Browsing Faculty of Natural Sciences by Title
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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
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Pagaling, Eulyn; Haigh, Richard D.; Grant, William D.; Cowan, Donald A.; Jones, Brian; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun (BioMed Central, 2007)[more][less]
Abstract: Background: We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus. Results: Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content of ~65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained. Conclusion: The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system. URI: http://hdl.handle.net/10566/140 Files in this item: 1
PagalingSequenceAnalysis2007.PDF (1.860Mb) -
Wu, Wilson; Radovanovic, Aleksandar; Tucker, William D. (Telkom, 2005)[more][less]
Abstract: This paper presents an innovative use of the Session Initiation Protocol (SIP) for the subscription and notification of geographic information in order to provide a privacy concerned location-based service. SIP is a signaling protocol used for establishing sessions in an IP network. It has been widely used for Internet conferencing and telephony. This research project aims to enhance the SIP presence model in order to protect sensitive geographic information. To achieve this goal, we thoroughly analyzed existing Location-Based Services (LBS), reviewed LBS designs’ pitfalls and identified several key privacy requirements. Based on this research, we presented a SIP flow that meets the privacy requirements. This SIP message flow includes SUBSCRIBE, NOTIFY and PUBLISH messages. A data format to carry geographic location information has also been introduced. The data format is based on Presence Information Data Format (PIDF). We define it as Location-enhanced PIDF, or LPIDF. LPIDF contains geographical information objects. We hope that the outcome of this research project will provide rich, convenient, privacy concerned architecture for LBS. Because LPIDF is based on SIP, this approach can be easily integrated into IP telephony services. LPIDF enables personalization of the Location-Based services address user privacy concerns and hereby increase their satisfaction. URI: http://hdl.handle.net/10566/494 Files in this item: 1
WuRadovanovicTuckerSIP2005.pdf (385.7Kb) -
Kobo, Hlabishi Isaac; Tucker, William D. (IIMC International Information Management Corporation, 2012)[more][less]
Abstract: This paper describes a situation-aware algorithm based on the current situation of a mesh network with mobile nodes that improves quality of service. After running laboratory performance tests, we concluded that a situation-aware mesh routing protocol offers potential to address issues pertaining to mobility, congestion and scalability in dynamic mesh networks with mobile nodes. Such networks appear promising to provide connectivity to people living in rural areas in developing regions of Africa, and can be easily interconnected to telco-styled networks through gateways for voice and Internet services. Such services can remain free in the mesh, yet can also be billed for interconnection. Our vision offers an attractive business model for up scaling a rural customer base for telcos, while at the same time offering increased quality of service for mobile users on rural mesh networks. URI: http://hdl.handle.net/10566/585 Files in this item: 1
KoboTuckerISTAfrica2012.pdf (465.0Kb) -
Roro, Zukile; Rey-Moreno, Carlos; Tucker, William D.; Siya, Masbulele Jay (Telkom, 2012)[more][less]
Abstract: This paper describes work in progress towards developing a business case and preliminary design for an 802.11-based mesh network in the remote rural community of Mankosi in the Eastern Cape province of South Africa. Aside from the technical challenges to building the network to be sustainable in the long term, this network needs to generate some revenue. Hence, there needs to be a business model that has revenue generation potential. This study will explore the economical and social aspects of voice over Internet- Protocol as a service for this community. After talking to the village leaders, we learned that there is a demand for telecommunication services and that most of them were interested only in telephony service. Very few villagers were interested in or had any knowledge about the Internet. We also learned that most of their cellular phone calls are local within the Mankosi community. This allows us to deploy an experimental local telephony service; a perfect opportunity for a low-cost and lowcosting inverse mesh infrastructure that can easily be connected to breakout and Internet services in the future. URI: http://hdl.handle.net/10566/594 Files in this item: 1
