Exploring grade 3 teachers’ resistance to ‘take up’progressive mathematics teaching roles
- Authors: Graven, Mellony , Westaway, Lise
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/69700 , vital:29568 , https://DOI: 10.1007/s13394-018-0237-7
- Description: This article addresses the question: Why teachers of mathematics have yet to ‘take up’ progressive roles? Drawing on the philosophy of critical realism and its methodological equivalent, social realism, we analyse interview and observation data of four grade 3 teachers, with the view to identifying the mechanisms conditioning the expression of teachers’ identities. In so doing, we show how post-apartheid changes in systemic roles of teachers create contradictory tensions for teachers as these bring their own mathematical learning and teaching experiences into contradiction with the new post-apartheid roles they are mandated to enact. We examine how this contradiction, together with beliefs about mathematics, pedagogy and learners, is expressed in the teaching of grade 3 mathematics. We maintain that the complementarity between teachers’ beliefs and old systemic roles provides an explanation for why teachers of grade 3 mathematics have yet to ‘take-up’ progressive roles. The implications point to the need for teacher development that creates enablers that lead to changes in classroom practices that align with policy-designated, progressive roles in teaching mathematics.
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Hepatitis C and HIV Coinfection in Developing Countries:
- Authors: Tastan Bishop, Özlem
- Date: 2018
- Language: English
- Type: text , book
- Identifier: http://hdl.handle.net/10962/148228 , vital:38721 , ISBN 9780128032343 , https://books.google.co.za/books?id=XSmlCgAAQBAJanddq=hepatitis+c+in+developing+countriesandsource=gbs_navlinks_s
- Description: Because of the common routes of transmission, hepatitis C virus (HCV) coinfection with HIV is frequent. Of the 36.6 million HIV-infected individuals worldwide, about 25% are also coinfected with HCV. Developing countries face the greatest burden of coinfection. HIV infection has been shown to have a significant impact on the progression of chronic HCV, with a higher risk of cirrhosis and hepatocellular carcinoma (HCC). Because of the improvements in the management and treatment of HIV/AIDS in resource-limited countries, HCV/HIV coinfection is becoming a significant clinical problem and a major cause of morbidity and mortality. HCV/HIV coinfection is characterized by aggressive hepatic fibrogenesis, incidence of cirrhosis, and HCC. HCC is currently a major cause for liver-related deaths in HIV patients. Viral eradication has been difficult to attain with interferon and ribavirin therapies. Novel therapies with direct-acting antiviral agents have been promising for this population. However, access to such expensive regimen is far beyond the capabilities of most resource-limited countries. Yet, studies lag behind those for HCV monoinfection.
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How are learning and training environments transforming with ESD
- Authors: O’Donoghue, R , Taylor, Jim , Venter, V
- Date: 2018
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/436718 , vital:73295 , ISBN 978-92-3-100244-1 , https://unesdoc.unesco.org/ark:/48223/pf0000261445
- Description: Action Area 2 of the Global Action Programme (GAP) on Edu-cation for Sustainable Development calls for the transformation of education and training environments1. This transformation can be interpreted in terms of changes in learning environ-ments brought about by the inclusion of ESD in education and training initiatives. This includes the integration of learning-led change found in whole-school approaches that emphasize in-clusive school governance, pedagogy and sustainable cam-pus management, as well as cooperation with partners and broader communities. These approaches are changing learn-ing environments in significant ways.
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How to be or not to be? A critical dialogue on the limitations and opportunities of academic development in the current higher education context
- Authors: Behari-Leak, Kasturi , Chitanand, N , Padayachee, Kershree , Masehela, L , Vorster, Jo-Anne E , Ganas, Rieta , Merckel, Vanessa
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/124217 , vital:35577 , https://hdl.handle.net/10520/EJC-13671ff578
- Description: In the tumultuous time we find ourselves, debates about pedagogy have taken centre stage once again. Concerns raised by the student protests of 2015 and 2016 have highlighted the urgent need to re-think traditional teaching, learning and assessment practices, as well as the development of decolonised and transformative curricula.Traditional notions of academic and professional development are now being tested and contested, insofar as they are able to respond to student challenges in appropriate, responsive, legitimate and relevant ways. As a professional organisation dedicated to supporting learning and teaching, the executive team of HELTASA responded to the challenge in this article by engaging with perspectives on the purpose, role and conceptualisation of academic development in the current decolonial moment in the South African Higher Education landscape. Critical processes that enable academics to engage, share thoughts and debate epistemological, pedagogical and methodological options to support students and academics are much needed. And the context and spirit in which these debates occur may be as important as the debates themselves.At its annual conference, the executive team facilitated a critical dialogue with conference delegates on the limitations and opportunities of AD in our current context. Given the diverse teaching and learning contexts and institutional differentiation in the sector, this article explores individual and collective theorised observations, reflections and experiences of the seven facilitators who led the CD. These reflections were analysed and discussed against the backdrop of AD as well as the affordances of CD as a participatory learning and engagement methodology. The findings showed that there is dire need to re-imagine, not only AD’s role but alternative forms of critical engagement in the sector.
