The effectiveness and impacts of subsidies to film industries
- Authors: Collins, Alan , Snowball, Jeanette D
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/68511 , vital:29273 , https://www.southafricanculturalobservatory.org.za/
- Description: Publisher version , Conference paper presented at the South African Cultural Observatory, First National Conference: Counting Culture, The Cultural and Creative Industries in National and International Context, 16-17 May 2016, The Boardwalk International Convention Centre, Nelson Mandela Bay.
- Full Text:
- Date Issued: 2016
The effects of silica based nanoparticles on the photophysicochemical properties, in vitro dark viability and photodynamic therapy study of zinc monocarboxyphenoxy phthalocyanine
- Authors: Oluwole, David O , Uddin, Imran , Prinsloo, Earl , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/240371 , vital:50828 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.07.002"
- Description: Aminopropyl triethoxysilane functionalized core SiO2 and core/shell ZnO/SiO2 nanoparticles (NP) were covalently linked to zinc monocarboxyphenoxy phthalocyanine (ZnMCPPc, complex 1) via amide bond formation. The photophysicochemical behavior, in vitro dark viability and photodynamic therapy (PDT) activity against human breast adenocarcinoma cell line (MCF-7 cells) of the conjugates were studied. The nanoconjugates showed enhanced photophysicochemical behavior as compared to complex 1 alone. Complex 1 showed higher dark toxicity against MCF-7 cells when compared to the conjugates. In the dark, complex 1 accounted for less than 50% viable cells at 28.6 μg/mL and 57.1 μg/mL compared to the conjugates which accounted for more than 50% cell viability at these concentrations. The in vitro dark viability and PDT activity of complex 1 was reduced in the presence of these nanoparticles.
- Full Text:
- Date Issued: 2016
The emancipatory potential of nursing practice in relation to sexuality: a systematic literature review of nursing research 2009–2014
- Authors: Macleod, Catriona I , Nhamo-Murire, Mercy
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/446312 , vital:74489 , xlink:href="https://doi.org/10.1111/nin.12131"
- Description: Nurses play a key role in the provision of services in relation to sexuality in both primary and sexual and reproductive health-care. Given the intersection of sexualities with a range of social injustices, this study reviews research on nursing practice concerning sexuality from an emancipatory/social justice perspective. A systematic review of English articles published in nursing journals appearing on the Web of Science database from 2009 to 2014 was conducted. Thirty-eight articles met the inclusion criteria. Analysis consisted of a descriptive phase (types and location of studies, aspects of sexualities focused on, target health users and aspects of nursing practice focused on) and a critical/emancipatory phase. In terms of practice, our analysis revealed that: barriers exist to the integration of issues relating to sexuality in nursing practice; the social location of nurses and their personal feelings regarding sexuality influence their practice; content that addresses gendered norms and media that assist in communication underpin some emancipatory practices. Few studies locate analyses of nursing practice within gendered, cultural and social norms; consider advocacy as part of the practice of nurses; or analyse the promotion of health user participation in health services and structures. The implications for emancipatory practice are drawn out.
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- Date Issued: 2016
The evaluation of a talent management programme within a global multinational organisation: a case study
- Authors: Ferguson, Alana Paulette
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MCom
- Identifier: http://hdl.handle.net/10962/64747 , vital:28597
- Description: Expected release date-May 2018
- Full Text:
- Date Issued: 2016
The good African society index
- Authors: Botha, Ferdi
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/396194 , vital:69157 , xlink:href="https://doi.org/10.1007/s11205-015-0891-z"
- Description: This paper constructs a Good Society Index for 45 African countries, termed the Good African Society Index (GASI). The GASI consists of nine main indexes: (1) economic sustainability, (2) democracy and freedom, (3) child well-being, (4) environment and infrastructure, (5) safety and security, (6) health and health systems, (7) integrity and justice, (8) education, and (9) social sustainability and social cohesion. Each component is split into four sub-components for a total of 36 indicators. Tunisia ranks highest on the GASI, followed by Cape Verde and Botswana. Chad has the lowest GASI score, followed by Central African Republic and Cote d’Ivoire. The GASI is strongly related to the 2012 Human Development Index and Fragile States Index, to a lesser extent, GNI per capita.
