Accelerating a hydrological uncertainty ensemble model using graphics processing units (GPUs)
- Tristram, Dale, Hughes, Denis A, Bradshaw, Karen L
- Authors: Tristram, Dale , Hughes, Denis A , Bradshaw, Karen L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/475173 , vital:77781 , xlink:href="https://doi.org/10.1016/j.cageo.2013.07.011"
- Description: The practical application of hydrological uncertainty models that are designed to generate multiple ensembles can be severely restricted by the available computer processing power and thus, the time taken to generate the results. CPU clusters can help in this regard, but are often costly to use continuously and maintain, causing scientists to look elsewhere for speed improvements. The use of powerful graphics processing units (GPUs) for application acceleration has become a recent trend, owing to their low cost per FLOP, and their highly parallel and throughput-oriented architecture, which makes them ideal for many scientific applications. However, programming these devices efficiently is non-trivial, seemingly making their use impractical for many researchers. In this study, we investigate whether redesigning the CPU code of an adapted Pitman rainfall-runoff uncertainty model is necessary to obtain a satisfactory speedup on GPU devices. A twelvefold speedup over a multithreaded CPU implementation was achieved by using a modern GPU with minimal changes to the model code. This success leads us to believe that redesigning code for the GPU is not always necessary to obtain a worthwhile speedup.
- Full Text:
- Authors: Tristram, Dale , Hughes, Denis A , Bradshaw, Karen L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/475173 , vital:77781 , xlink:href="https://doi.org/10.1016/j.cageo.2013.07.011"
- Description: The practical application of hydrological uncertainty models that are designed to generate multiple ensembles can be severely restricted by the available computer processing power and thus, the time taken to generate the results. CPU clusters can help in this regard, but are often costly to use continuously and maintain, causing scientists to look elsewhere for speed improvements. The use of powerful graphics processing units (GPUs) for application acceleration has become a recent trend, owing to their low cost per FLOP, and their highly parallel and throughput-oriented architecture, which makes them ideal for many scientific applications. However, programming these devices efficiently is non-trivial, seemingly making their use impractical for many researchers. In this study, we investigate whether redesigning the CPU code of an adapted Pitman rainfall-runoff uncertainty model is necessary to obtain a satisfactory speedup on GPU devices. A twelvefold speedup over a multithreaded CPU implementation was achieved by using a modern GPU with minimal changes to the model code. This success leads us to believe that redesigning code for the GPU is not always necessary to obtain a worthwhile speedup.
- Full Text:
Collection of urban tree products by households in poorer residential areas of three South African towns
- Kaoma, Humphrey, Shackleton, Charlie M
- Authors: Kaoma, Humphrey , Shackleton, Charlie M
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/180980 , vital:43678 , xlink:href="https://doi.org/10.1016/j.ufug.2014.02.002"
- Description: The high rates of urban in-migration and poverty common in many developing country towns potentially increases the reliance of urban populations on the direct benefits provided by trees. Yet understanding of the extent of such use and the sources of these tree products is limited. Here we report on the extent of use of urban tree products by 450 households in the poorer areas of three towns along a rainfall gradient based on household questionnaires. We considered the proportion of households making use of each of several tree products and the collection or purchasing frequency which we disaggregated by source of the product, including trees in homesteads, urban spaces, edges of towns and via purchase from traders. Most households (91%) used firewood, which was most frequently collected from the urban fringe or purchased, although one-third at times also collected firewood from trees on their home plot. All households used fruits, most commonly sourced through purchase (98%), but nearly half of whom also supplemented by harvesting fruits from their home plot. Other products used included wood for building, fencing and utensils, herbal medicines, planting material and mulch. Collection of products from urban homestead trees was highest amongst households in the informal settlements and least in the more established townships. Residents of new low-cost housing areas made extensive use of urban tree products harvested in urban spaces because they had fewer homestead trees than residents of informal areas or townships. Overall, urban residents made use of a wide array of tangible products from trees which they sourced from a variety of places, including their homestead plot. This urges that planning agencies ensure that homestead plot sizes or other urban spaces that provide tree products are large enough to support the direct needs of poorer urban residents.
- Full Text:
- Authors: Kaoma, Humphrey , Shackleton, Charlie M
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/180980 , vital:43678 , xlink:href="https://doi.org/10.1016/j.ufug.2014.02.002"
- Description: The high rates of urban in-migration and poverty common in many developing country towns potentially increases the reliance of urban populations on the direct benefits provided by trees. Yet understanding of the extent of such use and the sources of these tree products is limited. Here we report on the extent of use of urban tree products by 450 households in the poorer areas of three towns along a rainfall gradient based on household questionnaires. We considered the proportion of households making use of each of several tree products and the collection or purchasing frequency which we disaggregated by source of the product, including trees in homesteads, urban spaces, edges of towns and via purchase from traders. Most households (91%) used firewood, which was most frequently collected from the urban fringe or purchased, although one-third at times also collected firewood from trees on their home plot. All households used fruits, most commonly sourced through purchase (98%), but nearly half of whom also supplemented by harvesting fruits from their home plot. Other products used included wood for building, fencing and utensils, herbal medicines, planting material and mulch. Collection of products from urban homestead trees was highest amongst households in the informal settlements and least in the more established townships. Residents of new low-cost housing areas made extensive use of urban tree products harvested in urban spaces because they had fewer homestead trees than residents of informal areas or townships. Overall, urban residents made use of a wide array of tangible products from trees which they sourced from a variety of places, including their homestead plot. This urges that planning agencies ensure that homestead plot sizes or other urban spaces that provide tree products are large enough to support the direct needs of poorer urban residents.