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Jesus, Che, Luaty: on the relationship between a digital picture and an iconic image in political iconography in Angola
- Authors: Siegert, Nadine
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/145919 , vital:38478 , DOI: 10.2979/africatoday.65.1.04
- Description: This essay makes a close examination of a selection of images of the Angolan rapper Luaty Beirão, who became internationally known as a political activist during his imprisonment in June 2015, accused of staging a coup d'état. By analyzing and interpreting images that were highly mediatized during that period, this article shows how political iconography can be traced back to Christian iconography and other images. Such filiations of images and their mediatization invoke a power that contributes to the formation of political and popular icons. This article analyzes this nexus by deconstructing the transmutation of a photograph into a popular icon.
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Niq Mhlongo told us# FeesMustFall, or why the surface matters in Dog Eat Dog:
- Authors: Dass, Minesh
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/142609 , vital:38095 , DOI: 10.4314/eia.v45i3.6
- Description: In this paper, I investigate some of the reasons for the relative paucity of scholarly attention given to Niq Mhlongo’s debut novel, Dog Eat Dog. I argue that this text anticipates and articulates themes that are vital to contemporary South African culture generally, and to the academic space of the university specifically. For this reason, I contend that it is a work worthy of consideration, both because of its unusual form (it is a novel of ordeal rather than a Bildungsroman), and its prescient depiction of issues to do with institutional racism and academic exclusion – subjects which were central during the student-led protests on South African campuses in 2015 and 2016. A principal thesis of this article is that one of the reasons for literary study’s unwillingness to engage with the novel is the discipline’s predisposition to a hermeneutics of suspicion, a method of analysis that I show is unsuited to Mhlongo’s text. Instead, I argue for the use of surface reading as a valid and appropriate praxis given the form and the content of Dog Eat Dog.
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The “Pleasure Streets” of exile: queer subjectivities and the body in Arthur Nortje’s London poems
- Authors: Thorpe, Andrea
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68432 , vital:29255 , https://doi.org/10.1080/02564718.2018.1447865
- Description: Publisher version , In this article, I aim to expand our understanding of Arthur Nortje as a poet of “exile” by exploring the dialectic between self-loathing and pleasure, as well as between engagement and isolation, which he portrays performatively through his London poetry. While critics have emphasised Nortje’s “marginality” or “liminality”, both as an “exile” and a “coloured” South African, I draw on the critical writing of Zoë Wicomb in order to extend readings of his poetry beyond this tragic paradigm. I furthermore take up Sarah Nuttall’s suggestion that Nortje’s London poetry describes a degree of immersion within the city and that this aspect of his work demands further study. After tracing Nortje’s playful use of literary influences and his reworking of the trope of flânerie, I provide a series of close readings of poems in which Nortje depicts an exploration of queer subjectivities, staged within the city. In his London poetry, Nortje subverts and eludes fixed racial, sexual, national and class identities. Nortje’s London poetry exemplifies how South African literature was developed in response to the alienating condition of exile, but also through engagement with the places where exile occurred.
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Understanding Collective Learning and Human Agency in Diverse Social, Cultural and Material Settings
- Authors: Olvitt, Lausanne L , Lotz-Sisitka, Heila , Læssøe, Jeppe , Jordt Jørgensen, Nanna
- Date: 2018
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/127226 , vital:35979 , https://www.ajol.info/index.php/sajee/article/view/172221/161620
- Description: The significance of environment and sustainability education research and practice, and its potential contribution to a sustainable future for humanity, is conveyed by the International Social Science Council (n.d.), which explains: People everywhere will need to learn how to create new forms of human activity and new social systems that are more sustainable and socially just. However, we have limited knowledge about the type of learning that creates such change, how such learning emerges, or how it can be scaled-up to create transformations at many levels.Here, the important shift is towards considering what social systems, forms of knowledge, learning processes and questions of justice are associated with perpetuating or halting the decline of Earth’s bio-geo-chemical systems. This edition of the Southern African Journal of Environmental Education contributes three research papers and a themed Think Piece collection to these international deliberations about the role of education in enabling transformations to sustainability. Collectively, the articles highlight how relationality and the formation of human agency in socio-cultural and material settings in past–present–future configurations underpin all environment-oriented learning processes. The three research papers constituting the first part of this volume offer glimpses into how current unsustainable socio-cultural and material configurations might be transformed to address social inequalities and damaged people–nature relations. The Think Piece collection, introduced by Lotz-Sisitka, Læssøe and Jørgensen later in this editorial, focuses on how learning can foster and contribute to the development of change agents and collective agency for climate-resilient development.