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- Date Issued: 2016
The GULLS project: a comparison of vulnerabilities across selected ocean hotspots and implications for adaptation to global change
- Authors: Cochrane, Kevern L , Hobday, Alistair J , Aswani, Shankar , Byfield, Val , Dutra, Leo X C , Gasalla, Maria A , Haward, Marcus , Paytan, Adina , Pecl, Gretta T , Popova, Katya , Sainulabdeen, Shyam S , Savage, Candida , Sauer, Warwick H H , van Putten, Ingrid E , Visser, Natascha , TG Team
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/422037 , vital:71906
- Description: The GULLS project, `Global learning for local solutions: Reducing vulnerability of marine-dependent coastal communities' has been underway since October 2014. The project has been investigating six regional `hotspots': marine areas experiencing rapid warming. These are south-east Australia, Brazil, India, Solomon Islands, South Africa, and the Mozambique Channel and Madagascar. Rapid warming could be expected to have social, cultural and economic impacts that could affect these countries in different ways and may already be doing so. GULLS has focused on contributing to assessing and reducing the vulnerability of coastal communities and other stakeholders dependent on marine resources and to facilitate adaptation to climate change and variability through an integrated and trans-disciplinary approach. It includes participants from Australia, Brazil, India, Madagascar, New Zealand, South Africa, the United Kingdom and the United States of America. The research programme has been divided into six inter-linked components: ocean models, biological and ecological sensitivity analyses, system models, social vulnerability, policy mapping, and communication and education. This presentation will provide a brief overview of each of these components and describe the benefits that have resulted from the collaborative and transdisciplinary approach of GULLS. Following the standard vulnerability elements of exposure, sensitivity and adaptive capacity, the vulnerabilities of coastal communities and other stakeholders dependent on marine resources in the five hotspots will be compared using a set of indicators derived and populated from results of the research programme. The implications of similarities and differences between the hotspots for adaptation planning and options will be described.
- Full Text:
- Date Issued: 2016
The influence of photoperiod on the reproductive physiology of the greater red musk shrew: Crocidura flavescens
- Authors: Hoole, C , McKechnie, Andrew E , Parker, Daniel M , Bennett, Nigel C
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/70157 , vital:29626 , https://doi.org/10.1139/cjz-2015-0128
- Description: Photoperiodism involves the use of both absolute measures of day length and the direction in which day length is changing as a cue for regulating seasonal changes in physiology and behaviour so that birth and lactation coincide with optimal resource availability, increasing offspring survival. Induced ovulation and opportunistic breeding is often found in species that are predominantly solitary and territorial. In this study, the photoperiodic reproductive responses of male greater red musk shrews (Crocidura flavescens (I. Geoffroy Saint-Hilaire, 1827)) were investigated in the laboratory. The presence of spermatozoa regardless of the light cycle, suggest that although the shrews are photoresponsive, they may be capable of breeding throughout the year. Significantly greater testicular volume and eminiferous tubule diameter following exposure to a short day-light cycle suggests that these animals may have breeding peaks that correspond to short days. The presence of epidermal spines on the penis indicates that the shrew is likely also an induced ovulator. Flexible breeding patterns combined with induced ovulation affords this solitary species the greatest chance of reproductive success.
- Full Text:
- Date Issued: 2016
The interaction between graphene quantum dots grafted with polyethyleneimine and Au@ Ag nanoparticles
- Authors: Achadu, Ojodomo John , Uddin, Imran , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188679 , vital:44775 , xlink:href="https://doi.org/10.1016/j.jphotochem.2016.03.016"
- Description: Graphene quantum dots grafted with polyethyleneimine (GQDs-PEI) and Au@Ag core-shell nanoparticles blend was demonstrated to be a novel biosensing nanoprobe for the rapid and highly sensitive detection of biothiols such as cysteine (Cys), homocysteine (Hcys) and glutathione (GSH). The fluorescence emission of GQDs-PEI was quenched efficiently upon interaction with Au@Ag core-shell nanoparticles. The quenched fluorescence emission of the GQDs-PEI was restored in the presence of the biothiols. The fluorimetric sensing is based on the strong affinity between the mercapto (SH) groups of the biothiols and the Au@Ag core-shell nanoparticles by which the interaction between GQDs-PEI and Au@Ag core-shell nanoparticles was disrupted with a consequent modulation (‘turn-on’) of the quenched GQDs-PEI emission. Thus, a new, simple, rapid and highly sensitive fluorescence nanoprobe for detecting biothiols has been developed in this work.
