Estimating rainfall and water balance over the Okavango River Basin for hydrological applications

A historical database for use in rainfall-runoff modeling of the Okavango River Basin in Southwest Africa is presented. The work has relevance for similar data-sparse regions. The parameters of main concern are rainfall and catchment water balance which are key variables for subsequent studies of the hydrological impacts of development and climate change. Rainfall estimates are based on a combination of in-situ gauges and satellite sources. Rain gauge measurements are most extensive from 1955 to 1972, after which they are drastically reduced due to the Angolan civil war. The sensitivity of the rainfall fields to spatial interpolation techniques and the density of gauges was evaluated. Satellite based rainfall estimates for the basin are developed for the period from 1991 onwards, based on the Tropical Rainfall Measuring Mission (TRMM) and Special Sensor Microwave Imager (SSM/I) data sets. The consistency between the gauges and satellite estimates was considered. A methodology was developed to allow calibration of the rainfall-runoff hydrological model against rain gauge data from 1960-1972, with the prerequisite that the model should be driven by satellite derived rainfall products for the 1990s onwards. With the rain gauge data, addition of a single rainfall station (Longa) in regions where stations earlier were lacking was more important than the chosen interpolation method. Comparison of satellite and gauge rainfall outside the basin indicated that the satellite overestimates rainfall by 20%. A non-linear correction was derived used by fitting the rainfall frequency characteristics to those of the historical rainfall data. This satellite rainfall dataset was found satisfactory when using the Pitman rainfall-runoff model (Hughes et al., this issue). Intensive monitoring in the region is recommended to increase accuracy of the comprehensive satellite rainfall estimate calibration procedur

Covid-19 and Inequity: A comparative spatial analysis of New York City and Chicago hot spots

There have been numerous reports that the impact of the ongoing COVID-19 epidemic has disproportionately impacted traditionally vulnerable communities, including well-researched social determinants of health, such as racial and ethnic minorities, migrants, and the economically challenged. The goal of this ecological cross-sectional study is to examine the demographic and economic nature of spatial hot and cold spots of SARS-CoV-2 rates in New York City and Chicago as of April 13, 2020. In both cities, cold spots (clusters of low SARS-CoV-2 rate ZIP code tabulation areas) demonstrated typical protective factors associated with the social determinants of health and the ability to social distance. These neighborhoods tended to be wealthier, have higher educational attainment, higher proportions of non-Hispanic white residents, and more workers in managerial occupations. Hot spots (clusters of high SARS-CoV-2 rate ZIP code tabulation areas) also had similarities, such as lower rates of college graduates and higher proportions of people of color. It also appears to be larger households (more people per household), rather than overall population density, that may to be a more strongly associated with hot spots. Findings suggest important differences between the cities’ hot spots as well. They can be generalized by describing the NYC hot spots as working-class and middle-income communities, perhaps indicative of service workers and other occupations (including those classified as “essential services” during the pandemic) that may not require a college degree but pay wages above poverty levels. Chicago’s hot spot neighborhoods, on the other hand, are among the city’s most vulnerable, low-income neighborhoods with extremely high rates of poverty, unemployment, and non-Hispanic Black residents

Adult HIV care resources, management practices and patient characteristics in the Phase 1 IeDEA Central Africa cohort

