Knowledge, perceptions and willingness to control designated invasive tree species in urban household gardens in South Africa
- Shackleton, Charlie M, Shackleton, Ross T
- Authors: Shackleton, Charlie M , Shackleton, Ross T
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/180445 , vital:43389 , xlink:href="https://doi.org/10.1007/s10530-016-1104-7"
- Description: Many biological invasions result in negative impacts on the environment and human livelihoods, but simultaneously some also provide benefits that are valued differently by various stakeholders. To inform policy and management of invasive species it is important to assess landowners’ and broader society’s knowledge and perceptions of invasive species, something which is lacking in many contexts, especially in urban settings. In this study we interviewed 153 householders living in a medium-sized South African town who had declared invasive alien trees in their gardens. Less than half of the respondents could identify the invasive tree on their property and only one-third knew that it was an invasive alien species. There was a positive association between income and education levels with exposure to media about invasive alien species and respondents’ ability to identify the species and name any other invasive alien tree species. Knowledge levels were unequal across species. Amongst those who knew the tree was an invasive alien species, reasons why they retained it in their gardens included that it would be costly or too much effort to remove, they liked the tree, that it was not causing any harm and that the property was rented and so its removal was not their responsibility. However, the majority of people (83 %) were willing to have it removed from their garden if done for free by appropriate agencies, which is promising for compliance with new regulations on invasive species implemented at the end of 2014 in South Africa. The results also highlight the need for targeted and appropriate education and awareness programs amongst urban householders on invasive alien species, relevant legislation and their obligations.
- Full Text:
- Date Issued: 2016
- Authors: Shackleton, Charlie M , Shackleton, Ross T
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/180445 , vital:43389 , xlink:href="https://doi.org/10.1007/s10530-016-1104-7"
- Description: Many biological invasions result in negative impacts on the environment and human livelihoods, but simultaneously some also provide benefits that are valued differently by various stakeholders. To inform policy and management of invasive species it is important to assess landowners’ and broader society’s knowledge and perceptions of invasive species, something which is lacking in many contexts, especially in urban settings. In this study we interviewed 153 householders living in a medium-sized South African town who had declared invasive alien trees in their gardens. Less than half of the respondents could identify the invasive tree on their property and only one-third knew that it was an invasive alien species. There was a positive association between income and education levels with exposure to media about invasive alien species and respondents’ ability to identify the species and name any other invasive alien tree species. Knowledge levels were unequal across species. Amongst those who knew the tree was an invasive alien species, reasons why they retained it in their gardens included that it would be costly or too much effort to remove, they liked the tree, that it was not causing any harm and that the property was rented and so its removal was not their responsibility. However, the majority of people (83 %) were willing to have it removed from their garden if done for free by appropriate agencies, which is promising for compliance with new regulations on invasive species implemented at the end of 2014 in South Africa. The results also highlight the need for targeted and appropriate education and awareness programs amongst urban householders on invasive alien species, relevant legislation and their obligations.
- Full Text:
- Date Issued: 2016
Knowledge-building: educational studies in Legitimation Code Theory
- Authors: Clarence, Sherran
- Date: 2016
- Language: English
- Type: book review , text
- Identifier: http://hdl.handle.net/10962/61300 , vital:28013 , http://dx.doi.org/10.1080/14703297.2016.1231751
- Description: A challenge facing higher education researchers, especially those new to the craft of research, is that of moving between theory and data effectively in order to mediate research findings clearly to readers. For postgraduate students and academics publishing their research, working with data and designing effective and fit-for-purpose methodologies can be a challenge. Moreover, this is not necessarily an easy area for supervisors and research mentors to assist with. In addition to researchers, practitioners working in academic development also need ways of using research – either empirical or conceptual – to augment their work with lecturers to improve teaching and learning. There are many handbooks that detail the differences between qualitative, quantitative and mixed-methods research. There are many theoretical texts to choose from. But there are few texts that offer researchers and those mentoring researchers insight into how methodology and theory connect in research studies, as well as practical tools to navigate the chaos of research, bringing theory and data into conversation in relevant and problem-oriented ways that can influence practice effectively. Karl Maton, in his introduction to this edited collection, argues that in spite of many claims within educational and social research for the need to connect research with theory more effectively, ‘the two frequently remain divorced or, at best, not on speaking terms’ (p. 1). The central premise of the book flows from this: we need to move beyond calls for more theory-informed research into education and society towards generating ways of demonstrating enactments of research that bring theory and research together meaningfully. The need for the research we publish to make clear its theoretical and methodological underpinning and enactments is crucial for effecting sustainable and meaningful change in practice within the field. This text, located within the growing field of Legitimation Code Theory (LCT) research, within the broader field of sociology of education, takes a generous step in that direction. Building on Maton’s 2014 text, Knowledge and knowers. Towards a realist sociology of education, this text delves into how LCT concepts – particularly in the dimensions of Specialisation and Semantics – can be enacted within educational research and practice.
- Full Text: false
- Date Issued: 2016
- Authors: Clarence, Sherran
- Date: 2016
- Language: English
- Type: book review , text
- Identifier: http://hdl.handle.net/10962/61300 , vital:28013 , http://dx.doi.org/10.1080/14703297.2016.1231751
- Description: A challenge facing higher education researchers, especially those new to the craft of research, is that of moving between theory and data effectively in order to mediate research findings clearly to readers. For postgraduate students and academics publishing their research, working with data and designing effective and fit-for-purpose methodologies can be a challenge. Moreover, this is not necessarily an easy area for supervisors and research mentors to assist with. In addition to researchers, practitioners working in academic development also need ways of using research – either empirical or conceptual – to augment their work with lecturers to improve teaching and learning. There are many handbooks that detail the differences between qualitative, quantitative and mixed-methods research. There are many theoretical texts to choose from. But there are few texts that offer researchers and those mentoring researchers insight into how methodology and theory connect in research studies, as well as practical tools to navigate the chaos of research, bringing theory and data into conversation in relevant and problem-oriented ways that can influence practice effectively. Karl Maton, in his introduction to this edited collection, argues that in spite of many claims within educational and social research for the need to connect research with theory more effectively, ‘the two frequently remain divorced or, at best, not on speaking terms’ (p. 1). The central premise of the book flows from this: we need to move beyond calls for more theory-informed research into education and society towards generating ways of demonstrating enactments of research that bring theory and research together meaningfully. The need for the research we publish to make clear its theoretical and methodological underpinning and enactments is crucial for effecting sustainable and meaningful change in practice within the field. This text, located within the growing field of Legitimation Code Theory (LCT) research, within the broader field of sociology of education, takes a generous step in that direction. Building on Maton’s 2014 text, Knowledge and knowers. Towards a realist sociology of education, this text delves into how LCT concepts – particularly in the dimensions of Specialisation and Semantics – can be enacted within educational research and practice.
