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Some studies suggest that higher body mass index is associated with increased susceptibility to bacterial vaginosis (BV), but results are conflicting., Methods: Female sex workers aged 16 to 45 years and participating in an open, prospective cohort study in Mombasa, Kenya between 2000 and 2014 were included in this analysis. Up to 2 years of follow-up were included per woman. Body mass index (BMI) was categorized as underweight (≤18.5), normal (18.5-24.9), overweight (25-29.9), and obese (≥30). Bacterial vaginosis was assessed using Nugent scores. Generalized estimating equations were used to estimate relative risks of the association between BMI and BV., Results: At baseline, 32.1% (n = 625) of 1946 women had BV. Half of women were overweight (31.1%, n = 606) or obese (20.1%, n = 391). Participants contributed 14,319 follow-up visits. Adjusting for age, compared to women with normal BMI, overweight (adjusted relative risk, 0.91; 95% confidence interval, 0.81-1.02) and obese (adjusted relative risk, 0.82; 95% confidence interval, 0.71-0.94) women were at lower risk for BV (joint P = 0.03)., Conclusions: Obese women had a nearly 20% lower risk of BV compared with women with normal BMI. Potential mechanisms for this effect, including possible effects of diet, obesity-associated changes in the gut microbiome, and systemic estrogen levels, should be explored.

Background: HIV-1-discordant couples that remain discordant despite repeated exposure may differ from the general population in their distribution of transmission risk factors, including low plasma viral load (PVL) in the infected partner even in the absence of antiretroviral therapy (ART)., Methods: We followed two cohorts of HIV-1-infected Kenyan women: females in discordant couples (FDC) and female sex workers (FSW). We compared the distribution of undetectable (<150 copies/mL) and low PVL (<1,000 copies/mL) between the cohorts using bootstrap methods and exact Poisson regression., Results: We evaluated 296 FDC and 220 FSW. At baseline, FDC were more likely to have undetectable (RR = 6.94, bootstrap 95% CI: 3.47, 20.81) and low PVL (RR = 3.53, bootstrap 95% CI: 2.57, 5.65) than FSW. Similarly, both repeat undetectable PVL (RR = 9.36, bootstrap 95% CI: 6.04, 10.97) and repeat low (RR = 4.99, bootstrap 95% CI: 2.33, 14.04) PVL were more likely among FDC than FSW during follow-up., Discussion: We observed higher prevalence of viral control in FDC compared to FSW in the absence of ART, suggesting potentially higher prevalence of biological HIV resistance factors among discordant couples., Competing Interests: The authors have declared that no competing interests exist.

Genetic resources have to be managed appropriately to mitigate the impact of climate change. For many wildland plants, conservation will require knowledge of the climatic factors affecting intraspecific genetic variation to minimize maladaptation. Knowledge of the interaction between traits and climate can focus management resources on vulnerable populations, provide guidance for seed transfer, and enhance fitness and resilience under changing climates. In this study, traits of big sagebrush (Artemisia tridentata) were examined among common gardens located in different climates. We focus on two subspecies, wyomingensis and tridentata, that occupy the most imperiled warm-dry spectrum of the sagebrush biome. Populations collected across the sagebrush biome were recorded for flower phenology and survival. Mixed-effects models examined each trait to evaluate genetic variation, environmental effects, and adaptive breadth of populations. Climate variables derived from population-source locations were significantly associated with these traits (P < 0.0001), explaining 31% and 11% of the flower phenology and survival variation, respectively. To illustrate our model and assess variability in prediction, we examine fixed and focal point seed transfer approaches to map contemporary and climate model ensemble projections in two different regions of the sagebrush biome. A comparison of seed transfer areas predicts that populations from warmer climates become more prevalent, replacing colder-adapted populations by mid-century. However, these warm-adapted populations are often located along the trailing edge, margins of the species range predicted to be lost due to a contraction of the climatic niche. Management efforts should focus on the collection and conservation of vulnerable populations and prudent seed transfer to colder regions where these populations are projected to occur by mid-century. Our models provide the foundation to develop an empirical, climate-based seed transfer system for current and future restoration of big sagebrush., (Published 2018. This article is a U.S. Government work and is in the public domain in the USA.)

A species' population structure and history are critical pieces of information that can help guide the use of available native plant materials in restoration treatments and decide what new native plant materials should be developed to meet future restoration needs. In the western United States, Pseudoroegneria spicata (bluebunch wheatgrass; Poaceae) is an important component of grassland and shrubland plant communities and commonly used for restoration due to its drought resistance and competitiveness with exotic weeds. We used next-generation sequencing data to investigate the processes that shaped P. spicata 's geographic pattern of genetic variation across the Intermountain West. Pseudoroegneria spicata 's genetic diversity is partitioned into populations that likely differentiated since the Last Glacial Maximum. Adjacent populations display varying magnitudes of historical gene flow, with migration rates ranging from multiple migrants per generation to multiple generations per migrant. When considering the commercial germplasm sources available for restoration, genetic identities remain representative of the wildland localities from which germplasm sources were originally developed, and they maintain high levels of heterozygosity and nucleotide diversity. However, the commercial germplasm sources represent a small fraction of the overall genetic diversity of P. spicata in the Intermountain West. Given the low migration rates and long divergence times between some pairs of P. spicata populations, using commercial germplasm sources could facilitate undesirable restoration outcomes when used in certain geographic areas, even if the environment in which the commercial materials thrive is similar to that of the restoration site. As such, population structure and history can be used to provide guidance on what geographic areas may need additional native plant materials so that restoration efforts support species and community resilience and improve outcomes.

Introduction: Spontaneous interferon-γ (IFNγ) released detected by enzyme-linked immunospot (ELISpot) assays may be a biological phenomenon. Markers of immune activation levels were assessed as correlates of high background among individuals in Kenya., Methods: Couples concordantly seronegative for HIV-1 were enrolled. IFN-γ ELISpot assays were conducted and negative control wells were categorized as having either high or low background (≥50 and <50 SFU/10 6 peripheral blood mononuclear cells [PBMC], respectively). PBMC were stained for CD4, CD8, and immune activation markers (CD38 and HLA-DR) and analyzed using flow cytometry. Proportions of activated T-cells were compared between those with low and high background by Mann-Whitney U test. Correlates of background SFU and immune activation were assessed using regression models., Results: Among 58 individuals, 14 (24%) had high background. Frequencies of CD4 + CD38 + HLA-DR + and CD8 + CD38 + HLA-DR + cells were higher in individuals with high background compared to those with low background (P = 0.02). Higher background SFU was associated with history of sexually transmitted infections (P = 0.03), and illness in the past 3 months (P = 0.005), in addition to increased levels of activated CD4 + and CD8 + cells (P range = 0.008-0.03). Female gender and male circumcision decreased levels of CD4 + and CD8 + immune activation (P range = 0.002-0.03). Additionally, higher background SFU and activated CD4 + and CD8 + cells were individually associated with positive ELISpot responses to HIV-1 peptide pools (P range = 0.01-0.03)., Conclusions: These findings suggest that increased basal immune responses may be a biological mechanism contributing to higher background ELISpot SFU. Systematic exclusion of data from individuals with increased background in IFN-γ release assays may bias results in population-based studies., (© 2018 The Authors. Immunity, Inflammation and Disease Published by John Wiley & Sons Ltd.)

Background: Little is known about fertility desire in HIV-positive female sex workers. Fertility desire could increase HIV transmission risk if it was associated with condomless sex or lower adherence to antiretroviral therapy., Methods: A prospective cohort study was conducted among 255 HIV-positive female sex workers in Mombasa, Kenya. Using generalized estimating equations, fertility desire was evaluated as a risk factor for semen detection in vaginal secretions by prostate-specific antigen (PSA) test, a biomarker of condomless sex, detectable plasma viral load (VL), and HIV transmission potential, defined as visits with positive PSA and detectable VL., Results: The effect of fertility desire on PSA detection varied significantly by nonbarrier contraception use (P-interaction < 0.01). At visits when women reported not using nonbarrier contraception, fertility desire was associated with higher risk of semen detection [82/385, 21.3% vs. 158/1007, 15.7%; adjusted relative risk (aRR) 1.58, 95% confidence interval (CI): 1.12 to 2.23]. However, when women used nonbarrier contraception, fertility desire was associated with lower risk of PSA detection (10/77, 13.0% vs. 121/536, 22.6%; aRR 0.58, 95% CI: 0.35 to 0.94). Fertility desire was not associated with detectable VL (31/219, 14.2% vs. 128/776, 16.5%; aRR 0.82, 95% CI: 0.46 to 1.45) or higher absolute risk of transmission potential (10/218, 4.6% vs. 21/769, 2.7%; adjusted risk difference = 0.011, 95% CI -0.031 to 0.050)., Conclusions: Fertility desire was associated with higher risk of biological evidence of semen exposure when women were not using nonbarrier contraceptives. Low HIV transmission potential regardless of fertility desire suggests that the combination of condoms and antiretroviral therapy adherence was effective.