- Full Text:
- Date Issued: 2016
The last stop
- Authors: Mofokeng, Thabiso
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MA
- Identifier: http://hdl.handle.net/10962/64567 , vital:28559
- Description: My novella is set in the taxi industry. Its main characters are a wealthy taxi owner, a poor taxi driver from another African country, and the taxi driver's girlfriend. The story is partly a ghost story and partly crime fiction, it combines gritty realism with magical elements. It shows what happens between people in times of taxi violence. As the plot develops, the driver finds out that his boss is sleeping with his girlfriend. In revenge, the boss bribes some policemen to arrest the driver and beat him, and he dies in the police cells. But it turns out that the detective investigating the driver’s death is not quite impartial, nor is he of this world only.
- Full Text:
- Date Issued: 2016
The limitations of current health literacy measures for use in developing countries:
- Authors: Dowse, Roslind
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/156607 , vital:40030 , DOI: 10.1080/17538068.2016.1147742
- Description: Health literacy measures have largely emanated from developed countries, reflecting the characteristics of their economies, populations, and health systems. In contrast, it is disconcerting that health literacy appears to be so under-researched in developing countries (DCs), despite the likelihood of inadequate health literacy being endemic. In this commentary, I highlight some challenges when using existing health literacy measures in DCs and conclude with a summary of considerations when using/developing a tool for these populations.
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- Date Issued: 2016
The Malarial Exported PFA0660w Is an Hsp40 Co-Chaperone of PfHsp70-x
- Authors: Daniyan, Michael O , Boshoff, Aileen , Prinsloo, Earl , Pesce, Eva-Rachele , Blatch, Gregory L
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/66098 , vital:28901 , https://doi.org/10.1371/journal.pone.0148517
- Description: publisher version , Plasmodium falciparum, the human pathogen responsible for the most dangerous malaria infection, survives and develops in mature erythrocytes through the export of proteins needed for remodelling of the host cell. Molecular chaperones of the heat shock protein (Hsp) family are prominent members of the exportome, including a number of Hsp40s and a Hsp70. PFA0660w, a type II Hsp40, has been shown to be exported and possibly form a complex with PfHsp70-x in the infected erythrocyte cytosol. However, the chaperone properties of PFA0660w and its interaction with human and parasite Hsp70s are yet to be investigated. Recombinant PFA0660w was found to exist as a monomer in solution, and was able to significantly stimulate the ATPase activity of PfHsp70-x but not that of a second plasmodial Hsp70 (PfHsp70-1) or a human Hsp70 (HSPA1A), indicating a potential specific functional partnership with PfHsp70-x. Protein binding studies in the presence and absence of ATP suggested that the interaction of PFA0660w with PfHsp70-x most likely represented a co-chaperone/chaperone interaction. Also, PFA0660w alone produced a concentration-dependent suppression of rhodanese aggregation, demonstrating its chaperone properties. Overall, we have provided the first biochemical evidence for the possible role of PFA0660w as a chaperone and as co-chaperone of PfHsp70-x. We propose that these chaperones boost the chaperone power of the infected erythrocyte, enabling successful protein trafficking and folding, and thereby making a fundamental contribution to the pathology of malaria. , This work was supported by grants from the National Research Foundation (NRF) and Medical Research Council (MRC) of South Africa. The ProteOn XPR36 IAS was purchased from a National Nanotechnology Equipment Programme grant from the Department of Science and Technology and the NRF of South Africa. Michael O. Daniyan was a recipient of the Education Trust Fund (ETF) Academic Staff Training and Development (AST and D) scholarship of Obafemi Awolowo University, Ile-Ife, Nigeria and a Rhodes University Council research bursary
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- Date Issued: 2016
The network society: A model for computing infrastructure in South African schools
- Authors: Siebörger, Ingrid , Terzoli, Alfredo
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/430651 , vital:72706 , 10.1109/ISTAFRICA.2016.7530673
- Description: Worldwide computers are being used in schools for, amongst other things, developing the knowledge and skills required for citizens to be able to operate within the 21st Century Information Age. Realising the potential of technology in uplifting the lives of its citizens the South Afri-can government has proposed the National Broadband Plan (SA Con-nect). However, unfortunately this plan only addresses the networking aspect of Information Communication Technologies (ICTs). In this pa-per we investigate appropriate Information Technologies for schools in the light of SA Connect, and propose a model for the computing infra-structure required in South African schools in order to support access to and adoption of technology and networks. This model is based on our multi-year experimentation in the Siyakhula Living Lab.
