Trust on the semantic web
- Authors: Cloran, Russell Andrew
- Date: 2007 , 2006-08-07
- Subjects: Semantic Web , RDF (Document markup language) , XML (Document markup language) , Knowledge acquisition (Expert systems) , Data protection
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4649 , http://hdl.handle.net/10962/d1006616 , Semantic Web , RDF (Document markup language) , XML (Document markup language) , Knowledge acquisition (Expert systems) , Data protection
- Description: The Semantic Web is a vision to create a “web of knowledge”; an extension of the Web as we know it which will create an information space which will be usable by machines in very rich ways. The technologies which make up the Semantic Web allow machines to reason across information gathered from the Web, presenting only relevant results and inferences to the user. Users of the Web in its current form assess the credibility of the information they gather in a number of different ways. If processing happens without the user being able to check the source and credibility of each piece of information used in the processing, the user must be able to trust that the machine has used trustworthy information at each step of the processing. The machine should therefore be able to automatically assess the credibility of each piece of information it gathers from the Web. A case study on advanced checks for website credibility is presented, and the site presented in the case presented is found to be credible, despite failing many of the checks which are presented. A website with a backend based on RDF technologies is constructed. A better understanding of RDF technologies and good knowledge of the RAP and Redland RDF application frameworks is gained. The second aim of constructing the website was to gather information to be used for testing various trust metrics. The website did not gain widespread support, and therefore not enough data was gathered for this. Techniques for presenting RDF data to users were also developed during website development, and these are discussed. Experiences in gathering RDF data are presented next. A scutter was successfully developed, and the data smushed to create a database where uniquely identifiable objects were linked, even where gathered from different sources. Finally, the use of digital signature as a means of linking an author and content produced by that author is presented. RDF/XML canonicalisation is discussed in the provision of ideal cryptographic checking of RDF graphs, rather than simply checking at the document level. The notion of canonicalisation on the semantic, structural and syntactic levels is proposed. A combination of an existing canonicalisation algorithm and a restricted RDF/XML dialect is presented as a solution to the RDF/XML canonicalisation problem. We conclude that a trusted Semantic Web is possible, with buy in from publishing and consuming parties.
- Full Text:
- Date Issued: 2007
- Authors: Cloran, Russell Andrew
- Date: 2007 , 2006-08-07
- Subjects: Semantic Web , RDF (Document markup language) , XML (Document markup language) , Knowledge acquisition (Expert systems) , Data protection
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4649 , http://hdl.handle.net/10962/d1006616 , Semantic Web , RDF (Document markup language) , XML (Document markup language) , Knowledge acquisition (Expert systems) , Data protection
- Description: The Semantic Web is a vision to create a “web of knowledge”; an extension of the Web as we know it which will create an information space which will be usable by machines in very rich ways. The technologies which make up the Semantic Web allow machines to reason across information gathered from the Web, presenting only relevant results and inferences to the user. Users of the Web in its current form assess the credibility of the information they gather in a number of different ways. If processing happens without the user being able to check the source and credibility of each piece of information used in the processing, the user must be able to trust that the machine has used trustworthy information at each step of the processing. The machine should therefore be able to automatically assess the credibility of each piece of information it gathers from the Web. A case study on advanced checks for website credibility is presented, and the site presented in the case presented is found to be credible, despite failing many of the checks which are presented. A website with a backend based on RDF technologies is constructed. A better understanding of RDF technologies and good knowledge of the RAP and Redland RDF application frameworks is gained. The second aim of constructing the website was to gather information to be used for testing various trust metrics. The website did not gain widespread support, and therefore not enough data was gathered for this. Techniques for presenting RDF data to users were also developed during website development, and these are discussed. Experiences in gathering RDF data are presented next. A scutter was successfully developed, and the data smushed to create a database where uniquely identifiable objects were linked, even where gathered from different sources. Finally, the use of digital signature as a means of linking an author and content produced by that author is presented. RDF/XML canonicalisation is discussed in the provision of ideal cryptographic checking of RDF graphs, rather than simply checking at the document level. The notion of canonicalisation on the semantic, structural and syntactic levels is proposed. A combination of an existing canonicalisation algorithm and a restricted RDF/XML dialect is presented as a solution to the RDF/XML canonicalisation problem. We conclude that a trusted Semantic Web is possible, with buy in from publishing and consuming parties.