Background: Treatment of human immunodeficiency virus (HIV)-infected women to prevent cervical cancer may stimulate HIV RNA cervical shedding and risk HIV transmission., Methods: From 2011 to 2014, 400 HIV-infected women diagnosed with cervical intraepithelial neoplasia 2/3 in Kenya were randomized to loop electrosurgical excision procedure (LEEP) or cryotherapy. Cervical samples were collected at baseline and 3 weekly intervals. Samples were tested for HIV RNA using the Gen-Probe Aptima HIV assay with a minimum detection level of 60 copies/swab and analyzed using generalized estimating equations., Results: Women who received LEEP had significantly higher cervical HIV RNA levels than those who received cryotherapy at weeks 2 (adjusted incident rate ratio [aIRR], 1.07; P = .038) and 3 (aIRR, 1.08; P = .046). Within LEEP, significantly higher cervical shedding was found at weeks 2 (2.03 log10 copies/swab; P < .001) and 3 (2.04 log10 copies/swab; P < .001) compared to baseline (1.80 log10 copies/swab). Cervical HIV RNA was significantly higher following LEEP for up to 3 weeks among women on antiretroviral treatment (ART) (0.18 log10 copies/swab increase; P = .003) and in ART-naive women (1.13 log10 copies/swab increase; P < .001) compared to baseline. Within cryotherapy, cervical shedding increased in ART-naive women (0.72 log10 copies/swab increase; P = 0.004) but did not increase in women on ART., Conclusions: Women randomized to LEEP had a larger increase in post-procedural cervical HIV shedding than cryotherapy. Benefits of cervical cancer prevention outweigh the risk of HIV sexual transmission; our findings underscore the importance of risk-reduction counseling., Clinical Trials Registration: NCT01298596.

Background: HIV assisted partner services (APS) are a notification and testing strategy for sex partners of HIV-infected index patients. This cluster-randomized controlled trial secondary data analysis investigated whether history of intimate partner violence (IPV) modified APS effectiveness and risk of relationship dissolution., Setting: Eighteen HIV testing and counseling sites in Kenya randomized to provide immediate APS (intervention) or APS delayed for 6 weeks (control)., Methods: History of IPV was ascertained at study enrollment and defined as reporting ever experiencing physical or sexual IPV. Those reporting IPV in the month before enrollment were excluded. We tested whether history of IPV modified intervention effectiveness and risk of relationship dissolution using population-averaged Poisson and log-binomial generalized estimating equation models. Exploratory analyses investigated associations between history of IPV and events that occurred after HIV diagnosis using log-binomial generalized estimating equation models., Results: The study enrolled 1119 index participants and 1286 partners. Among index participants, 81 (7%) had history of IPV. History of IPV did not modify APS effectiveness in testing, newly diagnosing, or linking partners to care. History of IPV did not modify the association between receiving immediate APS and relationship dissolution during the study., Conclusions: Among participants who had not experienced IPV in the last month but had experienced IPV in their lifetimes, our results suggest that APS is an effective and safe partner notification strategy in Kenya. As APS is scaled up in different contexts, these data support including those reporting past IPV and closely monitoring adverse events.

Background: Disruptions of vaginal microbiota might increase women's susceptibility to HIV infection. Advances in molecular microbiology have enabled detailed examination of associations between vaginal bacteria and HIV acquisition. Therefore, this study aimed to evaluate the association between the concentrations of specific vaginal bacteria and increased risk of HIV acquisition in African women., Methods: We did a nested case-control study of participants from eastern and southern Africa. Data from five cohorts of African women (female sex workers, pregnant and post-partum women, and women in serodiscordant relationships) were used to form a nested case-control analysis between women who acquired HIV infection versus those who remained seronegative. Deep sequence analysis of broad-range 16S rRNA gene PCR products was applied to a subset of 55 cases and 55 controls. From these data, 20 taxa were selected for bacterium-specific real-time PCR assays, which were examined in the full cohort as a four-category exposure (undetectable, first tertile, second tertile, and third tertile of concentrations). Conditional logistic regression was used to generate odds ratios (ORs) and 95% CIs. Regression models were stratified by cohort, and adjusted ORs (aORs) were generated from a multivariable model controlling for confounding variables. The Shannon Diversity Index was used to measure bacterial diversity. The primary analyses were the associations between bacterial concentrations and risk of HIV acquisition., Findings: Between November, 2004, and August, 2014, we identified 87 women who acquired HIV infection (cases) and 262 controls who did not acquire HIV infection. Vaginal bacterial community diversity was higher in women who acquired HIV infection (median 1·3, IQR 0·4-2·3) than in seronegative controls (0·7, 0·1-1·5; p=0·03). Seven of the 20 taxa showed significant concentration-dependent associations with increased odds of HIV acquisition: Parvimonas species type 1 (first tertile aOR 1·67, 95% CI 0·61-4·57; second tertile 3·01, 1·13-7·99; third tertile 4·64, 1·73-12·46; p=0·005) and type 2 (first tertile 3·52, 1·63-7·61; second tertile 0·85, 0·36-2·02; third tertile 2·18, 1·01-4·72; p=0·004), Gemella asaccharolytica (first tertile 2·09, 1·01-4·36; second tertile 2·02, 0·98-4·17; third tertile 3·03, 1·46-6·30; p=0·010), Mycoplasma hominis (first tertile 1·46, 0·69-3·11; second tertile 1·40, 0·66-2·98; third tertile 2·76, 1·36-5·63; p=0·048), Leptotrichia/Sneathia (first tertile 2·04, 1·02-4·10; second tertile 1·45, 0·70-3·00; third tertile 2·59, 1·26-5·34; p=0·046), Eggerthella species type 1 (first tertile 1·79, 0·88-3·64; second tertile 2·62, 1·31-5·22; third tertile 1·53, 0·72-3·28; p=0·041), and vaginal Megasphaera species (first tertile 3·15, 1·45-6·81; second tertile 1·43, 0·65-3·14; third tertile 1·32, 0·57-3·05; p=0·038)., Interpretation: Differences in the vaginal microbial diversity and concentrations of key bacteria were associated with greater risk of HIV acquisition in women. Defining vaginal bacterial taxa associated with HIV risk could point to mechanisms that influence HIV susceptibility and provide important targets for future prevention research., Funding: National Institute of Child Health and Human Development., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Introduction: Child mortality due to infectious diseases remains unacceptably high in much of sub-Saharan Africa. Children who are hospitalised represent an accessible population at particularly high risk of death, both during and following hospitalisation. Hospital discharge may be a critical time point at which targeted use of antibiotics could reduce morbidity and mortality in high-risk children., Methods and Analysis: In this randomised, double-blind, placebo-controlled trial (Toto Bora Trial), 1400 children aged 1-59 months discharged from hospitals in Western Kenya, in Kisii and Homa Bay, will be randomised to either a 5-day course of azithromycin or placebo to determine whether a short course of azithromycin reduces rates of rehospitalisation and/or death in the subsequent 6-month period. The primary analysis will be modified intention-to-treat and will compare the rates of rehospitalisation or death in children treated with azithromycin or placebo using Cox proportional hazard regression. The trial will also evaluate the effect of a short course of azithromycin on enteric and nasopharyngeal infections and cause-specific morbidities. We will also identify risk factors for postdischarge morbidity and mortality and subpopulations most likely to benefit from postdischarge antibiotic use. Antibiotic resistance in Escherichia coli and Streptococcus pneumoniae among enrolled children and their primary caregivers will also be assessed, and cost-effectiveness analyses will be performed to inform policy decisions., Ethics and Dissemination: Study procedures were reviewed and approved by the institutional review boards of the Kenya Medical Research Institute, the University of Washington and the Kenyan Pharmacy and Poisons Board. The study is being externally monitored, and a data safety and monitoring committee has been assembled to monitor patient safety and to evaluate the efficacy of the intervention. The results of this trial will be published in peer-reviewed scientific journals and presented at relevant academic conferences and to key stakeholders., Trial Registration Number: NCT02414399., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Background: Adolescent-friendly policies aim to tailor HIV services for adolescents and young adults aged 10-24 years (AYA) to promote health outcomes and improve retention in HIV care and treatment. However, few interventions focus on improving healthcare worker (HCW) competencies and skills for provision of high-quality adolescent care. Standardized patients (SPs) are trained actors who work with HCWs in mock clinical encounters to improve clinical assessment, communication, and empathy skills. This stepped-wedge randomized controlled trial will evaluate a clinical training intervention utilizing SPs to improve HCW skills in caring for HIV-positive AYA, resulting in increased retention in care., Methods/design: The trial will utilize a stepped-wedge design to evaluate a training intervention using SPs to train HCWs in assessment, communication, and empathy skills for AYA HIV care. We will recruit 24 clinics in Kenya with an active electronic medical record (EMR) system and at least 40 adolescents enrolled in HIV care per site. Stratified randomization by county will be used to assign clinics to one of four waves - time periods when they receive the intervention - with each wave including six clinics. From each clinic, up to 10 HCWs will participate in the training intervention. SP training includes didactic sessions in adolescent health, current guidelines, communication skills, and motivational interviewing techniques. HCW participants will rotate through seven standardized SP scenarios, followed by SP feedback, group debriefing, and remote expert evaluation. AYA outcomes will be assessed using routine clinic data. The primary outcome is AYA retention in HIV care, defined as returning for first follow-up visit within 6 months of presenting to care, or returning for a first follow-up visit after re-engagement in care in AYA with a previous history of being lost to follow-up. Secondary outcomes include HCW competency scores, AYA satisfaction with care, and AYA clinical outcomes including CD4 and viral load. Additional analyses will determine cost-effectiveness of the intervention., Discussion: This trial will contribute valuable information to HIV programs in Kenya and other low-resource settings, providing a potentially scalable strategy to improve quality of care and retention in critical HIV services in this population., Trial Registration: ClinicalTrials.gov, ID: NCT02928900. Registered 26 August 2016.

