Browsing Faculty of Natural Sciences by Issue Date
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Baker, Gillian; Cowan, Donald A. (Portland Press, 2004)[more][less]
Abstract: Our understanding of thermophile diversity is based predominantly on PCR studies of community DNA. ‘Universal’ and domain-specific rRNA gene PCR primers have historically been used for the assessment of microbial diversity without adequate regard to the degree of specificity of primer pairs to different prokaryotic groups. In a reassessment of the published primers commonly used for ‘universal’ and archaeal 16 S rDNA sequence amplification we note that substantial variations in specificity exist. An unconsidered choice of primers may therefore lead to significant bias in determination of microbial community composition. In particular, Archaea-specific primer sequences typically lack specificity for the Korarchaeota and Nanoarchaea and are often biased towards certain clades. New primer pairs specifically designed for ‘universal’ archaeal 16 S rDNA sequence amplification, with homology to all four archaeal groups, have been designed. Here we present the application of these new primers for preparation of 16 S libraries from thermophile communities. URI: http://hdl.handle.net/10566/144 Files in this item: 1
Baker2004rDNAPrimers.pdf (778.1Kb) -
Cowan, Donald A. (Elsevier, 2004)[more][less]
Abstract: The newly isolated hyperthermophilic archaeal strain 121 grows slowly at 121 8C and even survives short periods at 130 8C. This is another organism that grows best at temperatures well in excess of 100 8C! We should not be astonished so much by the numerical increments but by the biochemical implications of this fact, and we should be excited by the scope provided by this and similar organisms to further our understanding of the evolution and adaptation of molecular structures and systems. And what about the upper limit of life? It appears improbable that the end-point of this search is represented by strain 121. The consensus view is that the true upper limit, where the energetic burden imposed by molecular repair and resynthesis becomes unsustainable, will probably lie in the region of 140–150 8C URI: http://hdl.handle.net/10566/147 Files in this item: 1
CowanUpperTemperature2004.pdf (331.8Kb) -
Vuza, Xolisa; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: We intend adding video messaging and conferencing to Multimodal Telemedicine Intecommunicator (MuTI), a previous system that has already been in place in the target environment. This is to allow a semi-synchronous communication to occur over the Internet Protocol. Videoconferencing can be used to communicate synchronously and video messaging in a store and forward fashion can be used to communicate asynchronously. MuTI supports store and forward of still images, voicemail and text. The system also supports real time communication by means of audio. The aim of this research is to learn how to bridge the digital divide by building applications that are useful and relevant to the users we build for. We are developing this application together with the users of the application in an iterative fashion where we build the prototypes and show the users at each cycle. The feedback that we get from the users plays an important role in building a prototype for the next cycle. The software will be instrumented to provide statistics about the system usage. We are also going to get data from the users by using questionnaires and compare this data with the statistics about software usage to see how much the system has been used and which features in the system do the users like. We are using a rural South African context in conducting this research. We hope to bring about guidelines and recommendations on how to develop applications to bridge the digital divide in a developing world context. URI: http://hdl.handle.net/10566/435 Files in this item: 1
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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) -
Julius, Elroy P.; Tucker, William D. (Telkom, 2004)[more][less]
