of autoinflammatory and autoimmune disorders have been observed in female premutation carriers of CGG repeat expansion alleles of between 55-200 repeats in the fragile X mental retardation 1 (FMR1) gene. To determine whether an abnormal immune profile was present at a cellular level that may predispose female carriers to autoinflammatory conditions, we investigated dynamic cytokine production following stimulation of blood cells. In addition, splenocyte responses were examined in an FMR1 CGG knock-in mouse model of the fragile X premutation.MethodsHuman monocyte and peripheral blood leukocytes (PBLs) were isolated from the blood of 36 female FMR1 premutation carriers and 15 age-matched controls. Cells were cultured with media alone, LPS or PHA. In the animal model, splenocytes were isolated from 32 CGG knock-in mice and 32 wild type littermates. Splenocytes were cultured with media alone or LPS or PMA/Ionomycin. Concentrations of cytokines (GM-CSF, IL-1β, IL-6, IL-10, IL-13, IL-17, IFNγ, TNFα, and MCP-1) were determined from the supernatants of cellular cultures via Luminex multiplex assay. Additionally, phenotypic cellular markers were assessed on cells isolated from human subjects via flow cytometry.ResultsWe found decreases in cytokine production in human premutation carriers as well as in the FMR1 knock-in mice when compared with controls. Levels of cytokines were found to be associated with CGG repeat length in both human and mouse. Furthermore, T cells from human premutation carriers showed decreases in cell surface markers of activation when compared with controls.ConclusionsIn this study, FMR1 CGG repeat expansions are associated with decreased immune responses and immune dysregulation in both humans and mice. Deficits in immune responses in female premutation carriers may lead to increased susceptibility to autoimmunity and further research is warranted to determine the link between FMR1 CGG repeat lengths and onset of autoinflammatory conditions.

The extracellular environment possesses a rich milieu of biophysical and biochemical signaling cues that are simultaneously integrated by cells and influence cellular phenotype. Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (WWTR1; TAZ), two important signaling molecules of the Hippo pathway, have been recently implicated as nuclear relays of cytoskeletal changes mediated by substratum rigidity and topography. These proteins intersect with other important intracellular signaling pathways (e.g. Wnt and TGFβ). In the cornea, epithelial cells adhere to the stroma through a 3-dimensional topography-rich basement membrane, with features in the nano-submicron size-scale that are capable of profoundly modulating a wide range of fundamental cell behaviors. The influences of substratum-topography, YAP/TAZ knockdown, and HSP90 inhibition on cell morphology, YAP/TAZ localization, and the expression of TGFβ2 and CTGF, were investigated. The results demonstrate (a) that knockdown of TAZ enhances contact guidance in a YAP dependent manner, (b) that CTGF is predominantly regulated by YAP and not TAZ, and (c) that TGFβ2 is regulated by both YAP and TAZ in these cells. Additionally, inhibition of HSP90 resulted in nuclear localization and subsequent transcriptional-activation of YAP, formation of cell-cell junctions and co-localization of E-cadherin and β-catenin at adherens junctions. Results presented in this study reflect the complexities underlying the molecular relationships between the cytoskeleton, growth factors, heat shock proteins, and co-activators of transcription that impact mechanotransduction. The data reveal the importance of YAP/TAZ on the cell behaviors, and gene and protein expression.

Species distribution models (SDMs) are increasingly used to project the potential distribution of introduced species outside their native range. Such studies rarely explicitly evaluate potential conflicts with native species should the range of introduced species expand. Two snake species native to eastern North America, Nerodia fasciata and Nerodia sipedon, have been introduced to California where they represent a new stressor to declining native amphibians, fish, and reptiles. To project the potential distributions of these non-native watersnakes in western North America, we built ensemble SDMs using MaxEnt, Boosted Regression Trees, and Random Forests and habitat and climatic variables. We then compared the overlap between the projected distribution of invasive watersnakes and the distributions of imperiled native amphibians, fish, and reptiles that can serve as prey or competitors for the invaders, to estimate the risk to native species posed by non-native watersnakes. Large areas of western North America were projected to be climatically suitable for both species of Nerodia according to our ensemble SDMs, including much of central California. The potential distributions of both N. fasciata and N. sipedon overlap extensively with the federally threatened Giant Gartersnake, Thamnophis gigas, which inhabits a similar ecological niche. N. fasciata also poses risk to the federally threatened California Tiger Salamander, Ambystoma californiense, whereas N. sipedon poses risk to some amphibians of conservation concern, including the Foothill Yellow-legged Frog, Rana boylii. We conclude that non-native watersnakes in California can likely inhabit ranges of several native species of conservation concern that are expected to suffer as prey or competing species for these invaders. Action should be taken now to eradicate or control these invasions before detrimental impacts on native species are widespread. Our methods can be applied broadly to quantify the risk posed by incipient invasions to native biodiversity.