Background: Pre-antiretroviral-treatment drug resistance (PDR) is a predictor of human immunodeficiency virus (HIV) treatment failure. We determined PDR prevalence and correlates in a Kenyan cohort., Methods: We conducted a cross-sectional analysis of antiretroviral (ARV) treatment-eligible HIV-infected participants. PDR was defined as ≥2% mutant frequency in a participant's HIV quasispecies at pol codons K103N, Y181C, G190A, M184 V, or K65R by oligonucleotide ligation assay and Illumina sequencing. PDR prevalence was calculated by demographics and codon, stratifying by prior ARV experience. Poisson regression was used to estimate prevalence ratios., Results: PDR prevalences (95% confidence interval [CI]) in 815 ARV-naive adults, 136 ARV-experienced adults, and 36 predominantly ARV-naive children were 9.4% (7.5%-11.7%), 12.5% (7.5%-19.3%), and 2.8% (0.1%-14.5%), respectively. Median mutant frequency within an individual's HIV quasispecies was 67%. PDR prevalence in ARV-naive women 18-24 years old was 21.9% (9.3%-40.0%). Only age in females associated with PDR: A 5-year age decrease was associated with adjusted PDR prevalence ratio 1.20 (95% CI, 1.06-1.36; P = .004)., Conclusions: The high PDR prevalence may warrant resistance testing and/or alternative ARVs in high HIV prevalence settings, with attention to young women, likely to have recent infection and higher rates of resistance., Clinical Trials Registration: NCT01898754., (© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

Introduction: As adolescents and young women become sexually active, they are at risk of adverse reproductive health outcomes including sexually transmitted infections (STIs). We assessed feasibility and acceptability of STI screening among 15- to 24-year-old women in Mombasa, Kenya., Methods: After sensitization activities, participants were recruited from 3 high schools and 1 university. Study staff conducted informational sessions. Students interested in participating were given consent forms to take home, and invited to visit our clinic for STI screening. During clinic visits, participants completed a self-administered questionnaire and provided a urine specimen for STI testing using a nucleic acid amplification test., Results: Between August 2014 and March 2015, 463 high school and 165 university students collected consent forms. Of these, 293 (63%) from high schools versus 158 (95%) from university attended clinic for STI screening (P < 0.001). Of the 150 (33%) who reported any history of insertive vaginal sex, 78 (52.0%) reported condom use at the last sex act, 31 (20.7%) reported using modern nonbarrier contraceptive methods, and 37 (24.7%) reported not using any contraception at the last sex act. Twenty-six (5.8%) participants were diagnosed with STIs (7 [1.6%] Neisseria gonorrhoeae, 16 [3.6%] Chlamydia trachomatis, 3 [0.7%] Trichomonas vaginalis). In multivariable analyses, reporting receptive vaginal sex without a condom was associated with having a laboratory confirmed STI (odds ratio, 6.21; 95% confidence interval, 1.72-22.28)., Conclusions: These findings support the need for reproductive health interventions to reduce the risk of STIs in a population of adolescent girls and young women in East Africa.

Oral pre-exposure prophylaxis (PrEP) can prevent HIV transmission. Yet, some may prefer not to take systemic daily medication. MTN-017 was a 3-period, phase 2 safety and acceptability study of microbicide gel applied rectally either daily or before and after receptive anal intercourse (RAI), compared to daily oral tablet. At baseline, cisgender men and transgender women who reported RAI (N = 187) rated the daily oral regimen higher in overall liking, ease of use, and likelihood of future use than the gel regimens. After trying all three, 28% liked daily oral the least. Gel did not affect sexual enjoyment (88%) or improved it (7-8%). Most partners had no reaction to gel use. Ease of gel use improved significantly between the first and the last few times of daily use. A rectal gel used before and after RAI may constitute an attractive alternative to daily tablet. Experience with product use may increase acceptability.

Children with acute and chronic malnutrition are at increased risk of morbidity and mortality following a diarrheal episode. To compare diarrheal disease severity and pathogen prevalence among children with and without acute and chronic malnutrition, we conducted a cross-sectional study of human immunodeficiency virus-uninfected Kenyan children aged 6-59 months, who presented with acute diarrhea. Children underwent clinical and anthropometric assessments and provided stool for bacterial and protozoal pathogen detection. Clinical and microbiological features were compared using log binomial regression among children with and without wasting (mid-upper arm circumference ≤ 125 mm) or stunting (height-for-age z score ≤ -2). Among 1,363 children, 7.0% were wasted and 16.9% were stunted. After adjustment for potential confounders, children with wasting were more likely than nonwasted children to present with at least one Integrated Management of Childhood Illness danger sign (adjusted prevalence ratio [aPR]: 1.3, 95% confidence interval [CI]: 1.0 to 1.5, P = 0.05), severe dehydration (aPR: 2.4, 95% CI: 1.5 to 3.8, P < 0.01), and enteroaggregative Escherichia coli recovered from their stool (aPR: 1.8, 1.1-2.8, P = 0.02). There were no differences in the prevalence of other pathogens by wasting status after confounder adjustment. Stunting was not associated with clinical severity or the presence of specific pathogens. Wasted children with diarrhea presented with more severe disease than children without malnutrition which may be explained by a delay in care-seeking or diminished immune response to infection. Combating social determinants and host risk factors associated with severe disease, rather than specific pathogens, may reduce the disparities in poor diarrhea-associated outcomes experienced by malnourished children.

Background: p16 immunohistochemistry is used to evaluate for HPV-associated cervical intraepithelial neoplasia. The diagnostic performance of p16 in HIV infection is unclear., Methods: Between June-December 2009, HIV-infected women underwent Papanicolaou (Pap) smear, human papillomavirus (HPV) testing, visual inspection with acetic acid (VIA), and colposcopy-directed biopsy as the disease gold standard at a HIV clinic in Kenya. Pap smears were evaluated for p16 expression. Sensitivity, specificity, positive predictive value (PPV), and area under the receiver operating characteristic curve (AUC) of p16 to detect CIN2/3 on histology and the impact of immunosuppression and ART was assessed., Results: Of 331 cervical samples with p16 expression, p16 sensitivity and specificity to detect CIN2/3 was 54.1% and 72.4% respectively, which was lower than Pap and HPV in sensitivity, but higher in specificity than Pap, HPV, and VIA. Combining tests and p16 reduced sensitivity and increased specificity of Pap from 90.5% to 48.7% and 51.4% to 81.7%; of VIA from 59.5% to 37.8% and 67.6% to 89.9%; and of HPV from 82.4% to 50.0% and 55.3% to 84.8%. Combination p16 increased the PPV of Pap from 34.9% to 43.4%; of HPV from 34.7% to 48.7%; and VIA from 34.9% to 51.9%. Adjunctive p16 did not change AUC (P>0.05). P16 performance was not altered by immunosuppression or ART use. Combining p16 with HPV and VIA reduced the variation in HPV and VIA performance associated with CD4 and ART., Conclusion: As an adjunctive test in HIV-infected women, p16 immunohistochemistry increased specificity and PPV of HPV and VIA for CIN2/3, and was not altered in performance by immunosuppression, ART, or age.

Background: Few men are tested for syphilis or human immunodeficiency virus (HIV) during their partner's pregnancy, a high-risk period for HIV and syphilis transmission. Offering home-based rapid testing of syphilis to couples during pregnancy can support prevention efforts to reduce transmission of sexually transmitted diseases and adverse pregnancy outcomes., Methods: We assessed men's uptake of paired (separate tests, single blood draw) point-of-care syphilis and HIV tests within a randomized controlled trial of pregnant women who received clinic or home partner HIV testing. We evaluated acceptance of paired HIV-syphilis testing during pregnancy or at 6 months postpartum, and evaluated whether addition of syphilis testing affected the uptake of HIV testing among men., Results: Of 601 women, we were unable to meet 101 male partners, and 180 tested before syphilis tests were available. Paired syphilis and HIV testing was offered at home to 80 men during pregnancy and to 230 men postpartum. For syphilis, 93% of men agreed to test during pregnancy and 98% agreed postpartum. For paired syphilis and HIV testing, 91% of men tested for both during pregnancy and 96% tested postpartum. Before syphilis test introduction, 96% of men accepted HIV testing, compared with 95% of men who accepted HIV testing when paired testing was offered., Conclusions: Uptake of syphilis and HIV testing was high among male partners offered couple testing at home. Introducing syphilis testing did not adversely affect HIV testing among men. Point-of-care diagnostics outside facilities can increase testing of male partners who rarely accompany women to antenatal clinics.

