An appraisal of secure, wireless grid-enabled data warehousing

In most research, appropriate collections of data play a significant role in aiding decision-making processes. This is more critical if the data is being accessed across organisational barriers. Further, for the data to be mined and analysed efficiently, to aid decision-making processes, it must be harnessed in a suitably-structured fashion. There is, for example, a need to perform diverse data analyses and interpretation of structured (non-personal) HIV/AIDS patient-data from various quarters in South Africa. Although this data does exist, to some extent, it is autonomously owned and stored in disparate data storages, and not readily available to all interested parties. In order to put this data to meaningful use, it is imperative to integrate and store this data in a manner in which it can be better utilized by all those involved in the ontological field. This implies integration of (and hence, interoperability), and appropriate accessibility to, the information systems of the autonomous organizations providing data and data-processing. This is a typical problem-scenario for a Virtual Inter-Organisational Information System (VIOIS), proposed in this study. The VIOIS envisaged is a hypothetical, secure, Wireless Grid-enabled Data Warehouse (WGDW) that enables IOIS interaction, such as the storage and processing of HIV/AIDS patient-data to be utilized for HIV/AIDS-specific research. The proposed WDGW offers a methodical approach for arriving at such a collaborative (HIV/AIDS research) integrated system. The proposed WDGW is virtual community that consists mainly of data-providers, service-providers and information-consumers. The WGDW-basis resulted from systematic literaturesurvey that covered a variety of technologies and standards that support datastorage, data-management, computation and connectivity between virtual community members in Grid computing contexts. A Grid computing paradigm is proposed for data-storage, data management and computation in the WGDW. Informational or analytical processing will be enabled through data warehousing while connectivity will be attained wirelessly (for addressing the paucity of connectivity infrastructure in rural parts of developing countries, like South Africa)

An appraisal of secure, wireless grid-enabled data warehousing

In most research, appropriate collections of data play a significant role in aiding decision-making processes. This is more critical if the data is being accessed across organisational barriers. Further, for the data to be mined and analysed efficiently, to aid decision-making processes, it must be harnessed in a suitably-structured fashion. There is, for example, a need to perform diverse data analyses and interpretation of structured (non-personal) HIV/AIDS patient-data from various quarters in South Africa. Although this data does exist, to some extent, it is autonomously owned and stored in disparate data storages, and not readily available to all interested parties. In order to put this data to meaningful use, it is imperative to integrate and store this data in a manner in which it can be better utilized by all those involved in the ontological field. This implies integration of (and hence, interoperability), and appropriate accessibility to, the information systems of the autonomous organizations providing data and data-processing. This is a typical problem-scenario for a Virtual Inter-Organisational Information System (VIOIS), proposed in this study. The VIOIS envisaged is a hypothetical, secure, Wireless Grid-enabled Data Warehouse (WGDW) that enables IOIS interaction, such as the storage and processing of HIV/AIDS patient-data to be utilized for HIV/AIDS-specific research. The proposed WDGW offers a methodical approach for arriving at such a collaborative (HIV/AIDS research) integrated system. The proposed WDGW is virtual community that consists mainly of data-providers, service-providers and information-consumers. The WGDW-basis resulted from systematic literaturesurvey that covered a variety of technologies and standards that support datastorage, data-management, computation and connectivity between virtual community members in Grid computing contexts. A Grid computing paradigm is proposed for data-storage, data management and computation in the WGDW. Informational or analytical processing will be enabled through data warehousing while connectivity will be attained wirelessly (for addressing the paucity of connectivity infrastructure in rural parts of developing countries, like South Africa)

Identification of differentially expressed genes during lace plant leaf development