- Full Text:
- Date Issued: 2016
The optical limiting of blue and green ytterbium double-decker phthalocyanines in solution and in poly (acrylic acid) as thin films
- Authors: Sekhosana, Kutloana E , Nyokong, Tebello
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/188585 , vital:44767 , xlink:href="https://doi.org/10.1016/j.ica.2016.05.026"
- Description: Bis{1(4), 8(11), 15(18), 22(25)-tetra(4-tert-butylphenoxy)phthalocyaninato} ytterbium(III) (2a) (the green form) was synthesized and reduced to form 2b (the blue form). Nonlinear optical parameters for complex 2 in green and blue forms were determined using the Z-scan technique and the values of third-order imaginary susceptibility (Im[χ(3)]) and second-order hyperpolarizability (γ) of the order of 10−9 (for 2b) and 10−27 esu, respectively, were obtained in solution. In poly(acrylic acid) as a thin film, complex 2a showed extremely high Im[χ(3)] and γ values of the order 10−8 and 10−25 respectively. A low optical limiting threshold value of 0.075 J cm−2 was obtained for the thin film 2a.
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- Date Issued: 2016
The photobleaching of the free and encapsulated metallic phthalocyanine and its effect on the photooxidation of simple molecules
- Authors: Fanchiotti, Brenda Gomes , Machado, Marcella Piffer Zamprogno , de Paula, Letícia Camilato , Durmuş, Mahmut , Nyokong, Tebello , da Silva, Gonçalves , da Silva, André Romero
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/239687 , vital:50755 , xlink:href="https://doi.org/10.1016/j.jphotobiol.2016.10.007"
- Description: The photobleaching of an unsubstituted phthalocyanine (gallium(III) phthalocyanine chloride (GaPc)) and a substituted phthalocyanine (1,4-(tetrakis[4-(benzyloxy)phenoxy]phthalocyaninato) indium(III) chloride (InTBPPc)) was monitored for the free photosensitizers and for the phthalocyanines encapsulated into nanoparticles of PEGylated poly(D,L-lactide-co-glycolide) (PLGA-PEG). Phosphate-buffered solutions (PBS) and organic solutions of the free GaPc or the free InTBPPc, and suspensions of each encapsulated photosensitizer (2–15 μmol/L) were irradiated using a laser diode of 665 nm with a power of 1–104 mW and a light dose of 7.5 J/cm2. The relative absorbance (RA) of the free GaPc dissolved in 1-methyl-2-pyrrolidone (MP) decreased 8.4 times when the laser power increased from 1 mW to 104 mW. However, the free or encapsulated GaPc did not suffer the photobleaching in PBS solution. The RA values decreased 2.4 times and 22.2 times for the free InTBPPc dissolved in PBS solution and in dimethylformamide (DMF), respectively, but the encapsulated InTBPPc was only photobleached when the laser power was 104 mW at 8 μmol/L. The increase of the free GaPc concentration favored the photobleaching in MP until 8 μmol/L while the increase from 2 μmol/L to 5 μmol/L reduced the photodegradation in PBS solution. However, the photobleaching of the free InTBPPc in DMF or in PBS solution, and of each encapsulated photosensitizer was not influenced by increasing the concentration. The influence of the photobleaching on the capability of the free and encapsulated GaPc and InTBPPc to photooxidate the simple molecules was investigated monitoring the fluorescence of dimethylanthracene (DMA) and the tryptophan (Trp). Free InTBPPc was 2.0 and 1.8 times faster to photooxidate the DMA and Trp than it was the free GaPc, but the encapsulated GaPc was 3.4 times more efficient to photooxidize the Trp than it was the encapsulated InTBPPc due to the photodegradation suffered by the encapsulated InTBPPc. The participation of the singlet oxygen was confirmed with the sodium azide in the photobleaching of all free and encapsulated photosensitizer, and in the photooxidation of the DMA and Trp. The asymmetry of InTBPPc increased the solubility of the free compound, decreasing the aggregation state of the photosensitizer and favoring the photobleaching process. The encapsulation shows capability in decreasing the photobleaching of both photosensitizers but the confocal micrographs showed that the increase of the solubility favored the InTBPPc photobleaching during the acquisition of optical cross section. A novel low-symmetry A3B-type phthalocyanine annelated with a pyrazino[2,3-f]phenanthroline ring system and substituted