Studies on the effects of alcohol use on HIV disease progression have been contradictory, with at least one study finding a positive effect of low alcohol consumption on CD4 count. In addition, most such studies have taken place in the developed West. We investigated the association between alcohol use and immune reconstitution through CD4 count response among HIV-infected individuals on antiretroviral therapy (ART) at an urban sub-Saharan African clinic. This was a retrospective cohort study of treatment-naïve HIV-infected adults initiating ART in Nairobi, Kenya and followed for 12 months between January 2009 and December 2012. At enrollment, a standardized questionnaire was used to collect data on sociodemographic variables and alcohol consumption. CD4 count was measured every six months. Linear regression models assessed the association between CD4 count and alcohol consumption, categorized as abstinent, moderate, or hazardous. Overall, 854 participants were included, 522 of which were women, with 85 (25.6%) men and 50 (9.6%) women reporting any alcohol use, and 8 (2.4%) men and 7 (1.3%) women reporting hazardous drinking. At baseline, alcohol use was associated with higher education and socioeconomic status. Median CD4 count was higher among alcohol users compared to those who abstained at baseline and at 6 and 12 months post-ART initiation, although this was only significant at 6 months. There were no differences in adherence between abstainers and drinkers. While overall alcohol use was significantly associated with higher CD4 counts, moderate and hazardous use treated separately were not. We conclude that, while alcohol use was associated with higher CD4 counts at 12 months post-ART, the mechanism for this association is unclear but may reflect unmeasured socioeconomic or nutritional differences. Additional research is required on the specific drinking patterns of this population and the types of alcoholic beverages consumed to clarify this relationship.

Gogh, Vincent Van (1853-1890). The Starry Night. Saint Rémy, June 1889. Oil on canvas, 29 × 36 1/4″ (73.7 × 92.1 cm). Acquired through the Lillie P. Bliss Bequest. The Museum of Modern Art. Digital Image © The Museum of Modern Art/Licensed by SCALA/Art Resource, NY., (Copyright © 2017 by the Congress of Neurological Surgeons.)

In this paper, we evaluate the effectiveness of the first year of a federally-funded, evidence-based preschool through third grade intervention in Chicago. We use inverse probability weighting with regression adjustment to estimate the impacts of the Child-Parent Center (CPC) program on teacher assessments of school readiness for 1,289 low-income preschool and 591 comparison-group participants. Results indicated significant positive impacts of the program for all domains, including literacy, math, socio-emotional development, science and total score. The percentage of CPC children who met national norms in school readiness exceeded the comparison group by 12 to 18.5 percentage points. Full-day participants experienced greater school readiness gains while program impacts were similar by family income and home language. Compared to the original CPC evaluation of children born in 1980 in which few comparison group children attended preschool, we find evidence that the contemporary implementation performs at least as well even though the current comparison group participants had alternative preschool experience.

Trials to assess microbicide safety require strict adherence to prescribed regimens. If adherence is suboptimal, safety cannot be adequately assessed. MTN-017 was a phase 2, randomized sequence, open-label, expanded safety and acceptability crossover study comparing 1) daily oral emtricitabine/tenofovir disoproxil fumarate (FTC/TDF), 2) daily use of reduced-glycerin 1% tenofovir (RG-TFV) gel applied rectally, and 3) RG-TFV gel applied before and after receptive anal intercourse (RAI)-if participants had no RAI in a week, they were asked to use two doses of gel within 24 hours. Product use was assessed by mixed methods including unused product return count, text messaging reports, and qualitative plasma TFV pharmacokinetic (PK) results. Convergence interviews engaged participants in determining the most accurate number of doses used based on product count and text messaging reports. Client-centered adherence counseling was also used. Participants (N = 187) were men who have sex with men and transgender women enrolled in the United States (42%), Thailand (29%), Peru (19%) and South Africa (10%). Mean age was 31.4 years (range 18-64 years). Based on convergence interviews, over an 8-week period, 94% of participants had ≥80% adherence to daily tablet, 41% having perfect adherence; 83% had ≥80% adherence to daily gel, 29% having perfect adherence; and 93% had ≥80% adherence to twice-weekly use during the RAI-associated gel regimen, 75% having perfect adherence and 77% having ≥80% adherence to gel use before and after RAI. Only 4.4% of all daily product PK results were undetectable and unexpected (TFV concentrations <0.31 ng/mL) given self-reported product use near sampling date. The mixed methods adherence measurement indicated high adherence to product use in all three regimens. Adherence to RAI-associated rectal gel use was as high as adherence to daily oral PrEP. A rectal microbicide gel, if efficacious, could be an alternative for individuals uninterested in daily oral PrEP.

Rising temperatures have begun to shift flowering time, but it is unclear whether phenotypic plasticity can accommodate projected temperature change for this century. Evaluating clines in phenological traits and the extent and variation in plasticity can provide key information on assessing risk of maladaptation and developing strategies to mitigate climate change. In this study, flower phenology was examined in 52 populations of big sagebrush (Artemisia tridentata) growing in three common gardens. Flowering date (anthesis) varied 91 days from late July to late November among gardens. Mixed-effects modeling explained 79% of variation in flowering date, of which 46% could be assigned to plasticity and genetic variation in plasticity and 33% to genetics (conditional R 2  = 0.79, marginal R 2  = 0.33). Two environmental variables that explained the genetic variation were photoperiod and the onset of spring, the Julian date of accumulating degree-days >5 °C reaching 100. The genetic variation was mapped for contemporary and future climates (decades 2060 and 2090), showing flower date change varies considerably across the landscape. Plasticity was estimated to accommodate, on average, a ±13-day change in flowering date. However, the examination of genetic variation in plasticity suggests that the magnitude of plasticity could be affected by variation in the sensitivity to photoperiod and temperature. In a warmer common garden, lower-latitude populations have greater plasticity (+16 days) compared to higher-latitude populations (+10 days). Mapped climatypes of flowering date for contemporary and future climates illustrate the wide breadth of plasticity and large geographic overlap. Our research highlights the importance of integrating information on genetic variation, phenotypic plasticity and climatic niche modeling to evaluate plant responses and elucidate vulnerabilities to climate change., (Published 2016. This article is a U.S. Government work and is in the public domain in the USA.)

Background: Lifelong antiretroviral therapy (ART) (Option B+) is recommended for all HIV-infected pregnant/postpartum women, but high adherence is required to maximize HIV prevention potential and maintain maternal health. Mobile health (mHealth) interventions may provide treatment adherence support for women during, and beyond, the pregnancy and postpartum periods., Methods and Design: We are conducting an unblinded, triple-arm randomized clinical trial (Mobile WACh X) of one-way short message service (SMS) vs. two-way SMS vs. control (no SMS) to improve maternal ART adherence and retention in care by 2years postpartum. We will enroll 825 women from Nairobi and Western Kenya. Women in the intervention arms receive weekly, semi-automated motivational and educational SMS and visit reminders via an interactive, human-computer hybrid communication system. Participants in the two-way SMS arm are also asked to respond to a question related to the message. SMS are based in behavioral theory, are tailored to participant characteristics through SMS tracks, and are timed along the pregnancy/postpartum continuum. After enrollment, follow-up visits are scheduled at 6weeks; 6, 12, 18, and 24months postpartum. The primary outcomes, virological failure (HIV viral load ≥1000copies/mL), maternal retention in care, and infant HIV infection or death, will be compared in an intent to treat analysis. We will also measure ART adherence and drug resistance., Discussion: Personalized and tailored SMS to support HIV-infected women during and after pregnancy may be an effective strategy to motivate women to adhere to ART and remain in care and improve maternal and infant outcomes., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Background: Peripartum immunologic changes may affect latent tuberculosis infection (LTBI) diagnostic performance among HIV-infected women., Methods: HIV-infected women were serially tested with tuberculin skin test (TST) and interferon gamma release assay [QuantiFERON TB Gold In-tube (QFT)] in pregnancy and 6 weeks postpartum in Kenya. Prevalence, sensitivity and agreement, and correlates of QFT/TST positivity were assessed. Quantitative QFT mitogen and Mycobacterium tuberculosis antigen (Mtb-Ag) responses were compared by peripartum stage. Incidence of test conversion at 6 weeks postpartum was evaluated in baseline TST-/QFT- women., Results: Among 100 HIV-infected women, median age was 26 years, median CD4 was 555 cells per cubic millimeter, and 88% were on antiretrovirals. More women were QFT+ than TST+ in both pregnancy (35.4% vs. 13.5%, P = 0.001) and postpartum (29.6% vs. 14.8%, P < 0.001). Among 18 consistently QFT+ women, 8 (44%) converted from TST- to TST+, with improved test agreement postpartum (56.9%, κ = 0.20 to 82.4%, κ = 0.60). Three initially QFT-/TST- women had test conversion (TST+ and/or QFT+), suggesting new infection (incidence 13.4/100 person-years). Mean QFT mitogen (4.46 vs. 7.64 IU/mL, P < 0.001) and Mtb-Ag (1.03 vs. 1.54 IU/mL, P = 0.03) responses were lower among all women retested in pregnancy vs. postpartum, and specifically among persistently QFT+ women (Mtb-Ag: 3.46 vs. 4.48 IU/mL, P = 0.007). QFT indeterminate rate was higher in pregnancy (16%) compared with postpartum (0%) because of lower mitogen response., Conclusions: QFT identified >2-fold more women with LTBI compared with TST in pregnancy and postpartum. Lower QFT Mtb-Ag and mitogen responses in pregnancy compared with postpartum suggest that pregnancy-associated immunologic changes may influence LTBI test performance.