RoroRey-MorenoTuckerSiya-SATNAC2012.pdf (150.8Kb) -
Lewis, John; Tucker, William D.; Blake, Edwin H. (Telkom, 2003)[more][less]
Abstract: Instant Messaging is traditionally a text only a air. However, there are instances when it would be useful to bridge to other types of media, like speech. The SoftBridge is an application framework that enables this kind of communications bridging using instant messages. Its use of protocols like the Jabber Instant Messaging Protocol and the Simple Object Access Protocol makes it simple, open and extensible. It also allows bridging to non IP communications infrastructure, like the telephone network. We describe the design and architecture of the system, protocol and extensibility mechanism. Finally we describe our experimental methodology and discuss the results of our initial experiments. URI: http://hdl.handle.net/10566/537 Files in this item: 1
LewisTuckerBlakeInstantMessaging2003.pdf (202.4Kb) -
Lewis, John; Tucker, William D.; Blake, Edwin H. (Telkom, 2002)[more][less]
Abstract: Users and computing equipment have varying capabilities that include the abilities to exchange text and audio, engage in high bandwidth communication, etc. As the technological options increase, e ective communication between the di erent media has be able to bridge across these options: the bridges have to take into account network quality, end-user equipment capabilities as well as user preferences and capabilities. Our research proposes a Soft- Bridge, an abstracted communications platform for the construction of applications across disparate capabilities found in various Digital Divides. We outline the architecture and the requirements that the SoftBridge has to ful ll. An approach and some initial work is described. URI: http://hdl.handle.net/10566/606 Files in this item: 1
LewisTuckerBlake-SATNAC2002.pdf (126.3Kb) -
Tucker, William D.; Glaser, Meryl; Lewis, John (Telkom, 2003)[more][less]
Abstract: Following on several partial prototypes, we built an automated Deaf Telephony bridging application with the SoftBridge platform. The SoftBridge performs multi-modal bridging in real-time using Text-to-Speech (TTS) and Automatic Speech Recognition (ASR) utilities accessed via web services. To perform Action Research with the Deaf community in Cape Town, we invited a Deaf user (DU) to participate in a pilot study. We conducted three tests varying the input/output modalities of the hearing user (HU). The DU had a standard text in/text out Instant Messaging client. The HU client used the following specific modality combinations: Text & TTS in/Text out, TTS in/Text out and TTS in/Text & ASR out. The SoftBridge logged the conversations for subsequent analysis. The trial showed a largely successful conversation. Success factors include a) a text and computer literate DU who is familiar with research practise, b) using the system to explain the research as we conducted it and c) that the multi-modal bridging capabilities overcame the expected shortcomings of TTS and especially ASR. The lessons learned from this trial will be applied to the next trial once the necessary modifications have been implemented. URI: http://hdl.handle.net/10566/535 Files in this item: 1
TuckerDeafTelephony2003.pdf (108.8Kb) -
Sun, Tao; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: We have built a SoftBridge prototype within a JAIN (Java APIs for the Integrated Network) SLEE (Service Logic Execution Environment). A SoftBridge is a semi-synchronous multimodal IP (Internet Protocol) -based communication system and the first prototype has been built for deaf telephony. This research addresses service life-cycle management for a SoftBridge with carrier grade reliability. An approach is proposed that carrier grade reliability support for a SoftBridge is provided by moving it into a JAIN SLEE. A JAIN SLEE is a general application server, which provides execution and management environment for telecommunication services. An empirical evaluation methodology is adopted to verify that JAIN SLEE enables carrier grade support for a SoftBridge. This work includes the development of functions of a SoftBridge and life-cycle management of a SoftBridge within a JAIN SLEE. Current work is busy in developing multimodal media adaptation functions of the SoftBridge prototype. System test, experiments with PBX (Private Branch Exchange)/PSTN (Public Switched Telephone Network) and evaluation of the SoftBridge prototype will be carried out in the next steps. Carrier grade reliability enables a SoftBridge to access the PSTN. A highly reliable SoftBridge could bring more new value-added services for telecom providers. Using a SoftBridge as an example, we also can learn how to go about carrier grade enhancement for IP-based communication applications in the telecoms domain. URI: http://hdl.handle.net/10566/592 Files in this item: 1