Premise of research.The lace plant is an excellent and unique model for studying developmentally regulated programmed cell death (PCD) in plants. Perforations form in highly predictable and easily accessible and distinguishable areas in lace plant leaves. However, little is known about the genes involved in regulation of this PCD or leaf development. In this study, for the first time, a general gene expression profile for lace plant leaf development was investigated.Methodology.A cDNA-amplified fragment length polymorphism involving 64 primer combinations was used for a half-genome analysis of 4666 transcripts. Two hundred and thirty differentially expressed transcript-derived fragments (TDFs) were sequenced. A partial expressed sequence tag (EST) database for window-stage (in which PCD is occurring) leaves was also established. Through a reverse transcription polymerase chain reaction, the possible role of ubiquitin in lace plant PCD was investigated.Pivotal results.Seventy-nine TDFs were successfully annotated. The isolated TDFs and ESTs encoded genes involved in processes such as photosynthesis, biosynthesis pathways, gene regulation, stress responses, defense against pathogens, and PCD, among others. Indirect evidence through ubiquitin transcript levels suggests involvement of proteasome machinery in lace plant development and PCD. This study provides a foundation for selective studies on regulation of lace plant leaf development and PCD

The prevalence, composition and distribution of forageable plant species in different urban spaces in two medium-sized towns in South Africa

Globally, the importance of urban vegetation in the quality and maintenance of life in urban areas is increasingly recognized. As the basis of urban green infrastructure, urban vegetation provides a diversity of ecosystem services, including provisioning services. However, there is limited understanding of the potential of urban vegetation as a supply of forageable resources within urban landscapes. This study examined the prevalence and distribution of forageable plant species across different spaces in the towns of Potchefstroom and Thabazimbi, South Africa. A multi-stage sampling technique was employed for selecting study sites, with a total of 136 plots sampled. In total, 88 plant species (foraged and forageable) were encountered across the sample plots, with almost three-quarters (70%) being indigenous to South Africa. Most of the species had multiple uses, with medicine, food and firewood being the most common uses, in order of frequency. Species cover and richness significantly differed across the urban spaces, being markedly higher in protected areas as compared to other spaces. Moreover, five plant communities were identified, resembling various species uses. Overall, the findings show that the fragmented urban spaces are endowed with a diversity of forageable plant species, with many valuable to particular sectors of urban society, such as foragers. Moreover, the notable number of forageable plant species encountered across the different spaces demonstrates the potential of urban green infrastructure as a supply of provisioning and cultural ecosystem services. This provides the basis for the selection of a diversity of species in urban greening programs for enhancing liveability and overall well-being in urban areas

Overestimates of Survival after HAART: Implications for Global Scale-Up Efforts

Background: Monitoring the effectiveness of global antiretroviral therapy scale-up efforts in resource-limited settings is a global health priority, but is complicated by high rates of losses to follow-up after treatment initiation. Determining definitive outcomes of these lost patients, and the effects of losses to follow-up on estimates of survival and risk factors for death after HAART, are key to monitoring the effectiveness of global HAART scale-up efforts. Methodology/Principal Findings: A cohort study comparing clinical outcomes and risk factors for death after HAART initiation as reported before and after tracing of patients lost to follow-up was conducted in Botswana's National Antiretroviral Therapy Program. 410 HIV-infected adults consecutively presenting for HAART were evaluated. The main outcome measures were death or loss to follow-up within the first year after HAART initiation. Of 68 patients initially categorized as lost, over half (58.8%) were confirmed dead after tracing. Patient tracing resulted in reporting of significantly lower survival rates when death was used as the outcome and losses to follow-up were censored [1-year Kaplan Meier survival estimate 0.92 (95% confidence interval, 0.88–0.94 before tracing and 0.83 (95% confidence interval, 0.79–0.86) after tracing, log rank P<0.001]. In addition, a significantly increased risk of death after HAART among men [adjusted hazard ratio 1.74 (95% confidence interval, 1.05–2.87)] would have been missed had patients not been traced [adjusted hazard ratio 1.41 (95% confidence interval, 0.65–3.05)]. Conclusions/Significance: Due to high rates of death among patients lost to follow-up after HAART, survival rates may be inaccurate and important risk factors for death may be missed if patients are not actively traced. Patient tracing and uniform reporting of outcomes after HAART are needed to enable accurate monitoring of global HAART scale-up efforts

Outcomes of the Botswana national HIV/AIDS treatment programme from 2002 to 2010: a longitudinal analysis