Abstract: This research aims to find an empirical solution for guaranteeing the delivery of synchronous and asynchronous messages within a semi-synchronous IP-based communication domain. The communication infrastructure that is needed between the Deaf and hearing communities forms the application domain within which the research is situated. SoftBridging is a framework for multi-modal bridging as well as multiuser, multi-modal conversation sessions. An implementation of this concept called SoftBridge, is a communication platform that allows a hearing and Deaf person to communicate inside a single uniform space. The system is based on an asynchronous transport mechanism that makes use of various web services to do the actual data conversions such as voice to text and text to voice. Publish-subscribe systems are an emerging paradigm for building a range of distributed applications. The architecture of publish-subscribe systems make use of Message Oriented Middleware (MOM) to guarantee reliable delivery of messages within a communication domain. We will choose one of these systems and incorporate it within the overall architecture of a SoftBridge system. We will modify the existing architecture of a SoftBridge system to reliably transport synchronous as well as asynchronous data over a synchronous established session. We will use the Session Initiation Protocol (SIP) to establish a synchronous session between various users and a SoftBridge system. The system will then be used as a basis for developing a Deaf telephony application that guarantees the delivery of messages no matter the synchrony. URI: http://hdl.handle.net/10566/463 Files in this item: 1
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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) -
Ah Tow, Lemese; Cowan, Donald A. (Springer Verlag, 2005)[more][less]
Abstract: Continental Antarctic is perceived as a largely pristine environment, although certain localized regions (e.g., parts of the Ross Dependency Dry Valleys) are relatively heavy impacted by human activities. The procedures imposed on Antarctic field parties for the handling and disposal of both solid and liquid wastes are designed to minimise eutrofication and contamination (particularly by human enteric bacteria). However, little consideration has been given to the significance, if any, of less obvious forms of microbial contamination resulting from periodic human activities in Antarctica. The predominant commensal microorganism on human skin, Staphylococcus epidermidis, could be detected by PCR, in Dry Valley mineral soils collected from heavily impacted areas, but could not be detected in Dry Valley mineral soils collected from low impact and pristine areas. Cell viability of this non-enteric human commensal is rapidly lost in Dry Valley mineral soil. However, S. epidermidis can persist for long periods in Dry Valley mineral soil as non-viable cells and/or naked DNA. URI: http://hdl.handle.net/10566/146 Files in this item: 1
AhTowDissemination2005.pdf (393.6Kb) -
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) -
Adesemowo, A. Kayode; Tucker, William D. (SAICSIT in association with ACM, 2005)[more][less]
Abstract: Text communication can be perceived as lacking in chat spontaneity, or plastic, due to medium limitations during interaction. A form of text messaging, Instant Messaging (IM), is now on the uptake, even on mobile handhelds. This paper presents results of using affective gesture to rubberise IM chat in order to improve synchronous communication spontaneity. The experimental design makes use of a text-only IM tool, running on handhelds, built with the Session Initiation Protocol (SIP) and the SIP Instant Messaging and Presence Leveraging Extensions (SIMPLE). The tool was developed with a novel user-defined hotkey – a one-click context menu that fast-tracks the creation and transmission of text-gestures and emoticons. A hybrid quantitative and qualitative approach was taken in order to enable data triangulation. Data collected from user trials affirms that the affective gesture hotkey facility improves chat responsiveness, thus enhancing chat spontaneity. URI: http://hdl.handle.net/10566/464 Files in this item: 1
AdesemowoTuckerInstantMessaging2005.pdf (364.4Kb) -
Hersh, Marion A.; Tucker, William D. (Elsevier, 2005)[more][less]
Abstract: There are a number of pressures on researchers in academia and industry to behave unethically or compromise their ethical standards, for instance in order to obtain funding or publish frequently. In this paper a case study of Deaf telephony is used to discuss the pressures to unethical behaviour in terms of withholding information or misleading participants that can result from mono-disciplinary orthodoxies. The Deaf telephony system attempts to automate multiple aspects of relayed communication between Deaf and hearing users. The study is analysed in terms of consequentialist and deontological ethics, as well as multi-loop action learning. Discussion of a number of examples of bad practice is used to indicate both the compatibility of ethical behaviour and good scientific method and that ethical behaviour is a pre-requisite for obtaining meaningful results. URI: http://hdl.handle.net/10566/466 Files in this item: 1
HershTuckerUnethicalBehaviour2005.pdf (86.66Kb) -
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) -
Julius, Elroy P.; Tucker, William D. (Telkom, 2005)[more][less]
