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Characterization of the co-chaperones of Hsp70 and Hsp90 in Trypanosoma brucei and their potential partnerships

  • Authors: Mokoena, Fortunate
  • Date: 2015
  • Language: English
  • Type: text , Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10962/54543 , vital:26583
  • Description: African Trypanosomiasis, which is caused by Trypanosoma brucei, is one of the crippling agents of social and economic development in Africa. T. brucei cycles between the cold-blooded insect vector, the tsetse fly (Glossina spp), and warm-blooded mammalian hosts. T. brucei, T. cruzi and L. major are mammal infecting kinetoplastid parasites that are collectively referred to as TriTryps. These parasites experience extreme environments as they move between their warm-blooded mammalian hosts and cold-blooded insect vectors which trigger extensive morphological transformations during the life-cycle of the parasite. Molecular chaperones have been implicated in parasite differentiation. TriTryps display significant expansions and diversity in the gene complements encoding molecular chaperones, especially J-proteins. Generally, J-proteins function as co-chaperones of Hsp70s, forming part of vital protein homeostasis processes. Hsp70s show a high degree of conservation, while J-proteins appear to be an extreme case of taxonomic radiation. Although several studies have focused on the molecular and cell biology of Hsp70s in some kinetoplastid parasites, knowledge is still lacking pertaining to J-proteins and their partnerships with Hsp70s. This thesis focused on the classification of kinetoplastid Jproteins into the four types by examining the domain organizations using T. brucei as a guide. The potential partnership of J-proteins and Hsp70s were postulated based on predicted subcellular localization. Kinetoplastid parasites, particularly T. brucei, have evolved an expanded and specialized J-protein machinery, likely to be a consequence of an evolutionary fitness/trait to adapt to diverse environment present in hosts and vectors. These analyses will yield insight into the process of parasite differentiation as well as provide new leads for chemotherapeutic treatments. The presence of the STI1 mediated Hsp90 hetero-complex formation has not been confirmed in T. brucei. To this end, in silico and biochemical techniques were used to characterize the role of TbSTI1, as an adaptor protein of Hsp70 and Hsp90. Through domain architecture analysis, sequence alignments, phylogenetic analysis and three-dimensional structure prediction, TbSTI1 was demonstrated to be the most conserved TPR containing co-chaperone of Hsp70 and Hsp83 in T. brucei and also shown to be highly similar to its eukaryotic homologues. Recombinant TbSTI1 was overproduced and purified in E.coli cells and subsequently shown to associate with TcHsp70 in a concentration dependent manner and associate weakly with TbHsp70.4. TbSTI1 and TbHsp83 were also demonstrated to be expressed and upregulated upon exposure to heat shock at the bloodstream stage of parasite development. In conclusion, this study is the first to report the interaction of TbSTI1 with a chaperone. Interactions between TbSTI1 and Hsp70s were demonstrated and therefore, the formation of the hetero-complex is predicted based the similarity of TbSTI1 to other STI1 proteins.
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CHIP: a co-chaperone for degradation by the proteasome

  • Authors: Edkins, Adrienne L
  • Date: 2015
  • Language: English
  • Type: text , book
  • Identifier: http://hdl.handle.net/10962/164863 , vital:41179 , ISBN 978-3-319-11730-0 , DOI: 10.1007/978-3-319-11731-7_11
  • Description: Protein homeostasis relies on a balance between protein folding and protein degradation. Molecular chaperones like Hsp70 and Hsp90 fulfil well-defined roles in protein folding and conformational stability via ATP dependent reaction cycles. These folding cycles are controlled by associations with a cohort of non-client protein co-chaperones, such as Hop, p23 and Aha1. Pro-folding co-chaperones facilitate the transit of the client protein through the chaperone mediated folding process. However, chaperones are also involved in ubiquitin-mediated proteasomal degradation of client proteins. Similar to folding complexes, the ability of chaperones to mediate protein degradation is regulated by co-chaperones, such as the C terminal Hsp70 binding protein (CHIP).
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Classification System for Wetlands and Other Aquatic Ecosystems in South Africa:

