Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities.

The genome-editing Cas9 protein uses multiple amino-acid residues to bind the target DNA. Considering only the residues in proximity to the target DNA as potential sites to optimise Cas9's activity, the number of combinatorial variants to screen through is too massive for a wet-lab experiment. Here we generate and cross-validate ten in silico and experimental datasets of multi-domain combinatorial mutagenesis libraries for Cas9 engineering, and demonstrate that a machine learning-coupled engineering approach reduces the experimental screening burden by as high as 95% while enriching top-performing variants by ∼7.5-fold in comparison to the null model. Using this approach and followed by structure-guided engineering, we identify the N888R/A889Q variant conferring increased editing activity on the protospacer adjacent motif-relaxed KKH variant of Cas9 nuclease from Staphylococcus aureus (KKH-SaCas9) and its derived base editor in human cells. Our work validates a readily applicable workflow to enable resource-efficient high-throughput engineering of genome editor's activity.

Documenting patients' and providers' preferences when proposing a randomized controlled trial: a qualitative exploration.

BACKGROUND: With advances in cancer diagnosis and treatment, women with early-stage breast cancer (ESBC) are living longer, increasing the number of patients receiving post-treatment follow-up care. Best-practice survivorship models recommend transitioning ESBC patients from oncology-provider (OP) care to community-based care. While developing materials for a future randomized controlled trial (RCT) to test the feasibility of a nurse-led Telephone Survivorship Clinic (TSC) for a smooth transition of ESBC survivors to follow-up care, we explored patients' and OPs' reactions to several of our proposed methods. METHODS: We used a qualitative study design with thematic analysis and a two-pronged approach. We interviewed OPs, seeking feedback on ways to recruit their ESBC patients for the trial, and ESBC patients, seeking input on a questionnaire package assessing outcomes and processes in the trial. RESULTS: OPs identified facilitators and barriers and offered suggestions for study design and recruitment process improvement. Facilitators included the novelty and utility of the study and simplicity of methods; barriers included lack of coordination between treating and discharging clinicians, time constraints, language barriers, motivation, and using a paper-based referral letter. OPs suggested using a combination of electronic and paper referral letters and supporting clinicians to help with recruitment. Patient advisors reported satisfaction with the content and length of the assessment package. However, they questioned the relevance of some questions (childhood trauma) while adding questions about trust in physicians and proximity to primary-care providers. CONCLUSIONS: OPs and patient advisors rated our methods for the proposed trial highly for their simplicity and relevance then suggested changes. These findings document processes that could be effective for cancer-patient recruitment in survivorship clinical trials.

High-fidelity KKH variant of Staphylococcus aureus Cas9 nucleases with improved base mismatch discrimination.

The Cas9 nuclease from Staphylococcus aureus (SaCas9) holds great potential for use in gene therapy, and variants with increased fidelity have been engineered. However, we find that existing variants have not reached the greatest accuracy to discriminate base mismatches and exhibited much reduced activity when their mutations were grafted onto the KKH mutant of SaCas9 for editing an expanded set of DNA targets. We performed structure-guided combinatorial mutagenesis to re-engineer KKH-SaCas9 with enhanced accuracy. We uncover that introducing a Y239H mutation on KKH-SaCas9's REC domain substantially reduces off-target edits while retaining high on-target activity when added to a set of mutations on REC and RuvC domains that lessen its interactions with the target DNA strand. The Y239H mutation is modelled to have removed an interaction from the REC domain with the guide RNA backbone in the guide RNA-DNA heteroduplex structure. We further confirmed the greatly improved genome-wide editing accuracy and single-base mismatch discrimination of our engineered variants, named KKH-SaCas9-SAV1 and SAV2, in human cells. In addition to generating broadly useful KKH-SaCas9 variants with unprecedented accuracy, our findings demonstrate the feasibility for multi-domain combinatorial mutagenesis on SaCas9's DNA- and guide RNA- interacting residues to optimize its editing fidelity.

Aberrant cervical innate immunity predicts onset of dysbiosis and sexually transmitted infections in women of reproductive age.