Abstract: This paper presents an empirical solution for guaranteeing the delivery of synchronous and asynchronous messages within a semi-synchronous IPbased communication domain. The communication infrastructure that is needed between Deaf and hearing communities forms the application domain within which the research is situated. SoftBridging is a framework for multi-modal bridging as well as multi-user, multi-modal conversation sessions. An implementation of this concept called SoftBridge for Instant Messaging Bridging Application (SIMBA), is a communication platform that allows a hearing and Deaf person to communicate inside a single uniform space. The system makes use of various web services to do the actual data conversions such as voice to text and text to voice. Publish-subscribe systems are an emerging paradigm for building a range of distributed applications. The architecture of publishsubscribe systems make use of Message Oriented Middleware (MOM) to guarantee reliable delivery of messages within a communication domain. We have incorporated a publish-subscribe system within the overall architecture of SIMBA. We have thus modified the existing architecture of SIMBA to reliably transport semi-synchronous data over a synchronous established session. We have chosen to use the Session Initiation Protocol (SIP) for the establishment of a synchronous session between various users and SIMBA. The system is currently being used as a basis for developing a Deaf telephony application that guarantees the delivery of messages no matter the synchrony. URI: http://hdl.handle.net/10566/509 Files in this item: 1
JuliusTuckerSoftBridging2005.pdf (589.9Kb) -
Cowan, Donald A.; Stafford, William (ASM Press, 2007)[more][less]
URI: http://hdl.handle.net/10566/126 Files in this item: 1
CowanMetagenomicMethods2007.pdf (432.7Kb) -
Yi, Long; Connan, James (Association for Computing Machinery, 2007)[more][less]
Abstract: Self-tuning has been an elusive goal for operating systems and is becoming a pressing issue for modern operating systems. Well-trained system administrators are able to tune an operating system to achieve better system performance for a specific system class. Unfortunately, the system class can change when the running applications change. Our model for self-tuning operating system is based on a monitor-classify-adjust loop. The idea of this loop is to continuously monitor certain performance metrics, and whenever these change, the system determines the new system class and dynamically adjusts tuning parameters for this new class. This paper describes KernTune, a prototype tool that identifies the system class and improves system performance automatically. A key aspect of KernTune is the notion of Artificial Intelligence (AI) oriented performance tuning. It uses a support vector machine (SVM) to identify the system class, and tunes the operating system for that specific system class. This paper presents design and implementation details for KernTune. It shows how KernTune identifies a system class and tunes the operating system for improved performance. URI: http://hdl.handle.net/10566/53 Files in this item: 1
Yi_KernTune(2007).pdf (262.3Kb) -
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) -
Ma, Zhen Yu; Tucker, William D. (Telkom, 2007)[more][less]
Abstract: The South African Deaf community has very limited telephony options. They prefer to communicate in sign language, a visual medium. Realtime video over Internet Protocol is a promising option, but in reality, the quality is often not enough for the Deaf to be able to understand each other’s sign language. Furthermore, these applications were not design specifically for the Deaf. This paper introduces an asynchronous video chat system to provide better quality video at the expense of increased latency. It determined a codec/transmission protocol combination in the laboratory environment and tested it out with actual Deaf users. This paper will address the results based on comparison between different codecs, transmission protocol on asynchronous video communication for the Deaf. URI: http://hdl.handle.net/10566/486 Files in this item: 1
MaTuckerDeaf2007.pdf (875.1Kb) -
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) -
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) -
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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Yi, Long; Tucker, William D. (Telkom, 2008)[more][less]
Abstract: This paper describes Kiara, an open source SIPbased communication system that provides the building blocks to enable Deaf relay services. We have implemented a prototype that provides real-time text, voice and video to a variety of end user devices over a variety of networks. The work-in-progress concerns the addition of relay services for the Deaf. URI: http://hdl.handle.net/10566/523 Files in this item: 1
YiTuckerKiara2008.pdf (173.6Kb)