Browsing Faculty of Natural Sciences by Title
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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
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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)