Data-driven modelling for assessing trophic status in marine ecosystems using machine learning approaches.

Assessing eutrophication in coastal and transitional waters is of utmost importance, yet existing Trophic Status Index (TSI) models face challenges like multicollinearity, data redundancy, inappropriate aggregation methods, and complex classification schemes. To tackle these issues, we developed a novel tool that harnesses machine learning (ML) and artificial intelligence (AI), enhancing the reliability and accuracy of trophic status assessments. Our research introduces an improved data-driven methodology specifically tailored for transitional and coastal (TrC) waters, with a focus on Cork Harbour, Ireland, as a case study. Our innovative approach, named the Assessment Trophic Status Index (ATSI) model, comprises three main components: the selection of pertinent water quality indicators, the computation of ATSI scores, and the implementation of a new classification scheme. To optimize input data and minimize redundancy, we employed ML techniques, including advanced deep learning methods. Specifically, we developed a CHL prediction model utilizing ten algorithms, among which XGBoost demonstrated exceptional performance, showcasing minimal errors during both training (RMSE = 0.0, MSE = 0.0, MAE = 0.01) and testing (RMSE = 0.0, MSE = 0.0, MAE = 0.01) phases. Utilizing a novel linear rescaling interpolation function, we calculated ATSI scores and evaluated the model's sensitivity and efficiency across diverse application domains, employing metrics such as R2, the Nash-Sutcliffe efficiency (NSE), and the model efficiency factor (MEF). The results consistently revealed heightened sensitivity and efficiency across all application domains. Additionally, we introduced a brand new classification scheme for ranking the trophic status of transitional and coastal waters. To assess spatial sensitivity, we applied the ATSI model to four distinct waterbodies in Ireland, comparing trophic assessment outcomes with the Assessment of Trophic Status of Estuaries and Bays in Ireland (ATSEBI) System. Remarkably, significant disparities between the ATSI and ATSEBI System were evident in all domains, except for Mulroy Bay. Overall, our research significantly enhances the accuracy of trophic status assessments in marine ecosystems. The ATSI model, combined with cutting-edge ML techniques and our new classification scheme, represents a promising avenue for evaluating and monitoring trophic conditions in TrC waters. The study also demonstrated the effectiveness of ATSI in assessing trophic status across various waterbodies, including lakes, rivers, and more. These findings make substantial contributions to the field of marine ecosystem management and conservation.

Cluster randomized controlled trial analysis at the cluster level: The clan command.

In this article, we introduce a new command, clan, that conducts a cluster-level analysis of cluster randomized trials. The command simplifies adjusting for individual- and cluster-level covariates and can also account for a stratified design. It can be used to analyze a continuous, binary, or rate outcome.

Marine waters assessment using improved water quality model incorporating machine learning approaches.

In marine ecosystems, both living and non-living organisms depend on "good" water quality. It depends on a number of factors, and one of the most important is the quality of the water. The water quality index (WQI) model is widely used to assess water quality, but existing models have uncertainty issues. To address this, the authors introduced two new WQI models: the weight based weighted quadratic mean (WQM) and unweighted based root mean squared (RMS) models. These models were used to assess water quality in the Bay of Bengal, using seven water quality indicators including salinity (SAL), temperature (TEMP), pH, transparency (TRAN), dissolved oxygen (DOX), total oxidized nitrogen (TON), and molybdate reactive phosphorus (MRP). Both models ranked water quality between "good" and "fair" categories, with no significant difference between the weighted and unweighted models' results. The models showed considerable variation in the computed WQI scores, ranging from 68 to 88 with an average of 75 for WQM and 70 to 76 with an average of 72 for RMS. The models did not have any issues with sub-index or aggregation functions, and both had a high level of sensitivity (R2 = 1) in terms of the spatio-temporal resolution of waterbodies. The study demonstrated that both WQI approaches effectively assessed marine waters, reducing uncertainty and improving the accuracy of the WQI score.

Robust machine learning algorithms for predicting coastal water quality index.