- Full Text: false
- Date Issued: 2016
Land acquisition for and local livelihood implications of biofuel development in Zimbabwe
- Authors: Thondhlana, Gladman
- Date: 2016
- Subjects: Biomass energy -- Government policy -- Zimbabwe Biomass energy -- Economic aspects -- Zimbabwe Biomass energy -- Environmental aspects -- Zimbabwe
- Language: English
- Type: text
- Identifier: http://hdl.handle.net/10962/49940 , vital:25944
- Description: In recent years, proponents of 'green and clean fuel' have argued that the costs of overreliance on fossil fuels could be reduced through transition to biofuels such as bio-ethanol. Global biofuel discourses suggest that any transition to biofuel invariably results in significant benefits, including energy independence, job creation, development of agro-industrial centres at local level and high revenue generations for the state with minimum negative impacts on the environment. With many risks and costs associated with traditional 'dirty' fuels, it is likely that many countries, particularly African countries, will move towards the 'green and clean fuel' alternative. However, until recently research has arguably paid limited attention to the local livelihood impacts related to land acquisition for biofuel development or the policy frameworks required to maximise biofuel benefits. With regards to biofuel benefits, some recent studies suggest that the much bandied potential for greater tax revenue, lowered fuel costs and wealth distribution from biofuel production have all been perverted with relatively little payoff in wage labour opportunities in return (e.g. Richardson, 2010; Wilkinson and Herrera, 2010). Based on work done in Chisumbanje communal lands of Zimbabwe (Thondhlana, 2015), this policy brief highlights the local livelihood impacts of biofuel development and discusses policy implications of the findings. By highlighting the justifications of biofuel development at any cost by the state, the study sheds some light on the conflicts between state interests and local livelihood needs.
- Full Text:
- Date Issued: 2016
- Authors: Thondhlana, Gladman
- Date: 2016
- Subjects: Biomass energy -- Government policy -- Zimbabwe Biomass energy -- Economic aspects -- Zimbabwe Biomass energy -- Environmental aspects -- Zimbabwe
- Language: English
- Type: text
- Identifier: http://hdl.handle.net/10962/49940 , vital:25944
- Description: In recent years, proponents of 'green and clean fuel' have argued that the costs of overreliance on fossil fuels could be reduced through transition to biofuels such as bio-ethanol. Global biofuel discourses suggest that any transition to biofuel invariably results in significant benefits, including energy independence, job creation, development of agro-industrial centres at local level and high revenue generations for the state with minimum negative impacts on the environment. With many risks and costs associated with traditional 'dirty' fuels, it is likely that many countries, particularly African countries, will move towards the 'green and clean fuel' alternative. However, until recently research has arguably paid limited attention to the local livelihood impacts related to land acquisition for biofuel development or the policy frameworks required to maximise biofuel benefits. With regards to biofuel benefits, some recent studies suggest that the much bandied potential for greater tax revenue, lowered fuel costs and wealth distribution from biofuel production have all been perverted with relatively little payoff in wage labour opportunities in return (e.g. Richardson, 2010; Wilkinson and Herrera, 2010). Based on work done in Chisumbanje communal lands of Zimbabwe (Thondhlana, 2015), this policy brief highlights the local livelihood impacts of biofuel development and discusses policy implications of the findings. By highlighting the justifications of biofuel development at any cost by the state, the study sheds some light on the conflicts between state interests and local livelihood needs.
- Full Text:
- Date Issued: 2016
Latrunculid sponges, their microbial communities and secondary metabolites: connecting conserved bacterial symbionts to pyrroloiminoquinone production
- Dorrington, Rosemary A, Hilliar, Storm Hannah, Kalinski, Jarmo-Charles J, Krause, Rui W M, McPhail, Kerry L, Parker-Nance, Shirley, Wlalmsley, Tara A, Waterworth, Samantha C
- Authors: Dorrington, Rosemary A , Hilliar, Storm Hannah , Kalinski, Jarmo-Charles J , Krause, Rui W M , McPhail, Kerry L , Parker-Nance, Shirley , Wlalmsley, Tara A , Waterworth, Samantha C
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65915 , vital:28858 , https://doi.org/10.1055/s-0036-1596655
- Description: publisher version , The Latrunculiidae are cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids (e.g. makaluvamines, discorhabdins and tsitsikammamines). Since pyrroloiminoquinones have also been isolated from sponges belonging to other families, ascidians and microorganisms, the biosynthetic origin of these alkaloids in latrunculid sponges is likely microbial. This study focuses on the secondary metabolites produced by closely-related Tsitsikamma species and Cyclacanthia bellae, all latrunculid sponges endemic to Algoa Bay on the South African southeast coast. The sponges produced suites of related pyrroloiminoquinones, including tsitsikammine A and B, and discohabdin C and V, the combination and relative abundance of which is species-specific. Characterisation of the diversity of sponge-associated bacterial communities revealed the unprecedented conservation of two dominant bacterial species. The first, a Betaproteobacterium, is also found in other latrunculids and related sponge families, representing a novel clade of sponge endosymbionts that have co-evolved with their hosts. The second conserved bacterial symbiont is a spirochaete found only in Cyclacanthia and Tsitsikamma species that is likely to have been recruited from free-living spirochaetes in the environment. This study sheds new light on the interactions between latrunculid sponges, their dominant bacterial symbionts, and the potential involvement of these bacteria in pyrroloiminoquinone biosynthesis.
- Full Text: false
- Date Issued: 2016
- Authors: Dorrington, Rosemary A , Hilliar, Storm Hannah , Kalinski, Jarmo-Charles J , Krause, Rui W M , McPhail, Kerry L , Parker-Nance, Shirley , Wlalmsley, Tara A , Waterworth, Samantha C
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/65915 , vital:28858 , https://doi.org/10.1055/s-0036-1596655
- Description: publisher version , The Latrunculiidae are cold water sponges known for their production of bioactive pyrroloiminoquinone alkaloids (e.g. makaluvamines, discorhabdins and tsitsikammamines). Since pyrroloiminoquinones have also been isolated from sponges belonging to other families, ascidians and microorganisms, the biosynthetic origin of these alkaloids in latrunculid sponges is likely microbial. This study focuses on the secondary metabolites produced by closely-related Tsitsikamma species and Cyclacanthia bellae, all latrunculid sponges endemic to Algoa Bay on the South African southeast coast. The sponges produced suites of related pyrroloiminoquinones, including tsitsikammine A and B, and discohabdin C and V, the combination and relative abundance of which is species-specific. Characterisation of the diversity of sponge-associated bacterial communities revealed the unprecedented conservation of two dominant bacterial species. The first, a Betaproteobacterium, is also found in other latrunculids and related sponge families, representing a novel clade of sponge endosymbionts that have co-evolved with their hosts. The second conserved bacterial symbiont is a spirochaete found only in Cyclacanthia and Tsitsikamma species that is likely to have been recruited from free-living spirochaetes in the environment. This study sheds new light on the interactions between latrunculid sponges, their dominant bacterial symbionts, and the potential involvement of these bacteria in pyrroloiminoquinone biosynthesis.
- Full Text: false
- Date Issued: 2016
LCT and systemic functional linguistics: Enacting complimentary theories for explanatory power
- Maton, Karl, Martin, James R, Matruglio, Erika S
- Authors: Maton, Karl , Martin, James R , Matruglio, Erika S
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/66491 , vital:28955
- Description: publisher version , Interdisciplinarity is the future. Such is the thrust of pronouncements repeatedly heard across the social sciences and humanities. Interdisciplinarity is often equated with intellectually and socially progressive stances and greater responsiveness to business and workplace needs. Yet such axiological and economic benefits are more often assumed or proclaimed than evidenced or demonstrated (Moore 2011). Moreover，what is declared to be 'interdisciplinary' often comprises the appropriation by literary or philosophical discourses of ideas from other fields rather than genuinely interdisciplinary dialogue. Nonetheless，to highlight the vacuity of much written in its name is not to dismiss the potential of interdisciplinarity itself. There are serious ontological and epistemological arguments for bringing disciplines together in substantive research (Bhaskar and Danermark 2006). Simply put，the social world comprises more than the phenomena addressed by any one discipline. Education，for example，involves at least knowledges， knowers， knowing， and the known, implicating insights from, among others，sociology，linguistics，psychology，and philosophy (Maton 2014b: 212-13). This is not to suggest a single study must encompass the disciplinary map in order to recreate reality in its entirety, Rather，it highlights that drawing on more than one disciplinary approach may offer greater explanatory power when exploring a specific problem-situation.
- Full Text: false
- Date Issued: 2016
- Authors: Maton, Karl , Martin, James R , Matruglio, Erika S
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/66491 , vital:28955
- Description: publisher version , Interdisciplinarity is the future. Such is the thrust of pronouncements repeatedly heard across the social sciences and humanities. Interdisciplinarity is often equated with intellectually and socially progressive stances and greater responsiveness to business and workplace needs. Yet such axiological and economic benefits are more often assumed or proclaimed than evidenced or demonstrated (Moore 2011). Moreover，what is declared to be 'interdisciplinary' often comprises the appropriation by literary or philosophical discourses of ideas from other fields rather than genuinely interdisciplinary dialogue. Nonetheless，to highlight the vacuity of much written in its name is not to dismiss the potential of interdisciplinarity itself. There are serious ontological and epistemological arguments for bringing disciplines together in substantive research (Bhaskar and Danermark 2006). Simply put，the social world comprises more than the phenomena addressed by any one discipline. Education，for example，involves at least knowledges， knowers， knowing， and the known, implicating insights from, among others，sociology，linguistics，psychology，and philosophy (Maton 2014b: 212-13). This is not to suggest a single study must encompass the disciplinary map in order to recreate reality in its entirety, Rather，it highlights that drawing on more than one disciplinary approach may offer greater explanatory power when exploring a specific problem-situation.
- Full Text: false
- Date Issued: 2016
LCT in mixed-methods research: evolving an instrument for quantitative data
- Maton, Karl, Howard, Sarah Katherine
- Authors: Maton, Karl , Howard, Sarah Katherine
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/66479 , vital:28954
- Description: publisher version , A mantra of social science declares a fundamental divide between the quantitative and the qualitative that involves more than methods. According to this depiction, the two methodologies are intrinsically associated with a range of ontological, epistemological, political and moral stances. Each of these constellations of stances is strongly integrated, such that choice of method is held to involve a series of associated choices. Each constellation is also strongly opposed to the other, along axes labelled positivism/constructivism, scientism/humanism, conservative/critical, old/new, among others. These ‘binary constellations’ (Maton 2014b: 148-70) offer a forced choice between two tightly-knit sets of practices that are portrayed as jointly exhaustive and mutually exclusive. So widespread is this methodological binarism that many scholars ‘are left with the impression that they have to pledge allegiance to one research school of thought or the other’ (Johnson and Onwuegbuzie 2004: 14). A competing mantra disclaims this divide. Distinctions underpinning the picture of binary constellations have been regularly dissolved. Arguments that one deals with numbers, the other with words, one studies behaviour, the other reveals meanings, one is hypothetico-deductive, the other inductive, one enables generalization, the other explores singular depth, among others, have been repeatedly undermined (e.g. Hammersley 1992). Indeed, the death of the divide is frequently declared. Calls for ‘transcending’ (Salomon 1991) or ‘getting over’ (Howe 1992) the quantitative-qualitative debate and arguments for mixed-methods research (Brannen 2005; Johnson and Onwuegbuzie 2004) are recurrent. These calls highlight how the methodologies offer complementary insights for research and demonstrate that eschewing either methodology on principle is unnecessarily renouncing potential explanatory power. However, the call to mixed-methods research remains more breached than honoured. Methodological monotheism remains dominant – studies of education and society typically adopt either quantitative or qualitative methods. As we shall discuss, the former is typically associated with the influence of psychology and the latter is often claimed as emblematic of sociology. Studies utilizing the sociological frameworks on which Legitimation Code Theory (LCT) builds have echoed this pattern by overwhelmingly adopting qualitative methods. Accordingly, Part I of this volume begins by exploring how LCT concepts can be enacted in qualitative research (Chapter 2). However, LCT is not limited to one methodology and a growing body of mixed-methods research is engaging with both qualitative and quantitative data. In this chapter we illustrate how this research works and the gains it offers. For resolutely qualitative researchers, the prospect of reading anything quantitative, even in mixed-methods research, may be unenticing. However, it would be a mistake to pass over this chapter, for several reasons. First, we offer insights into research practice that might surprise such scholars. As Bourdieu argued, ‘methodological indictments are too often no more than a disguised way of making a virtue out of necessity, of feigning to dismiss, to ignore in an active way, what one is ignorant of in fact’ (Bourdieu and Wacquant 1992: 226). Our aim is to contribute towards removing this reason for one-sidedness. We show, for example, how quantitative methods confound their common portrayal as neat, straightforward and procedural; they are complex and involved and require craft work and judgement. Our focus is, therefore, more practical than metaphysical. We shall not enter seemingly endless debates over whether the ‘quantitative-qualitative divide’ refers to paradigms, epistemologies or methods and whether these are complementary or incommensurable. Rather, we discuss the development of an instrument for enacting LCT concepts in quantitative methods and ground this account in real examples of mixed-methods research. Specifically, we trace the evolution of an instrument for embedding specialization codes within questionnaires through its creation for research into school music and then its development within studies of educational technology. Given that mathematics can be off-putting to the noviciate, we minimize discussion of statistics and explain measures in lay terms. Second, this is much more than a story of quantitative methods. The evolution of the instrument both shaped qualitative methods and was shaped by the data they generated, offering insights into how qualitative research can more fully engage with LCT. Its development also involved intimate dialogue with theory that shed fresh light on LCT itself, making explicit the ‘gaze’ embodied by the framework (Chapter 1, this volume). We shall highlight wider lessons learned about the craft of enacting LCT in research, lessons of direct relevance for studies using any methods. Third, we shall illustrate the explanatory power offered by using quantitative and qualitative methods together, such as providing a robust basis for detailed findings, identifying wider-scale trends typically inaccessible to qualitative methods that provide a context for their data, and facilitating knowledge-building through greater replicability across contexts and over time. For example, the technology studies built directly on the music studies to cumulatively develop the instrument and generated probably the largest data set in code sociology: 97,386 responses (83,937 student and 13,449 staff surveys) on the organizing principles of academic subjects, alongside 20 in-depth qualitative case studies of secondary schools. This offers a foundation of substantial breadth and depth for making claims about knowledge practices across the disciplinary map and a firm basis on which future research into disciplinary differences can build. Moreover, the quantitative instrument itself can be adopted or adapted in new studies, further enabling cumulative knowledge-building. Given these substantive, methodological and theoretical gains, it is perhaps surprising there exists any temptation to skip past discussion of mixed-methods research. This reflects the methodological character of the fields in which LCT emerged. We thus begin by briefly illustrating how the sociological frameworks on which the theory builds have become distanced from quantitative methods.
