Inferring direct DNA binding from ChIP-seq
- Bailey, Timothy L, Machanick, Philip
- Authors: Bailey, Timothy L , Machanick, Philip
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439314 , vital:73565 , https://doi.org/10.1093/nar/gks433
- Description: Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo . However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose ‘central motif enrichment analysis’ (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. We describe a novel visualization and statistical analysis tool—CentriMo—that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions and displays the positional distributions of predicted sites. Using CentriMo for motif enrichment analysis, we provide evidence that one transcription factor (Nanog) has different binding affinity in vivo than in vitro , that another binds DNA cooperatively (E2f1), and confirm the in vivo affinity of NFIC, rescuing a difficult ChIP-seq data set. In another data set, CentriMo strongly suggests that there is no evidence of direct DNA binding by the ChIP-ed factor (Smad1). CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net . All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a .
- Full Text:
- Date Issued: 2012
- Authors: Bailey, Timothy L , Machanick, Philip
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439314 , vital:73565 , https://doi.org/10.1093/nar/gks433
- Description: Genome-wide binding data from transcription factor ChIP-seq experiments is the best source of information for inferring the relative DNA-binding affinity of these proteins in vivo . However, standard motif enrichment analysis and motif discovery approaches sometimes fail to correctly identify the binding motif for the ChIP-ed factor. To overcome this problem, we propose ‘central motif enrichment analysis’ (CMEA), which is based on the observation that the positional distribution of binding sites matching the direct-binding motif tends to be unimodal, well centered and maximal in the precise center of the ChIP-seq peak regions. We describe a novel visualization and statistical analysis tool—CentriMo—that identifies the region of maximum central enrichment in a set of ChIP-seq peak regions and displays the positional distributions of predicted sites. Using CentriMo for motif enrichment analysis, we provide evidence that one transcription factor (Nanog) has different binding affinity in vivo than in vitro , that another binds DNA cooperatively (E2f1), and confirm the in vivo affinity of NFIC, rescuing a difficult ChIP-seq data set. In another data set, CentriMo strongly suggests that there is no evidence of direct DNA binding by the ChIP-ed factor (Smad1). CentriMo is now part of the MEME Suite software package available at http://meme.nbcr.net . All data and output files presented here are available at: http://research.imb.uq.edu.au/t.bailey/sd/Bailey2011a .
- Full Text:
- Date Issued: 2012
Institutional economics and the environment
- Authors: Fraser, Gavin C G
- Date: 2012
- Language: English
- Type: Text
- Identifier: vital:573 , http://hdl.handle.net/10962/d1006130
- Description: [From text] What is Institutional Economics? Before delving into the concept of institutional economics, it will be useful to explain what is meant by institutions because institutions in economics have a particular meaning. The most commonly agreed upon definition for institutions is a set of formal and informal rules of conduct that facilitate coordination or govern relationships between individuals or groups. The formal rules include laws, contracts, political systems, organisations, and markets, while the informal rules of conduct consist of norms, traditions, customs, value systems, religions and sociological trends. Institutions provide for more certainty in human interaction (North, 1990) and have an influence on outcomes such as economic performance, efficiency, economic growth and development. They can either benefit or hinder these economic measures. Williamson (2000) noted that new institutional economics operates at both the macro and micro levels. The macro level deals with the institutional environment, or the rules of the game, which affect the behaviour and performance of economic actors and in which organisational forms and transactions are embedded. Williamson (1993) described it as the set of fundamental political, social and legal ground rules that establish the basis for production, exchange and distribution. The micro level analysis known as the institutional arrangement, on the other hand, deals with the institutions of governance. These refer to the modes of managing transaction costs and include issues of social capital, property rights and collective action. Here the focus is on the individual transaction and the questions regarding organisational forms (private property versus common pool resources) are analysed. An institutional arrangement is an arrangement between economic units that govern the ways in which its members can co-operate or compete.
- Full Text:
- Date Issued: 2012
- Authors: Fraser, Gavin C G
- Date: 2012
- Language: English
- Type: Text
- Identifier: vital:573 , http://hdl.handle.net/10962/d1006130
- Description: [From text] What is Institutional Economics? Before delving into the concept of institutional economics, it will be useful to explain what is meant by institutions because institutions in economics have a particular meaning. The most commonly agreed upon definition for institutions is a set of formal and informal rules of conduct that facilitate coordination or govern relationships between individuals or groups. The formal rules include laws, contracts, political systems, organisations, and markets, while the informal rules of conduct consist of norms, traditions, customs, value systems, religions and sociological trends. Institutions provide for more certainty in human interaction (North, 1990) and have an influence on outcomes such as economic performance, efficiency, economic growth and development. They can either benefit or hinder these economic measures. Williamson (2000) noted that new institutional economics operates at both the macro and micro levels. The macro level deals with the institutional environment, or the rules of the game, which affect the behaviour and performance of economic actors and in which organisational forms and transactions are embedded. Williamson (1993) described it as the set of fundamental political, social and legal ground rules that establish the basis for production, exchange and distribution. The micro level analysis known as the institutional arrangement, on the other hand, deals with the institutions of governance. These refer to the modes of managing transaction costs and include issues of social capital, property rights and collective action. Here the focus is on the individual transaction and the questions regarding organisational forms (private property versus common pool resources) are analysed. An institutional arrangement is an arrangement between economic units that govern the ways in which its members can co-operate or compete.