Sexually transmitted infections (STIs) and vaginal dysbiosis (disturbed resident microbiota presenting with abnormal Nugent score or candidiasis) have been associated with mucosal inflammation and risk of HIV-1 infection, cancer and poor reproductive outcomes. To date, the temporal relationships between aberrant cervical innate immunity and the clinical onset of microbial disturbance have not been studied in a large population of reproductive age women. We examined data from a longitudinal cohort of 934 Ugandan and Zimbabwean women contributing 3,274 HIV-negative visits who had complete laboratory, clinical and demographic data. Among those, 207 women later acquired HIV, and 584 women were intermittently diagnosed with C. trachomatis (CT), N. gonorrhoeae (NG), genital herpes (HSV-2), T. vaginalis (TV), candidiasis, and abnormal intermediate (4-6) or high (7-10) Nugent score, i.e. bacterial vaginosis (BV). Immune biomarker concentrations in cervical swabs were analyzed by generalized linear and mixed effect models adjusting for site, age, hormonal contraceptive use (HC), pregnancy, breastfeeding, genital practices, unprotected sex and overlapping infections. High likelihood ratios (1.5-4.9) denoted the values of cervical immune biomarkers to predict onset of abnormal Nugent score and candidiasis at the next visits. When controlling for covariates, higher levels of ß-defensin-2 were antecedent to BV, CT and HSV-2, lower anti-inflammatory ratio IL-1RA:IL-1ß-to intermediate Nugent scores and candida, lower levels of the serine protease inhibitor SLPI-to candida, lower levels of the adhesion molecule ICAM-1 -to TV, and lower levels of the oxidative stress mitigator and endothelial activation marker VEGF-to NG. Changes in innate immunity following onset of dysbiosis and infections were dependent on HC use when controlling for all other covariates. In conclusion, imminent female genital tract dysbiosis or infection can be predicted by distinct patterns of innate immunity. Future research should characterize biotic and abiotic determinants of this pre-existing innate immunity state.

The effect of child hunger on educational attainment and early childbearing outcomes in a longitudinal population sample of Canadian youth.

PURPOSE: Early childhood experiences of poverty are associated with adverse developmental outcomes that have impli cations for individual and population health. Low educational attainment and early childbearing are two such important outcomes that can perpetuate childhood poverty into adulthood. Child hunger, or severe food insecurity, is an extreme manifestation of household food insecurity that is associated with the stressful experience of deep family poverty. Life-course theories suggest that childhood experiences of hunger could have adverse effects in the developmental pathway. The objective of this study was to examine the independent contribution of the child hunger experience to subsequent educational attainment and early childbearing in young adult men and women, in consideration of other latent, cumulative or shock effects associated with child poverty. METHODS: We analyzed National Longitudinal Survey of Children and Youth data using logistic regression based on 15,468 Canadian children followed over 16 years. RESULTS: The prevalence of the experience of child hunger was 5.0%. Child hunger was independently predictive of youth leaving high school, yet was not a factor in the achievement of higher educational attainment if youth were able to graduate from high school. Having always lived in rental accommodation and repeated reports of child hunger over time were predictive of early childbearing. CONCLUSIONS: Interventions directed at children and youth who are at risk of poor developmental outcomes because of severe food insecurity should focus on steering families toward their income entitlements, and providing support for youth to complete high school and to avoid early fertility.

A Longitudinal Assessment of Cervical Inflammation and Immunity Associated with HIV-1 Infection, Hormonal Contraception, and Pregnancy.

Hormonal contraception (HC), particularly injectable depot-medroxyprogesterone acetate (DMPA), has been associated with increased HIV acquisition and higher levels of cervical regulated upon activation, normal T-cell expressed, and secreted (RANTES), also associated with HIV seroconversion. Longitudinal changes in cervical immunity associated with DMPA and combined oral contraceptives (COCs) have not been studied. Cervical samples from 216 HIV seroconverters in Uganda and Zimbabwe with matched samples from 727 HIV-uninfected controls were collected at two quarterly visits before (t - 2, t - 1), at (t0), and two visits following (t + 1, t + 2) HIV seroconversion and corresponding visits for HIV-negative controls. We measured 10 biomarkers of inflammation and immunity and used generalized linear models to estimate and compare biomarker levels across HIV status, contraceptive, and pregnancy groups. Biomarkers remained relatively stable across visits for controls, while in HIV-infected women cervical immunity started to change before seroconversion with RANTES and BD-2 increased and secretory leukocyte protease inhibitor (SLPI) decreased at t - 1 and continued to change at t0 with ICAM-1 up and IL-8 down and with more biomarkers after seroconversion (IL-1ß, IL-6, MIP-3α, VEGF, and IL-1RA down and IL-1RA:IL-1ß ratio up). In multivariable analyses, seroconverters had higher BD-2 at t - 1, higher RANTES and lower SLPI from t - 1 through t + 2, and lower IL-8 and IL-1RA at and/or after seroconversion compared to nonseroconverters. Compared to non-HC users, DMPA users had higher RANTES at all visits and lower BD-2 at t - 2 through t0, while COC users and pregnant women had higher IL-8 and SLPI at all visits; COC users also had lower BD-2 preseroconversion; pregnant women had lower RANTES at t0 - t + 2. Longitudinal patterns of cervical immunity differ between HIV seroconverters and HIV-negative women; seroconverters demonstrate increased RANTES and decreased SLPI starting before and continuing postseroconversion. Furthermore, these patterns are differentially regulated by DMPA, COC, and pregnancy.