Population genetic information can provide valuable insight for the conservation and management of threatened and endangered plant species. Tamarix taklamakanensis is an endangered shrub endemic to arid basins of northwestern China. This species serves to stabilize soils in this region, but has seen substantial loss in its abundance due to depletion of ground water. The populations of this species have become small and fragmented, warranting conservation. Seven microsatellite loci were used to assess the genetic diversity and structure of 15 populations in the Tarim Basin, China. Among populations, the expected heterozygosity and total gene diversity were both moderate ( H E = 0.392, h T = 0.432), however the allelic diversity was low ( A = 2.4). Eleven populations were detected to have experienced recent bottlenecks using Wilcoxon's test and a model-shift test. Most populations of T. taklamakanensis in the centre of Tarim Basin showed low levels of genetic differentiation, but higher levels in geographically outlying populations. Genetic structure based on Bayesian assignment, the neighbour-joining network and principal coordinates analyses produced similar results, supporting five groups in the Tarim Basin. Gene flow was high among Bayesian groups based on historical gene flow estimated by private alleles. The genetic structure of T. taklamakanensis supports a pattern where gene flow principally occurs along river corridors through hydrochory of seeds and insect-mediated pollination. Populations upstream have contributed to a more diverse mixture of populations near the confluence of several rivers near the centre of Tarim Basin. This pattern of genetic structure could be influenced by the flow of water from different river systems. Conservation efforts should focus on fostering the regeneration of this species, maintaining genetic diversity and preserving the extant genetic structure. Conservation efforts are contingent upon maintaining ground water and streamflows in this arid basin.

Objective: Many HIV-positive women now live well beyond menopause. Postmenopausal women are no longer at risk for pregnancy, and some studies suggest that they may use condoms less often than premenopausal women. This study tests the hypothesis that, in HIV-positive women who report trading sex for cash or in-kind payment, unprotected sex is more common at postmenopausal visits compared with premenopausal visits., Design: Prospective cohort study of HIV-positive women ≥16 years old in Mombasa, Kenya., Methods: At enrollment and monthly follow-up visits, participants completed a standardized interview. Study clinicians collected genital samples at enrollment and quarterly visits. Menopausal status was assessed annually. The primary outcome of unprotected sex was determined by detection of prostate specific antigen (PSA) in vaginal secretions., Results: This study followed 404 HIV-positive women who contributed 2753 quarterly examination visits. Detection of PSA was less frequent at postmenopausal visits compared with premenopausal visits [55/554, 10.5% versus 394/2199, 17.9%; relative risk (RR) 0.58, 95% confidence interval (CI): 0.39 to 0.87]. Adjusting for age diminished the association between menopause and PSA detection (adjusted RR 0.73, 95% CI: 0.47 to 1.14). At visits where women reported sexual activity in the past week, they reported similar rates of 100% condom use at postmenopausal and premenopausal visits (RR 0.99, 95% CI: 0.87 to 1.13)., Conclusions: In this population of high-risk HIV-positive Kenyan women, postmenopausal status was not associated with a greater risk of unprotected sex. The relationship between menopause and unprotected sex is likely context specific and may differ with varying risk groups, regions, and levels of exposure to sexual health education.

A genecological approach was used to explore genetic variation for survival in Artemisia tridentata (big sagebrush). Artemisia tridentata is a widespread and foundational shrub species in western North America. This species has become extremely fragmented, to the detriment of dependent wildlife, and efforts to restore it are now a land management priority. Common-garden experiments were established at three sites with seedlings from 55 source-populations. Populations included each of the three predominant subspecies, and cytotype variations. Survival was monitored for 5 years to assess differences in survival between gardens and populations. We found evidence of adaptive genetic variation for survival. Survival within gardens differed by source-population and a substantial proportion of this variation was explained by seed climate of origin. Plants from areas with the coldest winters had the highest levels of survival, while populations from warmer and drier sites had the lowest levels of survival. Survival was lowest, 36%, in the garden that was prone to the lowest minimum temperatures. These results suggest the importance of climatic driven genetic differences and their effect on survival. Understanding how genetic variation is arrayed across the landscape, and its association with climate can greatly enhance the success of restoration and conservation.

Background: Human immunodeficiency virus (HIV) disproportionately affects men who have sex with men (MSM) and transgender women (TGW). Safe and acceptable topical HIV prevention methods that target the rectum are needed., Methods: MTN-017 was a phase 2, 3-period, randomized sequence, open-label, expanded safety and acceptability crossover study comparing rectally applied reduced-glycerin (RG) 1% tenofovir (TFV) and oral emtricitabine/TFV disoproxil fumarate (FTC/TDF). In each 8-week study period participants were randomized to RG-TFV rectal gel daily, or RG-TFV rectal gel before and after receptive anal intercourse (RAI; or at least twice weekly in the event of no RAI), or daily oral FTC/TDF., Results: MSM and TGW (n = 195) were enrolled from 8 sites in the United States, Thailand, Peru, and South Africa with mean age of 31.1 years (range 18-64). There were no differences in ≥grade 2 adverse event rates between daily gel (incidence rate ratio [IRR], 1.09; P = .59) or RAI gel (IRR, 0.90; P = .51) compared to FTC/TDF. High adherence (≥80% of prescribed doses assessed by unused product return and Short Message System reports) was less likely in the daily gel regimen (odds ratio [OR], 0.35; P < .001), and participants reported less likelihood of future daily gel use for HIV protection compared to FTC/TDF (OR, 0.38; P < .001)., Conclusions: Rectal application of RG TFV gel was safe in MSM and TGW. Adherence and product use likelihood were similar for the intermittent gel and daily oral FTC/TDF regimens, but lower for the daily gel regimen., Clinical Trials Registration: NCT01687218., (© The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

Background: Understanding sexual behaviors and vaginal practices of pregnant and breastfeeding women in sub-Saharan Africa is critical to inform HIV prevention strategies during these periods., Methods: HIV-uninfected women presenting for antenatal care in western Kenya were enrolled and followed through 36 weeks postpartum. Sexual behavior and vaginal practices were ascertained by structured questionnaires. Logistic regression was used to assess correlates of unprotected sex, vaginal washing, and vaginal drying., Results: Among 1252 women enrolled, 78.4% were married (of whom 15.1% were in polygamous unions), 1.4% had a known HIV-infected partner, and 33.6% had a partner of unknown HIV status. At enrollment, 58.5% reported sex in the past month (94.3% unprotected) and 4.5% reported forced sex. Odds of unprotected sex at enrollment was >11-fold higher in married than in unmarried women (P < 0.001) and lower among women who reported partners of unknown HIV status or HIV-infected compared with HIV-uninfected partners. Median time to postpartum resumption of sex was 7 weeks (interquartile range 4-12). Prevalence of unprotected sex in the past week increased from 6.6% to 60.0% between 2 and 36 weeks postpartum (P < 0.001). Vaginal washing was reported by 60.1% of women at enrollment and prevalence remained stable postpartum; vaginal drying was reported by 17.9% at enrollment and decreased to 6.1% at 36 weeks postpartum (P < 0.001). Vaginal washing and drying were associated with forced sex., Conclusions: High rates of unknown partner HIV status, polygamy, and less frequent condom use among pregnant/postpartum women underscore the need for female-controlled HIV prevention interventions. Vaginal washing and drying may present challenges to microbicide use.