- Full Text:
- Date Issued: 2012
Large pollen loads of a South African asclepiad do not interfere with the foraging behaviour or efficiency of pollinating honey bees
- Coombs, Gareth, Dold, Anthony P, Brassine, Eleanor I, Peter, Craig I
- Authors: Coombs, Gareth , Dold, Anthony P , Brassine, Eleanor I , Peter, Craig I
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6509 , http://hdl.handle.net/10962/d1005936
- Description: The pollen of asclepiads (Asclepiadoideae, Apocynaceae) and most orchids (Orchidaceae) are packaged as large aggregations known as pollinaria that are removed as entire units by pollinators. In some instances, individual pollinators may accumulate large loads of these pollinaria. We found that the primary pollinator of Cynanchum ellipticum (Apocynaceae-Asclepiadoideae), the honey bee Apis mellifera, accumulate very large agglomerations of pollinaria on their mouthparts when foraging on this species. We tested whether large pollinarium loads negatively affected the foraging behaviour and foraging efficiency of honey bees by slowing foraging speeds or causing honey bees to visit fewer flowers, and found no evidence to suggest that large pollinarium loads altered foraging behaviour. C. ellipticum displayed consistently high levels of pollination success and pollen transfer efficiency (PTE). This may be a consequence of efficiently loading large numbers of pollinaria onto pollinators even when primary points of attachment on pollinators are already occupied and doing so in a manner that does not impact the foraging behaviour of pollinating insects.
- Full Text:
- Date Issued: 2012
- Authors: Coombs, Gareth , Dold, Anthony P , Brassine, Eleanor I , Peter, Craig I
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6509 , http://hdl.handle.net/10962/d1005936
- Description: The pollen of asclepiads (Asclepiadoideae, Apocynaceae) and most orchids (Orchidaceae) are packaged as large aggregations known as pollinaria that are removed as entire units by pollinators. In some instances, individual pollinators may accumulate large loads of these pollinaria. We found that the primary pollinator of Cynanchum ellipticum (Apocynaceae-Asclepiadoideae), the honey bee Apis mellifera, accumulate very large agglomerations of pollinaria on their mouthparts when foraging on this species. We tested whether large pollinarium loads negatively affected the foraging behaviour and foraging efficiency of honey bees by slowing foraging speeds or causing honey bees to visit fewer flowers, and found no evidence to suggest that large pollinarium loads altered foraging behaviour. C. ellipticum displayed consistently high levels of pollination success and pollen transfer efficiency (PTE). This may be a consequence of efficiently loading large numbers of pollinaria onto pollinators even when primary points of attachment on pollinators are already occupied and doing so in a manner that does not impact the foraging behaviour of pollinating insects.
- Full Text:
- Date Issued: 2012
Mapping the most significant computer hacking events to a temporal computer attack model
- Van Heerden, Renier, Pieterse, Heloise, Irwin, Barry V W
- Authors: Van Heerden, Renier , Pieterse, Heloise , Irwin, Barry V W
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429950 , vital:72654 , https://doi.org/10.1007/978-3-642-33332-3_21
- Description: This paper presents eight of the most significant computer hacking events (also known as computer attacks). These events were selected because of their unique impact, methodology, or other properties. A temporal computer attack model is presented that can be used to model computer based attacks. This model consists of the following stages: Target Identification, Reconnaissance, Attack, and Post-Attack Recon-naissance stages. The Attack stage is separated into: Ramp-up, Dam-age and Residue. This paper demonstrates how our eight significant hacking events are mapped to the temporal computer attack model. The temporal computer attack model becomes a valuable asset in the protection of critical infrastructure by being able to detect similar attacks earlier.
- Full Text:
- Date Issued: 2012
- Authors: Van Heerden, Renier , Pieterse, Heloise , Irwin, Barry V W
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/429950 , vital:72654 , https://doi.org/10.1007/978-3-642-33332-3_21
- Description: This paper presents eight of the most significant computer hacking events (also known as computer attacks). These events were selected because of their unique impact, methodology, or other properties. A temporal computer attack model is presented that can be used to model computer based attacks. This model consists of the following stages: Target Identification, Reconnaissance, Attack, and Post-Attack Recon-naissance stages. The Attack stage is separated into: Ramp-up, Dam-age and Residue. This paper demonstrates how our eight significant hacking events are mapped to the temporal computer attack model. The temporal computer attack model becomes a valuable asset in the protection of critical infrastructure by being able to detect similar attacks earlier.
- Full Text:
- Date Issued: 2012
Peat formation in the context of the development of the Mkuze floodplain on the coastal plain of Maputaland, South Africa:
- Ellery, William F N, Grenfell, Suzanne E, Grenfell, Michael C, Humphries, M S, Barnes, K, Dahlberg, S, Kindness, A
- Authors: Ellery, William F N , Grenfell, Suzanne E , Grenfell, Michael C , Humphries, M S , Barnes, K , Dahlberg, S , Kindness, A
- Date: 2012
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/144354 , vital:38338 , DOI: 10.1016/j.geomorph.2011.11.009
- Description: This paper examines the geomorphological and sedimentological development of blocked-valley lakes in the Mkuze floodplain on the coastal plain of Maputaland, northern KwaZulu-Natal, South Africa. Blocked tributary valley lakes north of the floodplain become progressively shorter, broader, and less linear toward the eastern (downstream) end of the east–west oriented Mkuze floodplain. Clastic sediment forms surface sedimentary fill in tributary valleys in the west, while peat predominates tributary valley fill in the east. Two contrasting adjacent tributary valleys were examined, the more western Yengweni dominated by clastic sediment at the surface, and the more eastern Totweni with peat.
- Full Text:
- Date Issued: 2012
- Authors: Ellery, William F N , Grenfell, Suzanne E , Grenfell, Michael C , Humphries, M S , Barnes, K , Dahlberg, S , Kindness, A
- Date: 2012
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/144354 , vital:38338 , DOI: 10.1016/j.geomorph.2011.11.009
- Description: This paper examines the geomorphological and sedimentological development of blocked-valley lakes in the Mkuze floodplain on the coastal plain of Maputaland, northern KwaZulu-Natal, South Africa. Blocked tributary valley lakes north of the floodplain become progressively shorter, broader, and less linear toward the eastern (downstream) end of the east–west oriented Mkuze floodplain. Clastic sediment forms surface sedimentary fill in tributary valleys in the west, while peat predominates tributary valley fill in the east. Two contrasting adjacent tributary valleys were examined, the more western Yengweni dominated by clastic sediment at the surface, and the more eastern Totweni with peat.
- Full Text:
- Date Issued: 2012
Performance optimisation of sequential programs on multi-core processors
- Tristram, Waide B, Bradshaw, Karen
- Authors: Tristram, Waide B , Bradshaw, Karen
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/477111 , vital:78046 , ISBN 9781450313087 , https://doi.org/10.1145/2389836.2389851
- Description: With the increasing availability of multi-core processors, the sequential programming paradigm is no longer capable of harnessing the full power of processors. Parallel programming is however, generally complex and requires more expertise than the traditional sequential programming model. On the other hand, there are a multitude of optimisations for sequential programs that can exploit multiple cores without much effort by the programmer. The primary goal of this research is to identify available tools and techniques to aid programmers in the process of optimising C/C++ programs for execution on multi-processors. Using a couple of example programs we show that improved performance is possible using the proposed methodology. However, the choice of optimisation is dependent on the type of problem being solved and there is no generic best choice for all classes of problems.
- Full Text:
- Date Issued: 2012
- Authors: Tristram, Waide B , Bradshaw, Karen
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/477111 , vital:78046 , ISBN 9781450313087 , https://doi.org/10.1145/2389836.2389851
- Description: With the increasing availability of multi-core processors, the sequential programming paradigm is no longer capable of harnessing the full power of processors. Parallel programming is however, generally complex and requires more expertise than the traditional sequential programming model. On the other hand, there are a multitude of optimisations for sequential programs that can exploit multiple cores without much effort by the programmer. The primary goal of this research is to identify available tools and techniques to aid programmers in the process of optimising C/C++ programs for execution on multi-processors. Using a couple of example programs we show that improved performance is possible using the proposed methodology. However, the choice of optimisation is dependent on the type of problem being solved and there is no generic best choice for all classes of problems.
- Full Text:
- Date Issued: 2012
Prediction of water temperature metrics using spatial modelling in the Eastern and Western Cape, South Africa
- Rivers-Moore, Nick A, Mantel, Sukhmani K, Dallas, Helen F
- Authors: Rivers-Moore, Nick A , Mantel, Sukhmani K , Dallas, Helen F
- Date: 2012
- Language: English
- Type: text , Article
- Identifier: vital:7071 , http://hdl.handle.net/10962/d1003947 , http://www.scielo.org.za/scielo.php?pid=S1816-79502012000200002&script=sci_arttext
- Description: Key aspects of a river's temperature regime are described by magnitudes, timing and durations of thermal events, and frequencies of extreme exceedance events. To understand alterations to thermal regimes, it is necessary to describe thermal time series based on these statistics. Classification of sites based on their thermal metrics, and understanding of spatial patterns of these thermal statistics, provides a powerful approach for comparing study sites against reference sites. Water temperature regime dynamics should be viewed regionally, where regional divisions have an inherent underpinning by an understanding of natural thermal variability. The aim of this research was to link key water temperature metrics to readily-mapped environmental surrogates, and to produce spatial images of temperature metrics: 37 temperature metrics were derived for 12 months of sub-daily water temperatures at 90 sites in the Eastern Cape and Western Cape provinces, South Africa. These metrics were correlated with 16 environmental variables. Correlations enabled development of multiple regression models which facilitated mapping of temperature metrics over the study area. This approach has the potential to be applied at a national scale as more thermal time series are collected nationally. It is argued that the appropriateness of management decisions in rivers can be improved by including guidelines for thermal metrics at a regional scale. Such maps could facilitate incorporation of a temperature component into management guidelines for water resources.
- Full Text:
- Date Issued: 2012
- Authors: Rivers-Moore, Nick A , Mantel, Sukhmani K , Dallas, Helen F
- Date: 2012
- Language: English
- Type: text , Article
- Identifier: vital:7071 , http://hdl.handle.net/10962/d1003947 , http://www.scielo.org.za/scielo.php?pid=S1816-79502012000200002&script=sci_arttext
- Description: Key aspects of a river's temperature regime are described by magnitudes, timing and durations of thermal events, and frequencies of extreme exceedance events. To understand alterations to thermal regimes, it is necessary to describe thermal time series based on these statistics. Classification of sites based on their thermal metrics, and understanding of spatial patterns of these thermal statistics, provides a powerful approach for comparing study sites against reference sites. Water temperature regime dynamics should be viewed regionally, where regional divisions have an inherent underpinning by an understanding of natural thermal variability. The aim of this research was to link key water temperature metrics to readily-mapped environmental surrogates, and to produce spatial images of temperature metrics: 37 temperature metrics were derived for 12 months of sub-daily water temperatures at 90 sites in the Eastern Cape and Western Cape provinces, South Africa. These metrics were correlated with 16 environmental variables. Correlations enabled development of multiple regression models which facilitated mapping of temperature metrics over the study area. This approach has the potential to be applied at a national scale as more thermal time series are collected nationally. It is argued that the appropriateness of management decisions in rivers can be improved by including guidelines for thermal metrics at a regional scale. Such maps could facilitate incorporation of a temperature component into management guidelines for water resources.