Correction: Prevalence of sexually transmitted infections and bacterial vaginosis among women in sub-Saharan Africa: An individual participant data meta-analysis of 18 HIV prevention studies.

[This corrects the article DOI: 10.1371/journal.pmed.1002511.].

Prevalence of sexually transmitted infections and bacterial vaginosis among women in sub-Saharan Africa: An individual participant data meta-analysis of 18 HIV prevention studies.

BACKGROUND: Estimates of sexually transmitted infection (STI) prevalence are essential for efforts to prevent and control STIs. Few large STI prevalence studies exist, especially for low- and middle-income countries (LMICs). Our primary objective was to estimate the prevalence of chlamydia, gonorrhea, trichomoniasis, syphilis, herpes simplex virus type 2 (HSV-2), and bacterial vaginosis (BV) among women in sub-Saharan Africa by age, region, and population type. METHODS AND FINDINGS: We analyzed individual-level data from 18 HIV prevention studies (cohort studies and randomized controlled trials; conducted during 1993-2011), representing >37,000 women, that tested participants for ≥1 selected STIs or BV at baseline. We used a 2-stage meta-analysis to combine data. After calculating the proportion of participants with each infection and standard error by study, we used a random-effects model to obtain a summary mean prevalence of each infection and 95% confidence interval (CI) across ages, regions, and population types. Despite substantial study heterogeneity for some STIs/populations, several patterns emerged. Across the three primary region/population groups (South Africa community-based, Southern/Eastern Africa community-based, and Eastern Africa higher-risk), prevalence was higher among 15-24-year-old than 25-49-year-old women for all STIs except HSV-2. In general, higher-risk populations had greater prevalence of gonorrhea and syphilis than clinic/community-based populations. For chlamydia, prevalence among 15-24-year-olds was 10.3% (95% CI: 7.4%, 14.1%; I2 = 75.7%) among women specifically recruited from higher-risk settings for HIV in Eastern Africa and was 15.1% (95% CI: 12.7%, 17.8%; I2 = 82.3%) in South African clinic/community-based populations. Among clinic/community-based populations, prevalence was generally greater in South Africa than in Southern/Eastern Africa for most STIs; for gonorrhea, prevalence among 15-24-year-olds was 4.6% (95% CI: 3.3%, 6.4%; I2 = 82.8%) in South Africa and was 1.7% (95% CI: 1.2%, 2.6%; I2 = 55.2%) in Southern/Eastern Africa. Across the three primary region/population groups, HSV-2 and BV prevalence was high among 25-49-year-olds (ranging from 70% to 83% and 33% to 44%, respectively). The main study limitation is that the data are not from random samples of the target populations. CONCLUSIONS: Combining data from 18 HIV prevention studies, our findings highlight important features of STI/BV epidemiology among sub-Saharan African women. This methodology can be used where routine STI surveillance is limited and offers a new approach to obtaining critical information on STI and BV prevalence in LMICs.

Higher sequence diversity in the vaginal tract than in blood at early HIV-1 infection.

