TeleWeaver: an architectural overview of a customised application server for rurality
- Authors: Tsietsi, Mosiuoa , Terzoli, Alfredo , Gumbo, Sibukelo
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/430624 , vital:72704 , 10.1109/ISTAFRICA.2016.7530616
- Description: The Siyakhula Living Lab in the rural Eastern Cape province of South Africa has been in existence for over a decade now. In this time, sever-al software artefacts have been developed by students and partners with the aim of providing contextually-relevant services to the rural community. However, reliance on different platforms and paradigms has meant that the deployment of such services would be difficult to implement and maintain reliably in actual practice. What is required is a single software platform that can act as a docking station for multiple applications, as well as a routing substrate for applications living inside and outside the platform. A candidate platform to enable this is currently being integrated under the codename Teleweaver and is built from a free, open source J2EE application server and integrates with other software components. This paper provides an architectural overview of the platform and demonstrates how it provides a sustainable context for application development going forward.
- Full Text:
- Date Issued: 2016
Temperature-dependent performance and potential distribution of Pareuchaetes insulata, a biological control agent of Chromolaena odorata in South Africa
- Authors: Uyi, Osariyekemwen O , Zachariades, Costas , Hill, Martin P , McConnachie, Andrew J
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/418067 , vital:71505 , xlink:href="https://doi.org/10.1007/s10526-016-9760-1"
- Description: Despite the release of about 1.9 million individuals of Pareuchaetes insulata (Walker) (Lepidoptera: Erebidae) in KwaZulu-Natal for the biological control of Chromolaena odorata (L.) King and Robinson (Asteraceae) in South Africa, the moth probably only established at one of the 30 release sites and its population level is generally low in the field. To determine whether climate incompatibility in South Africa is responsible for the poor performance of P. insulata, the effects of temperature on life-history traits were investigated under several constant temperatures. Although a degree-day model estimated between 3.9 and 10.0 generations of the moth per year in the weed’s invaded range, survival and fecundity declined while development time was prolonged at constant temperatures below 25 °C, indicating that both direct and indirect negative impacts of low winter temperatures, such as increased mortality, slow development and reduced fecundity as well as exposure to natural enemies, may partly explain the poor performance of P. insulata in South Africa.
- Full Text:
- Date Issued: 2016
The Bero Volcanic Complex: extension of the Paraná-Etendeka Igneous Province into SW Angola
- Authors: Marsh, Julian S , Swart, Roger S
- Date: 2016
- Language: English
- Type: article , text
- Identifier: http://hdl.handle.net/10962/60763 , vital:27827 , https://www.sciencedirect.com/science/article/pii/S0377027316304176
- Description: An extension of the Etendeka-Paraná Igneous Province into SW Angola occurs as minor basalt lavas, intrusive gabbro sheets, minor mafic dykes and thick sheets and lava flows (with minor pyroclastics) of quartz latite composition This suite crops out along the eastern margin of the Cretaceous Namibe Basin in SW Angola. The quartz latites from one locality have been referred to informally as the Giraul volcanics but the name ‘Giraul’ has previously been used for Cretaceous conglomerates. We propose the name Bero Volcanic Complex for this suite of intrusive and extrusive rocks on the basis that the full compositional range of this diverse suite crops out along the Rio Bero. Major and trace element compositions and Sr-, Nd-, and Pb-isotopic compositions indicate that the basalts and gabbros are equivalent to the high-Ti Khumib/Urubici and Pitanga types from the Etendeka and Paraná. The basalts underlie the quartz latites which are cut by mafic dykes some of which are compositionally equivalent to the Paranapanema lavas in the Paraná. Five different geochemical types of high-Ti quartz latite are recognised amongst the silicic volcanics, 3 of which have very close geochemical affinities to the Ventura, Sarusas, and Khoraseb types of the northern Etendeka. Their relative stratigraphic position in the Bero volcanic sequence is the same as in the Etendeka sequence and extend significantly the area over which these types were erupted. The two remaining types, Chinguau and High-Nb are not known from either the Etendeka or the Paraná provinces.
- Full Text:
- Date Issued: 2016
The development of computational biology in South Africa: successes achieved and lessons learnt
- Authors: Mulder, Nicola J , Christoffels, Alan , De Oliveira, Tulio , Gamieldien, Junaid , Hazelhurst, Scott , Joubert, Fourie , Kumuthini, Judit , Pillay, Ché S , Snoep, Jacky L , Tastan Bishop, Özlem , Tiffin, Nicki
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/148347 , vital:38731 , DOI: 10.1371/journal.pcbi.1004395
- Description: Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
- Full Text:
- Date Issued: 2016
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 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.
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- Date Issued: 2016
The impact of shift work on the health and wellbeing of campus security guards
- Authors: Bazana, Sandiso , Campbell, Kerry , Kabungaidze, Trust
- Date: 2016
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/453779 , vital:75285 , xlink:href="https://hdl.handle.net/10520/EJC-ccdf3bd65"
- Description: The health and wellbeing of campus security guards continues to be ignored in academia particularly by the researchers and by those who employ these guards. The main aim of the study was to gain a clearer understanding of the impact of shift work on the health and wellbeing of campus security guards. The evidence from the study clarifies what many other researchers’ have revealed about the negative impact of shift work on the health and wellbeing of employees. However, more specifically, the study revealed five issues around how shift work has an impact on the health and wellbeing of campus security guards. These issues were deduced through the application of semi-structured interviews and thematic analysis. The study showed that shift work has an impact on a number of underlying factors such as disrupted family lives and religious gatherings; limited control leading to stress; working conditions’ impact on health; and disturbed sleeping patterns. All of these had a role in decreasing employees’ job performance and ultimately impacting on the organisation’s effectiveness. Apart from regulation, the study calls on government to be more involved in the health and wellbeing of the South African workforce, especially security guards. The study makes a number of suggestions to that effect.
- 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.
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- 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.
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- 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.
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- 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
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.
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- 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