Background Short-term mortality rates among patients with HIV receiving antiretroviral therapy (ART) in sub- Saharan Africa are higher than those recorded in high-income countries, but systematic long-term comparisons have not been made because of the scarcity of available data. We analysed the eff ect of the implementation of Botswana’s national ART programme, known as Masa, from 2002 to 2010. Methods The Masa programme started on Jan 21, 2002. Patients who were eligible for ART according to national guidelines had their data collected prospectively through a clinical information system developed by the Botswana Ministry of Health. A dataset of all available electronic records for adults (≥18 years) who had enrolled by April 30, 2010, was extracted and sent to the study team. All data were anonymised before analysis. The primary outcome was mortality. To assess the eff ect of loss to follow-up, we did a series of sensitivity analyses assuming varying proportions of the population lost to follow-up to be dead. Findings We analysed the records of 126 263 patients, of whom 102 713 had documented initiation of ART. Median follow-up time was 35 months (IQR 14–56), with a median of eight follow-up visits (4–14). 15 270 patients were deemed lost to follow-up by the end of the study. 63% (78 866) of the study population were women; median age at baseline was 34 years for women (IQR 29–41) and 38 years for men (33–45). 10 230 (8%) deaths were documented during the 9 years of the study. Mortality was highest during the fi rst 3 months after treatment initiation at 12·8 deaths per 100 person-years (95% CI 12·4–13·2), but decreased to 1·16 deaths per 100 person-years (1·12–1·2) in the second year of treatment, and to 0·15 deaths per 100 person-years (0·09–0·25) over the next 7 years of follow-up. In each calendar year after the start of the Masa programme in 2002, average CD4 cell counts at enrolment increased (from 101 cells/μL [IQR 44–156] in 2002, to 191 cells/μL [115–239] in 2010). In each year, the proportion of the total enrolled population who died in that year decreased, from 63% (88 of 140) in 2002, to 0·8% (13 of 1599) in 2010. A sensitivity analysis assuming that 60% of the population lost to follow-up had died gave 3000 additional deaths, increasing overall mortality from 8% to 11–13%. Interpretation The Botswana national HIV/AIDS treatment programme reduced mortality among adults with HIV to levels much the same as in other low-income or middle-income countries

A tale of two countries: progress towards UNAIDS 90‐90‐90 targets in Botswana and Australia

UNAIDS 90‐90‐90 targets and Fast‐Track commitments are presented as precursors to ending the AIDS epidemic by 2030, through effecting a 90% reduction in new HIV infections and AIDS‐related deaths from 2010 levels (HIV epidemic control). Botswana, a low to middle‐income country with the third‐highest HIV prevalence, and Australia, a low‐prevalence high‐income country with an epidemic concentrated among men who have sex with men (MSM), have made significant strides towards achieving the UNAIDS 90‐90‐90 targets. These two countries provide lessons for different epidemic settings. This paper discusses the lessons that can be drawn from Botswana and Australia with respect to their success in HIV testing, treatment, viral suppression and other HIV prevention strategies for HIV epidemic control. Botswana and Australia are on target to achieving the 90‐90‐90 targets for HIV epidemic control, made possible by comprehensive HIV testing and treatment programmes in the two countries. As of 2015, 70% of all people assumed to be living with HIV had viral suppression in Botswana and Australia. However, HIV incidence remains above one per cent in the general population in Botswana and in MSM in Australia. The two countries have demonstrated that rapid HIV testing that is accessible and targeted at key and vulnerable populations is required in order to continue identifying new HIV infections. All citizens living with HIV in both countries are eligible for antiretroviral therapy (ART) and viral load monitoring through government‐funded programmes. Notwithstanding their success in reducing HIV transmission to date, programmes in both countries must continue to be supported at current levels to maintain epidemic suppression. Scaled HIV testing, linkage to care, universal ART, monitoring patients on treatment over and above strengthened HIV prevention strategies (e.g. male circumcision and pre‐exposure prophylaxis) will all continue to require funding. The progress that Botswana and Australia have made towards meeting the 90‐90‐90 targets is commendable. However, in order to reduce HIV incidence significantly towards 2030, there is a need for sustained HIV testing, linkage to care and high treatment coverage. Botswana and Australia provide useful lessons for developing countries with generalized epidemics and high‐income countries with concentrated epidemics

What do the Universal Test and Treat Trials tell us about the path to HIV epidemic control?