In the majority of cases, human immunodeficiency virus type 1 (HIV-1) infection is transmitted through sexual intercourse. A single founder virus in the blood of the newly infected donor emerges from a genetic bottleneck, while in rarer instances multiple viruses are responsible for systemic infection. We sought to characterize the sequence diversity at early infection, between two distinct anatomical sites; the female reproductive tract vs. systemic compartment. We recruited 72 women from Uganda and Zimbabwe within seven months of HIV-1 infection. Using next generation deep sequencing, we analyzed the total genetic diversity within the C2-V3-C3 envelope region of HIV-1 isolated from the female genital tract at early infection and compared this to the diversity of HIV-1 in plasma. We then compared intra-patient viral diversity in matched cervical and blood samples with three or seven months post infection. Genetic analysis of the C2-V3-C3 region of HIV-1 env revealed that early HIV-1 isolates within blood displayed a more homogeneous genotype (mean 1.67 clones, range 1-5 clones) than clones in the female genital tract (mean 5.7 clones, range 3-10 clones) (p<0.0001). The higher env diversity observed within the genital tract compared to plasma was independent of HIV-1 subtype (A, C and D). Our analysis of early mucosal infections in women revealed high HIV-1 diversity in the vaginal tract but few transmitted clones in the blood. These novel in vivo finding suggest a possible mucosal sieve effect, leading to the establishment of a homogenous systemic infection.

A natural experimental study of the protective effect of home ownership on household food insecurity in Canada before and after a recession (2008-2009).

OBJECTIVES: Home ownership as opposed to renting is associated with lower rates of food insecurity, the latter being a marker of household economic deprivation associated with adverse health outcomes. It is unclear whether this relationship persists during a major economic decline, or whether different subgroups of home owners are equally protected. The 2008-2009 recession in Canada was tied to events in the United States related to inappropriate mortgage financing; the impact of the recession on food insecurity among home owners may identify policies to mitigate recessionary outcomes. METHODS: We used a before-and-after natural experimental design using data from the Canadian Community Health Survey (CCHS) cycles 2007/2008 (pre-recession) and 2009/2010 (post-recession) with information on household food insecurity, home ownership versus renting, and socio-demographics. Applying multivariable logistic regression, we examined changes in household food insecurity by housing tenure and sex over the period. RESULTS: Pre-recession, food insecurity affected 3.3% of home owners and 17.1% of renter households. Among home owners, the risk of food insecurity increased post-recession by 10%, which was not statistically significant. Post-recession, and with adjustment, although renters' higher absolute risk of food insecurity persisted, male-respondent home owners experienced the highest rate of increase in food insecurity prevalence by subgroup (OR = 1.26, 95% CI: 1.06-1.50) versus renters (OR = 1.17, 95% CI: 1.05-1.29). CONCLUSION: Housing policies in Canada protected most home owners from precarity during the 2008-2009 economic recession; however, male-respondent home owners exhibited a unique economic vulnerability during this time. Implications of Canadian home ownership policies are discussed in light of differential vulnerability of home owner groups.

The pervasive effect of youth self-report of hunger on depression over 6 years of follow up.

PURPOSE: We used longitudinal data to clarify the association between self-report of hunger and subsequent depression risk among youth and young adults, accounting for other risk factors. METHODS: Youth self-report of ever experiencing hunger data were collected from cycles 4-6 of the National Longitudinal Survey of Children and Youth cohort of Canadian youth 16 years and older (n = 4139). Data on depressive symptoms (CES-D 12) were collected over three cycles (2004-2009, cycles 6-8). We used multivariable regression based on generalized estimating equations (GEE) to examine prior youth hunger on later depression risk, adjusting for time-stable, time-varying, and lagged variables (e.g., depressive symptoms in previous cycle), thereby clarifying the temporal relationship. RESULTS: The prevalence of youth hunger experience and depression risk reached 5.9 and 15.0%, respectively. The adjusted odds ratio of depression for participants reporting hunger was 2.31 (95% CI 1.54, 3.46) and changed little [2.17 (95% CI 1.29, 3.67)] after accounting for previous CES-D 12 scores, suggesting a temporal relationship in which hunger contributes to depression risk. Unlike never-hungry youth, depression in ever-hungry youth remained comparatively elevated over time. CONCLUSIONS: Our models support an independent and temporal relationship between youth self-report of hunger and depression in adolescence and young adulthood.

Persons living with HIV infection on antiretroviral therapy also consulting traditional healers: a study in three African countries.