Coastal water quality assessment is an essential task to keep "good water quality" status for living organisms in coastal ecosystems. The Water quality index (WQI) is a widely used tool to assess water quality but this technique has received much criticism due to the model's reliability and inconsistence. The present study used a recently developed improved WQI model for calculating coastal WQIs in Cork Harbour. The aim of the research is to determine the most reliable and robust machine learning (ML) algorithm(s) to anticipate WQIs at each monitoring point instead of repeatedly employing SI and weight values in order to reduce model uncertainty. In this study, we compared eight commonly used algorithms, including Random Forest (RF), Decision Tree (DT), K-Nearest Neighbors (KNN), Extreme Gradient Boosting (XGB), Extra Tree (ExT), Support Vector Machine (SVM), Linear Regression (LR), and Gaussian Naïve Bayes (GNB). For the purposes of developing the prediction models, the dataset was divided into two groups: training (70%) and testing (30%), whereas the models were validated using the 10-fold cross-validation method. In order to evaluate the models' performance, the RMSE, MSE, MAE, R2, and PREI metrics were used in this study. The tree-based DT (RMSE = 0.0, MSE = 0.0, MAE = 0.0, R2 = 1.0 and PERI = 0.0) and the ExT (RMSE = 0.0, MSE = 0.0, MAE = 0.0, R2 = 1.0 and PERI = 0.0) and ensemble tree-based XGB (RMSE = 0.0, MSE = 0.0, MAE = 0.0, R2 = 1.0 and PERI = +0.16 to -0.17) and RF (RMSE = 2.0, MSE = 3.80, MAE = 1.10, R2 = 0.98, PERI = +3.52 to -25.38) models outperformed other models. The results of model performance and PREI indicate that the DT, ExT, and GXB models could be effective, robust and significantly reduce model uncertainty in predicting WQIs. The findings of this study are also useful for reducing model uncertainty and optimizing the WQM-WQI model architecture for predicting WQI values.

Risk Factors for Middle East Respiratory Syndrome Coronavirus Infection among Camel Populations, Southern Jordan, 2014-2018.

After the first detection of Middle East respiratory syndrome coronavirus (MERS-CoV) in camels in Jordan in 2013, we conducted 2 consecutive surveys in 2014-2015 and 2017-2018 investigating risk factors for MERS-CoV infection among camel populations in southern Jordan. Multivariate analysis to control for confounding demonstrated that borrowing of camels, particularly males, for breeding purposes was associated with increased MERS-CoV seroprevalence among receiving herds, suggesting a potential route of viral transmission between herds. Increasing age, herd size, and use of water troughs within herds were also associated with increased seroprevalence. Closed herd management practices were found to be protective. Future vaccination strategies among camel populations in Jordan could potentially prioritize breeding males, which are likely to be shared between herds. In addition, targeted management interventions with the potential to reduce transmission between herds should be considered; voluntary closed herd schemes offer a possible route to achieving disease-free herds.

Exploring Perceived Barriers and Facilitators of PrEP Uptake among Young People in Uganda, Zimbabwe, and South Africa.

Pre-exposure prophylaxis (PrEP) is an effective HIV prevention strategy. Few studies have explored adolescents and young people's perspectives toward PrEP. We conducted 24 group discussions and 60 in-depth interviews with males and females aged 13-24 years in Uganda, Zimbabwe, and South Africa between September 2018 and February 2019. We used the framework approach to generate themes and key concepts for analysis following the social ecological model. Young people expressed a willingness to use PrEP and identified potential barriers and facilitators of PrEP uptake. Barriers included factors at individual (fear of HIV, fear of side effects, and PrEP characteristics), interpersonal (parental influence, absence of a sexual partner), community (peer influence, social stigma), institutional (long waiting times at clinics, attitudes of health workers), and structural (cost of PrEP and mode of administration, accessibility concerns) levels. Facilitators included factors at individual (high HIV risk perception and preventing HIV/desire to remain HIV negative), interpersonal (peer influence, social support and care for PrEP uptake), community (adequate PrEP information and sensitization, evidence of PrEP efficacy and safety), institutional (convenient and responsive services, provision of appropriate and sufficiently resourced services), and structural (access and availability of PrEP, cost of PrEP) levels. The findings indicated that PrEP is an acceptable HIV prevention method. PrEP uptake is linked to personal and environmental factors that need to be considered for successful PrEP roll-out. Multi-level interventions needed to promote PrEP uptake should consider the social and structural drivers and focus on ways that can inspire PrEP uptake and limit the barriers.

Power and sample-size calculations for trials that compare slopes over time: Introducing the slopepower command.

