Prediction of protein secondary structure using binary classificationtrees, naive Bayes classifiers and the Logistic Regression Classifier
- Authors: Eldud Omer, Ahmed Abdelkarim
- Date: 2016
- Subjects: Bayesian statistical decision theory , Logistic regression analysis , Biostatistics , Proteins -- Structure
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5581 , http://hdl.handle.net/10962/d1019985
- Description: The secondary structure of proteins is predicted using various binary classifiers. The data are adopted from the RS126 database. The original data consists of protein primary and secondary structure sequences. The original data is encoded using alphabetic letters. These data are encoded into unary vectors comprising ones and zeros only. Different binary classifiers, namely the naive Bayes, logistic regression and classification trees using hold-out and 5-fold cross validation are trained using the encoded data. For each of the classifiers three classification tasks are considered, namely helix against not helix (H/∼H), sheet against not sheet (S/∼S) and coil against not coil (C/∼C). The performance of these binary classifiers are compared using the overall accuracy in predicting the protein secondary structure for various window sizes. Our result indicate that hold-out cross validation achieved higher accuracy than 5-fold cross validation. The Naive Bayes classifier, using 5-fold cross validation achieved, the lowest accuracy for predicting helix against not helix. The classification tree classifiers, using 5-fold cross validation, achieved the lowest accuracies for both coil against not coil and sheet against not sheet classifications. The logistic regression classier accuracy is dependent on the window size; there is a positive relationship between the accuracy and window size. The logistic regression classier approach achieved the highest accuracy when compared to the classification tree and Naive Bayes classifiers for each classification task; predicting helix against not helix with accuracy 77.74 percent, for sheet against not sheet with accuracy 81.22 percent and for coil against not coil with accuracy 73.39 percent. It is noted that it is easier to compare classifiers if the classification process could be completely facilitated in R. Alternatively, it would be easier to assess these logistic regression classifiers if SPSS had a function to determine the accuracy of the logistic regression classifier.
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- Date Issued: 2016
A psychobiography of Helen Martins
- Authors: Mitchell, Donna Leigh
- Date: 2014
- Subjects: Martins, Helen Elizabeth, 1897-1976 -- Criticism and interpretation , Psychology -- Biographical methods , Women sculptors -- Psychology , Psychohistory , Personality -- Social aspects , Personality -- Age factors , Personality assessment , Personality change
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3204 , http://hdl.handle.net/10962/d1011670 , Martins, Helen Elizabeth, 1897-1976 -- Criticism and interpretation , Psychology -- Biographical methods , Women sculptors -- Psychology , Psychohistory , Personality -- Social aspects , Personality -- Age factors , Personality assessment , Personality change
- Description: Helen Martins devoted approximately the last thirty years of her life to converting her family home into a unique fantasy world which she named the Owl House. Since her death in 1976 the Owl House has become a national monument and museum in South Africa. Throughout her life Helen was considered by most of the surrounding villagers to have been strange, and she withdrew increasingly from society. However, she appeared to have contained a desire for human connection. There are several instances in which she expressed this desire, such as through the numerous letters which she wrote to fellow artists. The existing body of literature on Helen illustrates the complex nature of her personality; however the question of which personality style she best typifies has remained unanswered. In order to answer this question a psychobiography was conducted on Helen. Psychobiographies entail a biographical representation of a person's life history to which a psychological theory is applied. The psychological theory utilised within the current study was Millon's (1969/1996) Biosocial- Learning Theory. Thus, the chief objective of this study was to describe and interpret Helen's personality style through the use of Millon's (1969/1996) Biosocial-Learning Theory. Alexander's model of data extraction and Miles and Huberman's three step approach were implemented in order to reduce, organise and analyse the data. The findings of this study reflected that Helen deteriorated from one of Millon's (1969/1996) proposed personality styles to another as she aged. The current findings may illuminate Helen's motives for obsessively devoting her life to the creation of her fantasy world.