Background: Assisted partner services for index patients with HIV infections involves elicitation of information about sex partners and contacting them to ensure that they test for HIV and link to care. Assisted partner services are not widely available in Africa. We aimed to establish whether or not assisted partner services increase HIV testing, diagnoses, and linkage to care among sex partners of people with HIV infections in Kenya., Methods: In this cluster randomised controlled trial, we recruited non-pregnant adults aged at least 18 years with newly or recently diagnosed HIV without a recent history of intimate partner violence who had not yet or had only recently linked to HIV care from 18 HIV testing services clinics in Kenya. Consenting sites in Kenya were randomly assigned (1:1) by the study statistician (restricted randomisation; balanced distribution in terms of county and proximity to a city) to immediate versus delayed assisted partner services. Primary outcomes were the number of partners tested for HIV, the number who tested HIV positive, and the number enrolled in HIV care, in those who were interviewed at 6 week follow-up. Participants within each cluster were masked to treatment allocation because participants within each cluster received the same intervention. This trial is registered with ClinicalTrials.gov, number NCT01616420., Findings: Between Aug 12, 2013, and Aug 31, 2015, we randomly allocated 18 clusters to immediate and delayed HIV assisted partner services (nine in each group), enrolling 1305 participants: 625 (48%) in the immediate group and 680 (52%) in the delayed group. 6 weeks after enrolment of index patients, 392 (67%) of 586 partners had tested for HIV in the immediate group and 85 (13%) of 680 had tested in the delayed group (incidence rate ratio 4·8, 95% CI 3·7-6·4). 136 (23%) partners had new HIV diagnoses in the immediate group compared with 28 (4%) in the delayed group (5·0, 3·2-7·9) and 88 (15%) versus 19 (3%) were newly enrolled in care (4·4, 2·6-7·4). Assisted partner services did not increase intimate partner violence (one intimate partner violence event related to partner notification or study procedures occurred in each group)., Interpretation: Assisted partner services are safe and increase HIV testing and case-finding; implementation at the population level could enhance linkage to care and antiretroviral therapy initiation and substantially decrease HIV transmission., Funding: National Institutes of Health., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

In many regions of sub-Saharan Africa, both HIV and helminth infections are prevalent. HIV-1 (human immunodeficiency virus type 1) and helminth infections can both compromise immune responses in humans. To determine whether the presence of helminth infection or the treatment of helminth infection alters unstimulated vaccine responses among HIV-1 infected individuals, we conducted two nested serologic studies. Blood samples were collected for HIV disease monitoring and vaccine-specific serologic assays, while stool was evaluated by direct microscopy methods. We compared antibody responses to measles and tetanus vaccines in helminth-infected ( Ascaris, Trichuris , hookworm and/or Schistosoma mansoni) and uninfected adults 18 years and older (n=100). We also compared measles and tetanus antibody responses in Ascaris only -infected adults receiving 400 mg albendazole daily for 3 days (n=16) vs. placebo (n=19) in a separate study. In both cohorts, over 70% of participants had measles and tetanus responses above the protective threshold. Prevalence of measles responses were similar between helminth-infected and uninfected individuals (82%, 95% CI: 71-93% vs 72%, 95% CI: 59-85%), as well as log 10 tetanus antibody levels (-0.133 IU/mL vs -0.190 IU/mL, p>0.05), and did not differ by helminth species. In the Ascaris -infected cohort, changes in measles responses and tetanus responses did not differ between those who received anthelminthic vs. placebo (p>0.05 for both). In these studies, neither helminth infection, nor deworming, appeared to affect previously administered vaccine responsiveness in HIV-1 infected, ART naïve, adults in Kenya.

Population genetic studies provide a foundation for conservation planning, especially for endangered species. Three chloroplast SSRs ( mtrnSf-trnGr, mtrnL2-trnF , and mtrnL5-trnL3 ) and the internal transcribed spacer were used to examine the population structure of Helianthemum in northwestern China. A total of 15 populations of the genus were collected. Nine chloroplast haplotypes and two nuclear genotypes were detected. Both the nuclear and chloroplast data showed two lineages in Helianthemum songaricum , respectively, distributed in Yili Valley and western Ordos Plateau. A total of 66.81% ( p < 0.001) of the genetic variation was supported by this lineage split. A Mantel test showed a significant correlation between genetic distance and geographical distance ( r = 0.937, p < 0.001). Based on genetic analyses, cpSSRs data support strong genetic divergence between regions. We speculate that the climate change during the late Tertiary and early Quaternary isolated H. songaricum into their current distribution, resulting in interruption of gene flow, leading to isolation and genetic divergence between the two regions. Meanwhile, possible selfing would increase genetic drift in small fragmented populations, that might account for the observed genetic divergence in both regions. Given the loss of genetic diversity and genetic divergence in small populations of Helianthemum in northwestern China immediate conservation management steps should be taken on the species.

Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Background: With malaria declining, other causes of fever may account for a substantial portion of severe childhood illness in sub-Saharan Africa. We determined prevalence, etiologies, and correlates of bacteremia among children in Western Kenya., Methods: In a cross-sectional study, febrile children aged 6 months to 15 years presenting to Kisii (low malaria endemicity) and Homabay (high malaria endemicity) Hospitals were enrolled and screened for malaria, human immunodeficiency virus (HIV) infection and bacteremia. Correlates of bacteremia were evaluated using logistic regression., Results: Among 1476 children enrolled, 48 (3.3%) had bacteremia (23 of 734, 3.1% in Kisii and 25 of 734, 3.4% in Homabay). Salmonella spp (19 typhi and 21 nontyphoidal salmonella) accounted for 83% (40 of 48) of isolates. The distribution of Salmonella spp was similar between sites. Bacteremia was associated with incomplete vaccination (adjusted odds ratio [aOR] = 2.1; 95% confidence interval [CI], 1.1-4.1), before treatment with antimalarials (aOR = 2.7; 95% CI, 1.4-4.1), having sought care elsewhere (aOR = 2.2; 95% CI, 1.2-4.0) and lower education of caregiver (aOR = 2.5; 95% CI, 1.1-4.8). Nontyphoidal salmonella bacteremia was associated with HIV (aOR = 6.8; 95% CI, 1.1-35.1) and anemia (hemoglobin <8 g/dL) (aOR = 5.2; 95% CI, 1.4-18.9)., Conclusions: Bacteremia was relatively uncommon, but children with HIV, anemia, incomplete vaccination, and/or persistent fever despite malaria treatment may have higher risk and may benefit from targeted bacterial culture and/or empiric antibiotic therapy., (© The Author 2015. Published by Oxford University Press on behalf of the Pediatric Infectious Diseases Society. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Background: Antiretroviral medications that are used as prophylaxis can prevent acquisition of human immunodeficiency virus type 1 (HIV-1) infection. However, in clinical trials among African women, the incidence of HIV-1 infection was not reduced, probably because of low adherence. Longer-acting methods of drug delivery, such as vaginal rings, may simplify use of antiretroviral medications and provide HIV-1 protection., Methods: We conducted a phase 3, randomized, double-blind, placebo-controlled trial of a monthly vaginal ring containing dapivirine, a non-nucleoside HIV-1 reverse-transcriptase inhibitor, involving women between the ages of 18 and 45 years in Malawi, South Africa, Uganda, and Zimbabwe., Results: Among the 2629 women who were enrolled, 168 HIV-1 infections occurred: 71 in the dapivirine group and 97 in the placebo group (incidence, 3.3 and 4.5 per 100 person-years, respectively). The incidence of HIV-1 infection in the dapivirine group was lower by 27% (95% confidence interval [CI], 1 to 46; P=0.046) than that in the placebo group. In an analysis that excluded data from two sites that had reduced rates of retention and adherence, the incidence of HIV-1 infection in the dapivirine group was lower by 37% (95% CI, 12 to 56; P=0.007) than that in the placebo group. In a post hoc analysis, higher rates of HIV-1 protection were observed among women over the age of 21 years (56%; 95% CI, 31 to 71; P<0.001) but not among those 21 years of age or younger (-27%; 95% CI, -133 to 31; P=0.45), a difference that was correlated with reduced adherence. The rates of adverse medical events and antiretroviral resistance among women who acquired HIV-1 infection were similar in the two groups., Conclusions: A monthly vaginal ring containing dapivirine reduced the risk of HIV-1 infection among African women, with increased efficacy in subgroups with evidence of increased adherence. (Funded by the National Institutes of Health; ClinicalTrials.gov number, NCT01617096 .).

Background: Disclosure of HIV serostatus can have significant benefits for people living with HIV/AIDS. However, there is limited data on whether partner disclosure influences ART treatment response., Methods: We conducted a retrospective cohort study of newly diagnosed, ART-naïve HIV-infected adults (>18 years) who enrolled at the Coptic Hope Center in Nairobi, Kenya between January 1st 2009 and July 1st 2011 and initiated ART within 3 months. Analysis was restricted to adults who reported to have either disclosed or not disclosed their HIV status to their partner. Analysis of CD4 response at 6 and 12 months post-ART was stratified by age group., Results: Among 615 adults newly initiating ART with partner disclosure data and 12 month follow-up, mean age was 38 years and 52% were male; 76% reported that they had disclosed their HIV-status to their partner. Those who disclosed were significantly younger and more likely to be married/cohabitating than non-disclosers. At baseline, median CD4 counts were similar between disclosure groups. Among younger adults (< 38 years) those who disclosed had higher CD4 recovery than those who did not at 6 months post- ART (mean difference = 31, 95% CI 3 to 58 p = 0.03) but not at 12 months (mean difference = 17, 95% CI -19 to 52, p = 0.4). Among older adults (≥ 38years) there was no observed difference in CD4 recovery at 6 or 12 months between disclosure groups., Conclusion: Among younger adults, disclosure of HIV status to partners may be associated with CD4 recovery following ART., Competing Interests: The authors have declared that no competing interests exist.