Trials of interventions that aim to slow disease progression may analyze a continuous outcome by comparing its change over time-its slope-between the treated and the untreated group using a linear mixed model. To perform a sample-size calculation for such a trial, one must have estimates of the parameters that govern the between- and within-subject variability in the outcome, which are often unknown. The algebra needed for the sample-size calculation can also be complex for such trial designs. We have written a new user-friendly command, slopepower, that performs sample-size or power calculations for trials that compare slope outcomes. The package is based on linear mixed-model methodology, described for this setting by Frost, Kenward, and Fox (2008, Statistics in Medicine 27: 3717-3731). In the first stage of this approach, slopepower obtains estimates of mean slopes together with variances and covariances from a linear mixed model fit to previously collected user-supplied data. In the second stage, these estimates are combined with user input about the target effectiveness of the treatment and design of the future trial to give an estimate of either a sample size or a statistical power. In this article, we present the slopepower command, briefly explain the methodology behind it, and demonstrate how it can be used to help plan a trial and compare the sample sizes needed for different trial designs.

Cytomegalovirus Antibody Responses Associated With Increased Risk of Tuberculosis Disease in Ugandan Adults.

BACKGROUND: Recent evidence highlights human cytomegalovirus (HCMV) and immune activation as risk factors for tuberculosis disease. It is not known whether other herpesviruses are also implicated, nor whether a dose-response relationship exists between tuberculosis risk and herpes coinfection. METHODS: This nested case-control study used stored serum samples from 25 persons with tuberculosis up to 10 years before tuberculosis diagnosis and between 3 and 6 matched controls without tuberculosis from a rural Ugandan cohort. Samples were investigated for Epstein-Barr virus, herpes simplex virus, and HCMV-specific immunoglobulin G (IgG), serum markers of inflammation, and mycobacterial antibody levels. RESULTS: Humoral response to HCMV, but not Epstein-Barr or herpes simplex virus, was associated with increased risk of active tuberculosis disease up to 10 years before diagnosis. Individuals with medium HCMV IgG were 2.8 times more likely to have tuberculosis (P = .055), and those with high HCMV IgG 3.4 times more likely to have tuberculosis (P = .007). Mycobacterial antibody levels were not associated with differences in odds of tuberculosis disease. Interferon-induced protein 10 was independently associated with increased odds of tuberculosis (odds ratio, 4.2; P = .009). CONCLUSIONS: These data provide evidence of a dose response between magnitude of HCMV IgG with risk of tuberculosis disease. An inflammatory environment, characterized by serum interferon-induced protein 10 and interleukin 1α, is independently associated with increased risk of tuberculosis disease.

Comparison of retention in observational cohorts and nested simulated HIV vaccine efficacy trials in the key populations in Uganda.

BACKGROUND: Outcomes in observational studies may not best estimate those expected in the HIV vaccine efficacy trials. We compared retention in Simulated HIV Vaccine Efficacy Trials (SiVETs) and observational cohorts drawn from two key populations in Uganda. METHODS: Two SiVETs were nested within two observational cohorts, one in Fisherfolk (FF) and another one in Female Sex Workers (FSW). Adult participants in each observational cohort were screened for enrolment into SiVETs. Those screened-out or not screened continued participation in the observational (non-SiVET) cohorts. SiVET participants were administered a licensed hepatitis B vaccine in a schedule that mimicked an actual HIV vaccine efficacy trial. Both cohorts were followed for 12 months and retention was assessed through dropout, defined as lost to follow up, being uncontactable, refusal to continue or missing the last study clinic visit. Dropout rates were compared using Poisson models giving rate ratios and 95% confidence intervals (95%CI). RESULTS: Out of 1525 participants (565 FF and 960 FSW), 572 (38%) were enrolled into SiVETs (282-FF and 290-FSW), and 953 (62%) remained in the non-SiVET cohorts. Overall, 326 (101 SiVET, 225 non-SiVET) dropped out in 1260 Person Years of Observation (PYO), a dropout rate of 25.9 /100 PYO (95%CI: 23.2-28.8); fewer dropped out in the SiVET cohorts (18.4, 95% CI: 15.1-22.4) than in the non-SiVET cohorts (31.6, 95% CI: 27.8-36.1), rate ratio (RR) =0.58, 95% CI: 0.46-0.73. In all cohorts, the dropout was more marked in FSW than in FF population. Duration lived in community was associated with dropout in both SiVETs and religion in both non-SiVET cohorts. CONCLUSION: The rate of dropout was lower in SiVET compared to non-SiVET cohort. Though the difference in dropout between SiVET and non-SiVET was generally similar, the actual dropout rates were higher in the FSW population. Conduct of SiVETs in these key populations could mean that designing HIV Vaccine Efficacy Trials will benefit from lower dropout rate shown in SiVET than non-SiVET observational cohort.