- Full Text:
- Date Issued: 2012
Prediction of water temperature metrics using spatial modelling in the Eastern and Western Cape, South Africa
- Rivers-Moore, Nick A, Mantel, Sukhmani K, Dallas, Helen F
- Authors: Rivers-Moore, Nick A , Mantel, Sukhmani K , Dallas, Helen F
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/438180 , vital:73441 , ISBN 1816-7950 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2651.pdf
- Description: Key aspects of a river’s temperature regime are described by magnitudes, timing and durations of thermal events, and frequencies of extreme exceedance events. To understand alterations to thermal regimes, it is necessary to describe thermal time series based on these statistics. Classification of sites based on their thermal met-rics, and understanding of spatial patterns of these thermal statistics, provides a powerful approach for comparing study sites against reference sites. Water tem-perature regime dynamics should be viewed regionally, where regional divisions have an inherent underpinning by an understanding of natural thermal variability. The aim of this research was to link key water temperature metrics to readi-lymapped environmental surrogates, and to produce spatial images of temperature metrics: 37 temperature metrics were derived for 12 months of sub-daily water temperatures at 90 sites in the Eastern Cape and Western Cape provinces, South Africa.
- Full Text:
- Date Issued: 2012
- Authors: Rivers-Moore, Nick A , Mantel, Sukhmani K , Dallas, Helen F
- Date: 2012
- Subjects: To be catalogued
- Language: English
- Type: text , report
- Identifier: http://hdl.handle.net/10962/438180 , vital:73441 , ISBN 1816-7950 , https://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2651.pdf
- Description: Key aspects of a river’s temperature regime are described by magnitudes, timing and durations of thermal events, and frequencies of extreme exceedance events. To understand alterations to thermal regimes, it is necessary to describe thermal time series based on these statistics. Classification of sites based on their thermal met-rics, and understanding of spatial patterns of these thermal statistics, provides a powerful approach for comparing study sites against reference sites. Water tem-perature regime dynamics should be viewed regionally, where regional divisions have an inherent underpinning by an understanding of natural thermal variability. The aim of this research was to link key water temperature metrics to readi-lymapped environmental surrogates, and to produce spatial images of temperature metrics: 37 temperature metrics were derived for 12 months of sub-daily water temperatures at 90 sites in the Eastern Cape and Western Cape provinces, South Africa.
- Full Text:
- Date Issued: 2012
Treatment of post traumatic stress disorder following an armed robbery : a case study testing the transportability of trauma-focused cognitive-behavioural therapy to urban Africans
- Drake, B, Edwards, David J A
- Authors: Drake, B , Edwards, David J A
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6225 , http://hdl.handle.net/10962/d1007775
- Description: John, an urban African male who developed post traumatic stress disorder (PTSD) following an armed robbery at the petrol station where he worked, was treated with 12 sessions of Trauma-focused cognitive behaviour therapy. Intervention involved a combination of psycho-education, prolonged imaginal exposure, cognitive restructuring and behavioural assignments. This article is a systematic case study of his treatment which included a comprehensive narrative and tracking of progress by means of the Post traumatic Diagnostic Scale. John responded well to the treatment, finding it acceptable and credible and remained free of PTSD symptoms at 15 months follow up. It is argued, based on the principles of Elliott’s Hermeneutic Single Case Efficacy Design, that there is evidence from within the narrative that it was the treatment that led to remission of symptoms. This case study demonstrates the cognitive, emotional and behavioural processes underlying John’s PTSD, which fits with those extensively described in the research literature, and that this evidence-based treatment developed in a westernised context is transportable to work with urban Africans.
- Full Text:
- Date Issued: 2012
- Authors: Drake, B , Edwards, David J A
- Date: 2012
- Language: English
- Type: Article
- Identifier: vital:6225 , http://hdl.handle.net/10962/d1007775
- Description: John, an urban African male who developed post traumatic stress disorder (PTSD) following an armed robbery at the petrol station where he worked, was treated with 12 sessions of Trauma-focused cognitive behaviour therapy. Intervention involved a combination of psycho-education, prolonged imaginal exposure, cognitive restructuring and behavioural assignments. This article is a systematic case study of his treatment which included a comprehensive narrative and tracking of progress by means of the Post traumatic Diagnostic Scale. John responded well to the treatment, finding it acceptable and credible and remained free of PTSD symptoms at 15 months follow up. It is argued, based on the principles of Elliott’s Hermeneutic Single Case Efficacy Design, that there is evidence from within the narrative that it was the treatment that led to remission of symptoms. This case study demonstrates the cognitive, emotional and behavioural processes underlying John’s PTSD, which fits with those extensively described in the research literature, and that this evidence-based treatment developed in a westernised context is transportable to work with urban Africans.
- Full Text:
- Date Issued: 2012
A ring-closing metathesis approach to eight-membered benzannelated scaffolds and subsequent internal alkene isomerizations
- Taher, Abu, Aderibigbe, Blessing A, Morgans, Garreth L, Madeley, Lee G, Khanye, Setshaba D, Van der Westhuizen, Leandi, Fernandes, Manuel A, Smith, Vincent J, Michael, Joseph P, Green, Ivan R, Van Otterlo, Willem A L
- Authors: Taher, Abu , Aderibigbe, Blessing A , Morgans, Garreth L , Madeley, Lee G , Khanye, Setshaba D , Van der Westhuizen, Leandi , Fernandes, Manuel A , Smith, Vincent J , Michael, Joseph P , Green, Ivan R , Van Otterlo, Willem A L
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66252 , vital:28925 , https://doi.org/10.1016/j.tet.2012.12.043
- Description: publisher version , A set of eight-membered benzannelated heterocycles containing two heteroatoms (O,O, NR,NR and O,NR where R=protecting group) was synthesized by ring-closing metathesis from the corresponding ortho-bis-allyl precursors. In this manner, 7-methoxy-2,5-dihydro-1,6-benzodioxocine, 1,2,5,6-tetrahydro-1,6-benzodiazocines, 5,6-dihydro-2H-1,6-benzoxazocines and 5,6,9,10-tetrahydropyrido[2,3-b][1,4]diazocine were synthesized. A number of these compounds were then treated with the catalyst [RuClH(CO)(PPh3)3] to facilitate isomerization of the alkene into conjugation with the heteroatoms in the eight-membered ring. Quite surprisingly, an equal ratio of regioisomers was obtained, even if the heteroatoms were different.
- Full Text: false
- Date Issued: 2013
- Authors: Taher, Abu , Aderibigbe, Blessing A , Morgans, Garreth L , Madeley, Lee G , Khanye, Setshaba D , Van der Westhuizen, Leandi , Fernandes, Manuel A , Smith, Vincent J , Michael, Joseph P , Green, Ivan R , Van Otterlo, Willem A L
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66252 , vital:28925 , https://doi.org/10.1016/j.tet.2012.12.043
- Description: publisher version , A set of eight-membered benzannelated heterocycles containing two heteroatoms (O,O, NR,NR and O,NR where R=protecting group) was synthesized by ring-closing metathesis from the corresponding ortho-bis-allyl precursors. In this manner, 7-methoxy-2,5-dihydro-1,6-benzodioxocine, 1,2,5,6-tetrahydro-1,6-benzodiazocines, 5,6-dihydro-2H-1,6-benzoxazocines and 5,6,9,10-tetrahydropyrido[2,3-b][1,4]diazocine were synthesized. A number of these compounds were then treated with the catalyst [RuClH(CO)(PPh3)3] to facilitate isomerization of the alkene into conjugation with the heteroatoms in the eight-membered ring. Quite surprisingly, an equal ratio of regioisomers was obtained, even if the heteroatoms were different.
- Full Text: false
- Date Issued: 2013
Ancient and modern hybridization between Lucilia sericata and L. cuprina (Diptera: Calliphoridae)
- Williams, Kirstin A, Villet, Martin H
- Authors: Williams, Kirstin A , Villet, Martin H
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442633 , vital:74017 , 10.14411/eje.2013.029
- Description: There are important but inconsistent differences in breeding site preference between the blow flies Lucilia sericata (Meigen, 1826) and L. cuprina (Wiedemann, 1830)(Diptera: Calliphoridae) that have significance for medical and veterinary science. These inconsistencies might arise from hybridisation. The species are difficult to distinguish using external morphology, although the male genitalia are distinctive and there are reliable molecular markers. Molecular evidence of modern hybridisation, derived from a newly developed nuclear marker, the period (per) gene, is presented here. This has implications for identifications of these species based on mtDNA, and may lead to an explanation of the medical and veterinary anomalies noted in these species.
- Full Text:
- Date Issued: 2013
- Authors: Williams, Kirstin A , Villet, Martin H
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/442633 , vital:74017 , 10.14411/eje.2013.029
- Description: There are important but inconsistent differences in breeding site preference between the blow flies Lucilia sericata (Meigen, 1826) and L. cuprina (Wiedemann, 1830)(Diptera: Calliphoridae) that have significance for medical and veterinary science. These inconsistencies might arise from hybridisation. The species are difficult to distinguish using external morphology, although the male genitalia are distinctive and there are reliable molecular markers. Molecular evidence of modern hybridisation, derived from a newly developed nuclear marker, the period (per) gene, is presented here. This has implications for identifications of these species based on mtDNA, and may lead to an explanation of the medical and veterinary anomalies noted in these species.
- Full Text:
- Date Issued: 2013
Being South African and belonging: the status and practice of mediated citizenship in a new democracy
- Wasserman, Herman, Garman, Anthea
- Authors: Wasserman, Herman , Garman, Anthea
- Date: 2013
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/159769 , vital:40342 , ISBN 978-1-84888-186-0
- Description: Democratic South Africa, with its highly inclusive constitution and embrace of all races, creeds and colours, could be understood as having an ideal form of citizenship to be emulated by other nations. At the heart of the 1996 constitution is the eradication of apartheid separation and the provision that all South Africans have shared humanity (‘ubuntu’). The Truth and Reconciliation Commission entrenched three founding critical ideas in public life: the right to talk, the recognition of shared humanity and the impulse to speak out about the horrors of the past. As a result the public sphere is filled with a great outpouring of personal stories and experiences in both the mainstream and popular forms of media. But South Africans continue to be preoccupied with the status of their citizenship; who a South African is and who belongs is uppermost in many public conversations.
- Full Text:
- Date Issued: 2013
- Authors: Wasserman, Herman , Garman, Anthea
- Date: 2013
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/159769 , vital:40342 , ISBN 978-1-84888-186-0
- Description: Democratic South Africa, with its highly inclusive constitution and embrace of all races, creeds and colours, could be understood as having an ideal form of citizenship to be emulated by other nations. At the heart of the 1996 constitution is the eradication of apartheid separation and the provision that all South Africans have shared humanity (‘ubuntu’). The Truth and Reconciliation Commission entrenched three founding critical ideas in public life: the right to talk, the recognition of shared humanity and the impulse to speak out about the horrors of the past. As a result the public sphere is filled with a great outpouring of personal stories and experiences in both the mainstream and popular forms of media. But South Africans continue to be preoccupied with the status of their citizenship; who a South African is and who belongs is uppermost in many public conversations.