- Full Text: false
- Date Issued: 2016
- Authors: Maton, Karl , Howard, Sarah Katherine
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/66479 , vital:28954
- Description: publisher version , A mantra of social science declares a fundamental divide between the quantitative and the qualitative that involves more than methods. According to this depiction, the two methodologies are intrinsically associated with a range of ontological, epistemological, political and moral stances. Each of these constellations of stances is strongly integrated, such that choice of method is held to involve a series of associated choices. Each constellation is also strongly opposed to the other, along axes labelled positivism/constructivism, scientism/humanism, conservative/critical, old/new, among others. These ‘binary constellations’ (Maton 2014b: 148-70) offer a forced choice between two tightly-knit sets of practices that are portrayed as jointly exhaustive and mutually exclusive. So widespread is this methodological binarism that many scholars ‘are left with the impression that they have to pledge allegiance to one research school of thought or the other’ (Johnson and Onwuegbuzie 2004: 14). A competing mantra disclaims this divide. Distinctions underpinning the picture of binary constellations have been regularly dissolved. Arguments that one deals with numbers, the other with words, one studies behaviour, the other reveals meanings, one is hypothetico-deductive, the other inductive, one enables generalization, the other explores singular depth, among others, have been repeatedly undermined (e.g. Hammersley 1992). Indeed, the death of the divide is frequently declared. Calls for ‘transcending’ (Salomon 1991) or ‘getting over’ (Howe 1992) the quantitative-qualitative debate and arguments for mixed-methods research (Brannen 2005; Johnson and Onwuegbuzie 2004) are recurrent. These calls highlight how the methodologies offer complementary insights for research and demonstrate that eschewing either methodology on principle is unnecessarily renouncing potential explanatory power. However, the call to mixed-methods research remains more breached than honoured. Methodological monotheism remains dominant – studies of education and society typically adopt either quantitative or qualitative methods. As we shall discuss, the former is typically associated with the influence of psychology and the latter is often claimed as emblematic of sociology. Studies utilizing the sociological frameworks on which Legitimation Code Theory (LCT) builds have echoed this pattern by overwhelmingly adopting qualitative methods. Accordingly, Part I of this volume begins by exploring how LCT concepts can be enacted in qualitative research (Chapter 2). However, LCT is not limited to one methodology and a growing body of mixed-methods research is engaging with both qualitative and quantitative data. In this chapter we illustrate how this research works and the gains it offers. For resolutely qualitative researchers, the prospect of reading anything quantitative, even in mixed-methods research, may be unenticing. However, it would be a mistake to pass over this chapter, for several reasons. First, we offer insights into research practice that might surprise such scholars. As Bourdieu argued, ‘methodological indictments are too often no more than a disguised way of making a virtue out of necessity, of feigning to dismiss, to ignore in an active way, what one is ignorant of in fact’ (Bourdieu and Wacquant 1992: 226). Our aim is to contribute towards removing this reason for one-sidedness. We show, for example, how quantitative methods confound their common portrayal as neat, straightforward and procedural; they are complex and involved and require craft work and judgement. Our focus is, therefore, more practical than metaphysical. We shall not enter seemingly endless debates over whether the ‘quantitative-qualitative divide’ refers to paradigms, epistemologies or methods and whether these are complementary or incommensurable. Rather, we discuss the development of an instrument for enacting LCT concepts in quantitative methods and ground this account in real examples of mixed-methods research. Specifically, we trace the evolution of an instrument for embedding specialization codes within questionnaires through its creation for research into school music and then its development within studies of educational technology. Given that mathematics can be off-putting to the noviciate, we minimize discussion of statistics and explain measures in lay terms. Second, this is much more than a story of quantitative methods. The evolution of the instrument both shaped qualitative methods and was shaped by the data they generated, offering insights into how qualitative research can more fully engage with LCT. Its development also involved intimate dialogue with theory that shed fresh light on LCT itself, making explicit the ‘gaze’ embodied by the framework (Chapter 1, this volume). We shall highlight wider lessons learned about the craft of enacting LCT in research, lessons of direct relevance for studies using any methods. Third, we shall illustrate the explanatory power offered by using quantitative and qualitative methods together, such as providing a robust basis for detailed findings, identifying wider-scale trends typically inaccessible to qualitative methods that provide a context for their data, and facilitating knowledge-building through greater replicability across contexts and over time. For example, the technology studies built directly on the music studies to cumulatively develop the instrument and generated probably the largest data set in code sociology: 97,386 responses (83,937 student and 13,449 staff surveys) on the organizing principles of academic subjects, alongside 20 in-depth qualitative case studies of secondary schools. This offers a foundation of substantial breadth and depth for making claims about knowledge practices across the disciplinary map and a firm basis on which future research into disciplinary differences can build. Moreover, the quantitative instrument itself can be adopted or adapted in new studies, further enabling cumulative knowledge-building. Given these substantive, methodological and theoretical gains, it is perhaps surprising there exists any temptation to skip past discussion of mixed-methods research. This reflects the methodological character of the fields in which LCT emerged. We thus begin by briefly illustrating how the sociological frameworks on which the theory builds have become distanced from quantitative methods.
- Full Text: false
- Date Issued: 2016
Learning style of Chinese event management students
- Louw, Mattheus J, Louw, Lynette, Li, Yanxia
- Authors: Louw, Mattheus J , Louw, Lynette , Li, Yanxia
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/69167 , vital:29438 , https://doi.org/10.1515/9783110366778-028
- Description: There is a demand for social development in China by establishing, inter alia, a framework focusing on the employability of university graduates and developing self-directed learners. The key to achieving this would be to gain a better understanding of how learning styles, as one of the cognitive factors, contribute towards academic performance in order to provide meaningful learning experiences.
- Full Text: false
- Date Issued: 2016
- Authors: Louw, Mattheus J , Louw, Lynette , Li, Yanxia
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/69167 , vital:29438 , https://doi.org/10.1515/9783110366778-028
- Description: There is a demand for social development in China by establishing, inter alia, a framework focusing on the employability of university graduates and developing self-directed learners. The key to achieving this would be to gain a better understanding of how learning styles, as one of the cognitive factors, contribute towards academic performance in order to provide meaningful learning experiences.
- Full Text: false
- Date Issued: 2016
Legal ethics education in South Africa: possibilities, challenges and opportunities
- Robertson, Michael, Kruuse, Helen
- Authors: Robertson, Michael , Kruuse, Helen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68941 , vital:29341 , http://dx.doi.org/10.1080/02587203.2016.1210934
- Description: Publisher version , The South African legal profession has been subject to harsh criticism in the last few years, leading to what some have called ‘an ethical crisis.’ Although this perception may or may not be warranted, there have been numerous calls for improved ethical legal practices by South African lawyers. This article seeks to contribute to a discussion about the importance of implementing legal ethics education in South African law schools. The authors (a) explore the meaning of ‘ethical legal practice’ by reference to the international literature; (b) examine the way in which legal ethics has so far been presented in the limited South African literature on the topic; (c) argue the need for a more thorough and critical literature on South African lawyers’ ethics, coupled with a commitment to developing a stronger legal ethics culture within the profession and the legal academia; and (d) suggest a possible approach for South African legal ethics education in the future, with reference to recent developments in other countries.
- Full Text: false
- Date Issued: 2016
- Authors: Robertson, Michael , Kruuse, Helen
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68941 , vital:29341 , http://dx.doi.org/10.1080/02587203.2016.1210934
- Description: Publisher version , The South African legal profession has been subject to harsh criticism in the last few years, leading to what some have called ‘an ethical crisis.’ Although this perception may or may not be warranted, there have been numerous calls for improved ethical legal practices by South African lawyers. This article seeks to contribute to a discussion about the importance of implementing legal ethics education in South African law schools. The authors (a) explore the meaning of ‘ethical legal practice’ by reference to the international literature; (b) examine the way in which legal ethics has so far been presented in the limited South African literature on the topic; (c) argue the need for a more thorough and critical literature on South African lawyers’ ethics, coupled with a commitment to developing a stronger legal ethics culture within the profession and the legal academia; and (d) suggest a possible approach for South African legal ethics education in the future, with reference to recent developments in other countries.
- Full Text: false
- Date Issued: 2016
Linking the ‘know-that’ and ‘know-how’ knowledge through games: a quest to evolve the future for science and engineering education
- Vahed, Anisa, McKenna, Sioux, Singh, S
- Authors: Vahed, Anisa , McKenna, Sioux , Singh, S
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66785 , vital:28993 , ISSN 1573-174X , https://doi.org/10.1007/s10734-015-9956-9
- Description: Publisher version , This paper responds to Muller’s notions of ‘knowing-that’ and ‘knowing how’. The paper addresses how educational interventions that are designed in line with targeted discipline-specific subjects can enhance the balance between professional practice and disciplinary knowledge in professionally accredited programmes at universities of technology. The context is a Dental Technology programme at a University of Technology in South Africa. Teaching through discipline-specific games, conceptualised from a game literacies perspective, is proposed as an engaging, interactive pedagogy for learning disciplinary knowledge that potentially encourages access to a particular affinity group. The authors use concepts from Bernstein and Maton to investigate whether epistemic relations or social relations are emphasised through board and digital games designed for two Dental Technology subjects. This paper offers valuable insight into alternative pedagogies that can be adopted into science, technology, engineering, and mathematics education with the aim of paving a pathway towards Muller’s Scenario 3.
- Full Text: false
- Date Issued: 2016
- Authors: Vahed, Anisa , McKenna, Sioux , Singh, S
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66785 , vital:28993 , ISSN 1573-174X , https://doi.org/10.1007/s10734-015-9956-9
- Description: Publisher version , This paper responds to Muller’s notions of ‘knowing-that’ and ‘knowing how’. The paper addresses how educational interventions that are designed in line with targeted discipline-specific subjects can enhance the balance between professional practice and disciplinary knowledge in professionally accredited programmes at universities of technology. The context is a Dental Technology programme at a University of Technology in South Africa. Teaching through discipline-specific games, conceptualised from a game literacies perspective, is proposed as an engaging, interactive pedagogy for learning disciplinary knowledge that potentially encourages access to a particular affinity group. The authors use concepts from Bernstein and Maton to investigate whether epistemic relations or social relations are emphasised through board and digital games designed for two Dental Technology subjects. This paper offers valuable insight into alternative pedagogies that can be adopted into science, technology, engineering, and mathematics education with the aim of paving a pathway towards Muller’s Scenario 3.
- Full Text: false
- Date Issued: 2016
Listening to the ‘Born Frees’: politics and disillusionment in South Africa
- Malila, Vanessa, Garman, Anthea
- Authors: Malila, Vanessa , Garman, Anthea
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158884 , vital:40237 , https://doi.org/10.1080/23743670.2015.1084587
- Description: In 2014 South Africa celebrated 20 years of democracy, and for many of the ‘Born Frees’ – those who came of age politically after 1996 – this was their first opportunity to vote in national elections. With democracy came the promise for South Africa's marginalised majority of voice and agency, but also the implicit promise that their democratically elected government would listen to them. In addition, the South African media have long championed their role as a voice for the voiceless. This article presents work done with youngsters from South Africa's poorest province, the Eastern Cape, in an effort to listen to their experience of politics and to understand their use of the media – especially whether it enables them to speak out and be heard in the public sphere.
- Full Text:
- Date Issued: 2016
- Authors: Malila, Vanessa , Garman, Anthea
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/158884 , vital:40237 , https://doi.org/10.1080/23743670.2015.1084587
- Description: In 2014 South Africa celebrated 20 years of democracy, and for many of the ‘Born Frees’ – those who came of age politically after 1996 – this was their first opportunity to vote in national elections. With democracy came the promise for South Africa's marginalised majority of voice and agency, but also the implicit promise that their democratically elected government would listen to them. In addition, the South African media have long championed their role as a voice for the voiceless. This article presents work done with youngsters from South Africa's poorest province, the Eastern Cape, in an effort to listen to their experience of politics and to understand their use of the media – especially whether it enables them to speak out and be heard in the public sphere.
- Full Text:
- Date Issued: 2016
Lives "on hold": the Daily Sun and the South African identity document
- Authors: Boshoff, Priscilla A
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/143538 , vital:38255 , https://hdl.handle.net/10520/EJC195358
- Description: The relationship between a personal identity and the state-issued Identity Document (ID) is the focus of this article, which examines stories published in the "Horror Affairs" column of the popular South African tabloid, the Daily Sun. These highly emotional stories tell of the despair and desperation felt by individuals at the lack of an ID book, which is blamed on the inefficiency of the state Department of Home Affairs. In order to explicate this relationship I make use of Agamben's notion of "bare life" and the camp in conjunction with Lacan's idea of the Symbolic Order to argue that if the Identity Document provides the means by which the individual is made to signify, the lack of an Identity Document threatens to reduce the individual to "bare life". By publishing the stories of those deprived of the visibility that the ID provides, the Daily Sun, I show, directly engages in this exchange, and, in contrast to Home Affairs, bestows its own even stronger gift of identity by the fact of appearance in its pages.
- Full Text:
- Date Issued: 2016
- Authors: Boshoff, Priscilla A
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/143538 , vital:38255 , https://hdl.handle.net/10520/EJC195358
- Description: The relationship between a personal identity and the state-issued Identity Document (ID) is the focus of this article, which examines stories published in the "Horror Affairs" column of the popular South African tabloid, the Daily Sun. These highly emotional stories tell of the despair and desperation felt by individuals at the lack of an ID book, which is blamed on the inefficiency of the state Department of Home Affairs. In order to explicate this relationship I make use of Agamben's notion of "bare life" and the camp in conjunction with Lacan's idea of the Symbolic Order to argue that if the Identity Document provides the means by which the individual is made to signify, the lack of an Identity Document threatens to reduce the individual to "bare life". By publishing the stories of those deprived of the visibility that the ID provides, the Daily Sun, I show, directly engages in this exchange, and, in contrast to Home Affairs, bestows its own even stronger gift of identity by the fact of appearance in its pages.
- Full Text:
- Date Issued: 2016
Local versus landscape effects of bush encroachment on plant available light, soil moisture, frost occurrence and herbaceous productivity and composition
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
- Authors: Klopper, Chrisna
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3137 , vital:20376
- Description: Bush encroachment is a global phenomenon and a pressing concern for South Africa rangelands. The expansion and increase in density of Vachellia karroo (hereafter referred to aAcacia karroo) has been documented in the Eastern Cape and KwaZulu Natal in South Africa. This increase in woody species in savannas is often at the expense of grass cover and thus is causing concern about how this will impact agriculture due to possible loss of grazing capacity. To understand the impacts of bush encroachment the effect of trees on their micro-climate and abiotic factors and in turn on the herbaceous layer needs to be examined. The objective of this study was to quantify the effect of Acacia karroo encroachment on the light environment, soil moisture and frost occurrence in the sub-canopy and inter-canopy micro-habitats, and how these changes affected herbaceous player productivity and composition. Another question that is being addressed here is whether, and how, the local tree effects scale up in the landscape and whether prediction can be made based on the effects of individual trees. The study was undertaken on a farm, Endwell, in the Smaldeel, Eastern Cape. At the study site, a semi-arid savanna, Acacia karroo has been encroaching since the 1980’s. The study was conducted at three scales: landscape, stand-wide and local scale. The landscape scale was represented by four areas with 0, 21, 45 and 72% tree canopy cover, the stand-wide scale consisted of transects with varying percentages of tree canopy cover within each of the four levels of encroachment. The local scale was represented by the sub-canopy and inter-canopy environment to test the effect of trees. At the local scale plant available light and soil moisture were lower in the sub-canopy than intercanopy regions, with leaf area index being higher in the sub-canopy. This local negative effect of the tree canopy on light and soil moisture in the sub-canopy did not scale up predictably in the landscape. At the stand-wide scale light in the inter-canopy was reduced as shading increased. Frost was excluded from under the canopies and frost incidence decreased at higher tree cover. Grass productivity was reduced in the sub-canopy, possibly due to lower light and soil moisture. Overall biomass increased from the low to medium level of encroachment but lowest at the high level of encroachment. Grass composition and cover was only slightly affected by tree canopies cover and C4 grass species were still present in the sub-canopy and at lower light environments. At the levels of Acacia karroo encroachment encountered at this study site, it seems unlikely that palatable or desirable C4 would be excluded from the system and that a shift from C4 to shade-tolerant species would occur. This is due to tree canopies at the site not reducing light to such anextent that they would outcompete grasses, and likely the very low grazing pressure at thesesites. Herbaceous biomass at these sites were still sufficient to carry a fire in the inter-canopyregion and sufficient grazing for herbivores. In the sub-canopy region fires will be excluded thus with higher the portion of sub-canopy areas increasing at the high levels of encroachment they may interrupt fire spread. Thus it was concluded that Acacia karroo encroachment up to 45% tree cover is currently not creating negative feedback on herbivory, but low stocking rates appear to be key to maintain this.
- Full Text:
- Date Issued: 2016
Louder than the frame:
- Podesva, K L, Beasley, M, Kataoka, M, Ntombela, N
- Authors: Podesva, K L , Beasley, M , Kataoka, M , Ntombela, N
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146211 , vital:38505 , ISBN 9783863359140
- Description: Book abstract. Almost 30 years after the founding of the first curatorial studies program (at the École du Magasin, Grenoble), with the curator remaining a figure of curiosity and fascination in the contemporary art world, a new question has emerged: how do we educate curators? Great Expectations: Prospects for the Future of Curatorial Education explores this question, focusing in particular on the challenges, opportunities and subjects that motivate educators and students. How has curatorial education changed in the past 25 years, and what will the next 25 years bring?.
- Full Text:
- Date Issued: 2016
- Authors: Podesva, K L , Beasley, M , Kataoka, M , Ntombela, N
- Date: 2016
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/146211 , vital:38505 , ISBN 9783863359140
- Description: Book abstract. Almost 30 years after the founding of the first curatorial studies program (at the École du Magasin, Grenoble), with the curator remaining a figure of curiosity and fascination in the contemporary art world, a new question has emerged: how do we educate curators? Great Expectations: Prospects for the Future of Curatorial Education explores this question, focusing in particular on the challenges, opportunities and subjects that motivate educators and students. How has curatorial education changed in the past 25 years, and what will the next 25 years bring?.
- Full Text:
- Date Issued: 2016
Mapping epistemic cultures and learning potential of participants in citizen science projects
- Vallabh, Priya, Lotz-Sisitka, Heila, O'Donoghue, Rob, Schudel, Ingrid J
- Authors: Vallabh, Priya , Lotz-Sisitka, Heila , O'Donoghue, Rob , Schudel, Ingrid J
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/128939 , vital:36192 , https://doi.org/10.1111/cobi.12701
- Description: The ever-widening scope and range of global change and interconnected systemic risks arising from people–environment relationships (social‐ecological risks) appears to be increasing concern among, and involvement of, citizens in an increasingly diversified number of citizen science projects responding to these risks. We examined the relationship between epistemic cultures in citizen science projects and learning potential related to matters of concern. We then developed a typology of purposes and a citizen science epistemic‐cultures heuristic and mapped 56 projects in southern Africa using this framework. The purpose typology represents the range of knowledge‐production purposes, ranging from laboratory science to social learning, whereas the epistemic‐cultures typology is a relational representation of scientist and citizen participation and their approach to knowledge production. Results showed an iterative relationship between matters of fact and matters of concern across the projects; the nexus of citizens’ engagement in knowledge‐production activities varied. The knowledge‐production purposes informed and shaped the epistemic cultures of all the sampled citizen science projects, which in turn influenced the potential for learning within each project. Through a historical review of 3 phases in a long‐term river health‐monitoring project, we found that it is possible to evolve the learning curve of citizen science projects. This evolution involved the development of scientific water monitoring tools, the parallel development of pedagogic practices supporting monitoring activities, and situated engagement around matters of concern within social activism leading to learning‐led change. We conclude that such evolutionary processes serve to increase potential for learning and are necessary if citizen science is to contribute to wider restructuring of the epistemic culture of science under conditions of expanding social-ecological risk.
- Full Text:
- Date Issued: 2016
- Authors: Vallabh, Priya , Lotz-Sisitka, Heila , O'Donoghue, Rob , Schudel, Ingrid J
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/128939 , vital:36192 , https://doi.org/10.1111/cobi.12701
- Description: The ever-widening scope and range of global change and interconnected systemic risks arising from people–environment relationships (social‐ecological risks) appears to be increasing concern among, and involvement of, citizens in an increasingly diversified number of citizen science projects responding to these risks. We examined the relationship between epistemic cultures in citizen science projects and learning potential related to matters of concern. We then developed a typology of purposes and a citizen science epistemic‐cultures heuristic and mapped 56 projects in southern Africa using this framework. The purpose typology represents the range of knowledge‐production purposes, ranging from laboratory science to social learning, whereas the epistemic‐cultures typology is a relational representation of scientist and citizen participation and their approach to knowledge production. Results showed an iterative relationship between matters of fact and matters of concern across the projects; the nexus of citizens’ engagement in knowledge‐production activities varied. The knowledge‐production purposes informed and shaped the epistemic cultures of all the sampled citizen science projects, which in turn influenced the potential for learning within each project. Through a historical review of 3 phases in a long‐term river health‐monitoring project, we found that it is possible to evolve the learning curve of citizen science projects. This evolution involved the development of scientific water monitoring tools, the parallel development of pedagogic practices supporting monitoring activities, and situated engagement around matters of concern within social activism leading to learning‐led change. We conclude that such evolutionary processes serve to increase potential for learning and are necessary if citizen science is to contribute to wider restructuring of the epistemic culture of science under conditions of expanding social-ecological risk.