Traditional healers provide healthcare to a substantial proportion of people living with HIV infection (PLHIV) in high HIV burden countries in sub-Saharan Africa. However, the impact on the health of retained patients visiting traditional healers is unknown. In 2011, a study to asses adherence to anti-retroviral therapy (ART) performed in 18 purposefully selected HIV treatment centers in Tanzania, Zambia and Uganda showed that 'consulting a traditional healer/herbalist because of HIV' was an independent risk factor for incomplete ART adherence. To identify characteristics of PLHIV on ART who were also consulting traditional healers, we conducted a secondary analysis of the data from this study. It was found that 260 (5.8%) of the 4451 patients enrolled in the study had consulted a traditional healer during the last three months because of HIV. In multivariable analysis, patients with fewer HIV symptoms, those who had been on ART for >5.3 years and those from Tanzania were more likely to have consulted a traditional healer. However, at the time of the study, there was a famous healer in Manyara district, Loliondo village of Tanzania who claimed his herbal remedy was able to cure all chronic diseases including HIV. HIV treatment programs should be aware that patients with fewer HIV symptoms, those who have been on ART for five or more years, and patients attending ART centers near famous traditional healers are likely to consult traditional healers. Such patients may need more support or counseling about the risks of both stopping ART and poor adherence. Considering the realities of inadequate human resources for health and the burden of disease caused by HIV in sub-Saharan Africa, facilitating a collaboration between allopathic and traditional health practitioners is recommended.

Infecting HIV-1 Subtype Predicts Disease Progression in Women of Sub-Saharan Africa.

INTRODUCTION: Long-term natural history cohorts of HIV-1 in the absence of treatment provide the best measure of virulence by different viral subtypes. METHODS: Newly HIV infected Ugandan and Zimbabwean women (N=303) were recruited and monitored for clinical, social, behavioral, immunological and viral parameters for 3 to 9.5years. RESULTS: Ugandan and Zimbabwean women infected with HIV-1 subtype C had 2.5-fold slower rates of CD4 T-cell declines and higher frequencies of long-term non-progression than those infected with subtype A or D (GEE model, P<0.001), a difference not associated with any other clinical parameters. Relative replicative fitness and entry efficiency of HIV-1 variants directly correlated with virulence in the patients, subtype D>A>C (P<0.001, ANOVA). DISCUSSION: HIV-1 subtype C was less virulent than either A or D in humans; the latter being the most virulent. Longer periods of asymptomatic HIV-1 subtype C could explain the continued expansion and dominance of subtype C in the global epidemic.

Impact of a guaranteed annual income program on Canadian seniors' physical, mental and functional health.

OBJECTIVE: Although there is widespread recognition that poverty is a key determinant of health, there has been less research on the impact of poverty reduction on health. Recent calls for a guaranteed annual income (GAI), defined as regular income provided to citizens by the state regardless of work status, raise questions about the impact, relative to the costs, of such a population health intervention. The objective of this study was to determine the impact of Canadian seniors' benefits (Old Age Security/Guaranteed Income Supplement, analogous to a GAI program) on the self-reported health, self-reported mental health and functional health of age-eligible, low-income seniors. METHODS: We used the 2009-2010 Canadian Community Health Survey to examine unattached adult respondents with an annual income of $20,000 or less, stratified by seniors' benefits/GAI eligibility (55-64 years: ineligible; 65-74 years: eligible). Using regression, we assessed self-reported health, selfreported mental health and functional health as measured by the Health Utilities Index, as outcomes for seniors' benefits/GAI-eligible and -ineligible groups. RESULTS: We found that individuals age-eligible for seniors' benefits/GAI had better health outcomes than recipients of conditional income assistance programs. Eligibility for seniors' benefits/GAI after age 64 was associated with better self-reported health, functional health and self-reported mental health outcomes, and these effects were observed until age 74. CONCLUSION: Using seniors' benefits as an example, a GAI leads to significantly better mental health and improved health overall. These improvements are likely to yield reduced health care costs, which may offset the costs associated with program expansion.

Serum vitamin D status and bacterial vaginosis prevalence and incidence in Zimbabwean women.