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- Date Issued: 2014
The epibiotic relationship between mussels and barnacles
- Authors: Bell, Caroline Margaret
- Date: 2014
- Subjects: Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5847 , http://hdl.handle.net/10962/d1011460 , Epibiosis , Mussels -- Ecology -- South Africa , Mussels -- Behavior -- South Africa , Mussels -- Habitat -- South Africa , Barnacles -- Ecology -- South Africa , Barnacles -- Behavior -- South Africa , Barnacles -- Habitat -- South Africa , Perna -- Behavior -- South Africa , Mytilus galloprovincialis -- Behavior -- South Africa , Marine biodiversity -- South Africa
- Description: Epibiosis is an ecological relationship that has been described as one of the closest possible associations in marine ecosystems. In the space limited rocky intertidal, mussel beds provide important secondary space for barnacles. The epibiotic relationship between mussels and barnacles on the south-east coast of South Africa was considered at different scales, from large-scale, natural patterns of epibiosis on the rocky shore, to fine-scale settlement choices of barnacles and the effects on the condition and growth rates of individual mussels. Mussel and barnacle assemblages were generally stable over a 12-month period. The tracking of individual mussels with and without barnacle epibionts resulted in a significant increase in mortality rate of mussels with epibionts over 12 months (two-way ANOVA, p = 0.028). Barnacles on rocks, as well as on mussels, were also tracked with no significant effect of substratum on mortality of barnacles (two-way ANOVA, p = 0.119). Prevalence and intensity of barnacle infestations was also examined in relation to coastline topography on two co-occurring mussel species, the indigenous Perna perna and invasive Mytilus galloprovincialis. The results were complex, but bay status had significant effects on prevalence and intensity for both mussel species, depending on the time and zone. The effect of bay in relation to time was particularly relevant for M. galloprovincialis (four-way nested ANOVA, Season X Site(Bay): p = 0.0002), where summer prevalence was higher than that of winter in bays, regardless of zone, while in open coast sites, the effect of season was only significant in the mid zone. Patterns of intensity generally showed higher values in summer. Substratum preference by barnacles was investigated by recording settlement, survival and mortality of Chthamalus dentatus barnacles on various treatments. There was a strong preference for the rock-like plastic substratum by primary settlers (pair-wise tests of PERMANOVA: Dead < Rock mimic (p = 0.0001); Replica < Rock mimic (p = 0.019) and Live < Rock mimic (p = 0.0001)). This indicates that barnacles settle on mussel shells only as a secondary choice and that micro-topography is an important variable in barnacle settlement. The effect of barnacle epibiosis on condition index and growth of P. perna and M. galloprovincialis was also examined as a direct indication of the health of mussels subjected to the biological stress of epibiosis. Although not significant (PERMANOVA: P. perna: p(perm) = 0.890; M. galloprovincialis: p(perm) = 0.395), growth for both mussel species was slower for barnacle-infested individuals in summer, which is the main growing season for mussels in the region. Results from condition index calculations, however, showed no negative impacts of epibiotic barnacles (three-way ANCOVA: P. perna: p = 0.372; M. galloprovincialis: p = 0.762). Barnacle epibionts create a new interface between the mussel and its environment and this interaction can affect other members of the community. The possibility of the barnacle epibiont causing increased drag also needs further investigation. Biological processes operating within a wide range of physical stressors drive the interactions on the rocky shore, such as epibiosis. Overall, the results of this study suggest that the epibiotic relationship between mussels and barnacles on the south-east coast of South Africa does not significantly affect the mussel species present and that barnacles only use mussel shells as a secondary choice of substratum.