with six solubilizing diisopropylphenoxy-groups (1) was synthesized by metalfree DBU-promoted cross-condensation of diiminoisoindolines derived from 4,5- bis(diisopropylphenoxy)phthalonitrile and pyrazino[2,3-f][1,10]phenanthroline-2,3-dicarbonitrile. The use of these particular precursors affords A3B phthalocyanine in 15% yield, while cross-condensation of the corresponding dinitriles yields only trace amounts of the target compound. Comparative studies of the A3B-type phthalocyanine and its symmetrical octa(diisopropylphenoxy)-substituted counterpart 2 reveal striking differences in the Q band regions of their UVevisible absorption (UVeVis) spectra, which could be readily rationalized through a comparison with calculated TD-DFT spectra. Since 1 can have two NH-tautomers with equivalent and non-equivalent NH-groups, and DFT calculations predict that the former tautomer is only 2.3 kcal/mol more stable than the latter one, a comprehensive analysis of 13C NMR spectra was carried out through the application of 1 He13C HMBC and HSQC techniques. It demonstrated that only the tautomer with equivalent NH-groups is present in solution.
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- Date Issued: 2016
The phytogeography of Southern Mistbelt Forests of the Eastern Cape, South Africa
- Authors: Matiwane, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/3224 , vital:20393
- Description: In the Eastern Cape, a moisture gradient (from west to east) exists along the Escarpment where patches of Southern Mistbelt Forests (SMF) occur. There is a notable profusion of plants in these forests, but the factors that drive plant species composition and abundance in these patches is poorly understood and such knowledge is critical if we are to address or mitigate the problems imposed by global change. Many of our ideas on plant community assembly are based on the premise that species differ in their environmental requirements for successful regeneration, especially when young. The aims of this study were to document the floristic diversity of poorly known patches of Southern Mistbelt Forests in the Eastern Cape and identify the environmental factors that influence plant community composition in these forest patches. Twenty six forest patches across the Eastern Cape were sampled. In each forest 400m2 circular plots were constructed. The diameter at breast height and stem counts for the tree species was taken and the % cover of the herbaceous species was recorded. General collections were also made to supplement the plot data in order to obtain a comprehensive flora for each forest patch. All sampling was done during the summer season of 2013 and 2014. Using plot data, Hierarchal Cluster Analysis and Multidimensional Scaling Analysis were done to compare similarities between patches. Plots from the same forest patch clustered which indicated that the species composition in each forest patch was unique. However, this pattern went down when only tree species were considered. Plant diversity also varied between patches; with those located in the east being generally more diverse than those in the west are. Clustering patterns in fragmented communities and differences in species diversity indicate evidence of species “nestedness”. Analysis of nestedness indicated that these forest patches were significantly nested. To identify which environmental variables might be correlated with both species diversity and nestedness, twelve environmental variables was selected for analysis using Canonical Correspondence Analysis and Principal Component Analysis. Results show that Mean Annual Precipitation, Mean Annual Potential Evapotranspiration, and percentage of Organic Matter of the soil were most strongly correlated with the patterns of diversity observed in these forest patches. Regression analysis indicated that Mean Annual Precipitation accounted for most of the variation in species diversity, especially for the herbaceous species. The herbaceous species thus show a greater sensitivity to “climate filtering” as a consequence of rainfall gradients. With the implementation of suitable monitoring programs, changes in abundance or even local extinction of these species can act as an early warning indicator of the possible long-term effects of climate change on forest communities.