BACKGROUND: Bacterial vaginosis, a highly prevalent vaginal condition, is correlated with many adverse reproductive outcomes. In some studies, low vitamin D status (measured as serum 25-hydroxyvitamin D, 25[OH]D) has been associated with increased prevalence of bacterial vaginosis. OBJECTIVES: We examined the cross-sectional association between vitamin D status and prevalence of bacterial vaginosis, separately for pregnant and nonpregnant women. Using prospectively collected data, we also characterized the effect of time-varying vitamin D status on incident bacterial vaginosis. STUDY DESIGN: We quantified 25(OH)D in stored sera collected quarterly from 571 Zimbabwean women participating in the Hormonal Contraception and Risk of HIV Acquisition Study. The analysis was restricted to women not using hormonal contraception. We characterized associations between vitamin D insufficiency (defined as 25[OH]D ≤ 30 ng/mL vs > 30 ng/mL) and prevalence of bacterial vaginosis among nonpregnant women at the enrollment visit and among pregnant women at the first follow-up visit that pregnancy was detected. Among women who were negative for bacterial vaginosis at enrollment (n = 380), we also assessed the effect of time-varying vitamin D status on incident bacterial vaginosis. We used the Liaison 25(OH)D total assay to measure 25(OH)D. Bacterial vaginosis was diagnosed via Nugent score. RESULTS: At enrollment, the prevalence of bacterial vaginosis was 31% and overall median 25(OH)D was 29.80 ng/mL (interquartile range, 24.70-34.30 ng/mL): 29.75 ng/mL (interquartile range, 25.15-33.95 ng/mL) among women with bacterial vaginosis, and 29.90 ng/mL (interquartile range, 24.70-34.50 ng/mL) among women without bacterial vaginosis. Among pregnant women, the prevalence of bacterial vaginosis was 27% and overall median 25(OH)D was 29.90 ng/mL (interquartile range, 24.10-34.00 ng/mL): 30.80 ng/mL (interquartile range, 26.10-36.90 ng/mL) among women with bacterial vaginosis, and 29.10 ng/mL (interquartile range, 23.80-33.45 ng/mL) among women without bacterial vaginosis. Vitamin D levels ≤ 30 ng/mL were not associated with a prevalence of bacterial vaginosis in nonpregnant women (adjusted prevalence ratio, 1.04; 95% confidence interval, 0.81-1.34) or pregnant women (adjusted prevalence ratio, 0.88, 95% confidence interval, 0.51-1.54). Vitamin D levels ≤ 30 ng/mL were similarly not associated with incident bacterial vaginosis (adjusted hazard ratio, 0.98, 95% confidence interval, 0.73-1.31). Our findings were robust to alternative specifications of vitamin D status including using a cut point for vitamin D deficiency of < 20 ng/mL vs ≥ 20 ng/mL and modeling 25(OH)D as a continuous variable. CONCLUSION: Among reproductive-age Zimbabwean women, insufficient vitamin D was not associated with increased bacterial vaginosis prevalence or incidence. Given established associations between bacterial vaginosis and poor reproductive outcomes, identification of factors leading to high bacterial vaginosis prevalence is urgently needed.

Infant feeding practices and childhood diet at Apollonia Pontica: Isotopic and dental evidence.

OBJECTIVE: This study analyzes deciduous dental pathology and stable isotopes to investigate the relationship between diet, feeding practices, and oral health in a subadult skeletal sample from the Greek colonial site of Apollonia Pontica, Bulgaria (mid-5th to mid-3rd Centuries BC). METHODS: Stable carbon and nitrogen isotope analysis was conducted on 74 bone collagen samples, and the deciduous dentitions of 85 individuals aged 8.5 months to 11 years were examined for evidence of caries, calculus, antemortem tooth loss, abscesses, and occlusal tooth wear. RESULTS: δ(13) C and δ(15) N values of the collagen samples indicate that weaning began between the ages of 6 months and 1 year, and was complete for most individuals by the age of 3. The isotopic data are consistent with a mixed diet of primarily terrestrial C3 resources. The dental pathology data indicate that complementary foods provided to young children had an impact on their oral health early on. Four outliers exhibited elevated δ(15) N values compared with the adult female range and lower levels of tooth wear than other members of their age groups. Possible explanations include prolonged breastfeeding, the consumption of diets elevated in (15) N, and physiological/nutritional stress. CONCLUSIONS: The deciduous dental data correlate well with the isotopic data and are consistent with later textual sources regarding the timing and duration of weaning, and the composition of complementary foods. The results of this research demonstrate the value of combining isotopic and dental evidence to investigate the dietary practices of infants and young children and the impact of these practices on oral health.