Introduction: Despite recent advances in the management of HIV infection and increased access to treatment, prevention, care and support, the HIV/AIDS epidemic continues to be a major global health problem, with sub-Saharan Africa suffering by far the greatest humanitarian, demographic and socio-economic burden of the epidemic. Information on HIV/AIDS clinical care and established cohorts’ characteristics in the Central Africa region are sparse. Methods: A survey of clinical care resources, management practices and patient characteristics was undertaken among 12 adult HIV care sites in four countries of the International Epidemiologic Databases to Evaluate AIDS Central Africa (IeDEA-CA) Phase 1 regional network in October 2009. These facilities served predominantly urban populations and offered primary care in the Democratic Republic of Congo (DRC; six sites), secondary care in Rwanda (two sites) and tertiary care in Cameroon (three sites) and Burundi (one site). Results: Despite some variation in facility characteristics, sites reported high levels of monitoring resources, including electronic databases, as well as linkages to prevention of mother-to-child HIV transmission programs. At the time of the survey, there were 21,599 HIV-positive adults (median age=37 years) enrolled in the clinical cohort. Though two-thirds were women, few adults (6.5%) entered HIV care through prevention of mother-to-child transmission services, whereas 55% of the cohort entered care through voluntary counselling and testing. Two-thirds of patients at sites in Cameroon and DRC were in WHO Stage III and IV at baseline, whereas nearly all patients in the Rwanda facilities with clinical stage information available were in Stage I and II. WHO criteria were used for antiretroviral therapy initiation. The most common treatment regimen was stavudine/lamivudine/nevirapine (64%), followed by zidovudine/lamivudine/nevirapine (19%). Conclusions: Our findings demonstrate the feasibility of establishing large clinical cohorts of HIV-positive individuals in a relatively short amount of time in spite of challenges experienced by clinics in resource-limited settings such as those in this region. Country differences in the cohort's site and patient characteristics were noted. This information sets the stage for the development of research initiatives and additional programs to enhance adult HIV care and treatment in Central Africa

Adaptation and conservation insights from the koala genome

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as ‘vulnerable’ due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala’s ability to detoxify eucalypt foliage may be due to expansions within a cytochrome P450 gene family, and its ability to smell, taste and moderate ingestion of plant secondary metabolites may be due to expansions in the vomeronasal and taste receptors. We characterized novel lactation proteins that protect young in the pouch and annotated immune genes important for response to chlamydial disease. Historical demography showed a substantial population crash coincident with the decline of Australian megafauna, while contemporary populations had biogeographic boundaries and increased inbreeding in populations affected by historic translocations. We identified genetically diverse populations that require habitat corridors and instituting of translocation programs to aid the koala’s survival in the wild

Declining Tuberculosis Incidence Among People Receiving HIV Care and Treatment Services in East Africa, 2007–2012

Background: Antiretroviral therapy (ART) reduces the risk of Tuberculosis (TB) among people living with HIV (PLWH). With ART scale-up in sub-Saharan Africa over the past decade, incidence of TB among PLWH engaged in HIV care is predicted to decline. Methods: We conducted a retrospective analysis of routine clinical data from 168,330 PLWH receiving care at 35 facilities in Kenya, Tanzania, and Uganda during 2003–2012, participating in the East African region of the International Epidemiologic Databases to Evaluate AIDS. Temporal trends in facility-based annual TB incidence rates (per 100,000 person years) among PLWH and country-specific standardized TB incidence ratios using annual population-level TB incidence data from the World Health Organization were computed between 2007 and 2012. We examined patient-level and facility-level factors associated with incident TB using multivariable Cox models. Results: Overall, TB incidence rates among PLWH in care declined 5-fold between 2007 and 2012 from 5960 to 985 per 100,000 person years [P = 0.0003] (Kenya: 7552 to 1115 [P = 0.0007]; Tanzania: 7153 to 635 [P = 0.0025]; Uganda: 3204 to 242 [P = 0.018]). Standardized TB incidence ratios significantly decreased in the 3 countries, indicating a narrowing gap between incidence rates among PLWH and the general population. We observed lower hazards of incident TB among PLWH on ART and/or isoniazid preventive therapy and receiving care in facilities offering TB treatment onsite. Conclusions: Annual TB incidence rates among PLWH significantly declined during ART scale-up but remained higher than the general population. Increasing access to ART and isoniazid preventive therapy and co-location of HIV and TB treatment may further reduce TB incidence among PLWH

Conceptualizing Care Continua: Lessons from Hiv, Hepatitis C virus, Tuberculosis and implications for the Development of Improved Care and Prevention Continua