- Full Text:
- Date Issued: 2016
MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs
- Kibet, Caleb K, Machanick, Philip
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61155 , vital:27985 , http://dx.doi.org/10.1101/065615
- Description: We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that `correct motifs' are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 { this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif.
- Full Text:
- Date Issued: 2016
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61155 , vital:27985 , http://dx.doi.org/10.1101/065615
- Description: We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that `correct motifs' are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 { this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif.
- Full Text:
- Date Issued: 2016
MCD spectroscopy and TD-DFT calculations of magnesium tetra-(15-crown-5-oxanthreno)-phthalocyanine
- Mack, John, Mkhize, Scebi, Safonoya, Evgeniya A, Gorbunova, Yulia G, Tsivadze, Aslan Yu, Nyokong, Tebello
- Authors: Mack, John , Mkhize, Scebi , Safonoya, Evgeniya A , Gorbunova, Yulia G , Tsivadze, Aslan Yu , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/240743 , vital:50867 , xlink:href="https://doi.org/10.1142/S1088424616500322"
- Description: An analysis of the MCD spectroscopy and TD-DFT calculations of magnesium tetra-(15-crown-5-oxanthreno)-phthalocyanine is reported. This study provides a reassessment of an earlier study on the nature of the bands in UV-visible absorption spectra of magnesium and zinc tetra-(15-crown-5-oxanthreno)-phthalocyanine that was based on an analysis of TD-DFT calculations for a series of model complexes with the B3LYP functional. A detailed analysis of MCD spectral data and TD-DFT calculations with the CAM-B3LYP functional for the complete Mg(II) complex provides an additional insight into the optical properties and electronic structures of tetra-(15-crown-5-oxanthreno)-phthalocyanines. Thus, the bands in the Q-band region are reassigned as being due exclusively to the Q transition of Gouterman’s 4-orbital model, since intense pseudo-A1𝒜1 terms are observed in the MCD spectrum in a spectral region that had previously been assigned as charge transfer bands.
- Full Text:
- Date Issued: 2016
- Authors: Mack, John , Mkhize, Scebi , Safonoya, Evgeniya A , Gorbunova, Yulia G , Tsivadze, Aslan Yu , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/240743 , vital:50867 , xlink:href="https://doi.org/10.1142/S1088424616500322"
- Description: An analysis of the MCD spectroscopy and TD-DFT calculations of magnesium tetra-(15-crown-5-oxanthreno)-phthalocyanine is reported. This study provides a reassessment of an earlier study on the nature of the bands in UV-visible absorption spectra of magnesium and zinc tetra-(15-crown-5-oxanthreno)-phthalocyanine that was based on an analysis of TD-DFT calculations for a series of model complexes with the B3LYP functional. A detailed analysis of MCD spectral data and TD-DFT calculations with the CAM-B3LYP functional for the complete Mg(II) complex provides an additional insight into the optical properties and electronic structures of tetra-(15-crown-5-oxanthreno)-phthalocyanines. Thus, the bands in the Q-band region are reassigned as being due exclusively to the Q transition of Gouterman’s 4-orbital model, since intense pseudo-A1𝒜1 terms are observed in the MCD spectrum in a spectral region that had previously been assigned as charge transfer bands.
- Full Text:
- Date Issued: 2016
Miscellaneous provisions
- Arendse, Jacqueline A, Clegg, David, Williams, Robert C
- Authors: Arendse, Jacqueline A , Clegg, David , Williams, Robert C
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/131276 , vital:36548 , https://store.lexisnexis.co.za/products/silke-on-tax-administration-skuZASKUPG1440
- Description: Miscellaneous provisions pertaining to tax administration are explained in this chapter.
- Full Text: false
- Date Issued: 2016
- Authors: Arendse, Jacqueline A , Clegg, David , Williams, Robert C
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/131276 , vital:36548 , https://store.lexisnexis.co.za/products/silke-on-tax-administration-skuZASKUPG1440
- Description: Miscellaneous provisions pertaining to tax administration are explained in this chapter.
- Full Text: false
- Date Issued: 2016
Modelling transport of inshore and deep-spawned chokka squid (Loligo reynaudi) paralarvae off South Africa: the potential contribution of deep spawning to recruitment
- Downey-Breedt, Nicola, Roberts, Michael J, Sauer, Warwick H H, Chang, N
- Authors: Downey-Breedt, Nicola , Roberts, Michael J , Sauer, Warwick H H , Chang, N
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125183 , vital:35742 , https://doi.10.1111/fog.12132
- Description: The South African chokka squid, Loligo reynaudi, spawns both inshore (≤70 m) and on the mid-shelf (71–130 m) of the Eastern Agulhas Bank. The fate of these deep-spawned hatchlings and their potential contribution to recruitment is as yet unknown. Lagrangian ROMS-IBM (Regional Ocean Modelling System-Individual-Based Model) simulations confirm westward transport of inshore and deep-spawned hatchlings, but also indicate that the potential exists for paralarvae hatched on the Eastern Agulhas Bank deep spawning grounds to be removed from the shelf ecosystem. Using a ROMS-IBM, this study determined the transport and recruitment success of deepspawned hatchlings relative to inshore-hatched paralarvae. A total of 12 release sites were incorporated into the model, six inshore and six deep-spawning sites. Paralarval survival was estimated based on timely transport to nursery grounds, adequate retention within the nursery grounds and retention on the Agulhas Bank shelf. Paralarval transport and survival were dependent on both spawning location and time of hatching. Results suggest the importance of the south coast as a nursery area for inshore-hatched paralarvae, and similarly the cold ridge nursery grounds for deep-hatched paralarvae. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off the Tsitsikamma coast, and the beneficial currents during this period (as indicated by the model results) it can be concluded that deep spawning may at times contribute significantly to recruitment.
- Full Text:
- Date Issued: 2016
- Authors: Downey-Breedt, Nicola , Roberts, Michael J , Sauer, Warwick H H , Chang, N
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125183 , vital:35742 , https://doi.10.1111/fog.12132
- Description: The South African chokka squid, Loligo reynaudi, spawns both inshore (≤70 m) and on the mid-shelf (71–130 m) of the Eastern Agulhas Bank. The fate of these deep-spawned hatchlings and their potential contribution to recruitment is as yet unknown. Lagrangian ROMS-IBM (Regional Ocean Modelling System-Individual-Based Model) simulations confirm westward transport of inshore and deep-spawned hatchlings, but also indicate that the potential exists for paralarvae hatched on the Eastern Agulhas Bank deep spawning grounds to be removed from the shelf ecosystem. Using a ROMS-IBM, this study determined the transport and recruitment success of deepspawned hatchlings relative to inshore-hatched paralarvae. A total of 12 release sites were incorporated into the model, six inshore and six deep-spawning sites. Paralarval survival was estimated based on timely transport to nursery grounds, adequate retention within the nursery grounds and retention on the Agulhas Bank shelf. Paralarval transport and survival were dependent on both spawning location and time of hatching. Results suggest the importance of the south coast as a nursery area for inshore-hatched paralarvae, and similarly the cold ridge nursery grounds for deep-hatched paralarvae. Possible relationships between periods of highest recruitment success and spawning peaks were identified for both spawning habitats. Based on the likely autumn increase in deep spawning off the Tsitsikamma coast, and the beneficial currents during this period (as indicated by the model results) it can be concluded that deep spawning may at times contribute significantly to recruitment.
