Risk charts to guide targeted HIV-1 viral load monitoring of ART: development and validation in patients from resource-limited settings.

BACKGROUND HIV-1 RNA viral load (VL) testing is recommended to monitor antiretroviral therapy (ART) but not available in many resource-limited settings. We developed and validated CD4-based risk charts to guide targeted VL testing. METHODS We modeled the probability of virologic failure up to 5 years of ART based on current and baseline CD4 counts, developed decision rules for targeted VL testing of 10%, 20% or 40% of patients in seven cohorts of patients starting ART in South Africa, and plotted cut-offs for VL testing on colour-coded risk charts. We assessed the accuracy of risk chart-guided VL testing to detect virologic failure in validation cohorts from South Africa, Zambia and the Asia-Pacific. FINDINGS 31,450 adult patients were included in the derivation and 25,294 patients in the validation cohorts. Positive predictive values increased with the percentage of patients tested: from 79% (10% tested) to 98% (40% tested) in the South African, from 64% to 93% in the Zambian and from 73% to 96% in the Asia-Pacific cohorts. Corresponding increases in sensitivity were from 35% to 68% in South Africa, from 55% to 82% in Zambia and from 37% to 71% in Asia-Pacific. The area under the receiver-operating curve increased from 0.75 to 0.91 in South Africa, from 0.76 to 0.91 in Zambia and from 0.77 to 0.92 in Asia Pacific. INTERPRETATION CD4-based risk charts with optimal cut-offs for targeted VL testing may be useful to monitor ART in settings where VL capacity is limited.

Three-year changes of prothrombotic factors in a cohort of South Africans with a high clinical suspicion of obstructive sleep apnea.

A hypercoagulable state might be one important mechanism linking obstructive sleep apnea (OSA) with incident myocardial infarction and stroke. However, previous studies on prothrombotic factors in OSA are not uniform and cross-sectional. We longitudinally studied prothrombotic factors in relation to OSA risk, adjusting for baseline levels of prothrombotic factors, demographics, metabolic parameters, aspirin use, and life style factors. The Berlin Questionnaire and/or neck circumference were used to define high OSA risk in 329 South African teachers (48.0 % male, 44.6 % black) at baseline and at three-year follow-up. Von Willebrand factor (VWF), fibrinogen, D-dimer, plasminogen activator inhibitor-1, clot lysis time (CLT), and soluble urokinase-type plasminogen activator receptor (suPAR) were measured in plasma. At baseline 35.7 % of participants had a high risk of OSA. At follow-up, persistently high OSA risk, persistently low OSA risk, OSA risk remission, and new-onset OSA risk were present in 26.1 %, 53.2 %, 9.4 %, and 11.3 % of participants, respectively. New-onset OSA risk was associated with a significant and longitudinal increase in VWF, fibrinogen, CLT, and suPAR relative to persistently low OSA risk; in VWF, fibrinogen, and suPAR relative to remitted OSA risk; and in VWF relative to persistently high OSA risk. Persistently high OSA risk was associated with an increase in CLT and suPAR relative to persistently low OSA risk and in D-dimer relative to remitted OSA risk. Remitted OSA risk was associated with D-dimer decrease relative to persistently low OSA risk. In OSA, hypercoagulability is a dynamic process with a most prominent three-year increase in individuals with new-onset OSA risk.

Age in antiretroviral therapy programmes in South Africa: a retrospective, multicentre, observational cohort study.