Comparison of HIV Risk Behaviors Between Clinical Trials and Observational Cohorts in Uganda.

Many key populations have high-risk behaviors for HIV infection making them suitable for HIV vaccine efficacy trials. However, these behaviors may change when participants enroll into a trial. We used HIV simulated vaccine efficacy trials (SiVETs) nested within observational cohorts of fisherfolks and female sex workers in Uganda to evaluate this difference. We screened observational cohort participants for enrolment into SiVETs, until 572 were enrolled. Those not enrolled (n = 953) continued participation in the observational cohorts. We determined risk behaviors at baseline and at 1 year, assigned a numeric score to each behavior and defined composite score as the sum of reported behaviors. We compared changes in scores over 12 months. Both observational cohorts and SiVETs saw a significant decrease in score but greatest in the SiVETs. Investigators recruiting for trials from these populations should consider the likely effect of reduction in risk behaviors on incident HIV infection and trial statistical power.

Survival of people aged 50 years and older by HIV and HIV treatment status: findings from three waves of the SAGE-Wellbeing of Older People Study (SAGE-WOPS) in Uganda.

BACKGROUND: Data on the survival status of older adults on antiretroviral treatment (ART) are scarce in sub-Saharan Africa. The objective of this study was to determine the survival status of people aged 50 years and older who were HIV-negative, HIV-positive not on ART, and HIV-positive on ART. METHODS: We used three waves of data from the World Health Organisation Study on Global Ageing and adult health- Well Being of Older People Study cohort in Uganda, conducted in 2009, 2012-2013 and 2015-2016. The cohort included HIV-negative and HIV-positive persons aged 50 years and older recruited from multiple rural and peri-urban sites in Uganda. Data were collected using interviewer-administered questionnaire. Time-dependent ART data were collected from medical records using a data-abstraction form. This study was conducted before the universal test and treat policy came into effect. We fitted Cox survival models to estimate hazard ratios to compare the risk of death between groups, adjusted for age, sex, marital status and hypertension. RESULTS: Of 623 participants, 517 (82.9%) of respondents had follow-up data and were included in this analysis. We observed 1571 person-years of follow-up from 274 people who were HIV-negative, and 1252 from 243 who were HIV-positive. The estimated mortality adjusted hazard ratio (aHR) was 1.89 (95% CI 1.0-3.4; p = 0.04) among people living with HIV compared to HIV-negative people. The aHR for mortality among people receiving ART compared with HIV-negative people was 1.75 (95% CI 0.9-3.5). People who were HIV-positive and not receiving ART had the greatest risk of death (aHR = 2.09, 95% CI 1.0-4.4 compared with HIV negative participants). The aHR for HIV-positive people not receiving ART, compared to those who were on treatment, was 1.19 (95% CI 0.6-2.5). CONCLUSION: Older adults living with HIV on ART had a risk of mortality that was nearly twice as high as HIV-negative adults. Further analyses of longitudinal data should be done to understand factors that affect the survival of older adults on ART.

Birth attendants' hand hygiene compliance in healthcare facilities in low and middle-income countries: a systematic review.

BACKGROUND: With an increasing number of women delivering in healthcare facilities in Low and Middle Income Countries (LMICs), healthcare workers' hand hygiene compliance on labour wards is pivotal to preventing infections. Currently there are no estimates of how often birth attendants comply with hand hygiene, or of the factors influencing compliance in healthcare facilities in LMICs. METHODS: We conducted a systematic review to investigate the a) level of compliance, b) determinants of compliance and c) interventions to improve hand hygiene during labour and delivery among birth attendants in healthcare facilities of LMICs. We also aimed to assess the quality of the included studies and to report the intra-cluster correlation for studies conducted in multiple facilities. RESULTS: We obtained 797 results across four databases and reviewed 71 full texts. Of these, fifteen met our inclusion criteria. Overall, the quality of the included studies was particularly compromised by poorly described sampling methods and definitions. Hand hygiene compliance varied substantially across studies from 0 to 100%; however, the heterogeneity in definitions of hand hygiene did not allow us to combine or compare these meaningfully. The five studies with larger sample sizes and clearer definitions estimated compliance before aseptic procedures opportunities, to be low (range: 1-38%). Three studies described two multi-component interventions, both were shown to be feasible. CONCLUSIONS: Hand hygiene compliance was low for studies with larger sample sizes and clear definitions. This poses a substantial challenge to infection prevention during birth in LMICs facilities. We also found that the quality of many studies was suboptimal. Future studies of hand hygiene compliance on the labour ward should be designed with better sampling frames, assess inter-observer agreement, use measures to improve the quality of data collection, and report their hand hygiene definitions clearly.

HIV serostatus, inflammatory biomarkers and the frailty phenotype among older people in rural KwaZulu-Natal, South Africa.

Objective: We compared the prevalence of frailty by HIV serostatus and related biomarkers to the modified frailty phenotype among older individuals in a rural population in South Africa. Methods: Questionnaire data were from a cohort of people living with HIV (PWH) on antiretroviral therapy (ART) and HIV-uninfected people aged 50 years and older sampled from the Africa Health Research Institute Demographic Health and Surveillance area in northern KwaZulu-Natal. The prevalence of frailty was compared using five categories: (1) physical activity; (2) mobility; (3) fatigue; (4) gait speed; and (5) grip strength, and assessed for demographic, clinical, and inflammatory correlates of frailty. Results: Among 614 individuals in the study, 384 (62.5%) were women. The median age at study enrolment was 64 years [Interquartile range (IQR) (58.6-72.0)]. 292 (47.6%) were PWH. 499 (81%) were classified as either pre-frail or frail. 43 (7%) were frail and HIV positive, 185 (30%) were pre-frail and HIV positive, 57 were frail and HIV negative and 214 (35%) were pre-frail and HIV negative. Frailty was similar for HIV negative and PWH (17.7% vs 14.7%, p = 0.72). Women were more likely to be frail (18.3% vs 13.04%, p = 0.16). The prevalence of frailty increased with age for both HIV groups. In the multivariable analysis, the odds of being frail were higher in those aged 70 years and above than those aged between 50 and 59 years (p < 0.001). Females were less likely to be pre-frail than males (p < 0.001). There was no association between any of the inflammatory biomarkers and frailty and pre-frailty. Conclusion: In this population, the prevalence of frailty is similar for PWH and people without HIV, but higher for women than men. These data suggest that the odds of developing frailty is similar for PWH over the age of 50 years, who survive into older age, as for people without HIV.

The Impact of Intensive Versus Standard Anthelminthic Treatment on Allergy-related Outcomes, Helminth Infection Intensity, and Helminth-related Morbidity in Lake Victoria Fishing Communities, Uganda: Results From the LaVIISWA Cluster-randomized Trial.

BACKGROUND: The prevalence of allergy-related diseases is increasing in low-income countries. Parasitic helminths, common in these settings, may be protective. We hypothesized that intensive, community-wide, anthelminthic mass drug administration (MDA) would increase allergy-related diseases, while reducing helminth-related morbidity. METHODS: In an open, cluster-randomized trial (ISRCTN47196031), we randomized 26 high-schistosomiasis-transmission fishing villages in Lake Victoria, Uganda, in a 1:1 ratio to receive community-wide intensive (quarterly single-dose praziquantel plus albendazole daily for 3 days) or standard (annual praziquantel plus 6 monthly single-dose albendazole) MDA. Primary outcomes were recent wheezing, skin prick test positivity (SPT), and allergen-specific immunoglobulin E (asIgE) after 3 years of intervention. Secondary outcomes included helminths, haemoglobin, and hepatosplenomegaly. RESULTS: The outcome survey comprised 3350 individuals. Intensive MDA had no effect on wheezing (risk ratio [RR] 1.11, 95% confidence interval [CI] 0.64-1.93), SPT (RR 1.10, 95% CI 0.85-1.42), or asIgE (RR 0.96, 95% CI 0.82-1.12). Intensive MDA reduced Schistosoma mansoni infection intensity: the prevalence from Kato Katz examinations of single stool samples from each patient was 23% versus 39% (RR 0.70, 95% CI 0.55-0.88), but the urine circulating cathodic antigen test remained positive in 85% participants in both trial arms. Hookworm prevalence was 8% versus 11% (RR 0.55, 95% CI 0.31-1.00). There were no differences in anemia or hepatospenomegaly between trial arms. CONCLUSIONS: Despite reductions in S. mansoni intensity and hookworm prevalence, intensive MDA had no effect on atopy, allergy-related diseases, or helminth-related pathology. This could be due to sustained low-intensity infections; thus, a causal link between helminths and allergy outcomes cannot be discounted. Intensive community-based MDA has a limited impact in high-schistosomiasis-transmission fishing communities, in the absence of other interventions. CLINICAL TRIALS REGISTRATION: ISRCTN47196031.

On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil.

The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integrative taxonomic approach that includes phylogenomic analyses, pelage characters, and locality records. A reduced representation genome-wide approach was employed to assess phylogenetic relationships among species of the eastern Amazonian clade of the Plecturocebus moloch group. Using existing records, we calculated the Extent of Occurrence (EOO) of the new species and estimated future habitat loss for the region based on predictive models. We then evaluated the species' conservation status using the IUCN Red list categories and criteria. The new species presents a unique combination of morphological characters: (1) grey agouti colouration on the crown and dorsal parts; (2) entirely bright red-brown venter; (3) an almost entirely black tail with a pale tip; and (4) light yellow colouration of the hair on the cheeks contrasting with bright red-brown hair on the sides of the face. Our phylogenetic reconstructions based on maximum-likelihood and Bayesian methods revealed well-supported species relationships, with the Alta Floresta taxon as sister to P. moloch + P. vieirai. The species EOO is 10,166,653 ha and we predict a total habitat loss of 86% of its original forest habitat under a "business as usual" scenario in the next 24 years, making the newly discovered titi monkey a Critically Endangered species under the IUCN A3c criterion. We give the new titi monkey a specific epithet based on: (1) clear monophyly of this lineage revealed by robust genomic and mitochondrial data; (2) distinct and diagnosable pelage morphology; and (3) a well-defined geographical distribution with clear separation from other closely related taxa. Urgent conservation measures are needed to safeguard the future of this newly discovered and already critically endangered primate.

Human Immunodeficiency Virus Incidence Among Women at High-Risk of Human Immunodeficiency Virus Infection Attending a Dedicated Clinic in Kampala, Uganda: 2008-2017.

BACKGROUND: High attrition and irregular testing for human immunodeficiency virus (HIV) in cohort studies for high-risk populations can bias incidence estimates. We compare incidence trends for high-risk women attending a dedicated HIV prevention and treatment clinic, using common methods for assigning when seroconversion occurs and whether seroconversion occurs among those with attrition. METHODS: Between April 2008 and May 2009, women were enrolled into cohort 1 and from January 2013 into cohort 2, then scheduled for follow-up once every 3 months. Incidence trends based on assuming a midpoint in the seroconversion interval were compared with those of assigning a random-point. We also compared estimates based on the random-point with and without multiple imputation (MI) of serostatuses for participants with attrition. RESULTS: By May 2017, 3084 HIV-negative women had been enrolled with 18,364 clinic visits. Before attrition, 27.6% (6990 of 25,354) were missed visits. By August 2017, 65.8% (426 of 647) of those enrolled in cohort 1 and 49.0% (1194 of 2437) in cohort 2 were defined with attrition. Among women with 1 or more follow-up visit, 93 of 605 in cohort 1 and 77 of 1601 in cohort 2 seroconverted. Periods with longer seroconversion intervals appeared to have noticeable differences in incidences when comparing the midpoint and random-point values. The MI for attrition is likely to have overestimated incidence after escalated attrition of participants. Based on random-point without MI for attrition, incidence at end of observation was 3.8/100 person-years in cohort 1 and 1.8/100 in cohort 2. CONCLUSIONS: The random-point approach attenuated variation in incidence observed using midpoint. The high incidence after years of ongoing prevention efforts in this vulnerable population should be investigated to further reduce incidence.

HIV, HCMV and mycobacterial antibody levels: a cross-sectional study in a rural Ugandan cohort.

OBJECTIVES: A growing evidence base implicates human cytomegalovirus (HCMV) as a risk factor for TB disease. We investigated total IgG and mycobacteria-specific antibodies in a cross-sectional study nested within a rural Ugandan General Population Cohort (GPC), in relation to HIV infection and the magnitude of HCMV IgG response. METHODS: Sera from 2189 individuals (including 27 sputum-positive TB cases) were analysed for antibodies against mycobacteria (Ag85A, PPD, LAM, ESAT6/CFP10) and HCMV, tetanus toxoid (TT) and total IgG. RESULTS: Anti-mycobacterial antibodies increased with age until approximately 20 years, when they plateaued. Higher HCMV exposure (measured by IgG) was associated with lower levels of some anti-mycobacterial antibodies, but no increase in total IgG. HIV infection was associated with a decrease in all anti-mycobacterial antibodies measured and with an increase in total IgG. CONCLUSIONS: The increase in anti-mycobacterial antibodies with age suggests increasing exposure to non-tuberculous mycobacteria (NTM), and to M.tb itself. HIV infection is associated with decreased levels of all mycobacterial antibodies studied here, and high levels of HCMV IgG are associated with decreased levels of some mycobacterial antibodies. These findings point towards the importance of humoral immune responses in HIV/TB co-infection and highlight a possible role of HCMV as a risk factor for TB disease.

Relationship Between Anemia, Malaria Coinfection, and Kaposi Sarcoma-Associated Herpesvirus Seropositivity in a Population-Based Study in Rural Uganda.

We examined anemia and malaria as risk factors for Kaposi sarcoma-associated herpesvirus (KSHV) seropositivity and antibody levels in a long-standing rural Ugandan cohort, in which KSHV is prevalent. Samples from 4134 children, aged 1-17 years, with a sex ratio of 1:1, and 3149 adults aged 18-103 years, 41% of whom were males, were analyzed. Among children, malaria infection was associated with higher KSHV prevalence (61% vs 41% prevalence among malaria infected and uninfected, respectively); malaria was not assessed in adults. Additionally, lower hemoglobin level was associated with an increased prevalence of KSHV seropositivity, both in children and in adults.

How many pygmy marmoset (Cebuella Gray, 1870) species are there? A taxonomic re-appraisal based on new molecular evidence.

The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventris Lönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed the mtDNA cytochrome b gene and, for the first time for any Neotropical primate, we used a reduced representation genome sequencing approach (ddRADseq) to obtain data for recently collected, geographically representative samples from the Rio Japurá, a northern tributary of the Rio Solimões and from the Javarí, Jutaí, Juruá, Madeira and Purus river basins, all tributaries south of the Solimões. We estimated phylogenies and diversification times under both maximum likelihood and Bayesian inference criteria. Our analysis showed two highly supported clades, with intraclade divergences much smaller than interclade divergences, indicating two species of Cebuella: one from the Rio Japurá and one to the south of Solimões. The interpretation of our results in light of the current taxonomy is not trivial however. Lönnberg stated that the type of Spix's pygmy marmoset (type locality 'near Tabatinga') was obtained from the south of the Solimões, and his description of the distinct niveiventris from Lago Ipixuna, south of the Solimões and several hundred kilometres east of Tabatinga, was based on a comparison with specimens that he determined as typical pygmaea that were from the upper Rio Juruá (south of the Solimões). As such it remains uncertain whether the name pygmaea should be applicable to the pygmy marmosets north of the Rio Solimões (Tabatinga type locality) or south (near Tabatinga but across the Solimões). Finally, our analysis of pelage coloration revealed three phenotypic forms: (1) south of the Rio Solimoes, (2) Eirunepé-Acre, upper Juruá basin; and (3) Japurá. More samples from both sides of Solimões in the region of Tabatinga will be necessary to ascertain the exact type locality for Spix's pygmaea and to resolve the current uncertainties surrounding pygmy marmoset taxonomy.

The validity of an area-based method to estimate the size of hard-to-reach populations using satellite images: the example of fishing populations of Lake Victoria.

BACKGROUND: Information on the size of populations is crucial for planning of service and resource allocation to communities in need of health interventions. In resource limited settings, reliable census data are often not available. Using publicly available Google Earth Pro and available local household survey data from fishing communities (FC) on Lake Victoria in Uganda, we compared two simple methods (using average population density) and one simple linear regression model to estimate populations of small rural FC in Uganda. We split the dataset into two sections; one to obtain parameters and one to test the validity of the models. RESULTS: Out of 66 FC, we were able to estimate populations for 47. There were 16 FC in the test set. The estimates for total population from all three methods were similar, with errors less than 2.2%. Estimates of individual FC populations were more widely discrepant. CONCLUSIONS: In our rural Ugandan setting, it was possible to use a simple area based model to get reasonable estimates of total population. However, there were often large errors in estimates for individual villages.