SunTucker-SATNAC2004.pdf (66.62Kb) -
Kimani, Serah W.; Agarkar, Vinod B.; Cowan, Donald A.; Sayed, Muhammed F.; Sewell, B. Trevor (International Union of Crystallography, 2007)[more][less]
Abstract: The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase superfamily and catalyzes the conversion of amides to the corresponding carboxylic acids and ammonia. It shows both amide-hydrolysis and acyl-transfer activities and also exhibits stereoselectivity for some enantiomeric substrates, thus making it a potentially important industrial catalyst. The crystal structure of G. pallidus RAPc8 amidase at a resolution of 1.9 A ˚ was solved by molecular replacement from a crystal belonging to the primitive cubic space group P4232. G. pallidus RAPc8 amidase is homohexameric in solution and its monomers have the typical nitrilase-superfamily α-β-β-α fold. Association in the hexamer preserves the eight-layered α-β-β-α:α-β-β-α structure across an interface which is conserved in the known members of the superfamily. The extended carboxy-terminal tail contributes to this conserved interface by interlocking the monomers. Analysis of the small active site of the G. pallidus RAPc8 amidase suggests that access of a water molecule to the catalytic triad (Cys, Glu, Lys) side chains would be impeded by the formation of the acyl intermediate. It is proposed that another active-site residue, Glu142, the position of which is conserved in the homologues, acts as a general base to catalyse the hydrolysis of this intermediate. The small size of the substrate-binding pocket also explains the specificity of this enzyme for short aliphatic amides and its asymmetry explains its enantioselectivity. URI: http://hdl.handle.net/10566/141 Files in this item: 1
KimaniAliphaticAmidase2007.pdf (2.155Mb) -
Ghaziasgar, Mehrdad; Connan, James (2008)[more][less]
Abstract: Current wireless human-computer interaction devices such as wireless mice and touchscreens, by and large, incorporate a sophisticated electronic architecture. The sophistication achieves wireless capabilities but carries over a cost overhead. In this paper we lay the foundation for developing a novel human-computer interaction device with reduced hardware sophistication. We developed a surface acoustic wave touchscreen-type device using only two transducers, as opposed to, typically, three or more transducers in conventional surface acoustic wave touchscreens. The transducers are mounted on a glass surface and connected into the line-in of a stereo sound card. User-initiated taps are detected, analysed and located on the surface, and the mouse cursor is moved to the computed screen location. URI: http://hdl.handle.net/10566/54 Files in this item: 1
Ghaziasgar_Surface(2008).pdf (454.3Kb) -
Felix, Cecil; Maiyalagan, Thandavarayan; Sivakumar, Pasupathi; Linkov, Vladimir (Bentham Science Publishers, 2012)[more][less]
Abstract: IrO2 as an anodic electrocatalyst for the oxygen evolution reaction (OER) in solid polymer electrolyte (SPE) electrolysers was synthesised by adapting the Adams fusion method. Optimisation of the IrO2 electrocatalyst was achieved by varying the synthesis duration (0.5 – 4 hours) and temperature (250 - 500°C). The physical properties of the electrocatalysts were characterised by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and x-ray diffraction (XRD). Electrochemical characterisation of the electrocatalysts toward the OER was evaluated by chronoamperometry (CA). CA analysis revealed the best electrocatalytic activity towards the OER for IrO2 synthesised for 2 hours at 350oC which displayed a better electrocatalytic activity than the commercial IrO2 electrocatalyst used in this study. XRD and TEM analyses revealed an increase in crystallinity and average particle size with increasing synthesis duration and temperature which accounted for the decreasing electrocatalytic activity. At 250°C the formation of an active IrO2 electrocatalyst was not favoured. URI: http://hdl.handle.net/10566/439 Files in this item: 1
FelixElectrocatalyst2012.pdf (3.090Mb) -
Felix, Cecil; Maiyalagan, Thandavarayan; Pasupathi, Sivakumar; Bladergroen, Bernard Jan; Linkov, Vladimir (Electochemical Society Inc., 2012)[more][less]