BACKGROUND As access to antiretroviral therapy (ART) expands, increasing numbers of older patients will start treatment and need specialised long-term care. However, the effect of age in ART programmes in resource-constrained settings is poorly understood. The HIV epidemic is ageing rapidly and South Africa has one of the highest HIV population prevalences worldwide. We explored the effect of age on mortality of patients on ART in South Africa and whether this effect is mediated by baseline immunological status. METHODS In this retrospective cohort analysis, we studied HIV-positive patients aged 16-80 years who started ART for the first time in six large South African cohorts of the International Epidemiologic Databases to Evaluate AIDS-Southern Africa collaboration, in KwaZulu-Natal, Gauteng, and Western Cape (two primary care clinics, three hospitals, and a large rural cohort). The primary outcome was mortality. We ascertained patients' vital status through linkage to the National Population Register. We used inverse probability weighting to correct mortality for loss to follow-up. We estimated mortality using Cox's proportional hazards and competing risks regression. We tested the interaction between baseline CD4 cell count and age. FINDINGS Between Jan 1, 2004, and Dec 31, 2013, 84,078 eligible adults started ART. Of these, we followed up 83,566 patients for 174,640 patient-years. 8% (1817 of 23,258) of patients aged 16-29 years died compared with 19% (93 of 492) of patients aged 65 years or older. The age adjusted mortality hazard ratio was 2·52 (95% CI 2·01-3·17) for people aged 65 years or older compared with those 16-29 years of age. In patients starting ART with a CD4 count of less than 50 cells per μL, the adjusted mortality hazard ratio was 2·52 (2·04-3·11) for people aged 50 years or older compared with those 16-39 years old. Mortality was highest in patients with CD4 counts of less than 50 cells per μL, and 15% (1103 of 7295) of all patients aged 50 years or older starting ART were in this group. The proportion of patients aged 50 years or older enrolling in ART increased with successive years, from 6% (290 of 4999) in 2004 to 10% (961 of 9657) in 2012-13, comprising 9% of total enrolment (7295 of 83 566). At the end of the study, 6304 (14%) of 44,909 patients still alive and in care were aged 50 years or older. INTERPRETATION Health services need reorientation towards HIV diagnosis and starting of ART in older individuals. Policies are needed for long-term care of older people with HIV. FUNDING National Institutes of Health (National Institute of Allergy and Infectious Diseases), US Agency for International Development, and South African Centre for Epidemiological Modelling and Analysis.

Implementation and Operational Research: Risk Charts to Guide Targeted HIV-1 Viral Load Monitoring of ART: Development and Validation in Patients From Resource-Limited Settings.

BACKGROUND HIV-1 RNA viral load (VL) testing is recommended to monitor antiretroviral therapy (ART) but not available in many resource-limited settings. We developed and validated CD4-based risk charts to guide targeted VL testing. METHODS We modeled the probability of virologic failure up to 5 years of ART based on current and baseline CD4 counts, developed decision rules for targeted VL testing of 10%, 20%, or 40% of patients in 7 cohorts of patients starting ART in South Africa, and plotted cutoffs for VL testing on colour-coded risk charts. We assessed the accuracy of risk chart-guided VL testing to detect virologic failure in validation cohorts from South Africa, Zambia, and the Asia-Pacific. RESULTS In total, 31,450 adult patients were included in the derivation and 25,294 patients in the validation cohorts. Positive predictive values increased with the percentage of patients tested: from 79% (10% tested) to 98% (40% tested) in the South African cohort, from 64% to 93% in the Zambian cohort, and from 73% to 96% in the Asia-Pacific cohort. Corresponding increases in sensitivity were from 35% to 68% in South Africa, from 55% to 82% in Zambia, and from 37% to 71% in Asia-Pacific. The area under the receiver operating curve increased from 0.75 to 0.91 in South Africa, from 0.76 to 0.91 in Zambia, and from 0.77 to 0.92 in Asia-Pacific. CONCLUSIONS CD4-based risk charts with optimal cutoffs for targeted VL testing maybe useful to monitor ART in settings where VL capacity is limited.

Physical-Biological Oceanographic Coupling Influencing Phytoplankton and Primary Production in the South China Sea