- Full Text:
- Date Issued: 2013
Comparisons of the thermal physiology of water hyacinth biological control agents: predicting establishment and distribution pre-and post-release
- May, Bronwen, Coetzee, Julie A
- Authors: May, Bronwen , Coetzee, Julie A
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123476 , vital:35446 , https://doi.10.1111/eea.120628
- Description: Investigations into the thermal physiology of weed biological control agents may elucidate reasons for establishment failure following release. Such studies have shown that the success of water hyacinth biological control in South Africa remains variable in the high-lying interior Highveld region, because the control agents are restricted to establishment and development due to extreme winter conditions. To determine the importance of thermal physiology studies, both pre- and post-release, this study compared the known thermal requirements of Eccritotarsus catarinensis (Carvalho) (Hemiptera: Miridae) released in 1996, with those of an agent released in 1990, Niphograpta albiguttalis (Warren) (Lepidoptera: Pyralidae) and a candidate agent, Megamelus scutellaris Berg (Hemiptera: Delphacidae), which is currently under consideration for release. The lower developmental threshold (to) and rate of development (K) were determined for N. albiguttalis and M. scutellaris, using a reduced axis regression, and incorporated into a degree-day model which compared the number of generations that E. catarinensis, N. albiguttalis, and M. scutellaris are capable of producing annually at any given site in South Africa. The degree-day models predicted that N. albiguttalis (K = 439.43, to = 9.866) can complete 4–11 generations per year, whereas M. scutellaris (K = 502.96, to = 11.458) can only complete 0–10 generations per year, compared with E. catarinensis (K = 342, to = 10.3) which is predicted to complete 3–14 generations per year. This suggests that the candidate agent, M. scutellaris, will not fare better in establishment than the other two agents that have been released in the Highveld, and that it may not be worth releasing an agent with higher thermal requirements than the agents that already occur in these high-lying areas. Thermal physiology studies conducted prior to release are important tools in biological control programmes, particularly those in resource-limited countries, to prevent wasting efforts in getting an agent established.
- Full Text:
- Date Issued: 2013
- Authors: May, Bronwen , Coetzee, Julie A
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/123476 , vital:35446 , https://doi.10.1111/eea.120628
- Description: Investigations into the thermal physiology of weed biological control agents may elucidate reasons for establishment failure following release. Such studies have shown that the success of water hyacinth biological control in South Africa remains variable in the high-lying interior Highveld region, because the control agents are restricted to establishment and development due to extreme winter conditions. To determine the importance of thermal physiology studies, both pre- and post-release, this study compared the known thermal requirements of Eccritotarsus catarinensis (Carvalho) (Hemiptera: Miridae) released in 1996, with those of an agent released in 1990, Niphograpta albiguttalis (Warren) (Lepidoptera: Pyralidae) and a candidate agent, Megamelus scutellaris Berg (Hemiptera: Delphacidae), which is currently under consideration for release. The lower developmental threshold (to) and rate of development (K) were determined for N. albiguttalis and M. scutellaris, using a reduced axis regression, and incorporated into a degree-day model which compared the number of generations that E. catarinensis, N. albiguttalis, and M. scutellaris are capable of producing annually at any given site in South Africa. The degree-day models predicted that N. albiguttalis (K = 439.43, to = 9.866) can complete 4–11 generations per year, whereas M. scutellaris (K = 502.96, to = 11.458) can only complete 0–10 generations per year, compared with E. catarinensis (K = 342, to = 10.3) which is predicted to complete 3–14 generations per year. This suggests that the candidate agent, M. scutellaris, will not fare better in establishment than the other two agents that have been released in the Highveld, and that it may not be worth releasing an agent with higher thermal requirements than the agents that already occur in these high-lying areas. Thermal physiology studies conducted prior to release are important tools in biological control programmes, particularly those in resource-limited countries, to prevent wasting efforts in getting an agent established.
- Full Text:
- Date Issued: 2013
Control protocol command translation for device interoperability on ethernet AVB networks
- Foss, Richard, Igumbor, Osedum P
- Authors: Foss, Richard , Igumbor, Osedum P
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426978 , vital:72405 , https://www.aes.org/e-lib/browse.cfm?elib=16707
- Description: Audio/Video Bridging (AVB) on Ethernet refers to a suite of standards that allows for deterministic and guaranteed delivery of audio and video content on Virtual Local Area Networks (VLAN). A requirement for the networking of audio devices is to allow for remote establishment and destruction of audio stream connections. There are a number of sound control protocols that utilize AVB transport, and this paper describes an approach for common control and interoperability among them. To demonstrate this approach, this paper describes the design and implementation of a command translator that enables communication between AES64 and OSC-networked AVB devices. Results from a quantitative analysis reveal that when a proxy is used for connection management, noticeable delays are not added to a user’s visual and auditory perception.
- Full Text:
- Date Issued: 2013
- Authors: Foss, Richard , Igumbor, Osedum P
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/426978 , vital:72405 , https://www.aes.org/e-lib/browse.cfm?elib=16707
- Description: Audio/Video Bridging (AVB) on Ethernet refers to a suite of standards that allows for deterministic and guaranteed delivery of audio and video content on Virtual Local Area Networks (VLAN). A requirement for the networking of audio devices is to allow for remote establishment and destruction of audio stream connections. There are a number of sound control protocols that utilize AVB transport, and this paper describes an approach for common control and interoperability among them. To demonstrate this approach, this paper describes the design and implementation of a command translator that enables communication between AES64 and OSC-networked AVB devices. Results from a quantitative analysis reveal that when a proxy is used for connection management, noticeable delays are not added to a user’s visual and auditory perception.
- Full Text:
- Date Issued: 2013
Eudicella trimeni Janson, 1884 (Coleoptera: Scarabaeidae: Cetoniinae: Goliathini): Description of larva with notes on conservation status, biology and taxonomy
- Perissinotto, Renzo, Orozco, Jesús (Entomologist)
- Authors: Perissinotto, Renzo , Orozco, Jesús (Entomologist)
- Date: 2013
- Subjects: Afrotropical , Goliathini , Eudicella trimeni , Scarab beetles , Fruit chafers , Flower chafers , Larva , Grubs , Rosenkäfer
- Language: English
- Type: Article
- Identifier: vital:6559 , http://hdl.handle.net/10962/d1006605 , http://africaninvertebrates.org/ojs/index.php/AI/article/view/307
- Description: Eudicella trimeni is reportedly one of the most endangered species of the genus, having been declared virtually extinct until recently. Present research has shown that the species occurs in an area wider than previously known. However, its habitat is disappearing at a fast rate and the Eastern Cape and KwaZulu-Natal populations appear to be sufficiently different from each other to warrant at least subspecies status and further investigation. Third instar larvae of the northern population were collected recently in the Karkloof Nature Reserve, KwaZulu-Natal. They were reared to adulthood under environmentally controlled conditions and are here described.