Abstract: IrO2, IrxRu1-xO2, IrxSnx-1O2 and IrxTax-1O2 (1 ≥ x ≥ 0.7) were synthesized, characterised and evaluated as electrocatalysts for the oxygen evolution reaction in solid polymer electrolyte electrolysers. The electrocatalysts were synthesised by adapting the Adams fusion method. The physical properties of the electrocatalysts were characterised by scanning electron microscopy, transmission electron microscopy and x-ray diffraction. Electrochemical activity of the electrocatalysts toward the oxygen evolution reaction was evaluated by cyclic voltammetry and chronoamperometry. X-ray diffraction revealed no phase separation when RuO2 or SnO2 was introduced into the IrO2 lattice suggesting that solid solutions were formed. Transmission electron microscope analysis revealed nanosize particles for all synthesised metal oxides. Crystallinity increased with the addition of RuO2 and SnO2 while a suppression of crystal growth was observed with the addition of Ta2O5 to IrO2. Chronoamperometry revealed that the addition of all the secondary metal oxides to IrO2 resulted in improved catalytic performance. Ir0.7Ru0.3O2 was identified as the most promising electrocatalyst for the oxygen evolution reaction. Keywords: URI: http://hdl.handle.net/10566/504 Files in this item: 1
FelixOxygenEvolutionReaction2012.pdf (1.464Mb) -
Glaser, Meryl; Tucker, William D. (2004)[more][less]
Abstract: This paper presents a description of telecommunications for Deaf people in South Africa by contrasting the situation in the developed world. We explain the main motivations for providing a locally appropriate solution. Research activity began with a community-based field trial of TTYs. The recommendations of the trial motivated an innovative approach to provide synchronous and accessible relay services. Drawing from international technological developments, we designed a software solution called the SoftBridge. We employ iterative Action Research cycles to drive technological modifications to the SoftBridge and to encourage adoption by the end-user community. URI: http://hdl.handle.net/10566/593 Files in this item: 1
GlaserTucker-CVHI2004.pdf (162.9Kb) -
Chetty, Marshini; Tucker, William D.; Blake, Edwin H. (Telkom, 2004)[more][less]
Abstract: Rural areas in South Africa have unique conditions such as remoteness and scarcity of reliable public facilities. Information and Communication Technologies (ICTs) introduced into these areas must be suitable for these conditions. Using a user-centred design approach based on Participatory Design and Action Research, we have developed a telemedicine application for a rural village in the Eastern Cape. This paper describes how we determined the requirements and design for the application and why we chose Voice over Internet Protocol (VoIP) combined with a store and forward approach to achieve our telemedicine goals. We present an overview of the methodology we are using, describe the software application we have developed and mention several challenges we have faced to date. Finally we conclude that VoIP and store and forward technologies are appropriate to the South African rural situation. URI: http://hdl.handle.net/10566/621 Files in this item: 1
ChettyTuckerBlake-SATNAC2004.pdf (287.0Kb) -
Penton, Jason; Tucker, William D.; Glaser, Meryl (Telkom, 2002)[more][less]
Abstract: We have developed a prototype bridge that relays text and speech between Teldem, a text telephone for the Deaf, and a standard telephone or H.323 endpoint. Telgo323 uses modified H.323 media gateways and open source Text to Speech and Speech to Text software. The approach allows for easy integration of new tools as the technologies mature. This paper presents the design of the implementation prototype, discusses Teldem tone decoding, and suggests directions for future work. The Telgo323 provides evidence that an automated relay bridge is imminently viable for the Deaf Community, and further demonstrates an attractive approach for building bridges over the Digital Divide. URI: http://hdl.handle.net/10566/612 Files in this item: 1
PentonTuckerGlaser-SATNAC2002.pdf (99.60Kb) -
Brierley, Andrew S.; Boyer, David C.; Axelson, Bjorn Erik; Lynam, Christopher P.; Sparks, Conrad A.J.; Boyer, Helen; Gibbons, Mark J. (Inter-Research, 2005)[more][less]
Abstract: Acoustic target strengths (TSs) of the 2 most common large medusae, Chrysaora hysoscella and Aequorea aequorea, in the northern Benguela (off Namibia) have previously been estimated (at 18, 38 and 120 kHz) from acoustic data collected in conjunction with trawl samples, using the ‘comparison method’. These TS values may have been biased because the method took no account of acoustic backscatter from mesozooplankton. Here we report our efforts to improve upon these estimates, and to determine TS additionally at 200 kHz, by conducting additional sampling for mesozooplankton and fish larvae, and accounting for their likely contribution to the total backscatter. Published sound scattering models were used to predict the acoustic backscatter due to the observed numerical densities of mesozooplankton and fish larvae (solving the forward problem). Mean volume backscattering due to jellyfish alone was then inferred by subtracting the model-predicted