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- Date Issued: 2014
Synthesis and evaluation of PGM-selective ligands
- Authors: Gxoyiya, Babalwa Siliziwe Blossom
- Date: 2013-05-28
- Subjects: Platinum group , Ligands , Ligands -- Evaluation
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4450 , http://hdl.handle.net/10962/d1007849 , Platinum group , Ligands , Ligands -- Evaluation
- Description: A series of polydentate POM-selective, sulfur-containing amide ligands have been synthesized from ro-dibromoalkanes and mercaptoacetanilide, The resulting 3,6- dithiaoctanediamides and 3,7-dithianonanediamides, some of which contain a polymerisable group, were all characterized by high-resolution MS, IR, I Hand I3C NMR spectroscopic methods. Various approaches to the polymerisable ligands were explored, the most efficient proving to be the incorporation of an allyl ether moiety in the mercaptoacetanilide. The corresponding Pd(U) and Pt(II) complexes were also prepared from the metal chloride salts and characterized by elemental analysis and spectroscopic methods. The NMR data indicates that both the cis- and transcomplexes were formed, while the IR data indicates cis- coordination of the chlorine . ligands. Molecularly imprinted polymers (MIP's), prepared using platinum(II) mercaptoacetanilide and 3,6-dithiadiamide complexes, showed high selectivity for , , palladium(II) [in the presence of Pt(II), CoCII), Cu(II) and Ni(II)] as determined by . ICP-MS analysis. The more kinetically inert Pt(II) ions however, slowly displaced Pd(II), confirming the Pt(II) selectivity of the MIP's. Solvent extraction studies were conducted to explore the selectivity of the 3,6- dithiaoctanediamides and 3,7-dithianonanediamides for Pd(U) over CoCII), Cu(U) and Ni(II). The ICP-MS data indicate that, in general, equilibration was achieved within ten minutes and that the longer-chain amides were less selective than the shorter-chain analogues. , KMBT_363 , Adobe Acrobat 9.54 Paper Capture Plug-in
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Videographic analysis of the Coelacanth, Latimeria Chalumnae, and associated habitats in the Isimangaliso Wetland Park, KwaZulu-Natal, South Africa
- Authors: Thornycroft, Rosanne Elizabeth
- Date: 2012
- Subjects: Isimangaliso Wetland Park , Coelacanth , Coelacanth -- South Africa -- KwaZulu-Natal , Habitat (Ecology) , Coelacanth -- Behavior -- South Africa -- KwaZulu-Natal , Coelacanth -- Habitat -- South Africa -- KwaZulu-Natal
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5333 , http://hdl.handle.net/10962/d1005179 , Isimangaliso Wetland Park , Coelacanth , Coelacanth -- South Africa -- KwaZulu-Natal , Habitat (Ecology) , Coelacanth -- Behavior -- South Africa -- KwaZulu-Natal , Coelacanth -- Habitat -- South Africa -- KwaZulu-Natal
- Description: Videography is a valuable tool in biological and ecological studies. Using video footage obtained during previous coelacanth surveys, this thesis investigated coelacanths and their associated habitats in the submarine canyons of iSimangaliso Wetland Park, South Africa. This thesis aimed to (1) describe the biological habitats within the submarine canyons, (2) determine coelacanth distribution within these habitats, and (3) assess the use of computer-aided identification to successfully identify individual coelacanths. Seven different habitat types were noted with the most distinctive being the canyon margins that consisted of dense agglomerations of gorgonians, wire and whip corals, and sponges. Results suggested that although substratum type has a great influence on invertebrate community structure in the canyons, depth is the principal factor. Coelacanths were associated with cave habitats within the steep rocky canyon walls. Habitat analyses allowed predictive classification tree models to be constructed. Depth, underlying percentage of rock, and percentage cover of gorgonians and sponges were the most important variables for determining coelacanth presence and absence. The overall correct classification rate for the model was estimated at 96.6%, correctly predicting coelacanth absence (> 99%) better than presence (60%). Because coelacanths have a unique spot pattern it was possible to quickly and accurately identify specific individuals photographically using computer-aided identification software. Without any manual intervention by an operator the software accurately identified between 56 and 92% of the individuals. Identification success increased to 100% if the operator could also manually select from other potential matching photographs. It was also shown that fish exhibiting a yaw angle not exceeding 60° could be accurately identified in photographs. Each of the sections presented in this thesis represent a possible step towards analysing coelacanth-related habitats, locating and then analysing new habitats. Steps include first locating a population and then performing a habitat analysis. Coelacanth location within the different habitats can then be determined allowing the development of predictive models to potentially identify possible locations of new populations. The final step is to identify individual fish within the population for assessing demographic parameters and population monitoring.