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Dangers of generic pedagogical panaceas: implementing sevice-learning differently in diverse disciplines
- Authors: Hlengwa, Amanda I , McKenna, Sioux
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61051 , vital:27933 , http://joe.ukzn.ac.za/Libraries/No_67_2017/Dangers_of_generic_pedagogical_panaceas_Implementing_service-learning_differently_in_diverse_disciplines.sflb.ashx
- Description: Descriptions of service-learning in the literature tend to position it as a powerful pedagogic tool as well as an exemplar of ‘best practice’ applicable across all disciplines and institutional contexts. Furthermore service-learning is couched as a moral imperative. In the South African context, this moral imperative is translated into policy pronouncements driving institutions of higher education to demonstrate responsiveness to the transformation needs of broader society. In this article, two departments, Philosophy and Environmental Science, at one university are used as case studies to interrogate what enables the uptake of service-learning as a pedagogic tool. Drawing on the work of Fairclough, this paper identifies the dominant discourses at play and considers how they constrain or enable the uptake of service-learning. We advocate for the infusion of service-learning in curricula, but argue that institutional culture, disciplinary values and the structure of knowledge impact on its uptake and should not be dismissed in the implementation process.
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Ecological dominance along rocky shores, with a focus on intertidal ascidians
- Authors: Rius, Marc , Teske, Peter R , Manriquez, Patricio H , Suarez-Jimenez, Rocio , McQuaid, Christopher D
- Date: 2017
- Subjects: To be catalogued
- Language: English
- Type: text , book chapter
- Identifier: http://hdl.handle.net/10962/453416 , vital:75252 , ISBN 9781138197862 , https://www.taylorfrancis.com/chapters/oa-edit/10.1201/b21944-4/ecological-dominance-along-rocky-shores-focus-intertidal-ascidians-marc-rius-peter-teske-patricio-manr%C3%ADquez-roc%C3%ADo-su%C3%A1rez-jim%C3%A9nez-christopher-mcquaid-juan-carlos-castilla?context=ubxandrefId=e4c0e0f7-2c0a-417f-8751-8225febf1536
- Description: The role of dominant species is of central importance in ecology. Such species play a key role in ecosystem structure, stability and function, regulating resource allocation across trophic levels and overall ecosystem productivity. Although ecological interactions between dominant and subordinate species are often considered to influence the latter negatively, the presence of dominant species can also be beneficial. These species commonly act as ecosystem engineers and enhance biodiversity by creating habitat for other species. Along rocky coastlines, dominant species are often sessile suspension-feeding organisms that can monopolize all available substrata. This is particularly noticeable in intertidal and shallow subtidal habitats where the number of species that achieve ecological dominance is limited. Here, we review the ecological and evolutionary mechanisms that facilitate dominance along rocky coastlines. We then focus on a prominent example, the members of the Pyura stolonifera species complex (Tunicata), which are an emerging model system for studying ecological dominance. These ascidians achieve the highest biomass levels ever reported in rocky intertidal habitats and, when invasive, can fundamentally transform entire ecosystems. Finally, we discuss conservation implications and conclude with directions for future research.
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Genetic analysis of native and introduced populations of the aquatic weed Sagittaria platyphylla – implications for biological control in Australia and South Africa
- Authors: Kwong, Raelene M , Broadhurst, Linda M , Keener, Brian R , Coetzee, Julie A , Knerr, Nunzio , Martin, Grant D
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/76991 , vital:30653 , https://doi.org/10.1016/j.biocontrol.2017.06.002
- Description: Sagittaria platyphylla (Engelm.) J.G. Sm. (Alismataceae) is an emergent aquatic plant native to southern USA. Imported into Australia and South Africa as an ornamental and aquarium plant, the species is now a serious invader of shallow freshwater wetlands, slow-flowing rivers, irrigation channels, drains and along the margins of lakes and reservoirs. As a first step towards initiating a classical biological control program, a population genetic study was conducted to determine the prospects of finding compatible biological control agents and to refine the search for natural enemies to source populations with closest genetic match to Australian and South African genotypes. Using AFLP markers we surveyed genetic diversity and population genetic structure in 26 populations from the USA, 19 from Australia and 7 from South Africa. Interestingly, we have established that populations introduced into South Africa and to a lesser extent Australia have maintained substantial molecular genetic diversity comparable with that in the native range. Results from principal coordinates analysis, population graph theory and Bayesian-based clustering analysis all support the notion that introduced populations in Australia and South Africa were founded by multiple sources from the USA. Furthermore, the divergence of some Australian populations from the USA suggests that intraspecific hybridization between genetically distinct lineages from the native range may have occurred. The implications of these findings in relation to biological control are discussed.