values from the observed water-column total associated with jellyfish net samples. Zooplankton-corrected echo intensity/jellyfish density data pairs were in close agreement with linear relationships determined previously from uncorrected data. Small sample sizes precluded recalculation of TS, but nonparametric pair-wise tests failed to detect any significant differences between echo intensities for jellyfish densities observed in the present study and echo intensities predicted for those densities by density–intensity relationships arising from the previous study. Previous linear density–intensity relationships had y-axis intercepts greater than zero. On the assumption that the positive intercepts were due to backscatter from unsampled mesozooplankton, new TS relationships were calculated from downward-adjusted density–intensity relationships. New values agreed closely with TS estimates determined elsewhere using single-target echo detection techniques. Given that estimates of jellyfish TS appear robust, it should now be feasible to identify jellyfish acoustically at sea and to assess their abundance, even in the presence of mixed mesozooplankton assemblages. URI: http://hdl.handle.net/10566/247 Files in this item: 1
BrierleyAcoustic2005.pdf (103.7Kb) -
Gibbons, Mark J.; Stuart, V; Verheye, H M (NISC and Taylor & Francis, 1992)[more][less]
Abstract: Carnivorous zooplankton in the Benguela system have tended to be ignored by all but early taxonomists and a handful of recent researchers. An attempt is made here to address the importance of carnivores in this system but, because the database is poor, it was necessary to apply material from outside the region. The taxa covered include ctenophores, cnidarians (Scyphozoa and Hydrozoa, including Siphonophora), chaetognaths and hyperiid amphipods as well as such minor groups as pelagic gastropods and decapods. Most groups of carnivores within the Benguela are represented by only one or two "common" species. These tend to be epiplanktonic and generally concentrated inshore of the shelf-break, where their distributions are influenced by changes in local hydrography. Their densities frequently exceed those of herbivores. The dominant carnivores share a number of attributes: wide-ranging diets, high assimilation and growth efficiencies and mostly a Type I functional response to food concentration. They fall into two categories. The first is the gelatinous species, which have short lifespans and exhibit rapid growth and often massive reproductive response to high concentrations of food. They are patchily distributed and some appear to have behavioural traits that enable them to stay within localized patches of prey on which they may be dependent because of high metabolic costs. In the second category are crustacean predators and chaetognaths which have slower response times to the food environment but may have longer lifespans, lower daily maintenance needs and an ability to store lipids. They are less dependent on high densities of food organisms and can survive throughout winter, when gelatinous predators are rare. The effect of predation on abundance of copepods is estimated on the basis of both published and unpublished data. Should swarms of predators coincide with a critical gateway of zooplankton or larvae, then there may be total depletion. This applies especially to the nearshore zone of the West Coast and to semi-enclosed bays. The role of carnivorous zooplankton in the diets of commercially important fish species is stressed, but their importance in the regeneration of nutrients may be insignificant. URI: http://hdl.handle.net/10566/305 Files in this item: 1
GibbonsTrophicEcology1992.pdf (1.199Mb) -
Gibbons, Mark J.; Hendricks, Martin G. J. (Magnolia Press, 2010)[more][less]
Abstract: Perepsilonema benguelae sp. nov. and Leptepsilonema saldanhae sp. nov. are described and illustrated from coarse sand sediments in Saldanha Bay, along the west coast of South Africa. Perepsilonema benguelae sp. nov. is characterised by a large swollen body in the genital region, the annuli are not clearly orientated into anteriorly and posteriorly directed margins and copulatory thorns are restricted to three pairs in the precloacal region. In Leptepsilonema saldanhae sp. nov. the somatic setae in the pharyngeal region are very long and the first ambulatory setae of the external subventral row are short. Other distinguishing features include the shape of the amphidial fovea and the copulatory apparatus, and the presence of six ventro-lateral copulatory thorns around the cloaca. These descriptions are the first for the family Epsilonematidae from the west coast of South Africa. URI: http://hdl.handle.net/10566/244 Files in this item: 1
HendricksGibbons2010.pdf (245.4Kb)