  • Authors: Ellery, William F N
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/144454 , vital:38347 , https://doi.org/10.2989/10220119.2015.1025843
  • Description: There have been several attempts to develop a wetland classification for South Africa, with merit in each, but a system that satisfies the needs of a wide range of professionals has been elusive. This is partly to be expected since classification systems are often user-specific. Nevertheless, and at last, the authors of Classification System for Wetlands and Other Aquatic Ecosystems in South Africa. User Manual: Inland Systems (SANBI Biodiversity Series 22) have developed a robust and comprehensive wetland classification system for South Africa that likely will have broad appeal and be widely used. Working for Wetlands, the Water Research Commission (WRC) and SANBI provided considerable support for the development of this system and there was expert input from a wide range of stakeholders.
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Coastal landscape change on the Cape St Francis/St Francis Bay peninsula from 1960 to 2014

  • Authors: Schroeder, Daniel Heiko
  • Date: 2015
  • Subjects: Coast changes -- South Africa -- Saint Francis, Cape , Peninsulas -- South Africa -- Saint Francis, Cape , Human ecology -- South Africa -- Saint Francis, Cape , Geographic information systems -- South Africa -- Saint Francis, Cape , Surveying -- South Africa -- Saint Francis, Cape
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:5086 , http://hdl.handle.net/10962/d1018203
  • Description: A large proportion of the human population, their settlements and socioeconomic activities occur on land directly adjacent to the coastline. The increased demand for coastal leisure and tourism has interfered with natural landscape features and their associated processes. The Cape St Francis/St Francis Bay peninsula located on the southeast coast of South Africa was rapidly developed and transformed from a little fishing village into an urban coastal developed area over a 50-year period (1961-2014). A system that once existed in a state of dynamic or non-equilibrium was interfered with through anthropogenic disturbances, resulting in more frequent and intense natural events, which ranged from floods to debris flows, decreased sand supply and resulting beach erosion. The aim of the project was to identify and map landscape features and changes on the peninsula using an interdisciplinary approach. The triangulated methods of a desktop study using Geographic Information Systems (GIS) and media reviews, a crowdsourcing/participatory approach based on interviews, and a one year land surveying period of measurable field based surveys of physical features gave a well balanced view. The research showed that the natural landscape has been altered dramatically by settlement and associated infrastructure development. In particular, the loss of dunefields and the artificial modification of river paths were major impact areas. Beach erosion is a continual issue for the peninsula residents, particularly in St Francis Bay.
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Comparative electrocatalytic studies of nanocomposites of mixed and covalently linked multiwalled carbon nanotubes and 4-(4, 6-diaminopyrimidin-2-ylthio) phthalocyaninato cobalt (II)

  • Authors: Nyoni, Stephen , Nyokong, Tebello
  • Date: 2015
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/189285 , vital:44834 , xlink:href="https://doi.org/10.1016/j.poly.2015.05.038"
  • Description: Electrocatalytic behavior of 4-(4,6-diaminopyrimidin-2-ylthio) phthalocyaninato cobalt(II) (CoPyPc) when mixed or covalently mixed to multiwalled carbon nanotubes (MWCNTs) is reported. Infra-red spectroscopy was used to confirm amide linkage of the covalently linked nanocomposite. Rotating disk electrode (RDE) and cyclic (CV) voltammetry studies were used for the electrochemical characterization of the prepared phthalocyanine and MWCNT nanocomposite. The electrocatalytic effects of the nanocomposites of the cobalt phthalocyanine derivative were then investigated towards L-cysteine oxidation using both RDE and CV experiments, and the electrocatalytic performance of the covalently linked cobalt phthalocyanine-MWCNT was found to be superior over the mixed nanocomposite.
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Comparative study of clan CA cysteine proteases: an insight into the protozoan parasites