Background: To examine the application of continuum models to tuberculosis, HIV, and other conditions; to theorize the concept of continua; and to learn lessons that could inform the development of improved care and prevention continua as public health metrics. Methods: An analytic review of literature drawn from several fields of health care. Results: The continuum construct is now part of public health evaluation systems for HIV, and is increasingly used in public health and the medical literature. Issues with the comparability and optimal design of care continuum models have been raised, and their methodologic and theoretic underpinnings and scope of focus have been underaddressed. Review of relevant publications suggests that a key limitation of current models is their lack of measures reflecting incidence and mortality. Issues relating to continua data being longitudinal or cross-sectional, definition of numerators and denominators for each step, data sources, measures of timeliness of step completion, theoretic models to facilitate inferences of causes of care continuum gaps, how measures of prevention efforts, reinfection/relapses, and interactions of continua for co-occurring comorbidities should be reflected, and how analyses of differences in retention over time, across geographic regions, and in response to interventions should be conducted are critical to the development of sound care and prevention continuum models. Conclusion: Lessons learned from the application of continuum models to HIV and other conditions suggest that the application of well-formulated constructs of care and prevention continua, that depict, in well defined, standardized steps, incidence and mortality, along with degrees of and time to screening, engagement in care and prevention, treatment and treatment outcomes, including relapse or reinfection, may be vital tools in evaluating intervention and program outcomes, and in improving population health and population health metrics for a wide range conditions

Untangling the Relationship Between Antiretroviral Therapy Use and Incident Pregnancy: A Marginal Structural Model Analysis Using Data From 47,313 HIV-Positive Women in East Africa

BACKGROUND: Scale-up of triple-drug antiretroviral therapy (ART) in Africa has transformed the context of childbearing for HIV-positive women and may impact pregnancy incidence in HIV programs. METHODS: Using observational data from 47,313 HIV-positive women enrolled at 26 HIV clinics in Kenya and Uganda between 2001 and 2009, we calculated the crude cumulative incidence of pregnancy for the pre-ART and on-ART periods. The causal effect of ART use on incident pregnancy was assessed using inverse probability weighted marginal structural models, and the relationship was further explored in multivariable Cox models. RESULTS: Crude cumulative pregnancy incidence at 1 year after enrollment/ART initiation was 4.0% and 3.9% during the pre-ART and on-ART periods, respectively. In marginal structural models, ART use was not significantly associated with incident pregnancy [hazard ratio = 1.06; 95% confidence interval (CI): 0.99 to 1.12]. Similarly, in Cox models, there was no significant relationship between ART use and incident pregnancy (cause-specific hazard ratio: 0.98; 95% CI: 0.91 to 1.05), but effect modification was observed. Specifically, women who were pregnant at enrollment and on ART had an increased risk of incident pregnancy compared to those not pregnant at enrollment and not on ART (cause-specific hazard ratio: 1.11; 95% CI: 1.01 to 1.23). CONCLUSIONS: In this large cohort, ART initiation was not associated with incident pregnancy in the general population of women enrolling in HIV care but rather only among those pregnant at enrollment. This finding further highlights the importance of scaling up access to lifelong treatment for pregnant women

Inferring random change point from left-censored longitudinal data by segmented mechanistic nonlinear models, with application in HIV surveillance study

The primary goal of public health efforts to control HIV epidemics is to diagnose and treat people with HIV infection as soon as possible after seroconversion. The timing of initiation of antiretroviral therapy (ART) treatment after HIV diagnosis is, therefore, a critical population-level indicator that can be used to measure the effectiveness of public health programs and policies at local and national levels. However, population-based data on ART initiation are unavailable because ART initiation and prescription are typically measured indirectly by public health departments (e.g., with viral suppression as a proxy). In this paper, we present a random change-point model to infer the time of ART initiation utilizing routinely reported individual-level HIV viral load from an HIV surveillance system. To deal with the left-censoring and the nonlinear trajectory of viral load data, we formulate a flexible segmented nonlinear mixed effects model and propose a Stochastic version of EM (StEM) algorithm, coupled with a Gibbs sampler for the inference. We apply the method to a random subset of HIV surveillance data to infer the timing of ART initiation since diagnosis and to gain additional insights into the viral load dynamics. Simulation studies are also performed to evaluate the properties of the proposed method

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT