Browsing Faculty of Natural Sciences by Title
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Mugabo, Pierre; Els, Ilse; Smith, Johan; Rabie, Helena; Smith, Peter; Mirochnick, Mark; Steyn, Wilhelm; Hall, David; Madsen, Richard; Cotton, Mark F (Health & Medical Publishing Group, 2011)[more][less]
Abstract: Background. No pharmacokinetic data exist for premature infants receiving single-dose nevirapine (sd NVP) for prevention of mother-to-child transmission (MTCT) of HIV. Aim. To describe NVP decay pharmacokinetics in two groups of premature infants - those whose mothers either received or did not receive NVP during labour. Methods. Infants less than 37 weeks' gestation were prospectively enrolled. Mothers received sd NVP during labour if time allowed. Infants received sd NVP and zidovudine. Blood was collected on specified days after birth and NVP concentrations were determined by liquid chromatography-mass spectrometry. Results. Data were obtained from 81 infants, 58 born to mothers who received sd NVP during labour (group I) and 23 to mothers who did not receive NVP (group II). Of the infants 29.6% were small for gestational age (SGA). Median (range) maximum concentration (Cmax), time to reach maximum concentration (Tmax), area under the plasma concentration-time curve (AUC) and halflife (T) were 1 438 (350-3 832) ng/ml, 25h50 (9h40-83h45), 174 134 (22 308-546 408) ng×h/ml and 59.0 (15.4-532.6) hours for group I and 1 535 (635-4 218) ng/ml, 17h35 (7h40-29h), 168 576 (20 268-476 712) ng×h/ml and 69.0 (22.12-172.3) hours for group II. For group II, the median (range) volume of distribution (Vd) and body clearance (Cl) were 1 702.6 (623.7-6 189.8) ml and 34.9 (6.2-163.8) ml/h. The AUC was higher (p=0.006) and Cl lower (p<0.0001) in SGA infants. Plasma concentrations exceeding 100 ng/ml were achieved over 8 days in 78% infants in group I and 70.0% in group II. The MTCT rate was 4.8%. Conclusion. Women in preterm labour often deliver with little advance warning. Our study suggests that NVP dosing of preterm infants as soon as possible after birth without maternal intrapartum dosing may be as effective as combined maternal and infant dosing. URI: http://hdl.handle.net/10566/405 Files in this item: 1
MugaboPrematureMTCT.pdf (503.0Kb) -
Buecher, Emmanuelle; Gibbons, Mark J. (NISC (Pty) Ltd and Taylor& Francis, 2003)[more][less]
Abstract: Diel vertical migration (DVM) of six common species of hydromedusae was investigated during two drogue studies conducted in St Helena Bay on the west coast of South Africa in February 1995. Clytia spp., Obelia spp. and Bougainvillia macloviana, were largely confined to surface waters and did not appear to display any DVM. By contrast, Leuckartiara octona and Euphysa aurata displayed clear DVM and, like Proboscidactyla menoni, were found at greater depths than the other species. The depth distribution and amplitude of migration varied between surveys for most species, so definitive interpretations of patterns could not be made. URI: http://hdl.handle.net/10566/377 Files in this item: 1
BuecherDielVerticalMigration2003.pdf (121.3Kb) -
Clarke, Dylan T.; Paterson, Gordon L. J.; Florence, Wayne K.; Gibbons, Mark J. (Iziko Museums of Cape Town, 2010)[more][less]
Abstract: A new species of Magelonidae, Magelona debeerei sp. nov., is described and illustrated from grab-samples collected at <100moff the southwest coast of Africa. Magelona debeerei sp. nov. has previously been identified from the region as M. papillicornis (Müller, 1858) by Day (1955, 1961, 1967) but differs from M. papillicornis sensu stricto by possessing dorsal medial lobes on chaetigers 4–8 and lateral pouches (Σ configuration) between chaetigers 10 and 11. Three species of Magelona have now been recorded from southern Africa (M. capensis Day, 1961, M. cincta Ehlers, 1908 and M. debeerei sp. nov.), and a key to Magelona from this region is provided. URI: http://hdl.handle.net/10566/245 Files in this item: 1
Clarke et al 2010.pdf (455.5Kb) -
Ah Tow, Lemese; Cowan, Donald A. (Society for General Microbiology, 2003)[more][less]
Abstract: Our results allow us to conclude that there appears to be significant conservation between the tuf genes of Planococcus, Planomicrobium and Staphylococcus spp., and that although the primer set TstaG422/TStag765 has been shown to possess high specificity, its use for the definitive identification of Staphylococcus spp. must be treated with some caution. Description: Published as a "Microbiology Comment": this provides a platform for readers of Microbiology to communicate their personal observations and opinions in a more informal way than through the submission of papers. URI: http://hdl.handle.net/10566/143 Files in this item: 1
AhTow&Cowan2003.PDF (251.5Kb) -
Gibbons, Mark J. (NISC (Pty) Ltd and Taylor& Francis, 1995)[more][less]
Abstract: A total of 24 species of euphausiid was collected during a survey along the South African south coast during January 1992. Communities over the Agulhas Bank were of low diversity and abundance and were dominated by Nycliphanes capensis. Those at the shelf-edge were of high diversity and abundance and were dominated by Euphausia recurI'll and Thysalloessa gregaria. Such high diversity may be maintained by vertical scgregation at night. Few species displayed obvious diel vertical migration, although N. capen sis may be able to maintain itself on the shelf by means of this behaviour. E. recurl'Cl appeared to feed on phytoplankton throughout the water column at night, reflecting the distribution of food. URI: http://hdl.handle.net/10566/374 Files in this item: 1
GibbonsEuphausiid1995.pdf (584.2Kb) -
Gibbons, Mark J.; Buecher, Emmanuelle; Thibault-Botha, Delphine (NISC (Pty) Ltd and Taylor& Francis, 2003)[more][less]
Abstract: The vertical distribution, abundance and size composition of a population of Pleurobrachia pileus was studied during a six-day drogue study conducted off the west coast of South Africa in February 1995. The population was centred in deep water, possibly because of the presence of a potential predator, Beroe sp., at shallower depths. The population of P. pileus failed to display clear patterns of migration, although nocturnal recruitment from deeper water resulted in a deepening of the depth of occupation then. The population was dominated by individuals <4 mm polar diameter, and large animals were confined to the upper water layers. These results are discussed with reference to possible spawning activities. Using published equations relating size to clearance rates, it was estimated that the population could remove up to 27% of integrated mesozooplankton standing stocks, and in excess of 100% (293%) at some depths. URI: http://hdl.handle.net/10566/373 Files in this item: 1
GibbonsPleurobrachia2003.pdf (270.1Kb) -
Barange, M; Macpherson, E; Gibbons, Mark J. (NISC and Taylor & Francis, 1994)[more][less]
Abstract: Information on vertical and horizontal distribution patterns, abundance and morphology of the decapod Pasiphaea semispinosa in the Benguela upwelling system is presented. P. semispinosa is the dominant pelagic decapod in the system, occurring between 19 and 32°S along the mid and inner shelf in concentrations of 10-100•m-2• Although it is more abundant during abated than during active upwelling in the northern Benguela, it would appear to be equally abundant during both upwelling scenarios in the southern Benguela. In the southern Benguela, reproductive females are present during winter and juveniles dominate during active upwelling, but juveniles appear to be more common during abated upwelling in the northern Benguela. The estimates of abundance of P. semispinosa presented in this study are subject to sampling biases attributable to their vertical migratory behaviour and net avoidance capabilities. URI: http://hdl.handle.net/10566/307 Files in this item: 1
GibbonsPasiphaea1994.pdf (692.3Kb) -
Tucker, William D.; Blake, Edwin H.; Marsden, Gary (Telkom, 2004)[more][less]
Abstract: We looked for and found two situations within the South African Digital Divide where constant and severe macro-scale latencies would most likely interfere with the usage of Information and Communication Technology (ICT) solutions. We describe how these systems tend to exhibit both social and technical macro-scale delays. Our experience building bridges for these communities has inspired several innovations with respect to the design, development and measurement of IP communications systems. The main contribution is the Open User Interconnect (OUI) stack, a communications system model that explicitly includes the user in relation to the underlying network. The OUI stack is orthogonal to the Open System Interconnect stack. There are two outcomes from including the user in the model. First, the OUI approach necessitates the adoption of usercentred methods such as Participatory Design and in the case of the South African Digital Divide, the adoption of Action Research principles. The second outcome is a user-centred measurement notion, called Quality of Communication (QoC), that is a macro-scale spin on Quality of Service. QoC explicitly includes the measurement of user behaviour in addition to system metrics. In conclusion, we suggest that these Digital Divide-inspired contributions may be applicable to IP communications system design, development and measurement in general. The paper concludes with a brief dissertation completion plan. URI: http://hdl.handle.net/10566/485 Files in this item: 1
TuckerDigitalDivide2004.pdf (131.4Kb) -
Baker, Gillian; Ah Tow, Lemese; Cowan, Donald A. (Elsevier, 2003)[more][less]
Abstract: PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in ‘pristine’ environments. For ‘pristine’ environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions. URI: http://hdl.handle.net/10566/149 Files in this item: 1
BakerPCRdetection2003.pdf (391.8Kb) -
Naidoo, Vaughn; Tucker, William D. (Telkom, 2001)[more][less]
Abstract: Next Generation Networks use policy-based network management and QoS protocols to provide voice services on IP networks. Large numbers of older equipment still push IP packets. We present several solutions that include legacy equipment into a PBNM and QoS system. A static design uses traffic shaping at the legacy edge. A dynamic solution uses a Quasi-PEP implemented over RSVP and COPS. Preliminary test results are presented for the static solution. Collected data shows that the solution decreases packet loss on the legacy side. URI: http://hdl.handle.net/10566/519 Files in this item: 1
NaidooTuckerNextGenNetworks2001.pdf (59.43Kb) -
Glaser, Meryl; Tucker, William D.; Mashao, Daniel (Telkom, 2004)[more][less]
Abstract: Following on the development of several prototypes, we have built a semi-automated Deaf Telephony prototype on the SoftBridge platform. This prototype relays text and speech between Deaf users on the Internet and hearing users on the telephone system. Previous work with a pilot trial in the laboratory revealed several opportunities for enhancement. We added a Wizard of Oz (WoOz) to replace the poorly performing automatic speech recognition functionality as well as H.323 breakout, more extensive logging and advanced call initiation functionality. In order to trial the current prototype, we initiated an Information and Communication Technology (ICT) training programme with the Deaf Community of Cape Town. Twenty Deaf users participated in the training. In addition to the training, much baseline user data was collected to give an indication of how Deaf users communicate with hearing users as well as how familiar they are with ICT devices and services. The work for the rest of this year requires us to recruit and train a WoOz operator. Subsequent trials will essentially consist of monthly cycles of prototype introduction, training, automated metric and log collection, user feedback and then feature enhancement. Linguistic analyses of the text output of the Deaf users will be analyzed. We hope to refine the SoftBridge prototype to fit the needs of the Deaf and hearing users, from both technical and social viewpoints. We expect that these iterative cycles will continue for some time and will teach us many lessons regarding multi-modal semi-synchronous IP-based communications systems. URI: http://hdl.handle.net/10566/447 Files in this item: 1
GlaserTuckerMashaoDeafTelephony2004.pdf (133.0Kb) -
Cowan, Donald A.; Sayed, Muhammed F.; Tsekoa, Tsepo L.; Cameron, Rory A.; Sewell, B. Trevor (Academy of Science of South Africa (ASSAf), 2004)[more][less]
Abstract: Microbial nitrile hydratases are important industrial enzymes that catalyse the conversion of nitriles to the corresponding amides. Bacillus strain RAPc8 nitrile hydratase has recently been cloned and functionally expressed in E. coli. Here, the purification, crystallization and preliminary X-ray diffraction data of this nitrile hydratase are described. The heterotetrameric enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 30% PEG 400, 0.1 M MES (pH 6.5) and 0.1 M magnesium chloride were selected for X-ray diffraction studies. A data set complete to 2.5 Å was collected under cryoconditions at the in-house X-ray source at the University of the Western Cape. The space group was determined to be primitive tetragonal (P41212) with unit cell dimensions a = 106.61 Å, b = 106.61 Å, c=83.23 Å, = = =90°; with one dimer per asymmetric unit. Solution of the three-dimensional structure via molecular replacement is in progress. URI: http://hdl.handle.net/10566/167 Files in this item: 1
TsekoaPurification2004.pdf (784.0Kb) -
Segers, Vaughn; Connan, James (2009)[more][less]
Abstract: This paper discusses an implementation for gesture recognition using eigenvectors under controlled conditions. This application of eigenvector recognition is trained on a set of defined hand images. Training images are processed using eigen techniques from the OpenCV image processing library. Test images are then compared in real-time. These techniques are outlined below. URI: http://hdl.handle.net/10566/63 Files in this item: 1
Segers_Real2009.pdf (179.9Kb) -
Tucker, William D.; Blake, Edwin H.; Marsden, Gary; Pearson, Murray; Westerveld, Rudi (Telkom, 2007)[more][less]
Abstract: This paper reports on three years of research and fieldwork with a rural wireless Internet Protocol communication project. We built a long-range WiFi network and custom communication software to support a rural telehealth project in the remote Eastern Cape. We report on our work using cellular networks, devices and applications as reference technologies because our users and beneficiaries are very comfortable with them. Of most concern are the technological and contextual issues affecting take up of the systems we designed. The paper intends to provide a summary analysis of our experience so that others in the field can learn from our successes and mistakes with respect to rural Information and Communication Technology for Development (ICT4D) in a South African context. URI: http://hdl.handle.net/10566/487 Files in this item: 1
TuckerIP-Communication2007.pdf (1.427Mb) -
Daniels, Francois; Tucker, William D. (Telkom, 2008)[more][less]
Abstract: This paper presents a fully decentralised peer-topeer voice communication tool intended for use across mobile ad hoc networks (MANET) by distributed groups who desired collaboration. We examined the synergy between MANETs and peer-to-peer virtual overlay networks which allowed the creation of ad hoc applications. One style of communication considered suitable for task oriented distributed group collaboration was push-to-talk. This research was focused on providing a push-to-talk communication platform suitable for deployment across MANETs. The research methodology employed was a proof of concept approach within a classical experimental computer science paradigm. We developed a prototype which used JXTA, a peer-to-peer virtual overlay network, to provide push-to-talk functionality across MANETs. Guaranteed delivery of messages was provided via a peer-to-peer voicemail delivery system. While the system did what intended we show that JXTA had a problem with the efficient delivery of voice samples. URI: http://hdl.handle.net/10566/508 Files in this item: 1
DanielsTuckerMANET2008.pdf (216.0Kb) -
Baker, Gillian; Smith, J.J.; Cowan, Donald A. (Elsevier, 2003)[more][less]
Abstract: The Polymerase Chain Reaction (PCR) has facilitated the detection of unculturable microorganisms in virtually any environmental source and has thus been used extensively in the assessment of environmental microbial diversity. This technique relies on the assumption that the gene sequences present in the environment are complementary to the “universal” primers used in their amplification. The recent discovery of new taxa with 16S rDNA sequences not complementary to standard universal primers suggests that current 16S rDNA libraries are not representative of true prokaryotic biodiversity. Here we re-assess the specificity of commonly used 16S rRNA gene primers and present these data in tabular form designed as a tool to aid simple analysis, selection and implementation. In addition, we present two new primer pairs specifically designed for effective ‘universal’ Archaeal 16S rDNA sequence amplification. These primers are found to amplify sequences from Crenarchaeote and Euryarchaeote type strains and environmental DNA. URI: http://hdl.handle.net/10566/169 Files in this item: 1