Background: Studies of alcohol use and sexual behavior in African populations have primarily been cross-sectional, used nonvalidated measures of alcohol use, or relied on self-reported sexual risk endpoints. Few have focused on human immunodeficiency virus (HIV)-positive women., Methods: Longitudinal data were collected from a cohort of HIV-positive Kenyan female sex workers. At enrollment and annual visits, participants were asked about past-year alcohol use using the Alcohol Use Disorders Identification Test (AUDIT). The primary endpoint was detection of prostate-specific antigen (PSA) in vaginal secretions at quarterly examinations. Associations between hazardous/harmful alcohol use (AUDIT score ≥7), PSA detection, and secondary measures of sexual risk were evaluated using generalized estimating equations with a log binomial regression model., Results: A total of 405 women contributed 2750 vaginal samples over 606 person-years of follow-up. Hazardous/harmful alcohol use was reported at 16.6% of AUDIT assessments and was associated with higher risk of PSA detection (relative risk 1.50; 95% confidence interval, 1.11-2.01) relative to no alcohol use. This association was attenuated and no longer statistically significant, after adjusting for age, work venue, intimate partner violence, depression, and partnership status (adjusted relative risk, 1.13; 95% confidence interval, 0.82-1.56). In exploratory analyses, alcohol use was associated with self-report of unprotected sex and with sexually transmitted infection acquisition., Conclusions: Although hazardous/harmful alcohol use was not associated with detection of PSA in adjusted analysis, associations with secondary outcomes suggest that alcohol use is at least a marker of sexual risk behavior.

Objective: Treatment interruption has been well tolerated and durable in some pediatric studies but none have compared treatment interruption with continued antiretroviral treatment (ART) following ART initiation in early HIV. The objective of this study was to compare outcomes in treatment interruption versus continued ART among early-treated infants., Design: Randomized trial (OPH-03; NCT00428116)., Methods: The trial included HIV-infected infants who initiated ART at less than 13 months of age, received ART for 24 months, and, if eligible (CD4% >25%, normal growth), were randomized to treatment interruption versus continued ART. Children in the treatment interruption group restarted ART if they met WHO ART-eligibility criteria. During 18-months postrandomization, primary outcomes were incidence of serious adverse events and growth. CD4%, viral load, morbidity, and growth were compared., Results: Of 140 infants enrolled, 121 started ART, of whom 75 completed at least 24 months ART and 42 were randomized (21 per arm). ART was initiated at median age 5 months and randomization at 30 months. Among 21 treatment interruption children, 14 met ART restart criteria within 3 months. Randomization was discontinued by Data and Safety Monitoring Board due to low treatment interruption durability. At 18 months postrandomization, growth and serious adverse events were comparable between arms; hypercholesteremia incidence was higher in the continued arm (P = 0.03). CD4% and viral load did not differ between arms [CD4% 35% and median viral load undetectable (<150 copies/ml) in both arms, P = 0.9 for each comparison]. No infants had post-treatment viral control., Conclusion: Short treatment interruption did not compromise 18-month CD4%, viral control, growth, or morbidity compared with continued ART among infants who started ART in early HIV infection.

Environmental enteropathy (EE), a subclinical intestinal disorder characterized by mucosal inflammation, reduced barrier integrity, and malabsorption, appears to be associated with increased risk of stunting in children in low- and middle-income countries. Fecal biomarkers indicative of EE (neopterin [NEO], myeloperoxidase [MPO], and alpha-1-antitrypsin [AAT]) have been negatively associated with 6-month linear growth. Associations between fecal markers (NEO, MPO, and AAT) and short-term linear growth were examined in a birth cohort of 246 children in Bangladesh. Marker concentrations were categorized in stool samples based on their distribution (< first quartile, interquartile range, > third quartile), and a 10-point composite EE score was calculated. Piecewise linear mixed-effects models were used to examine the association between markers measured quarterly (in months 3-21, 3-9, and 12-21) and 3-month change in length-for-age z-score (ΔLAZ). Children with high MPO levels at quarterly time points lost significantly more LAZ per 3-month period during the second year of life than those with low MPO (ΔLAZ = -0.100; 95% confidence interval = -0.167 to -0.032). AAT and NEO were not associated with growth; however, composite EE score was negatively associated with subsequent 3-month growth. In this cohort of children from an urban setting in Bangladesh, elevated MPO levels, but not NEO or AAT levels, were associated with decreases in short-term linear growth during the second year of life, supporting previous data suggesting the relevance of MPO as a marker of EE., (© The American Society of Tropical Medicine and Hygiene.)

We conducted a prospective cohort study to evaluate intimate partner violence (IPV) as a risk factor for detectable plasma viral load in HIV-positive female sex workers (FSWs) on antiretroviral therapy (ART) in Kenya. IPV in the past year was defined as ≥1 act of physical, sexual, or emotional violence by the index partner (i.e. boyfriend/husband). The primary outcome was detectable viral load (≥180 copies/ml). In-depth interviews and focus groups were included to contextualize results. Analyses included 195 women (570 visits). Unexpectedly, IPV was associated with significantly lower risk of detectable viral load (adjusted relative risk 0.21, 95 % CI 0.05-0.84, p-value = 0.02). Qualitative findings revealed that women valued emotional and financial support from index partners, despite IPV. IPV was not a major barrier to ART adherence. The observed association between IPV and lower risk of detectable viral load in FSWs may be due to unmeasured personal and relationship factors, warranting further research.

Volatile organic compounds (VOCs) play important roles in the environmental adaptation and fitness of plants. Comparison of the qualitative and quantitative differences in VOCs among closely related taxa and assessing the effects of environment on their emissions are important steps to deducing VOC function and evolutionary importance. Headspace VOCs from five taxa of sagebrush (Artemisia, subgenus Tridentatae) growing in two common gardens were collected and analyzed using GC-MS. Of the 74 total VOCs emitted, only 15 were needed to segregate sagebrush taxa using Random Forest analysis with a low error of 4%. All but one of these 15 VOCs showed qualitative differences among taxa. Ordination of results showed strong clustering that reflects taxonomic classification. Random Forest identified five VOCs that classify based on environment (2% error), which do not overlap with the 15 VOCs that segregated taxa. We show that VOCs can discriminate closely related species and subspecies of Artemisia, which are difficult to define using molecular markers or morphology. Thus, it appears that changes in VOCs either lead the way or follow closely behind speciation in this group. Future research should explore the functions of VOCs, which could provide further insights into the evolution of sagebrushes., (No claim to US Government works New Phytologist © 2016 New Phytologist Trust.)

We conducted a prospective cohort study to test the hypothesis that intimate partner violence (IPV) is associated with unprotected sex in HIV-positive female sex workers in Mombasa, Kenya. Women completed monthly visits and quarterly examinations. Any IPV in the past year was defined as ≥1 act of physical, sexual, or emotional violence by the current or most recent emotional partner ('index partner'). Unprotected sex with any partner was measured by self-report and prostate specific antigen (PSA) test. Recent IPV was associated with significantly higher risk of unprotected sex (adjusted relative risk [aRR] 1.91, 95 % CI 1.32, 2.78, p = 0.001) and PSA (aRR 1.54, 95 % CI 1.17, 2.04, p = 0.002) after adjusting for age, alcohol use, and sexual violence by someone besides the index partner. Addressing IPV in comprehensive HIV programs for HIV-positive women in this key population is important to improve wellbeing and reduce risk of sexual transmission of HIV.

Food webs of freshwater ecosystems can be subsidized by allochthonous resources. However, it is still unknown which environmental factors regulate the relative consumption of allochthonous resources in relation to autochthonous resources. Here, we evaluated the importance of allochthonous resources (litterfall) for the aquatic food webs in Neotropical tank bromeliads, a naturally replicated aquatic microcosm. Aquatic invertebrates were sampled in more than 100 bromeliads within either open or shaded habitats and within five geographically distinct sites located in four different countries. Using stable isotope analyses, we determined that allochthonous sources comprised 74% (±17%) of the food resources of aquatic invertebrates. However, the allochthonous contribution to aquatic invertebrates strongly decreased from shaded to open habitats, as light incidence increased in the tanks. The density of detritus in the tanks had no impact on the importance of allochthonous sources to aquatic invertebrates. This overall pattern held for all invertebrates, irrespective of the taxonomic or functional group to which they belonged. We concluded that, over a broad geographic range, aquatic food webs of tank bromeliads are mostly allochthonous-based, but the relative importance of allochthonous subsidies decreases when light incidence favors autochthonous primary production. These results suggest that, for other freshwater systems, some of the between-study variation in the importance of allochthonous subsidies may similarly be driven by the relative availability of autochthonous resources., (© 2016 by the Ecological Society of America.)