Biomarkers of Cervical Inflammation and Immunity Associated with Cervical Shedding of HIV-1.

BACKGROUND: Cervicovaginal HIV shedding is associated with increased female-to-male and mother-to-child transmission. Genital inflammation may increase shedding through cytokines/chemokines which recruit and activate HIV target cells. We evaluated whether cervical immune mediators present before seroconversion affected HIV shedding and whether mediators differed between shedders and nonshedders. METHODS: We used cervical samples from 187 African women with documented HIV seroconversion in the Hormonal Contraception and HIV study. Samples were from the two visits before seroconversion (T-2 and/or T-1), and/or at seroconversion (T0), and/or the two visits (T + 1 and/or T + 2) after seroconversion. We measured interleukin (IL)-1ß, IL-1 Receptor Antagonist (IL-1RA), IL-6, IL-8, RANTES (Regulated on Activation, Normal T-Cell Expressed and Secreted), MIP-3α, vascular endothelial growth factor (VEGF), Intercellular Adhesion Molecule-1 (ICAM-1), secretory leukocyte protease inhibitor (SLPI), and BD-2 and used the Wilcoxon test and generalized linear models to evaluate the association between mediators and shedding. RESULTS: The only immune mediator that differed at T-1 was RANTES, which was higher among shedders (p ≤ .05). HIV seroconversion was followed by significant decreases in many mediators, but a significant increase in RANTES. The magnitude of the change was significantly different for shedders versus nonshedders with regard to RANTES (increased in both groups, significantly more so in shedders), SLPI (decreased in both groups, significantly more so in shedders), and MIP-3α (decreased in shedders and increased in nonshedders). At T0, shedders had lower levels of SLPI and MIP-3α than nonshedders. CONCLUSIONS: In this study, a specific immune mediator profile was associated with risk of cervical HIV shedding. Higher and increasing levels of RANTES and lower and decreasing levels of SLPI and MIP-3α were associated with increased risk of HIV shedding.

Incident pregnancy and pregnancy outcomes among HIV-infected women in Uganda and Zimbabwe.

OBJECTIVE: To describe pregnancy outcomes among HIV-infected women and examine factors associated with live birth among those receiving and not receiving combination antiretroviral therapy (cART). METHODS: The present analysis included women with HIV from Uganda and Zimbabwe who participated in a prospective cohort study during 2001-2009. Incident pregnancies and pregnancy outcomes were recorded quarterly. The Kaplan-Meier method was used to estimate incident pregnancy probabilities; factors associated with live birth were evaluated by Poisson regression with generalized estimating equations. RESULTS: Among 306 HIV-infected women, there were 160 incident pregnancies (10.1 per 100 women-years). The pregnancy rate was higher among cART-naïve women than among those receiving cART (10.7 vs 5.5 per 100 women-years; P=0.047), and it was higher in Uganda than in Zimbabwe (14.4 vs 7.7 per 100 women-years; P<0.001). Significant associations were noted between a live birth and prenatal care (relative risk 3.9; 95% confidence interval 2.2-6.9) and illness during pregnancy (relative risk 0.8; 95% confidence interval 0.7-1.0). CONCLUSION: Women not receiving cART have higher pregnancy rates than do those receiving cART, but cART use might not affect the risk of adverse pregnancy outcomes. Timely prenatal care and monitoring of illnesses during pregnancy should be incorporated into treatment services for HIV-infected women.

The Contribution of Cervicovaginal Infections to the Immunomodulatory Effects of Hormonal Contraception.