Two cruises were carried out in the summer and winter of 1998 to study coupled physical-chemical-biological processes in the South China Sea and their effects on phytoplankton stock and production. The results clearly show that the seasonal distributions of phytoplankton were closely related to the coupled processes driven by the East Asian Monsoon. Summer southwesterly monsoon induced upwelling along the China and Vietnam coasts. Several mesoscale cyclonic cold eddies and anticyclonic warm pools were identified in both seasons. In the summer, the upwelling and cold eddies, both associated with rich nutrients, low dissolved oxygen ( DO), high chlorophyll a (Chl a) and primary production ( PP), were found in the areas off the coast of central Vietnam, southeast of Hainan Island and north of the Sunda shelf, whereas in the winter they form a cold trough over the deep basin aligning from southwest to northeast. The warm pools with poor nutrients, high DO, low Chl a, and PP were found in the areas southeast of Vietnam, east of Hainan, and west of Luzon during the summer, and a northwestward warm jet from the Sulu Sea with properties similar to the warm pools was encountered during the winter. The phytoplankton stock and primary production were lower in summer due to nutrient depletion near the surface, particularly PO4. This phosphorus depletion resulted in phytoplankton species succession from diatoms to dinoflagellates and cyanophytes. A strong subsurface Chl a maximum, dominated by photosynthetic picoplankton, was found to contribute significantly to phytoplankton stocks and production.

Rights at Risk: Refugees in the New South Africa

This thesis seeks to analyze the relationship between public attitudes toward refugees in a refugee receiving state and the realization of the legal rights afforded refugees (de facto rights). I hypothesize that the more negative a host culture is toward refugees, the less refugees are able to realize their rights. Conversely, the more positive a host culture is toward refugees, the more refugees are able to realize their rights. I test the hypothesis through a case study of refugee populations in Cape Town, South Africa, based on research conducted from May to June 2007. The orientation (positive or negative) of the host culture's perceptions toward a refugee group (Independent Variable) is measured through: (1) a coded content analysis of the South African media, (2) a coded content analysis of semi-structured interviews, and (3) an assessment of secondary source public opinion surveys and reports. The realization of refugee rights (Dependent Variable) is operationalized as a function of two rights: (1) the right to personal physical integrity and (2) the right to protection from unlawful detention. These rights are measured by coding (1) media reports and (2) interviews, and by (3) assessing NGO reports and secondary source public opinion surveys. My empirical data shows that the cultural orientation toward refugees is not overwhelmingly negative, and the realization of rights is not conclusively "low." However, the frequency of data coded "negative" and "low" versus "positive" or "high" suggest that South Africans regard refugees somewhat negatively and that rights are not fully realized. This finding is strengthened by the analysis of secondary sources and field notes.

Association between glycemic index and glycemic load and the risk of incident coronary heart disease among whites and African Americans with and without type 2 diabetes: The Atherosclerosis Risk in Communities study

Several studies have examined the association between high glycemic index (GI) and glycemic load (GL) diets and the risk for coronary heart disease (CHD). However, most of these studies were conducted primarily on white populations. The primary aim of this study was to examine whether high GI and GL diets are associated with increased risk for developing CHD in whites and African Americans, non-diabetics and diabetics, and within stratifications of body mass index (BMI) and hypertension (HTN). Baseline and 17-year follow-up data from ARIC (Atherosclerosis Risk in Communities) study was used. The study population (13,051) consisted of 74% whites, 26% African Americans, 89% non-diabetics, 11% diabetics, 43% male, 57% female aged 44 to 66 years at baseline. Data from the ARIC food frequency questionnaire at baseline were analyzed to provide GI and GL indices for each subject. Increases of 25 and 30 units for GI and GL respectively were used to describe relationships on incident CHD risk. Adjusted hazard ratios for propensity score with 95% confidence intervals (CI) were used to assess associations. During 17 years of follow-up (1987 to 2004), 1,683 cases of CHD was recorded. Glycemic index was associated with 2.12 fold (95% CI: 1.05, 4.30) increased incident CHD risk for all African Americans and GL was associated with 1.14 fold (95% CI: 1.04, 1.25) increased CHD risk for all whites. In addition, GL was also an important CHD risk factor for white non-diabetics (HR=1.59; 95% CI: 1.33, 1.90). Furthermore, within stratum of BMI 23.0 to 29.9 in non-diabetics, GI was associated with an increased hazard ratio of 11.99 (95% CI: 2.31, 62.18) for CHD in African Americans, and GL was associated with 1.23 fold (1.08, 1.39) increased CHD risk in whites. Body mass index modified the effect of GI and GL on CHD risk in all whites and white non-diabetics. For HTN, both systolic blood pressure and diastolic blood pressure modified the effect on GI and GL on CHD risk in all whites and African Americans, white and African American non-diabetics, and white diabetics. Further studies should examine other factors that could influence the effects of GI and GL on CHD risk, including dietary factors, physical activity, and diet-gene interactions. ^