  • Authors: Moyo, Sipho Dugunye
  • Date: 2015
  • Subjects: Cysteine proteinases , Proteolytic enzymes , Protozoan diseases , Parasites , Protozoan diseases -- Chemotherapy , Bioinformatics , Plasmodium , Antiprotozoal agents
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4165 , http://hdl.handle.net/10962/d1020309
  • Description: Protozoan infections such as Malaria, Leishmaniasis, Toxoplasmosis, Chaga’s disease and African trypanosomiasis caused by the Plasmodium, Leishmania, Toxoplasma and Trypanosoma genuses respectively; inflict a huge economic, health and social impact in endemic regions particularly tropical and sub-tropical regions. The combined infections are estimated at over a billion annually and approximately 1.1 million deaths annually. The global burden of the protozoan infections is worsened by the increased drug resistance, toxicity and the relatively high cost of treatment and prophylaxis. Therefore there has been a high demand for new drugs and drug targets that play a role in parasite virulence. Cysteine proteases have been validated as viable drug targets due to their role in the infectivity stage of the parasites within the human host. There is a variety of cysteine proteases hence they are subdivided into families and in this study we focus on the clan CA, papain family C1 proteases. The current inhibitors for the protozoan cysteine proteases lack selectivity and specificity which contributes to drug toxicity. Therefore there is a need to identify the differences and similarities between the host, vector and protozoan proteases. This study uses a variety of bioinformatics tools to assess these differences and similarities. The Plasmodium cysteine protease FP-2 is the most characterized protease hence it was used as a reference to all the other proteases and its homologs were retrieved, aligned and the evolutionary relationships established. The homologs were also analysed for common motifs and the physicochemical properties determined which were validated using the Kruskal-Wallis test. These analyses revealed that the host and vector cathepsins share similar properties while the parasite cathepsins differ. At sub-site level sub-site 2 showed greater variations suggesting diverse ligand specificity within the proteases, a revelation that is vital in the design of antiprotozoan inhibitors.
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Comparative study of the effect of silver nanoparticles on the hexokinase activity from human and Trypanosoma brucei

Comparison of protein binding microarray derived and ChIP-seq derived transcription factor binding DNA motifs

  • Authors: Hlatshwayo, Nkosikhona Rejoyce
  • Date: 2015
  • Subjects: Protein binding , DNA , DNA microarrays , Transcription factors , DNA-protein interactions , Gene regulatory networks
  • Language: English
  • Type: Thesis , Masters , MSc
  • Identifier: vital:4146 , http://hdl.handle.net/10962/d1017907
  • Description: Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .
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Comparisons of isotopic niche widths of some invasive and indigenous fauna in a South African river

  • Authors: Hill, Jaclyn M , Jones, Roy W , Hill, Martin P , Weyl, Olaf L F
  • Date: 2015
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/423711 , vital:72088 , xlink:href="https://doi.org/10.1111/fwb.12542"
  • Description: Biological invasions threaten ecosystem integrity and bio-diversity, with numerous adverse implications for native flora and fauna. Established populations of two notorious freshwater invaders, the snail Tarebia granifera and the fish Pterygoplichthys disjunctivus, have been reported on three continents and are frequently predicted to be in di-rect competition with native species for dietary resources.
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Composition portfolio

Conditions enabling or constraining the exercise of agency among new academics in higher education, conducive to the social inclusion of students