- Full Text:
- Date Issued: 2016
Molecular genetic, life-history and morphological variation in a coastal warm-temperate sciaenid fish: evidence for an upwelling-driven speciation event
- Henriques, Romina, Potts, Warren M, Sauer, Warwick H H, Santos, Carmen V D, Kruger, Jerraleigh, Thomas, Jessica A, Shaw, Paul W
- Authors: Henriques, Romina , Potts, Warren M , Sauer, Warwick H H , Santos, Carmen V D , Kruger, Jerraleigh , Thomas, Jessica A , Shaw, Paul W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125252 , vital:35750 , http://dx.doi.10.1111/jbi.12829
- Description: The marine environment is punctuated by biogeographical barriers that limit dispersal and gene flow in otherwise widespread species (Teske et al., 2011a,b; Briggs & Bowen, 2012; Luiz et al., 2012). These barriers may be physical obstacles such as landmasses (e.g. Isthmus of Panama) or less intuitive features such as deep water (Lessios et al., 2003), freshwater outflows (Floeter et al., 2008) or oceanographic features (Shaw et al., 2004; Galarza et al., 2009; von der Heyden et al., 2011). Upwelling cells and sea surface temperature (SSTs) gradients in particular are known to disrupt gene flow, leading to divergence of allopatric populations and species (Waters & Roy, 2004; Teske et al., 2011a; Henriques et al., 2012, 2014, 2015). However, as oceanographic features are seldom permanent and frequently subject to considerable environmental variability, many barriers often permit some level of permeability to dispersal (Floeter et al., 2008). Other processes may influence the persistence of differentiated allopatric taxa across such physical barriers (Bradbury et al., 2008), with ecological divergence (and diversifying selection) being reported as a major evolutionary process influencing the biogeographical distributions of marine species (Pelc et al., 2009; Teske et al., 2011a; Gaither et al., 2015).
- Full Text:
- Date Issued: 2016
- Authors: Henriques, Romina , Potts, Warren M , Sauer, Warwick H H , Santos, Carmen V D , Kruger, Jerraleigh , Thomas, Jessica A , Shaw, Paul W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/125252 , vital:35750 , http://dx.doi.10.1111/jbi.12829
- Description: The marine environment is punctuated by biogeographical barriers that limit dispersal and gene flow in otherwise widespread species (Teske et al., 2011a,b; Briggs & Bowen, 2012; Luiz et al., 2012). These barriers may be physical obstacles such as landmasses (e.g. Isthmus of Panama) or less intuitive features such as deep water (Lessios et al., 2003), freshwater outflows (Floeter et al., 2008) or oceanographic features (Shaw et al., 2004; Galarza et al., 2009; von der Heyden et al., 2011). Upwelling cells and sea surface temperature (SSTs) gradients in particular are known to disrupt gene flow, leading to divergence of allopatric populations and species (Waters & Roy, 2004; Teske et al., 2011a; Henriques et al., 2012, 2014, 2015). However, as oceanographic features are seldom permanent and frequently subject to considerable environmental variability, many barriers often permit some level of permeability to dispersal (Floeter et al., 2008). Other processes may influence the persistence of differentiated allopatric taxa across such physical barriers (Bradbury et al., 2008), with ecological divergence (and diversifying selection) being reported as a major evolutionary process influencing the biogeographical distributions of marine species (Pelc et al., 2009; Teske et al., 2011a; Gaither et al., 2015).
- Full Text:
- Date Issued: 2016
Molecular identification of Azolla invasions in Africa: The Azolla specialist, Stenopelmus rufinasus proves to be an excellent taxonomist
- Madeira, P T, Dray, F Allen, Coetzee, Julie A, Paterson, Iain D, Tipping, Philip W
- Authors: Madeira, P T , Dray, F Allen , Coetzee, Julie A , Paterson, Iain D , Tipping, Philip W
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424765 , vital:72182 , xlink:href="https://doi.org/10.1016/j.sajb.2016.03.007"
- Description: Biological control of Azolla filiculoides in South Africa with the Azolla specialist Stenopelmus rufinasus has been highly successful. However, field surveys showed that the agent utilized another Azolla species, thought to be the native Azolla pinnata subsp. africana, which contradicted host specificity trials. It is notoriously difficult to determine Azolla species based on morphology so genetic analyses were required to confirm the identity of the Azolla used by the agent. Extensive sampling was conducted and samples were sequenced at the trnL-trnF and trnG-trnR chloroplastic regions and the nuclear ITS1 region. Current literature reported A. filiculoides as the only Section Azolla species in southern Africa but 24 samples were identified as Azolla cristata, an introduced species within Section Azolla that was not used during host specificity trials. A. pinnata subsp. africana was only located at one site in southern Africa, while the alien A. pinnata subsp. asiatica was located at three. What was thought to be A. pinnata subsp. africana was in fact A. cristata, a closer relative of A. filiculoides and a suitable host according to specificity trials. This study confirms that S. rufinasus is a proficient Azolla taxonomist but also supports the use of molecular techniques for resolving taxonomic conundrums.
- Full Text:
- Date Issued: 2016
- Authors: Madeira, P T , Dray, F Allen , Coetzee, Julie A , Paterson, Iain D , Tipping, Philip W
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/424765 , vital:72182 , xlink:href="https://doi.org/10.1016/j.sajb.2016.03.007"
- Description: Biological control of Azolla filiculoides in South Africa with the Azolla specialist Stenopelmus rufinasus has been highly successful. However, field surveys showed that the agent utilized another Azolla species, thought to be the native Azolla pinnata subsp. africana, which contradicted host specificity trials. It is notoriously difficult to determine Azolla species based on morphology so genetic analyses were required to confirm the identity of the Azolla used by the agent. Extensive sampling was conducted and samples were sequenced at the trnL-trnF and trnG-trnR chloroplastic regions and the nuclear ITS1 region. Current literature reported A. filiculoides as the only Section Azolla species in southern Africa but 24 samples were identified as Azolla cristata, an introduced species within Section Azolla that was not used during host specificity trials. A. pinnata subsp. africana was only located at one site in southern Africa, while the alien A. pinnata subsp. asiatica was located at three. What was thought to be A. pinnata subsp. africana was in fact A. cristata, a closer relative of A. filiculoides and a suitable host according to specificity trials. This study confirms that S. rufinasus is a proficient Azolla taxonomist but also supports the use of molecular techniques for resolving taxonomic conundrums.
- Full Text:
- Date Issued: 2016