- Full Text:
- Date Issued: 2013
- Authors: Perissinotto, Renzo , Orozco, Jesús (Entomologist)
- Date: 2013
- Subjects: Afrotropical , Goliathini , Eudicella trimeni , Scarab beetles , Fruit chafers , Flower chafers , Larva , Grubs , Rosenkäfer
- Language: English
- Type: Article
- Identifier: vital:6559 , http://hdl.handle.net/10962/d1006605 , http://africaninvertebrates.org/ojs/index.php/AI/article/view/307
- Description: Eudicella trimeni is reportedly one of the most endangered species of the genus, having been declared virtually extinct until recently. Present research has shown that the species occurs in an area wider than previously known. However, its habitat is disappearing at a fast rate and the Eastern Cape and KwaZulu-Natal populations appear to be sufficiently different from each other to warrant at least subspecies status and further investigation. Third instar larvae of the northern population were collected recently in the Karkloof Nature Reserve, KwaZulu-Natal. They were reared to adulthood under environmentally controlled conditions and are here described.
- Full Text:
- Date Issued: 2013
Evaluating the acceleration of typical scientific problems on the GPU
- Tristram, Dale, Bradshaw, Karen L
- Authors: Tristram, Dale , Bradshaw, Karen L
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/477607 , vital:78103 , ISBN 9781450321129 , https://doi.org/10.1145/2513456.2513473
- Description: General-purpose computation on graphics processing units (GPGPU) has great potential to accelerate many scientific models and algorithms. However, some problems are considerably more difficult to accelerate than others, and it may be difficult for those new to GPGPU to ascertain the difficulty of accelerating a particular problem. Additionally, problems of different levels of difficulty require varying complexities of optimisations to achieve satisfactory results, and currently there is no clear separation between the different levels of known optimisations, which would be helpful to new users of GPGPU. Through what was learned in the acceleration of three problems, problem attributes have been identified to assist in evaluating the difficulty of accelerating a problem on a GPU. We envisage that with further development, these attributes could form the foundation of a difficulty classification system that could be used to determine whether GPU acceleration is practical for a candidate GPU acceleration problem, aid in identifying appropriate techniques and optimisations, and outline the required GPGPU knowledge.
- Full Text:
- Date Issued: 2013
- Authors: Tristram, Dale , Bradshaw, Karen L
- Date: 2013
- Subjects: To be catalogued
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/477607 , vital:78103 , ISBN 9781450321129 , https://doi.org/10.1145/2513456.2513473
- Description: General-purpose computation on graphics processing units (GPGPU) has great potential to accelerate many scientific models and algorithms. However, some problems are considerably more difficult to accelerate than others, and it may be difficult for those new to GPGPU to ascertain the difficulty of accelerating a particular problem. Additionally, problems of different levels of difficulty require varying complexities of optimisations to achieve satisfactory results, and currently there is no clear separation between the different levels of known optimisations, which would be helpful to new users of GPGPU. Through what was learned in the acceleration of three problems, problem attributes have been identified to assist in evaluating the difficulty of accelerating a problem on a GPU. We envisage that with further development, these attributes could form the foundation of a difficulty classification system that could be used to determine whether GPU acceleration is practical for a candidate GPU acceleration problem, aid in identifying appropriate techniques and optimisations, and outline the required GPGPU knowledge.
- Full Text:
- Date Issued: 2013
Halogenated oxindole and indoles from the South African marine ascidian Distaplia skoogi:
- Bromley, Candice L, Parker-Nance, Shirley, de la Mare, Jo-Anne, Edkins, Adrienne L, Beukes, Denzil R, Davies-Coleman, Michael T
- Authors: Bromley, Candice L , Parker-Nance, Shirley , de la Mare, Jo-Anne , Edkins, Adrienne L , Beukes, Denzil R , Davies-Coleman, Michael T
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/164918 , vital:41184
- Description: The known 3,6-dibromoindole (1), 6-bromo-3-chloroindole (2) and 6-bromo-2-oxindole (3) were isolated from the marine ascidian (sea squirt) Distapia skoogi collected from Algoa Bay, South Africa. Standard spectroscopic techniques were used to elucidate the structures of 1-3. All three compounds were found to be moderately cytotoxic to metastatic MDA-MB-231 breast cancer cells.
- Full Text:
- Date Issued: 2013
- Authors: Bromley, Candice L , Parker-Nance, Shirley , de la Mare, Jo-Anne , Edkins, Adrienne L , Beukes, Denzil R , Davies-Coleman, Michael T
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/164918 , vital:41184
- Description: The known 3,6-dibromoindole (1), 6-bromo-3-chloroindole (2) and 6-bromo-2-oxindole (3) were isolated from the marine ascidian (sea squirt) Distapia skoogi collected from Algoa Bay, South Africa. Standard spectroscopic techniques were used to elucidate the structures of 1-3. All three compounds were found to be moderately cytotoxic to metastatic MDA-MB-231 breast cancer cells.