- Full Text:
- Date Issued: 2007
Characterisation of Human Hsj1a : an HSP40 molecular chaperone similar to Malarial Pfj4
- Authors: McNamara, Caryn
- Date: 2007
- Subjects: Heat shock proteins , Protein folding , Proteins -- Analysis , Proteins -- Structure , Plasmodium , Malaria , Molecular chaperones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4083 , http://hdl.handle.net/10962/d1007603
- Description: Protein folding, translocation, oligomeric rearrangement and degradation are vital functions to obtain correctly folded proteins in any cell. The constitutive or stress-induced members of each of the heat shock protein (Hsp) families, namely Hsp70 and Hsp40, make up the Hsp70/Hsp40 chaperone system. The Hsp40 J-domain is important for the Hsp70-Hsp40 interaction and hence function. The type-II Hsp40 proteins, Homo sapiens DnaJ 1a (Hsj1a) and Plasmodium falciparum DnaJ 4 (Pfj4), are structurally similar suggesting possible similar roles during malarial infection. This thesis has focussed on identifying whether Hsj1a and Pfj4 are functionally similar in their interaction with potential partner Hsp70 chaperones. Analysis in silico also showed Pfj4 to have a potential chaperone domain, a region resembling a ubiquitin-interacting motif (UIM) corresponding to UIM1 of HsjIa, and another highly conserved region was noted between residues 232-241. The highly conserved regions within the Hsp40 J-domains, and those amino acids therein, are suggested to be responsible for mediating this Hsp70-Hsp40 partner interaction. The thermosensitive dnaJ cbpA Escherichia coli OD259 mutant strain producing type-I Agrobacterium tumefaciens DnaJ (AgtDnaJ) was used as a model heterologous expression system in this study. AgtDnaJ was able to replace the lack of two E coli Hsp40s in vivo, DnaJ and CbpA, whereas AgtDnaJ(H33Q) was unable to. AgtDnaJ-based chimeras containing the swapped J-domains of similar type-II Hsp40 proteins, namely Hsj1Agt and Pfj4Agt, were also able to replace these in E. coli OD259. Conserved J-domain amino acids were identified and were substituted in these chimeras. Of these mutant proteins, Hsj IAgt(L8A), Hsj1Agt(R24A), Hsj1Agt(H31Q), Pfj4Agt(L 11A) and Pfj4Agt(H34Q) were not able to replace the E. coli Hsp40s, whilst Pfj4Agt(Y8A) and Pfj4Agt(R27A) were only able to partially replace them. This shows the leucine of helix I and the histidine of the loop region are key in the in vivo function of both proteins and that the arginine of helix II is key for Hsj1a. The histidine-tagged Hsj1a protein was also successfully purified from the heterologous system. The in vitro stimulated ATPase activity of human Hsp70 by Hsj1a was found to be approximately 14 nmol Pí[subscript]/min/mg, and yet not stimulated by Pfj4, suggesting a possible species-specific interaction is occurring.
- Full Text:
- Date Issued: 2007
- Authors: McNamara, Caryn
- Date: 2007
- Subjects: Heat shock proteins , Protein folding , Proteins -- Analysis , Proteins -- Structure , Plasmodium , Malaria , Molecular chaperones
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4083 , http://hdl.handle.net/10962/d1007603
- Description: Protein folding, translocation, oligomeric rearrangement and degradation are vital functions to obtain correctly folded proteins in any cell. The constitutive or stress-induced members of each of the heat shock protein (Hsp) families, namely Hsp70 and Hsp40, make up the Hsp70/Hsp40 chaperone system. The Hsp40 J-domain is important for the Hsp70-Hsp40 interaction and hence function. The type-II Hsp40 proteins, Homo sapiens DnaJ 1a (Hsj1a) and Plasmodium falciparum DnaJ 4 (Pfj4), are structurally similar suggesting possible similar roles during malarial infection. This thesis has focussed on identifying whether Hsj1a and Pfj4 are functionally similar in their interaction with potential partner Hsp70 chaperones. Analysis in silico also showed Pfj4 to have a potential chaperone domain, a region resembling a ubiquitin-interacting motif (UIM) corresponding to UIM1 of HsjIa, and another highly conserved region was noted between residues 232-241. The highly conserved regions within the Hsp40 J-domains, and those amino acids therein, are suggested to be responsible for mediating this Hsp70-Hsp40 partner interaction. The thermosensitive dnaJ cbpA Escherichia coli OD259 mutant strain producing type-I Agrobacterium tumefaciens DnaJ (AgtDnaJ) was used as a model heterologous expression system in this study. AgtDnaJ was able to replace the lack of two E coli Hsp40s in vivo, DnaJ and CbpA, whereas AgtDnaJ(H33Q) was unable to. AgtDnaJ-based chimeras containing the swapped J-domains of similar type-II Hsp40 proteins, namely Hsj1Agt and Pfj4Agt, were also able to replace these in E. coli OD259. Conserved J-domain amino acids were identified and were substituted in these chimeras. Of these mutant proteins, Hsj IAgt(L8A), Hsj1Agt(R24A), Hsj1Agt(H31Q), Pfj4Agt(L 11A) and Pfj4Agt(H34Q) were not able to replace the E. coli Hsp40s, whilst Pfj4Agt(Y8A) and Pfj4Agt(R27A) were only able to partially replace them. This shows the leucine of helix I and the histidine of the loop region are key in the in vivo function of both proteins and that the arginine of helix II is key for Hsj1a. The histidine-tagged Hsj1a protein was also successfully purified from the heterologous system. The in vitro stimulated ATPase activity of human Hsp70 by Hsj1a was found to be approximately 14 nmol Pí[subscript]/min/mg, and yet not stimulated by Pfj4, suggesting a possible species-specific interaction is occurring.