We sought to understand patient perceptions of the emergency department/urgent care (ED/UC) HIV diagnosis experience as well as factors that may promote or discourage linkage to HIV care. We conducted in-depth interviews with patients (n=24) whose HIV infection was diagnosed in the ED/UC of a public hospital in San Francisco at least six months prior and who linked to HIV care at the hospital HIV clinic. Key diagnosis experience themes included physical discomfort and limited functionality, presence of comorbid diagnoses, a wide spectrum of HIV risk perception, and feelings of isolation and anxiety. Patients diagnosed with HIV in the ED/UC may not have their desired emotional supports with them, either because they are alone or they are with family members or friends to whom they do not want to immediately disclose. Other patients may have no one they can rely on for immediate support. Nearly all participants described compassionate disclosure of test results by ED/UC providers, although several noted logistical issues that complicated the disclosure experience. Key linkage to care themes included the importance of continuity between the testing site and HIV care, hospital admission as an opportunity for support and HIV education, and thoughtful matching by linkage staff to a primary care provider. ED/UC clinicians and testing programs should be sensitive to the unique roles of sickness, risk perception, and isolation in the ED/UC diagnosis experience, as these things may delay acceptance of HIV diagnosis. The disclosure and linkage to care experience is crucial in forming patient attitudes towards HIV and HIV care, thus staff involved in disclosure and linkage activities should be trained to deliver compassionate, informed, and thoughtful care that bridges HIV testing and treatment sites.

The extent of faith-based organizations' participation within the overall health systems of developing countries is unclear. Recent reports state that faith-based organizations play a substantial role in providing healthcare in developing countries, cited in some publications as up to 70% of all healthcare services. The data behind these numbers are sometimes difficult to pinpoint and seem at odds to national and regional survey data. In an effort to quantify the contribution of faith-based organizations to healthcare delivery in low- and middle-income countries, we undertook a systematic review of the literature and conducted a new analysis of relevant Demographic and Health Survey data from 47 countries. Our findings demonstrate that the magnitude of healthcare provided by faith-based organizations may be lower than previously estimated. Understanding the scale of FBO-provided medical care is important for health sector planning, and more accurate and complete estimates are needed.

The extent of faith-based organizations' participation within the overall health systems of developing countries is unclear. Recent reports state that faith-based organizations play a substantial role in providing healthcare in developing countries, cited in some publications as up to 70% of all healthcare services. The data behind these numbers are sometimes difficult to pinpoint and seem at odds to national and regional survey data. In an effort to quantify the contribution of faith-based organizations to healthcare delivery in low- and middle-income countries, we undertook a systematic review of the literature and conducted a new analysis of relevant Demographic and Health Survey data from 47 countries. Our findings demonstrate that the magnitude of healthcare provided by faith-based organizations may be lower than previously estimated. Understanding the scale of FBO-provided medical care is important for health sector planning, and more accurate and complete estimates are needed.

BackgroundBehavior change communication (BCC) interventions, while still a necessary component of HIV prevention, have not on their own been shown to be sufficient to stem the tide of the epidemic. The shortcomings of BCC interventions are partly due to barriers arising from structural or economic constraints. Arguments are being made for combination prevention packages that include behavior change, biomedical, and structural interventions to address the complex set of risk factors that may lead to HIV infection.MethodsIn 2009/2010 we conducted 216 in-depth interviews with a subset of study participants enrolled in the RESPECT study - an HIV prevention trial in Tanzania that used cash awards to incentivize safer sexual behaviors. We analyzed community diaries to understand how the study was perceived in the community. We drew on these data to enhance our understanding of how the intervention influenced strategies for risk reduction.ResultsWe found that certain situations provide increased leverage for sexual negotiation, and these situations facilitated opportunistic implementation of risk reduction strategies. Opportunities enabled by the RESPECT intervention included leveraging conditional cash awards, but participants also emphasized the importance of exploiting new health status knowledge from regular STI testing. Risk reduction strategies included condom use within partnerships and/or with other partners, and an unexpected emphasis on temporary abstinence.ConclusionsOur results highlight the importance of increasing opportunities for implementing risk reduction strategies. We found that an incentive-based intervention could be effective in part by creating such opportunities, particularly among groups such as women with limited sexual agency. The results provide new evidence that expanding regular testing of STIs is another important mechanism for providing opportunities for negotiating behavior change, beyond the direct benefits of testing. Exploiting the latent demand for STI testing should receive renewed attention as part of innovative new combination interventions for HIV prevention.