BakerReviewReanalysis2003.pdf (969.0Kb) -
Samaai, Toufiek; Gibbons, Mark J.; Kelly, Michelle (Cambridge University Press, 2009)[more][less]
Abstract: The sponge genus Strongylodesma is reviewed and redefined, and now accommodates eight closely related species. The type species of Strongylodesma Le´vi is redescribed and an additional two new species are described from the Indo-Pacific: S. novaecaledoniae sp. nov. and S. tongaensis sp. nov. Several specimens previously identified as species of Batzella (Poecilosclerida: Chondropsidae) have been re-assigned to Strongylodesma, as the new species S. purpureus sp. nov. and S. nigra sp. nov. With the description here of new species from the Pacific Ocean and Caribbean Atlantic, the biogeographical distribution of Strongylodesma now appears to be generally tropical with a subtropical South African component, whereas previously it was only known from South Africa. Although species of Strongylodesma have not previously been recorded from the intermediate locations (Western Indian Ocean, South-east Asia, central west Pacific, and New Zealand), re-evaluation here will facilitate more readily the recognition of taxa in these intermediate regions, if they exist, in the future. The species are not widespread, except perhaps along the south-east coast of South Africa, and where they occur they are not abundant. Species occur over a wide depth range, from the intertidal in Tsitsikamma, South Africa, to 140 m in the Caribbean. URI: http://hdl.handle.net/10566/248 Files in this item: 1
SamaaiRevision2009.pdf (893.7Kb) -
Tucker, William D.; Blake, Edwin H. (International Information Management Corporation, 2008)[more][less]
Abstract: We describe the use of Outcome Mapping to guide the design of a rural telemedicine consultation system in South Africa. While Outcome Mapping was not primarily intended to guide design, we show that it tied in well with a cyclical participatory design method for an Information and Communication Technology for Development project. URI: http://hdl.handle.net/10566/525 Files in this item: 1
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Burton, Stephanie; Cowan, Donald A.; Woodley, John M. (Nature Publishing Group, 2002)[more][less]
Abstract: While the use of enzymes as biocatalysts to assist in the industrial manufacture of fine chemicals and pharmaceuticals has enormous potential, application is frequently limited by evolution-led catalyst traits. The advent of designer biocatalysts, produced by informed selection and mutation through recombinant DNA technology, enables production of process-compatible enzymes. However, to fully realize the potential of designer enzymes in industrial applications, it will be necessary to tailor catalyst properties so that they are optimal not only for a given reaction but also in the context of the industrial process in which the enzyme is applied. URI: http://hdl.handle.net/10566/150 Files in this item: 1
BurtonCowanWoodley2002.pdf (768Kb) -
Poroye, Adeola; Tucker, William D.; Norman, Michael (Telkom, 2009)[more][less]
Abstract: This paper presents work in progress to explore the utility of Near Field Communication technology to secure mobile financial services. The objective is to evaluate the potential of this approach as an upcoming technology for mobile cash transactions. The paper argues that Near Field Communication technology offers a feasible solution and can be integrated into a standard cellular handset to turn it into a contactless smart card. The motivation is to create a new secure way for the unbanked to perform financial transactions. A prototype has been developed and tested with participants in a laboratory environment. This paper also reports on preliminary results. URI: http://hdl.handle.net/10566/540 Files in this item: 1