- Full Text:
- Date Issued: 2007
The effect of geography, cultivation and harvest technique on the umckalin concentration and growth of pelargonium sidoides (Geraniaceae)
- Authors: White, Andrew Graeme
- Date: 2007
- Subjects: Pelargoniums , Geraniaceae , Botany -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Eastern Cape , Medicinal plants -- South Africa -- Eastern Cape , Coumarins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4234 , http://hdl.handle.net/10962/d1003803 , Pelargoniums , Geraniaceae , Botany -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Eastern Cape , Medicinal plants -- South Africa -- Eastern Cape , Coumarins
- Description: Pelargonium sidoides DC. (Geraniaceae) root extracts are used in the Eastern Cape Province of South Africa as a traditional medicine for the treatment of respiratory tract and gastro-intestinal infections. Ethanolic extracts are used globally as herbal treatments for bronchitis, asthma and as an immune system booster. Despite documented exploitation of wild populations by illegal harvesters, this species has not been awarded a protected status. The high level of harvest in the years preceding this study prompted this investigation of the prospects for sustainable root harvest through wild harvest and greenhouse cultivation. A novel method was developed for the purification of umckalin, a bioactive constituent in root extracts, such that the root umckalin concentrations of wild and cultivated plants could be quantified by HPLC. As part of the cultivation experiments, the concentration of umckalin in roots was measured for plants across part of the species’ distribution range in the Eastern Cape Province. This survey revealed that root umckalin concentrations were inversely related to the average annual rainfall of the collection site (r² = 0.94, p = 0.007) and directly related to soil pH (r² = 0.97, p = 0.002). Thus, the possibility of inducing high umckalin concentrations in greenhouse-cultivated plants was investigated by subjecting plants to rapid and prolonged water stress treatments. Two leaf applied hormone treatments (cytokinin and gibberellin) and a root competition treatment with a fast growing annual (Conyza albida) were also investigated based on the potential function of umckalin in P. sidoides plants. These five treatments did not significantly affect root umckalin concentrations compared to well-watered controls. The results of further experiments suggested that umckalin production may have been influenced by the geographical origin and genetics of plants rather than environmental variation. Following wild harvest experiments, the regrowth of replanted shoots from which a standard proportion of the root was harvested showed that water availability affected shoot survival but not root regrowth rate. Regrowth rates were low, questioning the viability of wild harvest. In contrast, greenhouse cultivated plants showed ca. six times greater growth rates, supporting the cultivation of roots to supply future market demand.
- Full Text:
- Date Issued: 2007
- Authors: White, Andrew Graeme
- Date: 2007
- Subjects: Pelargoniums , Geraniaceae , Botany -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Eastern Cape , Medicinal plants -- South Africa -- Eastern Cape , Coumarins
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4234 , http://hdl.handle.net/10962/d1003803 , Pelargoniums , Geraniaceae , Botany -- South Africa -- Eastern Cape , Traditional medicine -- South Africa -- Eastern Cape , Medicinal plants -- South Africa -- Eastern Cape , Coumarins
- Description: Pelargonium sidoides DC. (Geraniaceae) root extracts are used in the Eastern Cape Province of South Africa as a traditional medicine for the treatment of respiratory tract and gastro-intestinal infections. Ethanolic extracts are used globally as herbal treatments for bronchitis, asthma and as an immune system booster. Despite documented exploitation of wild populations by illegal harvesters, this species has not been awarded a protected status. The high level of harvest in the years preceding this study prompted this investigation of the prospects for sustainable root harvest through wild harvest and greenhouse cultivation. A novel method was developed for the purification of umckalin, a bioactive constituent in root extracts, such that the root umckalin concentrations of wild and cultivated plants could be quantified by HPLC. As part of the cultivation experiments, the concentration of umckalin in roots was measured for plants across part of the species’ distribution range in the Eastern Cape Province. This survey revealed that root umckalin concentrations were inversely related to the average annual rainfall of the collection site (r² = 0.94, p = 0.007) and directly related to soil pH (r² = 0.97, p = 0.002). Thus, the possibility of inducing high umckalin concentrations in greenhouse-cultivated plants was investigated by subjecting plants to rapid and prolonged water stress treatments. Two leaf applied hormone treatments (cytokinin and gibberellin) and a root competition treatment with a fast growing annual (Conyza albida) were also investigated based on the potential function of umckalin in P. sidoides plants. These five treatments did not significantly affect root umckalin concentrations compared to well-watered controls. The results of further experiments suggested that umckalin production may have been influenced by the geographical origin and genetics of plants rather than environmental variation. Following wild harvest experiments, the regrowth of replanted shoots from which a standard proportion of the root was harvested showed that water availability affected shoot survival but not root regrowth rate. Regrowth rates were low, questioning the viability of wild harvest. In contrast, greenhouse cultivated plants showed ca. six times greater growth rates, supporting the cultivation of roots to supply future market demand.