Unlabelled: SETTINGp: Among human immunodeficiency virus (HIV) infected adults living in tuberculosis (TB) endemic settings, Mycobacterium tuberculosis is a common cause of bloodstream infections. Although young children have an increased propensity for M. tuberculosis dissemination, M. tuberculosis bacteremia is infrequently described in children., Objective: To determine the prevalence of M. tuberculosis bacteremia in adult and pediatric patients and to examine sources of heterogeneity between estimates., Design: Systematic review and meta-analysis., Results: Of 1077 reviewed abstracts, 27 publications met the inclusion criteria, yielding 29 independent M. tuberculosis bacteremia prevalence estimates: 22 in adults, 6 in children, and 1 not stratified by age group. The random effects pooled M. tuberculosis bacteremia prevalence in adults was 13.5% (95%CI 10.8-16.2) and 0.4% (95%CI 0-0.9) in children (P for difference = 0.004). Restricting analyses to HIV-infected participants, pooled M. tuberculosis bacteremia prevalence from 21 adult studies was 15.5% (95%CI 12.5-18.5) and 0.8% (95%CI 0-1.8) in three pediatric studies (P = 0.001). Inclusion of pre-determined study-level confounders did not account for observed differences in M. tuberculosis bacteremia prevalence between age groups., Conclusion: While M. tuberculosis bacteremia appears relatively common in adults, particularly those with HIV infection, bloodstream M. tuberculosis appears to be rare in children.

Objectives: To evaluate the impacts of the expansion of an evidence-based full- and part-day early childhood development program on multiple indicators of school readiness, attendance, and parental involvement for a large cohort of low-income children., Methods: This study involved the end-of-preschool follow-up of a nonrandomized, matched-group cohort of 2630 predominantly low-income, ethnic minority children who enrolled in the Midwest Child-Parent Centers (CPC) or alternative preschools in the fall of 2012 in 31 schools in Chicago, Illinois. The program provides comprehensive education, family support, and health services. In the preschool component assessed in this study, 1724 children aged 3 to 4 years in all 16 Chicago centers enrolled in the program. The comparison group included 906 children of the same age who participated in the usual preschool services in 14 matched schools., Results: Relative to the comparison group who enrolled in the usual preschool services and adjusted for covariates, CPC participants had higher mean scores on all performance-based assessments of literacy (59.4 vs 52.4; P = .001), socioemotional development (57.0 vs 51.8; P = .001), and physical health (34.5 vs 32.1; P = .001). They also had higher ratings of parental involvement in school (5.3 vs 4.0; P = .04). Group differences also translated into higher rates of meeting national assessment norms. Program estimates were similar for children attending new and established CPCs and according to age, race/ethnicity, and family income status., Conclusions: The findings show that expansion of the program to new schools and more diverse populations is feasible and effective in promoting school readiness skills and parental involvement., (Copyright © 2016 by the American Academy of Pediatrics.)

Objective: To develop and validate an HIV risk assessment tool to predict HIV acquisition among African women., Design: Data were analyzed from 3 randomized trials of biomedical HIV prevention interventions among African women (VOICE, HPTN 035, and FEM-PrEP)., Methods: We implemented standard methods for the development of clinical prediction rules to generate a risk-scoring tool to predict HIV acquisition over the course of 1 year. Performance of the score was assessed through internal and external validations., Results: The final risk score resulting from multivariable modeling included age, married/living with a partner, partner provides financial or material support, partner has other partners, alcohol use, detection of a curable sexually transmitted infection, and herpes simplex virus 2 serostatus. Point values for each factor ranged from 0 to 2, with a maximum possible total score of 11. Scores ≥5 were associated with HIV incidence >5 per 100 person-years and identified 91% of incident HIV infections from among only 64% of women. The area under the curve (AUC) for predictive ability of the score was 0.71 (95% confidence interval [CI]: 0.68 to 0.74), indicating good predictive ability. Risk score performance was generally similar with internal cross-validation (AUC = 0.69; 95% CI: 0.66 to 0.73) and external validation in HPTN 035 (AUC = 0.70; 95% CI: 0.65 to 0.75) and FEM-PrEP (AUC = 0.58; 95% CI: 0.51 to 0.65)., Conclusions: A discrete set of characteristics that can be easily assessed in clinical and research settings was predictive of HIV acquisition over 1 year. The use of a validated risk score could improve efficiency of recruitment into HIV prevention research and inform scale-up of HIV prevention strategies in women at highest risk.

Background: Many offenders with intellectual disabilities have substance use issues. Offending behaviour may be associated with substance use., Materials and Methods: Prisoners with and without intellectual disabilities were compared in terms of their substance use prior to imprisonment, the influence of substance use on offending, and their participation in alcohol and drug treatment programmes., Results: Substance use was similar in prisoners with and without intellectual disabilities in the year prior to their current prison terms. Prisoners with intellectual disabilities were much less likely to report that substance use was an antecedent to the offences leading to their imprisonment. The completion rate of alcohol and drug treatment programmes was much lower for those with intellectual disabilities., Conclusions: Substance use may be as common in prisoners with intellectual disabilities as those without this condition. Services may need to reflect on whether their treatment programmes are meeting the needs of all prisoners., (© 2015 John Wiley & Sons Ltd.)

Background: Cytomegalovirus (CMV) is associated with morbidity and mortality in human immunodeficiency virus (HIV)-exposed infants. We assessed the effect of and relative contribution of breastfeeding to CMV acquisition among infants delivered by HIV-infected mothers., Methods: Between 1993 and 1998 pregnant, HIV-infected women in Nairobi, Kenya, were randomly assigned to breastfeed or formula-feed their infants in an HIV transmission study. Women were allocated equally between treatment arms, and the study was not blinded. The primary endpoint of this nested study was time to infant CMV infection., Results: CMV infection was assessed in 138 breastfed and 134 formula-fed infants. Baseline characteristics were similar between arms. Breastfed infants acquired CMV earlier than formula-fed infants (median age of acquisition, 4.26 vs 9.87 months; P < .001) and had a higher 1-year probability of CMV infection (0.89 vs 0.69; P < .001). Breastfeeding was associated with a 1.6-fold increased risk of infant CMV acquisition independent of infant HIV status (multivariable hazard ratio, 1.61; 95% confidence interval, 1.20-2.16; P = .002). Approximately one third of CMV infections occurred during the peripartum period, with 40% acquired through breastfeeding and the remainder acquired through modes other than breast milk., Conclusions: Preventing CMV acquisition may be a priority for HIV-exposed infants, but there is a narrow window of opportunity for intervention. Approaches that reduce maternal cervical and breast milk CMV reactivation may help delay infant infection., (© The Author 2015. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.)

Unlabelled: Mother-to-child transmission (MTCT) of HIV provides a setting for studying immune correlates of protection. Neutralizing antibodies (NAbs) are suggested to contribute to a viral bottleneck during MTCT, but their role in blocking transmission is unclear, as studies comparing the NAb sensitivities of maternal viruses have yielded disparate results. We sought to determine whether transmitting mothers differ from nontransmitting mothers in the ability to neutralize individual autologous virus variants present at transmission. Ten transmitting and 10 nontransmitting HIV-infected mothers at high risk of MTCT were included in this study. Full-length HIV envelope genes (n = 100) were cloned from peripheral blood mononuclear cells obtained near transmission from transmitting mothers and at similar time points from nontransmitting mothers. Envelope clones were tested as pseudoviruses against contemporaneous, autologous maternal plasma in neutralization assays. The association between transmission and the log2 50% inhibitory concentration (IC50) for multiple virus variants per mother was estimated by using logistic regression with clustered standard errors. t tests were used to compare proportions of neutralization-resistant viruses. Overall, transmitting mothers had a median IC50 of 317 (interquartile range [IQR], 202 to 521), and nontransmitting mothers had a median IC50 of 243 (IQR, 95 to 594). Transmission risk was not significantly associated with autologous NAb activity (odds ratio, 1.25; P = 0.3). Compared to nontransmitting mothers, transmitting mothers had similar numbers of or fewer neutralization-resistant virus variants, depending on the IC50 neutralization resistance cutoff. In conclusion, HIV-infected mothers harbor mostly neutralization-sensitive viruses, although resistant variants were detected in both transmitting and nontransmitting mothers. These results suggest that MTCT during the breastfeeding period is not driven solely by the presence of maternal neutralization escape variants., Importance: There are limited data demonstrating whether NAbs can prevent HIV transmission and infection in humans, and for this reason, NAbs have been studied in MTCT, where maternal antibodies are present at the time of transmission. Results of these studies have varied, perhaps because of differences in methods. Importantly, studies often used cultured viruses and samples from time points outside the window of transmission, which could confound findings. Here, we considered the role of maternal NAbs against individual maternal virus variants near the time of transmission. We found no evidence that NAbs are associated with protection from infection. In fact, depending on the cutoff used to define neutralization resistance, we found evidence that nontransmitting mothers have more neutralization-resistant virus variants. These results suggest that lack of virus transmission in the early breastfeeding period is not simply due to an absence of maternal neutralization escape variants and likely includes multiple factors., (Copyright © 2016 Milligan et al.)