  • Authors: Behari-Leak, Kasturi
  • Date: 2015
  • Subjects: Social integration -- South Africa , Students -- South Africa -- Social conditions , Educational change -- South Africa , College teachers -- South Africa , Education, Higher -- South Africa , Critical realism , Social realism , Agent (Philosophy)
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:1333 , http://hdl.handle.net/10962/d1020295
  • Description: This study, which is part of a National Research Foundation project on Social Inclusion in Higher Education (HE), focuses on the exercise of agency among new academics, conducive to the social inclusion of students. Transitioning from varied entry points into higher education, new academics face numerous challenges as they embed themselves in disciplinary and institutional contexts. Given the complexity and contested nature of the current higher education landscape, new academics are especially vulnerable. Using Roy Bhaskar’s critical realism as meta-theoretical framing and Margaret Archer’s social realist theory, with its methodological focus on analytical dualism and morphogenesis, this study offers a social realist account of how new academics engage with enabling and constraining conditions at institutional, faculty, departmental and classroom levels. Through an analysis of six individual narratives of mediation, this study explicates and exemplifies the range of agential choices exercised by new academics to mediate their contested spaces. A nuanced social and critical account of the material, ideational and agential conditions in HE shows that the courses of action taken by these new academics are driven through their concerns, commitments and projects in higher education. Yet, despite the university’s espousal of embracing change, the current induction and transition of new academics is inadequate to the task of transformation in higher education. Systemic conditions in HE, conducive to critical agency and social justice, are not enabling. Bhaskar’s Seven Scalar Being, used as an analytical frame and heuristic, guides the cross-case analysis of the six narratives across seven levels of ontology. The findings highlight that, despite difficult contextual influences, the positive exercise of agency is a marked feature of new participants in HE in this study. This has immediate implications for ways in which professional and academic development, and disciplinary and departmental programmes, could create and sustain conducive conditions for the professionalisation of new academics through more sensitised practices. Using alternative research methods such as photovoice to generate its data, this doctoral study proposes that new research methodologies, located in the third space, are needed now more than ever in HE sociological research, to recognise the researcher and the research participants as independent, autonomous and causally efficacious beings. To this end, this study includes a Chapter Zero, which captures the narrative of the doctoral scholar as researcher, who, shaped and influenced by established doctoral practices and traditions in the field, exercises her own doctoral agency in particular ways.
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Condoms in pockets and HIV-free certificates: mother-daughter communication about sex and risk in a time of AIDS epidemic in South Africa

  • Authors: Wilbraham, Lindy
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/143693 , vital:38274 , https://ischp.files.wordpress.com/2015/08/ischp_2015_abstract_booklet.pdf
  • Description: Responsive to the perceived high risks of sexual coercion, unwanted pregnancy and HIV-infection of girls in particular, several South African sexual health promotion campaigns have used media targeting parents (mothers in particular) to instruct them on how sex should be talked about with young people to ‘risk-proof’ them. Such an instrumentalist public health discourse posits this intergenerational communication as an ‘ongoing discussion’ of events, feelings, issues and risk-safe practices around heterosexual sex negotiation. A Foucauldian view finds these conversational imperatives pitched against much-talked-about resistances to talking about sex; and the saturation with risk of ambivalent mothers and silent daughters. Mother-daughter communication about sex and sexualities – as an uneasy western ideal of attachment parenting – has tangled roots in psychoanalytic theory and feminisms where sex as the core of modern subjectivity is normalized, capacities for intimacy are trained, and affiliative sexuality is modelled in ways that balance the rights and responsibilities of sexual agency/citizenship. This paper begins with two narrative fragments from a sexual health campaign that addressed mothers and daughters, and recounts how these ‘stories’ produced derisive laughter when introduced into group discussions with young/older women. The paper follows two lines of exploration. Firstly, is western idealized fabrication of inter-subjectivity between mothers and daughters desirable and feasible in post-apartheid conditions of epidemic in South Africa? And secondly, what if the narratives of lives and experiences we offer by way of health education materials provoke uncertainties, gaps and interrogations about sex, mothering and communication, instead of offering homilies and solutions?
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Connectivity through allochthony: Reciprocal links between adjacent aquatic and terrestrial ecosystems in South Africa