BackgroundPeripheral blood interferon-gamma release assays (IGRAs) have sub-optimal sensitivity and specificity for diagnosis of active pulmonary tuberculosis (TB). However, assessment of local immune responses has been reported to improve the accuracy of TB diagnosis.MethodsWe enrolled HIV-infected adults with cough ≥2 weeks' duration admitted to Mulago Hospital in Kampala, Uganda and referred for bronchoscopy following two negative sputum acid-fast bacillus smears. We performed an ELISPOT-based IGRA (T-SPOT.TB®, Oxford Immunotec, Oxford, UK) using peripheral blood and bronchoalveolar lavage (BAL) fluid mononuclear cells, and determined the accuracy of IGRAs using mycobacterial culture results as a reference standard.Results94 HIV-infected patients with paired peripheral blood and BAL IGRA results were included. The study population was young (median age 34 years [IQR 28-40 years]) and had advanced HIV/AIDS (median CD4+ T-lymphocyte count 60 cells/µl [IQR 22-200 cells/µl]). The proportion of indeterminate IGRA results was higher in BAL fluid than in peripheral blood specimens (34% vs. 14%, difference 20%, 95% CI 7-33%, p = 0.002). BAL IGRA had moderate sensitivity (73%, 95% CI 50-89%) but poor specificity (48%, 95% CI 32-64%) for TB diagnosis. Sensitivity was similar (75%, 95% CI 57-89%) and specificity was higher (78%, 95% CI 63-88%) when IGRA was performed on peripheral blood.ConclusionsBAL IGRA performed poorly for the diagnosis of smear-negative TB in a high HIV/TB burden setting. Further studies are needed to examine reasons for the large proportion of indeterminate results and low specificity of BAL IGRA for active TB in high HIV/TB burden settings.

BackgroundDinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments.Methodology/principal findingsIn this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species.Conclusions/significanceCOI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.

BackgroundAntiretroviral therapy (ART) may influence the biological, social and behavioral determinants of pregnancy in HIV-infected women. However, there are limited longitudinal data on the reproductive intentions and outcomes among women on ART in Africa. METHODOLOGY /PRINCIPAL FINDINGS: Using a prospective cohort design, we analyzed trends in desire for children and predictors of pregnancy among a cohort of 733 HIV-infected women in rural Uganda who initiated ART between May 2003 and May 2004 and were followed up in their homes until June 2006. Women answered in-depth social and behavioral questionnaires administered every quarter in year 1 after initiating ART, and every 6 to 12 months thereafter. Use of family planning methods was assessed at 18 and 24 months after starting ART. We tested for non-constant pregnancy incidence by using a shape parameter test from the Weibull distribution. We modeled repeated measurements of all variables related to the women's desire for children over time using a generalized estimating equation (GEE) extension to the logistic regression model. Risk factors for pregnancy were examined using Cox proportional hazards model. 711 women eligible for the study were followed-up for a median time of 2.4 years after starting ART. During this time, less than 7% of women reported wanting more children at any time point yet 120 (16.9%) women experienced 140 pregnancies and pregnancy incidence increased from 3.46 per 100 women-years (WY) in the first quarter to 9.5 per 100 WY at 24 months (p18.5 (HR = 1.09, CI: 1.01-1.18) and not having used condoms consistently in the last 3 months (HR = 1.79, CI: 1.02-3.13) were independently associated with pregnancy.Conclusion/significanceWomen on ART and their partners should be consistently counseled on the effects of ART in restoring fertility, and offered regularly free and comprehensive family planning services as part of their standard package of care.