UNLABELLED: Particular types of hormonal contraceptives (HCs) and genital tract infections have been independently associated with risk of HIV-1 acquisition. We examined whether immunity in women using injectable depot medroxyprogesterone acetate (DMPA), combined oral contraceptives (COC), or no HCs differs by the presence of cervicovaginal infections. Immune mediators were quantified in cervical swabs from 832 HIV-uninfected reproductive-age Ugandans and Zimbabweans. Bacterial infections and HIV were diagnosed by PCR, genital herpes serostatus by enzyme-linked immunosorbent assay (ELISA), altered microflora by Nugent score, and Trichomonas vaginalis and Candida albicans infection by wet mount. Generalized linear models utilizing Box-Cox-Power transformation examined associations between levels of mediators, infection status, and HCs. In no-HC users, T. vaginalis was associated with broadest spectrum of aberrant immunity (higher interleukin 1ß [IL-1ß], IL-8, macrophage inflammatory protein 3α [MIP-3α], ß-defensin 2 [BD2], and IL-1 receptor antigen [IL-1RA]). In women with a normal Nugent score and no genital infection, compared to the no-HC group, COC users showed higher levels of IL-1ß, IL-6, IL-8, and IL-1RA, while DMPA users showed higher levels of RANTES and lower levels of BD2, both associated with HIV seroconversion. These effects of COC were blunted in the presence of gonorrhea, chlamydia, trichomoniasis, candidiasis, and an abnormal Nugent score; however, RANTES was increased among COC users with herpes, chlamydia, and abnormal Nugent scores. The effect of DMPA was exacerbated by lower levels of IL-1RA in gonorrhea, chlamydia, or herpes, SLPI in gonorrhea, and IL-1ß, MIP-3α, and IL-1RA/IL1ß ratio in trichomoniasis. Thus, the effects of HC on cervical immunity depend on the genital tract microenvironment, and a weakened mucosal barrier against HIV may be a combined resultant of genital tract infections and HC use. IMPORTANCE: In this article, we show that in young reproductive-age women most vulnerable to HIV, hormonal contraceptives are associated with altered cervical immunity in a manner dependent on the presence of genital tract infections. Through altered immunity, hormones may predispose women to bacterial and viral pathogens; conversely, a preexisting specific infection or disturbed vaginal microbiota may suppress the immune activation by levonorgestrel or exacerbate the suppressed immunity by DMPA, thus increasing HIV risk by their cumulative action. Clinical studies assessing the effects of contraception on HIV susceptibility and mucosal immunity may generate disparate results in populations that differ by microbiota background or prevalence of undiagnosed genital tract infections. A high prevalence of asymptomatic infections among HC users that remain undiagnosed and untreated raises even more concerns in light of their combined effects on biomarkers of HIV risk. The molecular mechanisms of the vaginal microbiome's simultaneous interactions with hormones and HIV remain to be elucidated.

Hormonal contraception and the risk of HIV acquisition: an individual participant data meta-analysis.

BACKGROUND: Observational studies of a putative association between hormonal contraception (HC) and HIV acquisition have produced conflicting results. We conducted an individual participant data (IPD) meta-analysis of studies from sub-Saharan Africa to compare the incidence of HIV infection in women using combined oral contraceptives (COCs) or the injectable progestins depot-medroxyprogesterone acetate (DMPA) or norethisterone enanthate (NET-EN) with women not using HC. METHODS AND FINDINGS: Eligible studies measured HC exposure and incident HIV infection prospectively using standardized measures, enrolled women aged 15-49 y, recorded ≥15 incident HIV infections, and measured prespecified covariates. Our primary analysis estimated the adjusted hazard ratio (aHR) using two-stage random effects meta-analysis, controlling for region, marital status, age, number of sex partners, and condom use. We included 18 studies, including 37,124 women (43,613 woman-years) and 1,830 incident HIV infections. Relative to no HC use, the aHR for HIV acquisition was 1.50 (95% CI 1.24-1.83) for DMPA use, 1.24 (95% CI 0.84-1.82) for NET-EN use, and 1.03 (95% CI 0.88-1.20) for COC use. Between-study heterogeneity was mild (I(2) < 50%). DMPA use was associated with increased HIV acquisition compared with COC use (aHR 1.43, 95% CI 1.23-1.67) and NET-EN use (aHR 1.32, 95% CI 1.08-1.61). Effect estimates were attenuated for studies at lower risk of methodological bias (compared with no HC use, aHR for DMPA use 1.22, 95% CI 0.99-1.50; for NET-EN use 0.67, 95% CI 0.47-0.96; and for COC use 0.91, 95% CI 0.73-1.41) compared to those at higher risk of bias (p(interaction) = 0.003). Neither age nor herpes simplex virus type 2 infection status modified the HC-HIV relationship. CONCLUSIONS: This IPD meta-analysis found no evidence that COC or NET-EN use increases women's risk of HIV but adds to the evidence that DMPA may increase HIV risk, underscoring the need for additional safe and effective contraceptive options for women at high HIV risk. A randomized controlled trial would provide more definitive evidence about the effects of hormonal contraception, particularly DMPA, on HIV risk.