  • Authors: Richoux, Nicole B , Moyo, Sydney , Chari, Lenin D , Bergamino, Leandro , Carassou, Laure , Dalu, Tatenda , Hean, Jeff W , Sikutshwa, Likho , Gininda, Simphiwe , Magoro, Mandla , Perhar, Gurbir , Ni, Felicity , Villet, Martin H , Whitfield, Alan K , Parker, Daniel M , Froneman, P William , Arhonditsis, George , Craig, Adrian J F K
  • Date: 2015
  • Subjects: To be catalogued
  • Language: English
  • Type: text , report
  • Identifier: http://hdl.handle.net/10962/438363 , vital:73454 , ISBN 978-1-4312-0679-7 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2186-1-15.pdf
  • Description: An important aspect of the dynamics of nutrients and pollutants in natural systems is captured in the concept of allochthony, founded on the observation that nutrients and energy in a variety of forms are transferred between adjacent habitats, com-munities and ecosystems that are not routinely considered as connected. Different forms of nutrients and energy move across the conceptual boundaries of habitats via organisms’ activities or physical processes such as wind or water currents, and these transfers can represent important food subsidies. Such cross-partition ecolog-ical subsidies can augment the nutritional condition, biomass and biodiversity of communities, particularly where local production (or autochthony) alone may be inadequate to support local food webs. Furthermore, organic subsidies can influ-ence population dynamics, community interactions and ecosystem processes, and can represent dominant flux inputs in ecosystem budgets. Our intention was to ex-plore organic nutrient fluxes in relation to a primarily lotic (i.e. flowing) aquatic sys-tem at the scale of a hydrological catchment.
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Conscientious objection and South African medical practitioners' constructions of termination of pregnancy and emergency contraception

  • Authors: Chiwandire, Desire
  • Date: 2015
  • Subjects: Abortion -- South Africa , Abortion -- Moral and ethical aspects -- South Africa , Emergency contraceptives -- South Africa , Contraception -- Moral and ethical aspects -- South Africa , Medical personnel -- Attitudes -- South Africa , Patients -- Legal status, laws, etc. -- South Africa , Reproductive rights -- South Africa , Women's rights -- South Africa , Liberty of conscience
  • Language: English
  • Type: Thesis , Masters , MSocSc
  • Identifier: vital:2888 , http://hdl.handle.net/10962/d1017863
  • Description: Aim: The 1996 Choice on Termination of Pregnancy Act decriminalized abortion in South Africa and the South African Medicines Control Council in 2000 approved the dispensing of emergency contraceptive methods by pharmacists to women without a doctor's prescription. This legislation has been hailed as among the most progressive in the world with respect to women's reproductive justice. However the realisation of these rights in practice has not always met expectations in part due to medical practitioners' ethical objections to termination of pregnancy and the provision of related services. The aim of this study was to interpret the varying ways in which medical practitioners frame termination of pregnancy and emergency contraceptive services, their own professional identities and that of their patients/clients. Methods: Sample of 58 doctors and 59 pharmacists drawn from all nine provinces of South Africa. Data collected using an anonymous confidential internet-based self-administered questionnaire. Participants were randomly recruited from online listings of South African doctors and pharmacists practicing in both private and public sectors. Data were analysed using theoretically derived qualitative content analysis. Results: Participants drew on eight frames to justify their willingness or unwillingness to provide termination-of-pregnancy related services: the foetal life frame, the women's rights frame, the balancing frame, the social justice frame, the do no harm frame, the legal and professional obligation frame, the consequences frame and the moral absolutist frame. Conclusion: Health professionals' willingness or unwillingness to provide termination of pregnancy related services is highly dependent on how they frame or understand termination of pregnancy, and how they understand their own professional identities and those of their patients/clients.
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Constructing sexualities: a critical overview of articles published in Feminism and Psychology

  • Authors: Marx, Jacqueline , Donaldson, Natalie
  • Date: 2015
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/142040 , vital:38044 , DOI: 10.1177/0959353515572704
  • Description: How have sexualities been dealt with in articles published in Feminism and Psychology since the inception of the journal in 1991? The idea for this overview arose from our experience of designing a critical sexualities course for graduate students in psychology. The articles featured in this overview form part of a Virtual Special Issue that can be located on the Feminism and Psychology website. Virtual Special Issues (VSI) are collections of previously published articles, which have been compiled by guest editors who are experts in the field. VSIs provide readers with an overview of feminist thought about a topic or theme, as well as an easy way to locate pertinent articles. Scholars who are approaching a new topic may find a VSI especially useful, as will instructors who are preparing course syllabi. This article introduces the Constructing Sexualities VSI.
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Consuming pasts : imaging food as Identity and (post)memory in post-apartheid South Africa

Contextualising work-family conflict, social support and gender ideologies of professional/registered nurses in the Cacadu District, Eastern Cape