- Full Text:
- Date Issued: 2013
Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), a potential biological control agent for the submerged aquatic weed, Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae)
- Martin, Grant D, Coetzee, Julie A, Baars, Jan-Robert
- Authors: Martin, Grant D , Coetzee, Julie A , Baars, Jan-Robert
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/103912 , vital:32322 , https://doi.org/10.4001/003.021.0118
- Description: The leaf-mining fly, Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), was investigated in its native range in South Africa, to determine its potential as a biological control agent for Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae), an invasive submerged macrophyte that is weedy in many parts of the world. The fly was found throughout the indigenous range of the plant in South Africa. High larval abundance was recorded at field sites with nearly all L. major shoots sampled ontaining larvae, with densities of up to 10 larvae per shoot. Adults laid batches of up to 15 eggs, usually on the abaxial sides of L. major leaves. The larvae mined internally, leaving the epidermal tissues of the upper and lower leaves intact. The larvae underwent three instars which took an average of 24 days and pupated within the leaf tissue, from which the adults emerged. Impact studies in the laboratory showed that H. lagarosiphon larval feeding significantly restricted the formation of L. major side branches. Based on its biology and damage caused to the plant, Hydrellia lagarosiphon could be considered as a useful biological control candidate for L. major in countries where the plant is invasive.
- Full Text:
- Date Issued: 2013
- Authors: Martin, Grant D , Coetzee, Julie A , Baars, Jan-Robert
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/103912 , vital:32322 , https://doi.org/10.4001/003.021.0118
- Description: The leaf-mining fly, Hydrellia lagarosiphon Deeming (Diptera: Ephydridae), was investigated in its native range in South Africa, to determine its potential as a biological control agent for Lagarosiphon major (Ridl.) Moss ex Wager (Hydrocharitaceae), an invasive submerged macrophyte that is weedy in many parts of the world. The fly was found throughout the indigenous range of the plant in South Africa. High larval abundance was recorded at field sites with nearly all L. major shoots sampled ontaining larvae, with densities of up to 10 larvae per shoot. Adults laid batches of up to 15 eggs, usually on the abaxial sides of L. major leaves. The larvae mined internally, leaving the epidermal tissues of the upper and lower leaves intact. The larvae underwent three instars which took an average of 24 days and pupated within the leaf tissue, from which the adults emerged. Impact studies in the laboratory showed that H. lagarosiphon larval feeding significantly restricted the formation of L. major side branches. Based on its biology and damage caused to the plant, Hydrellia lagarosiphon could be considered as a useful biological control candidate for L. major in countries where the plant is invasive.
- Full Text:
- Date Issued: 2013
Institutions and economic research: a case of location externalities on agricultural resource allocation in the Kat River basin, South Africa. A Rejoinder
- Mbatha, Cyril N, Antrobus, Geoffrey G
- Authors: Mbatha, Cyril N , Antrobus, Geoffrey G
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/143002 , vital:38184 , https://0-doi.org.wam.seals.ac.za/10.1080/03031853.2013.798069
- Description: In Mbatha and Antrobus (2008), an argument was put forward against an importation or adoption of universal models or general theorems to explain locally prevailing socio-economic conditions and predict outcomes in varied geographical contexts such as in the Kat River basin. In response to this argument a comment in this edition argues that our “results are caused by, metaphorically speaking, comparing apples and oranges. If, however, all of the relevant information is taken into account, a simple economic model may suffice to depict the situation within the KRV.” Here we illustrate that the comment comes from a misreading of basic details in the original discussion and in its construction and presentation of an alternative model of the KRV conditions the comment reiterates our original argument that general models and theorems are likely to fail to explain local intricacies primarily because they are not founded on local historical institutions.
- Full Text:
- Date Issued: 2013
- Authors: Mbatha, Cyril N , Antrobus, Geoffrey G
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/143002 , vital:38184 , https://0-doi.org.wam.seals.ac.za/10.1080/03031853.2013.798069
- Description: In Mbatha and Antrobus (2008), an argument was put forward against an importation or adoption of universal models or general theorems to explain locally prevailing socio-economic conditions and predict outcomes in varied geographical contexts such as in the Kat River basin. In response to this argument a comment in this edition argues that our “results are caused by, metaphorically speaking, comparing apples and oranges. If, however, all of the relevant information is taken into account, a simple economic model may suffice to depict the situation within the KRV.” Here we illustrate that the comment comes from a misreading of basic details in the original discussion and in its construction and presentation of an alternative model of the KRV conditions the comment reiterates our original argument that general models and theorems are likely to fail to explain local intricacies primarily because they are not founded on local historical institutions.
- Full Text:
- Date Issued: 2013
Media, citizenship and the politics of belonging in contemporary South Africa:
- Milton, Viola C, Wasserman, Herman, Garman, Anthea
- Authors: Milton, Viola C , Wasserman, Herman , Garman, Anthea
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/159802 , vital:40345 , DOI: 10.1080/02500167.2013.864447
- Description: Drawing on a wide range of theoretical and empirical studies, the articles in this special issue examine issues of citizenship and belonging in South Africa. Questions of belonging and citizenship are neither novel, nor particular to South Africa – they have been high on the intellectual (and popular) agenda internationally since at least the early 1990s. Yet South Africa's history of artificially separating and defining its citizens in the racial regimes of colonialism and apartheid still reverberates today, as is reflected in the continued inequalities marring South African society
- Full Text:
- Date Issued: 2013
- Authors: Milton, Viola C , Wasserman, Herman , Garman, Anthea
- Date: 2013
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/159802 , vital:40345 , DOI: 10.1080/02500167.2013.864447
- Description: Drawing on a wide range of theoretical and empirical studies, the articles in this special issue examine issues of citizenship and belonging in South Africa. Questions of belonging and citizenship are neither novel, nor particular to South Africa – they have been high on the intellectual (and popular) agenda internationally since at least the early 1990s. Yet South Africa's history of artificially separating and defining its citizens in the racial regimes of colonialism and apartheid still reverberates today, as is reflected in the continued inequalities marring South African society
- Full Text:
- Date Issued: 2013