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- Date Issued: 2012
A contribution to cabbage pest management by subsistence and small-scale farmers in the Eastern Cape, South Africa
- Authors: Mkize, Nolwazi
- Date: 2004
- Subjects: Cabbage -- Diseases and pests , Insect pests -- Integrated control -- South Africa -- Eastern Cape , Farms, Small -- South Africa -- Eastern Cape , Agriculture -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5659 , http://hdl.handle.net/10962/d1005342 , Cabbage -- Diseases and pests , Insect pests -- Integrated control -- South Africa -- Eastern Cape , Farms, Small -- South Africa -- Eastern Cape , Agriculture -- South Africa -- Eastern Cape
- Description: The interaction between farmers, agricultural scientists and extension workers is sometimes overlooked in agricultural entomology. In an attempt to respond to this reality this study examines some foundation of this interaction in relation to the pest management practices of subsistence and small-scale farmers and also highlights the problems that might arise in the implementation of IPM. Problems involving pests occurrence; language barriers; beliefs, knowledge and perception about insects, and visual literacy are examined. The thesis has a two-fold focus, firstly the study of pests on cabbages of subsistence farmers in Grahamstown and secondly a broader focus on other aspects such as cultural entomology, perception of insects and visual literacy specifically in relation to Xhosa speaking people in the Eastern Cape. The most important crop for emergent farmers in the Eastern Cape are cabbages, which have a variety of pests of which diamondback moths and are the most important. Traditional pest management practices tend to influence the development of IPM programmes adopted by these farmers. Eastern Cape farmers apply periodic cropping systems, which had an effect on the population densities of diamondback moth (DBM), other lepidopteran pests and their parasitoids. Considering the maximum population densities of DBM, which were 0.2 - 2.9 larvae/plant, there were no major pest problems. The availability of parasitoids, even in highly disturbed and patchy environments, showed good potential for biological control. Since some extension officers cannot speak the local farmers’ language, a dictionary of insect names was formulated in their language (isiXhosa) to assist communication. Response-frequency distribution analysis showed that the dictionary is essentially complete. The literal translations of some names show that isiXhosa speakers often relate insects to people, or to their habitat or classify them according to their behaviour. Farmers from eight sites in the Eastern Cape were interviewed regarding their knowledge and perception of insect pests and their control thereof. To some extent, farmers still rely on cultural control and have beliefs about insects that reflected both reality and superstition. There is no difference between the Ciskei and Transkei regions regarding insect-related beliefs. Farmers generally lack an understanding of insect ecology. There is a need for farmers to be taught about insects to assist with the implementation of IPM. Leftover pesticides from commercial farms or detergents are sometimes used to manage the pests. When training illiterate or semi-literate farmers, it is important to understand their media literacy so as to design useful graphic and object training media. Generally farmers showed that they either understand graphic or object media depending on the features of the insects being looked at. These findings are discussed with regard to the potential development of IPM training material for subsistence and small-scale farmers in a community.
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- Date Issued: 2004
An investigation into the viability of deploying thin client technology to support effective learning in a disadvantaged, rural high school setting
- Authors: Ndwe, Tembalethu Jama
- Date: 2002
- Subjects: Network computers , Education -- Data processing
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4627 , http://hdl.handle.net/10962/d1006500 , Network computers , Education -- Data processing
- Description: Computer Based Training offers many attractive learning opportunities for high school pupils. Its deployment in economically depressed and educationally marginalized rural schools is extremely uncommon due to the high technology skills and costs involved in its deployment and ongoing maintenance. This thesis puts forward thin client technology as a potential solution to the needs of education environments of this kind. A functional business case is developed and evaluated in this thesis, based upon a requirements analysis of media delivery in learning, and upon formal cost/performance models and a deployment field trial. Because of the economic constraints of the envisaged deployment area in rural education, an industrial field trial is used, and the aspects of this trial that can be carried over to the rural school situation have been used to assess performance and cost indicators. Our study finds that thin client technology could be deployed and maintained more cost effectively than conventional fat client solutions in rural schools, that it is capable of supporting the learning elements needed in this deployment area, and that it is able to deliver the predominantly text based applications currently being used in schools. However, we find that technological improvements are needed before future multimediaintensive applications can be adequately supported.
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- Date Issued: 2002