  • Authors: Koeberg, Richenda
  • Date: 2015
  • Subjects: Nursing -- Social aspects -- South Africa -- Eastern Cape , Nurses -- Job stress -- South Africa -- Eastern Cape , Work and family
  • Language: English
  • Type: Thesis , Masters , MA
  • Identifier: vital:3261 , http://hdl.handle.net/10962/d1017884
  • Description: The focus of this study was to investigate work-family conflict, social support and gender ideologies of professional/registered nurses in the South African context, specifically within the Cacadu District (Eastern Cape). The study had four aims: (a) to investigate the construct validity of the measuring instrument, (b) to investigate the relationship between social support provided by family and family interference with work (FIW), (c) to ascertain the influence of shift work on perceived work-family conflict, and lastly, (d) to determine whether there is a difference between the number of children in households and nurses’ perceptions of work-family conflict. A quantitative research design was used in the study. The sample (N = 106) was taken from five district hospitals in the Cacadu District, Eastern Cape. The measuring instrument consisted of three scales, namely the Multi-dimensional Work-Family Conflict Scale (Carlson, Kacmar, & Williams, 2000), the Social Support Questionnaire (Sarason, Sarason, Shearin, & Pierce, 1987), and an adapted Gender Ideology Scale (Tsai, 2008). The results indicated that the construct validity of the Multi-dimensional Work-Family Conflict scale was satisfactory. However, analysis of the Social Support Questionnaire and Gender Ideology scales both suggested that these scales have not been validated for use with diverse samples outside the contexts in which they were developed. The results also indicated that there is a relationship between social support provided by families and behaviour-based family interference with work. Additionally, there appeared to be a difference between the shifts worked by nurses and their perceived work-family conflict, except for strain-based work interference with family. And lastly, the only significant difference between the number of children in the household and work-family conflict was reported for strain-based work interference with family. The implications of the results for future research suggest the importance of developing and validating work-family conflict, social support and gender ideology scales that are dependent on the context of the research. In so doing, the constructs of the scale are made meaningful. Additionally, the findings provide preliminary evidence of tailoring work-family initiatives that address the needs of the nursing profession and the context of healthcare institutions
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Contrasting signals of genetic diversity and historical demography between two recently diverged marine and estuarine fish species

  • Authors: von Der Heyden, Sophie , Toms, Jessica A , Teske, Peter R , Lamberth, Stephen J , Holleman, Wouter
  • Date: 2015
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/445611 , vital:74407 , https://doi.org/10.3354/meps11191
  • Description: Estuaries, at the confluence of marine and freshwater systems, are mostly of geologically recent origin and as such make excellent models for understanding recent speciation events. Using molecular approaches, we compared genetic diversity and demographic histories in 2 closely related southern African klipfish species, the marine Clinus superciliosus and the estuarine C. spatulatus. Strong genetic differentiation was identified using both mtDNA control region and nDNA S7 sequencing, despite some haplotype sharing. Coalescent-based modelling suggests that species divergence occurred during the Late Pleistocene or, more likely, during the Early Holocene, when present-day estuaries formed. Analyses of population demography suggest that C. superciliosus has undergone historical population expansion, whereas C. spatulatus is characterized by a population decline, potentially driven by repeated cycles of population crashes linked to the opening and closing of estuarine systems. This is also reflected in values of genetic diversity, which are almost an order of magnitude lower in the estuarine than in the marine species. Given the unique evolutionary history of C. spatulatus, a species that is restricted to only 2 South African estuaries, we highlight the need for a better understanding of the processes that have shaped the evolution of estuarine populations. The identification of unique genetic lineages in estuaries can help to better guide conservation and management efforts for some of South Africa’s most fragile habitats.
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Contributions to the study of a class of optimal control problems on the orthogonal groups SO(3) and SO(4)