- Full Text:
- Date Issued: 2016
The trophic ecology of waterbirds in a small temperate estuary: a stable isotope and lipid tracer approach
- Authors: Hean, Jeffrey William
- Date: 2016
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/54356 , vital:26557
- Description: Waterbirds are often overlooked as predators in aquatic ecosystems, despite the fact that waterbirds congregate in great numbers in and around waterways, notably estuaries. To fully appreciate the effect that aquatic feeding waterbird species may have on aquatic prey communities and the role that they play in estuarine food webs, stable isotopes and fatty acid profiles were employed to examine the seasonal diet of selected waterbirds in the Kowie Estuary, Eastern Cape Province, South Africa. Population counts were conducted every month for four seasons to examine the demography of waterbirds in the lower reaches of the estuary. The mean monthly energy consumption, along with dry matter intake of all waterbird species observed, were calculated and compared to similar estuaries in South Africa and elsewhere. Three duck species, one migrant sandpiper and one piscivore were selected for more detailed investigation at several temporal scales. This thesis has revealed that stable isotope analysis of waterbird tissues provides more informative data than fatty acid analysis for investigating waterbird diet and basal resource-tertiary consumer nutrient coupling. Stable δ15N and δ13C isotopes from several body tissues, in conjunction with SIAR models, were used to determine the seasonal diet of each waterbird species, while fatty acid profiles were investigated to examine the trophic transfer of fatty acids from basal resources to waterbird predators via the benthic fauna. Stable isotopes revealed that Cape Shoveller, Cape Teal and Yellow-Billed Duck shifted their diet over both long and short temporal scales, while the migratory Ruff and piscivorous Little Egret maintained a relatively consistent diet over time. Isopods, amphipods, copepods and Mysidacea were the main foods of all three duck species and the Ruff (>30%). Little Egret fed mainly on flathead mullet throughout the year. Fatty acid analysis revealed evidence for trophic transfer of specific fatty acids from basal resources to waterbirds in the Kowie Estuary but provided little information on seasonal diet of waterbirds. Waterbirds foraging in the Kowie Estuary appeared to shift their diet to coincide with resource abundance pulses, but also displayed seasonal dietary overlap. This study highlights the role that waterbirds play in aquatic food webs. The subject requires more attention so that we can better understand all the predatory drivers on aquatic communities.
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- Date Issued: 2016
Towards malicious network activity mitigation through subnet reputation analysis
- Authors: Herbert, Alan , Irwin, Barry V W
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/427799 , vital:72463 , https://www.researchgate.net/profile/Barry-Ir-win/publication/327622788_Towards_Malicious_Network_Activity_Mitigation_through_Subnet_Reputation_Analysis/links/5b9a1a88458515310583fda6/Towards-Malicious-Network-Activity-Mitigation-through-Subnet-Reputation-Analysis.pdf
- Description: Analysis technologies that focus on partial packet rather than full packet analysis have shown promise in detection of malicious activity on net-works. NetFlow is one such emergent protocol that is used to log net-work flows through summarizing key features of them. These logs can then be exported to external NetFlow sinks and proper configuration can see effective bandwidth bottleneck mitigation occurring on net-works. Furthermore, each NetFlow source node is configurable with its own unique ID number. This feature enables a system that knows where a NetFlow source node ID number resides physically to say which network flows are occurring from which physical locations irre-spective of the IP addresses involved in these network flows.
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- Date Issued: 2016
Transcription factor motif quality assessment requires systematic comparative analysis
- Authors: Kibet, Cabel K , Machanick, Philip
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/439366 , vital:73570 , https://f1000research.com/articles/4-1429
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
Transcription factor motif quality assessment requires systematic comparative analysis [version 2; referees: 2 approved]
- Authors: Kibet, Caleb K , Machanick, Philip
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/61169 , vital:27987 , http://dx.doi.org/10.12688/f1000research.7408.2
- Description: Transcription factor (TF) binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs) have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.
- Full Text:
- Date Issued: 2016
Transforming the use of tutorials through academic staff development
- Authors: Clarence, Sherran , Wolff, Karin , Winberg, Simon , Farmer, Jean-Lee , Esambe, Emmanuel
- Date: 2016
- Language: English
- Type: text , conference publication
- Identifier: http://hdl.handle.net/10962/66982 , vital:29008
- Full Text:
- Date Issued: 2016