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Local setting influences the quantity of household food waste in mid-sized South African towns
- Authors: Chakona, Gamuchirai , Shackleton, Charlie M
- Date: 2017
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60866 , vital:27847 , https://doi.org/10.1371/journal.pone.0189407
- Description: The world faces a food security challenge with approximately 868 million people undernourished and about two billion people suffering from the negative health consequences of micronutrient deficiencies. Yet, it is believed that at least 33% of food produced for human consumption is lost or wasted along the food chain. As food waste has a negative effect on food security, the present study sought to quantify household food waste along the ruralurban continuum in three South African mid-sized towns situated along an agro-ecological gradient. We quantified the types of foods and drinks that households threw away in the previous 48 hours and identified the causes of household food waste in the three sites. More households wasted prepared food (27%) than unprepared food (15%) and drinks (8%). However, households threw away greater quantities of unprepared food in the 48-hour recall period (268.6±610.1 g, 90% confidence interval: 175.5 to 361.7 g) compared to prepared food (121.0±132.4 g, 90% confidence interval: 100.8 to 141.3 g) and drinks (77.0±192.5 ml, 90% confidence interval: 47.7 to 106.4 ml). The estimated per capita food waste (5±10 kg of unprepared food waste, 3±4 kg of prepared food waste and 1±3 litres of drinks waste per person per year) overlaps with that estimated for other developing countries, but lower than most developed countries. However, the estimated average amount of food waste per person per year for this study (12.35 kg) was higher relative to that estimated for developing countries (8.5 kg per person per year). Household food waste was mainly a result of consumer behavior concerning food preparation and storage. Integrated approaches are required to address this developmental issue affecting South African societies, which include promoting sound food management to decrease household food waste. Also, increased awareness and educational campaigns for household food waste reduction interventions are discussed.
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Looking underneath: deconstruction in Hogarth's Industry and Idleness
- Authors: Herbst, Michael
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/147803 , vital:38674 , https://doi.org/10.1080/00043389.2003.11877010
- Description: In Hogarth's engraved series Industry and Idleness two young men from lower-class backgrounds are apprenticed to Mr West, a weaver. The first plate (1) lays bare the two apprentices' marked difference in temperament: Francis Goodchild works contentedly at his well-lit loom with his 'Prentice's Guide- a standard manual of instruction and advice for London apprentices in various trades - open on the floor below him. In the gloomy foreground Thomas Idle snores crassly at his loom, oblivious of his 'Prentice's Guide, which has apparently been reduced to tatters by the cat that now toys with the abandoned shuttle.
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Reaching sideways, writing our ways: the orientation of the arts of Africa discourse
- Authors: Simbao, Ruth K , Miko, William B , Ijisakin, Eyitayo T , Tchibozo, Romuald , Hwati, Masimba , NG-Yang, Kristin , Mudekereza, Patrick , Nalubowa, Aidah , Hyacinthe. Genevieve , Jason, Lee-Roy , Abdou, Eman , Chachage, Rehema , Tumusiime, Amanda , Sousa, Suzana , Muchemwa, Fadzai
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/145886 , vital:38475 , https://0-doi.org.wam.seals.ac.za/10.1162/AFAR_a_00341
- Description: In Rehema Chachage's video installation, Kwa Baba Rithi Undugu (2010), sculptural objects representing old-fashioned transistor radios are mounted on the wall, side by side (Fig. 1). Embedded in each radio is a small video screen, which reveals a figure who stands in one place while the vertical line of the radio tuner crosses her body in search of the desired frequency (Figs. 2–3). A man's voice wafts in and out as it is periodically interrupted by unsolicited noise, revealing the difficulty of relating to others when sound is interrupted or there is an absence of voice. Voice, writes Chachage, is a “prerequisite for interlocution and the construction of discourse.” This work engages with the assertion that to “live means to participate in dialogue: to ask questions, to heed, to respond, to agree …” and to do so full heartedly with your “eyes, lips, hands, soul, spirit … whole body and deeds” (Bakhtin 1984:293).
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‘It’s tough being gay’: gay, lesbian and bisexual students’ experiences of being ‘at home’in South African university residence life
- Authors: Vincent, Louise , Munyuki, Chipo L
- Date: 2017
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/141734 , vital:38000 , DOI: 10.20853/31-2-869
- Description: In the post-apartheid era, a variety of commentators invoked the idea of making university campuses a ‘home for all’ so as to depict a vision of what transformed, inclusive higher education institutional cultures, might look like. In this article, we discuss the experiences of students who self-identified as gay, lesbian or bisexual of being ‘at home’ in university residence life on a largely residential South African campus. Drawing from many different disciplines, including anthropology, history, philosophy, geography, psychology, architecture and sociology, we distil the essential features of ‘at-homeness’ as incorporating comfort, privacy, security, acceptance, companionship, recognition and community – all of which are central to human flourishing. We find that while some participants reported being afforded the advantages of feeling at home in university residence life, others are routinely denied many of the essential comforts associated with being ‘at home’ that heterosexual students have the privilege of taking for granted as a component of their experience of university residence life.
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Back to the future: revival, relevance and route of an anarchist/syndicalist approach for twenty-first-century left, labour and national liberation movements
- Authors: van der Walt, Lucien
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/144812 , vital:38381 , DOI: 10.1080/02589001.2016.1235365
- Description: The failings of classical Marxism, social democracy and anti-imperialist nationalism point to the need for a radical left politics at a distance from the state. This paper examines the impact, revival and promise of the anarchist/syndicalist tradition, a rich, continuous praxis in labour, left, anti-imperialist, anti-racist and egalitarian movements, worldwide, since the 1860s. Outlining its core ideas – anti-hierarchy, anti-capitalism, anti-statism, opposition to social and economic inequality, internationalist class-based mobilisation – and critique of mainstream Marxism and nationalism, it highlights the arguments there is a basic incompatibility between state rule, and bottom-up, egalitarian, democratic, socialist relationships. The anarchist/syndicalist project cannot be reduced to an organising style, protest politics or spontaneism: for it, transition to a just, self-managed society requires organised popular capacity for a revolutionary rupture, developed through prefigurative, class-based, democratic organs of counter-power, including syndicalist unions aiming at collectivised property, and revolutionary counter-culture. Success needs formal organisation, unified strategy and anarchist / syndicalist political organisations.
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Festival fringe production and the long tail
- Authors: Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68855 , vital:29332 , http://www.econrsa.org/node/1170
- Description: Publisher version , In the past 15 years, there has been a worldwide proliferation of arts festivals, including so-called "fringe" festivals, which encouraged more experimental and avant-garde productions. While fringe festival productions had the potential to generate significant income for producers, their aims were primarily related to artistic innovation and it is well known that putting on a fringe show is highly unlikely to provide financial gain for most producers. This is what is referred to in statistics and marketing as a "long tail" distribution, in which a minority of producers in a particular market earn the vast majority of industry income. However, for individual producers of live theatre, such a distribution represents high risks and potentially large financial losses. This article uses producer data from two different fringe festivals in South Africa to explore determinants of ticket sales and box-office income. Included in the analysis is a consideration of the impact of genre and pricing strategies on the probability (Logit model) of shows being in the top 10%, 30% and 50% of best-selling and earning productions. Results support the long tail hypothesis.
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Knowledge and knowers in teaching and learning: an enhanced approach to curriculum alignment
- Authors: Clarence, Sherran
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/59823 , vital:27655 , http://www.legitimationcodetheory.com/pdf/2016Clarence-c.pdf
- Description: John Biggs’ well-known curriculum design approach, constructive alignment, is widely used in higher education in the United Kingdom, Australia and South Africa. Developed with one dominant account of learning through curriculum, this approach has a gap in terms of accounting for other kinds of knowledge building, and associated knower development. This paper proposes a complementary approach that accounts for different kinds of knowledge and knower building. Using Legitimation Code Theory’s concept of Specialisation, the paper argues that accounting for what makes a discipline ‘special’ in terms of its basis for legitimate achievement can enable curriculum writers to align curricula more effectively with that basis in different disciplines. Using a case study approach, this paper shows how this tool can provide lecturers and academic development practitioners with a useful mode of analysing curriculum alignment to more ably account for differential development of disciplinary knowledges and knowers.
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MARS Motif: Assessment and Ranking Suite for transcription factor binding motifs
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439339 , vital:73568 , https://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 discovery.
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MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs
- 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.
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