"Gangsterism," HIV, and "tik:" An exploration of Cape Town youth

Since early 2000, the Western Cape of South Africa has been documented as an area for monitoring the spread of HIV. The majority of HIV cases occur within individuals between the ages of 15-49 years, and the epidemic is believed to be complicated by the increased use of crystal methamphetamine (CM), or “tik.” Eighty percent of current CM users in Cape Town are under the age of 21 years, and almost 18% of current HIV cases are in individuals under the age of 24 years. Gang membership in youth may also be complicating the HIV problem as gangs feed the social acceptability of “tik” and encourage sexual violence. With almost half the population of Cape Town in their mid-twenties, the threat of a new HIV epidemic complicated by CM use has become a concern in the young adults of the city. Research into the relationships between gang membership and drugs/violence has been extensively studied in the Cape Flats. Yet, few have examined the role of gangs in the perpetuation of HIV. Therefore, the purpose of this investigation was exploratory in nature. Key informant interviews from Cape Town youth were used as case illustrations to generate potential hypotheses on the interrelationships between “gangsterism,” “tik” use, and HIV. Such awareness is important if effective efforts to reduce HIV incidence in Cape Town (and Sub-Saharan Africa) are to transpire. If the problem of CM is not addressed quickly, the Cape Flats may find itself with a higher rate of an already uncontrollable HIV epidemic. ^

A relationship between aerosol transport and compound-specific d13C land plant biomarker and pollen records

We examined near-surface, late Holocene deep-sea sediments at nine sites on a north-south transect from the Congo Fan (4°S) to the Cape Basin (30°S) along the Southwest African continental margin. Contents, distribution patterns and molecular stable carbon isotope signatures of long-chain n-alkanes (C27-C33) and n-alkanols (C22-C32) are indicators of land plant vegetation of different biosynthetic types, which can be correlated with concentrations and distributions of pollen taxa in the same sediments. Calculated clusters of wind trajectories and satellite Aerosol Index imagery afford information on the source areas for the lipids and pollen on land and their transport pathways to the ocean sites. This multidisciplinary approach on an almost continental scale provides clear evidence of latitudinal differences in lipid and pollen composition paralleling the major phytogeographic zonations on the adjacent continent. Dust and smoke aerosols are mainly derived from the western and central South African hinterland dominated by deserts, semi-deserts and savannah regions rich in C4 and CAM plants. The northern sites (Congo Fan area and northern Angola Basin), which get most of their terrestrial material from the Congo Basin and the Angolan highlands, may also receive some material from the Chad region. Very little aerosol from the African continent is transported to the most southerly sites in the Cape Basin. As can be expected from the present position of the phytogeographic zones, the carbon isotopic signatures of the n-alkanes and n-alkanols both become isotopically more enriched in 13C from north to south. The results of the study suggest that this combination of pollen data and compound-specific isotope geochemical proxies can be effectively applied in the reconstruction of past continental phytogeographic developments.

Model - data comparison of western African rainfall evolutions during the Last Interglacial (130-115 ka)

This dataset characterizes the evolution of western African precipitation indicated by marine sediment geochemical records in comparison to transient simulations using CCSM3 global climate model throughout the Last Interglacial (130-115 ka). It contains (1) defined tie-points (age models), newly published stable isotopes of benthic foraminifera and Al/Si log-ratios of eight marine sediment cores from the western African margin and (2) annual and seasonal rainfall anomalies (relative to pre-industrial values) for six characteristic latitudinal bands in western Africa simulated by CCSM3 (two transient simulations: one non-accelerated and one accelerated experiment).