  • Authors: Adams, Ross Montague
  • Date: 2015
  • Language: English
  • Type: text , Thesis , Doctoral , PhD
  • Identifier: http://hdl.handle.net/10962/64826 , vital:28608
  • Description: In this thesis we investigate a class of invariant optimal control problems, and their associated quadratic Hamilton-Poisson systems, on the orthogonal groups SO(3) and SO(4). Specifically, we are concerned with the class of left-invariant control affine systems. We begin by classifying all cost-extended systems on SO(3) under cost equivalence. (Cost-extended systems are closely related to optimal control problems.) A classification of all quadratic Hamilton-Poisson systems on the (minus) Lie-Poisson space so(3)*, under affine equivalence, is also obtained. For the normal forms obtained in our classification (of Hamilton-Poisson systems) we investigate the (Lyapunov) stability nature of the equilibria using spectral and energy-Casimir methods. For a subclass of these systems, we obtain analytic expressions for the integral curves of the associated Hamiltonian vector fields in terms of (basic) Jacobi elliptic functions. The explicit relationship between the classification of cost-extended systems on SO(3) and the classification of quadratic Hamilton- Poisson systems on so(3)* is provided. On SO(4), a classification of all left-invariant control affine systems under L-equivalence is obtained. We then determine which of these representatives are controllable, thus obtaining a classification under detached feedback equivalence. We also obtain a partial classification of quadratic Hamilton-Poisson systems on the Lie-Poisson space so(4)*. An investigation of the stability nature of the equilibria for a subclass of these systems is also done. Several illustrative examples of optimal control problems on the orthogonal group SO(3) are provided. More specifically, we consider an optimal control problem corresponding to a representative of our classification (of cost-extended system) for each possible number of control inputs. For each of these problems, we obtain explicit expressions for the extremal trajectories on the homogeneous space S2 by projecting the extremal trajectories on the group SO(3). The examples provided show how our classifications of cost-extended systems and Hamilton-Poisson systems can be used to obtain the optimal controls and the extremal trajectories corresponding to a large class of optimal control problems on SO(3). An example of a four-input optimal control problem on SO(4) is also provided. This example is provided to show how the solutions of certain problems on SO(4) can be related to the solutions of certain optimal control problems on SO(3).
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Control and vulnerability : reflections on the nature of human agency and personhood

  • Authors: Paphitis, Sharli Anne
  • Date: 2015
  • Subjects: Self-control , Vulnerability (Personality trait) , Self (Philosophy) , Social psychology , Cognitive science , Frankfurt, Harry G., 1929- -- Criticism and interpretation , Watson, Gary, 1943- -- Criticism and interpretation , Mele, Alfred R., 1951- -- Criticism and interpretation , Nietzsche, Friedrich Wilhelm, 1844-1900 -- Criticism and interpretation
  • Language: English
  • Type: Thesis , Doctoral , PhD
  • Identifier: vital:2750 , http://hdl.handle.net/10962/d1018671
  • Description: Following the writings of philosophers such as Harry Frankfurt, Gary Watson, and Alfred Mele, in this thesis I defend some central claims of the self-control view of human agency. However, I not only defend, but also supplement this view in the following two ways. First, drawing on work by Mary Midgley and Sigmund Freud I advance the claim that self-control requires the experience of internal conflict between an agent’s motivations and intentions. Second, drawing on insights from Simone de Beauvoir and Friedrich Nietzsche, as well as recent research in social psychology and cognitive science, I will argue in this thesis that self-control and vulnerability are inextricably intertwined with one another, and that as a result both are to be seen as constitutive of human agency. While it is the capacity for self-control that marks us out as human agents, I argue that it is also our uniquely human vulnerability which distinguishes our agency from the kind of agency which we might attribute to other potential or actual forms of sentience. Further, while the concepts of human agency and personhood are typically conflated in the analytic tradition of philosophy, in this thesis I will show that there are good reasons for understanding these two concepts as subtly distinct from one another. The term personhood, I will argue, can fruitfully be understood in substantive rather than purely formal terms. A person, in the superlative sense, is to be understood as someone who exercises their agency well; and, as such, persons are answerable to a number of normative prescriptions. Following Midgley, Nietzsche and Martha Nussbaum, I argue against Frankfurt’s normative prescription for personhood in the form of what he calls ‘wholeheartedness’, and offer four normative prescriptions for personhood of my own.
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