Introduction Achieving HIV epidemic control globally will require new strategies to accelerate reductions in HIV incidence and mortality. Universal test and treat (UTT) was evaluated in four randomized population‐based trials (BCPP/Ya Tsie, HPTN 071/PopART, SEARCH, ANRS 12249/TasP) conducted in sub‐Saharan Africa (SSA) during expanded antiretroviral treatment (ART) eligibility by World Health Organization guidelines and the UNAIDS 90‐90‐90 campaign. Discussion These three‐year studies were conducted in Botswana, Zambia, Uganda, Kenya and South Africa in settings with baseline HIV prevalence from 4% to 30%. Key observations across studies were: (1) Universal testing (implemented via a variety of home and community‐based testing approaches) achieved >90% coverage in all studies. (2) When coupled with robust linkage to HIV care, rapid ART start and patient‐centred care, UTT achieved among the highest reported population levels of viral suppression in SSA. Significant gains in population‐level viral suppression were made in regions with both low and high baseline population viral load; however, viral suppression gains were not uniform across all sub‐populations and were lower among youth. (3) UTT resulted in marked reductions in community HIV incidence when universal testing and robust linkage were present. However, HIV elimination targets were not reached. In BCPP and HPTN 071, annualized HIV incidence was approximately 20% to 30% lower in the intervention (which included universal testing) compared to control arms (no universal testing). In SEARCH (where both arms had universal testing), incidence declined 32% over three years. (4) UTT reduced HIV associated mortality by 23% in the intervention versus control communities in SEARCH, a study in which mortality was comprehensively measured. Conclusions These trials provide strong evidence that UTT inclusive of universal testing increases population‐level viral suppression and decreases HIV incidence and mortality faster than the status quo in SSA and should be adapted at a sub‐country level as a public health strategy. However, more is needed, including integration of new prevention interventions into UTT, in order to reach UNAIDS HIV elimination targets

Five-year follow up of genotypic resistance patterns in HIV-1 subtype C infected patients in Botswana after failure of thymidine analogue-based regimens

Objective: Our objective was to establish genotypic resistance profiles among the 4% of Batswana patients who experienced virologic failure while being followed within Botswana's National Antiretroviral Treatment Program between 2002 and 2007. Methods: At the beginning of the national program in 2002, almost all patients received stavudine (d4T), together with didanosine (ddI), as part of their first nucleoside reverse transcriptase inhibitor (NRTI)-based regimen (Group 1). In contrast, the standard of care for all patients subsequently enrolled (2002-2007) included zidovudine/lamivudine (ZDV/3TC) (Group 2). Genotypes were analyzed in 26 patients from Group 1 and 37 patients from Group 2. Associations between mutations were determined using Pearson's correlation coefficient and Jaccard's coefficient of similarity. Results: Seventy-eight percent of genotyped patients possessed mutations associated with protease inhibitor (PI) resistance while 87% and 90%, respectively, exhibited mutations associated with NRTIs and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The most frequent PI mutations involving resistance to NFV were L90M (25.2%) and D30N (16.2%), but mutations at positions K45Q and D30N were often observed in tandem (P = 60.5, J = 50; p = 0.002; Group 2) alongside Q61E in 42.8% of patients who received ZDV/3TC. Both major patterns of thymidine analogue mutations, TAM 1 (48%) and TAM 2 (59%), were represented in patients from Group 1 and 2, although M184V was higher among individuals who had initially received ddI (61% versus 40.5%). In contrast, L74V was more frequent among individuals from Group 2 (16.2% versus 7.7%). Differences in regard to NNRTI mutations were also observed between Group 1 and Group 2 patients. Conclusion: Despite a low rate of therapeutic failure (4%) among these patients, those who failed possessed high numbers of resistance mutations as well as novel resistance mutations and/or polymorphisms at sites within reverse transcriptase and protease