Plants growing near the cargo packing station, and seed occurrence in cargo and luggage destined for Gough and Marion Island and the Antarctic

Globalization has resulted in unprecedented movements of people, goods, and alien species across the planet. Although the impacts of biological invasions are widely appreciated, a bias exists in research effort to post-dispersal processes because of the difficulties of measuring propagule pressure. The Antarctic provides an ideal model system in which to investigate propagule movements because of the region's isolation and small number of entry routes. Here we investigated the logistics operations of the South African National Antarctic Programme (SANAP) and quantified the initial dispersal of alien species into the region. we found that over 1400 seeds from 99 taxa are transported into the Antarctic each field season in association with SANAP passenger luggage and cargo. The first ever assessment of propagule drop-off indicated that 30-50% of these propagules will enter the recipient environment. Many of the taxa include cosmopolitan weeds and known aliens in the Antarctic, indicating that logistics operations form part of a globally self-perpetuating cycle moving alien species between areas of human disturbance. in addition, propagules of some taxa native to the Antarctic region were also found, suggesting that human movements may be facilitating intra-regional homogenization. Several relatively simple changes in biosecurity policy that could significantly reduce the threat of introduction of nonnative species are suggested.

Stable carbon and oxygen isotope ratios of foraminifera in surface sediments of the South China Sea

The relationship between planktonic and benthic foraminiferal stable-isotope values and oceanographic conditions and factors controlling isotopic variations are discussed on the basis of oxygen and carbon isotopic analyses of 192 modern surface and Last Glacial Maximum (LGM) samples from the South China Sea (SCS). The harmonic variation of benthic delta18O in surface sediments with water depth and temperature implies that the temperature is the main factor influencing benthic delta18O variations. Planktonic delta18O fluctuates with sea surface temperature (SST) and salinity (SSS). The N-S temperature gradient results in planktonic delta18O decreasing from the northeast to the south. Cool, saline waters driven by the winter monsoon are interpreted to have been responsible for the high delta18O values in the northeast SCS. The East Asian monsoons not only bring nutrients into the South China Sea and maintain high nutrient concentration levels at the southwestern and northeastern ends, which cause depleted delta13C both in planktonic (surface) and benthic (bottom) samples but also reduce planktonic/benthic delta18O differences. The distribution of delta18O and delta13C in the surface and LGM samples are strikingly similar, indicating that the impact of SST and SSS has been maintained, and nutrient inputs, mainly from the northeastern and southwestern ends, have been controlled by monsoons since the LGM. Comparisons of the modern and LGM delta18O indicate a difference of about 3.6 °C in bottom-water temperature and a large surface-to-bottom temperature gradient during the LGM as compared to today.

Stable carbon and oxygen isotope composition of Late Cretaceous benthic foraminifera from the southern South Atlantic

The stable carbon and oxygen isotope composition of different benthic foraminiferal species of the latest Campanian and earliest Maastrichtian from Ocean Drilling Project Hole 690C (Weddell Sea, southern South Atlantic, ~1800 m paleowater depth) have been investigated. The total range of measured isotope values of all samples exceeds ~4 per mil for delta 13C and 1.1 per mil for delta 18O. Carbon isotope values of proposed deep infaunal species are generally similar or only slightly lower when compared to proposed epifaunal to shallow infaunal species. Interspecific differences vary between samples probably reflecting temporal changes in organic carbon fluxes to the sea floor. Constantly lower delta 13C values for Pullenia marssoni and Pullenia reussi suggest the deepest habitat for these species. The strong depletion of delta 13C values by up to 3 per mil within lenticulinids may be attributed to a deep infaunal microhabitat, strong vital effects, or different feeding strategy when compared to other species or modern lenticulinids. The mean delta 18O values reveal a strong separation of epifaunal to shallow infaunal and deep infaunal species. Epifaunal to shallow infaunal species are characterized by low delta 18O values, deep infaunal species by higher values. This result possibly reflects lower metabolic rates and longer life cycles of deep infaunal species or the operating of a pore water [CO3]2- effect on the benthic foraminiferal stable isotopes. Pyramidina szajnochae shows an enrichment of oxygen isotopes with test size comprising a total of 0.6 per mil between 250 and 1250 µm shell size. Although delta 13C lacks a corresponding trend these data likely represent the presence of changes in metabolic rates during ontogenesis. These results demonstrate the general applicability of multi-species stable isotope measurements of pristine Cretaceous benthic foraminifera to reconstruct past microhabitats and to evaluate biological and environmental effects on the stable isotope composition.