- Full Text:
- Date Issued: 2007
Constructing a low-cost, open-source, VoiceXML
- Authors: King, Adam
- Date: 2007 , 2013-07-01
- Subjects: VoiceXML (Document markup language) , Asterisk (Computer file) , Internet telephony , Open source software
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4585 , http://hdl.handle.net/10962/d1004735 , VoiceXML (Document markup language) , Asterisk (Computer file) , Internet telephony , Open source software
- Description: Voice-enabled applications, applications that interact with a user via an audio channel, are used extensively today. Their use is growing as speech related technologies improve, as speech is one of the most natural methods of interaction. They can provide customer support as IVRs, can be used as an assistive technology, or can become an aural interface to the Internet. Given that the telephone is used extensively throughout the globe, the number of potential users of voice-enabled applications is very high. VoiceXML is a popular, open, high-level, standard means of creating voice-enabled applications which was designed to bring the benefits of web based development to services. While VoiceXML is an ideal language for creating these applications, VoiceXML gateways, the hardware and software responsible for interpreting VoiceXML applications and interfacing with the PSTN, are still expensive and so there is a need for a low-cost gateway. Asterisk, and open-source, TDM/VoIP telephony platform, can be used as a low-cost PSTN interface. This thesis investigates adding a VoiceXML service to Asterisk, creating a low-cost VoiceXML prototype gateway which is able to render voice-enabled applications. Following the Component-Based Software Engineering (CBSE) paradigm, the VoiceXML gateway is divided into a set of components which are sourced from the open-source community, and integrated to create the gateway. The browser requires a VoiceXML interpreter (OpenVXI), a Text-To-Speech engine (Festival) and a speech recognition engine (Sphinx 4). The integration of the components results in a low-cost, open-source VoiceXML gateway. System tests show that the integration of the components was successful, and that the system can handle concurrent calls. A fully compliant version of the gateway can be used in the real world to render voice-enabled applications at a low cost. , KMBT_363 , Adobe Acrobat 9.55 Paper Capture Plug-in
- Full Text:
- Date Issued: 2007
- Authors: King, Adam
- Date: 2007 , 2013-07-01
- Subjects: VoiceXML (Document markup language) , Asterisk (Computer file) , Internet telephony , Open source software
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4585 , http://hdl.handle.net/10962/d1004735 , VoiceXML (Document markup language) , Asterisk (Computer file) , Internet telephony , Open source software
- Description: Voice-enabled applications, applications that interact with a user via an audio channel, are used extensively today. Their use is growing as speech related technologies improve, as speech is one of the most natural methods of interaction. They can provide customer support as IVRs, can be used as an assistive technology, or can become an aural interface to the Internet. Given that the telephone is used extensively throughout the globe, the number of potential users of voice-enabled applications is very high. VoiceXML is a popular, open, high-level, standard means of creating voice-enabled applications which was designed to bring the benefits of web based development to services. While VoiceXML is an ideal language for creating these applications, VoiceXML gateways, the hardware and software responsible for interpreting VoiceXML applications and interfacing with the PSTN, are still expensive and so there is a need for a low-cost gateway. Asterisk, and open-source, TDM/VoIP telephony platform, can be used as a low-cost PSTN interface. This thesis investigates adding a VoiceXML service to Asterisk, creating a low-cost VoiceXML prototype gateway which is able to render voice-enabled applications. Following the Component-Based Software Engineering (CBSE) paradigm, the VoiceXML gateway is divided into a set of components which are sourced from the open-source community, and integrated to create the gateway. The browser requires a VoiceXML interpreter (OpenVXI), a Text-To-Speech engine (Festival) and a speech recognition engine (Sphinx 4). The integration of the components results in a low-cost, open-source VoiceXML gateway. System tests show that the integration of the components was successful, and that the system can handle concurrent calls. A fully compliant version of the gateway can be used in the real world to render voice-enabled applications at a low cost. , KMBT_363 , Adobe Acrobat 9.55 Paper Capture Plug-in
- Full Text:
- Date Issued: 2007