- Full Text:
Effects of analytes on the fluorescence properties of CdTe@ ZnS quantum dots decorated with cobalt tetraamino-phthalocyanine
- Adegoke, Oluwasesan, Nyokong, Tebello
- Authors: Adegoke, Oluwasesan , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189829 , vital:44935 , xlink:href="https://doi.org/10.1016/j.jlumin.2013.09.079"
- Description: In this work, we have carried out an investigation on the effects of different biologically active analytes on the fluorescence response of glutathione-capped CdTe@ZnS quantum dots (QDs)-colbalt tetraamino-phthalocyanine nanoconjugate system. Firstly, fluorescence quenching occurred. Experimental results showed that some analytes either “turned on”, others further quenched or showed no effect on the fluorescence emission of the nanoprobe.
- Full Text:
- Authors: Adegoke, Oluwasesan , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/189829 , vital:44935 , xlink:href="https://doi.org/10.1016/j.jlumin.2013.09.079"
- Description: In this work, we have carried out an investigation on the effects of different biologically active analytes on the fluorescence response of glutathione-capped CdTe@ZnS quantum dots (QDs)-colbalt tetraamino-phthalocyanine nanoconjugate system. Firstly, fluorescence quenching occurred. Experimental results showed that some analytes either “turned on”, others further quenched or showed no effect on the fluorescence emission of the nanoprobe.
- Full Text:
Electrochemical behaviour of gold nanoparticles and Co tetraaminophthalocyanine on glassy carbon electrode
- Maringa, Audacity, Antunes, Edith M, Nyokong, Tebello
- Authors: Maringa, Audacity , Antunes, Edith M , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/241573 , vital:50951 , xlink:href="https://doi.org/10.1016/j.electacta.2013.12.132"
- Description: We report on the electrodeposition of gold nanoparticles (AuNPs) onto the glassy carbon electrode (GCE) followed by polymerization of cobalt tetraamino phthalocyanine (CoPc(NH2)4) on top (represented as poly-CoPc(NH2)4-/AuNPs-GCE). The modified electrode where CoPc(NH2)4 is polymerized first followed by deposition of AuNPs is represented as AuNPs/poly-CoPc(NH2)4-GCE. In the absence of AuNPs, the electrode is represented as poly-CoPc(NH2)4-GCE or for AuNPs alone (AuNPs-GCE). The surface coverage was 1.5 × 10−9 mol cm−2 for AuNPs-GCE and 3.0 × 10−9 mol cm−2 for the rest of the modified electrodes. AuNPs/CoPc(NH2)4-GCE exhibited high electrocatalytic activity towards the oxidation of nitrite, with detection potential of 0.76 V. The catalytic rate constant of 3.96 × 107 cm3 mol−1 s−1 was obtained for nitrite oxidation.
- Full Text:
- Authors: Maringa, Audacity , Antunes, Edith M , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/241573 , vital:50951 , xlink:href="https://doi.org/10.1016/j.electacta.2013.12.132"
- Description: We report on the electrodeposition of gold nanoparticles (AuNPs) onto the glassy carbon electrode (GCE) followed by polymerization of cobalt tetraamino phthalocyanine (CoPc(NH2)4) on top (represented as poly-CoPc(NH2)4-/AuNPs-GCE). The modified electrode where CoPc(NH2)4 is polymerized first followed by deposition of AuNPs is represented as AuNPs/poly-CoPc(NH2)4-GCE. In the absence of AuNPs, the electrode is represented as poly-CoPc(NH2)4-GCE or for AuNPs alone (AuNPs-GCE). The surface coverage was 1.5 × 10−9 mol cm−2 for AuNPs-GCE and 3.0 × 10−9 mol cm−2 for the rest of the modified electrodes. AuNPs/CoPc(NH2)4-GCE exhibited high electrocatalytic activity towards the oxidation of nitrite, with detection potential of 0.76 V. The catalytic rate constant of 3.96 × 107 cm3 mol−1 s−1 was obtained for nitrite oxidation.
- Full Text:
Improved l-cysteine electrocatalysis through a sequential drop dry technique using multi-walled carbon nanotubes and cobalt tetraaminophthalocyanine conjugates
- Nyoni, Stephen, Mugadza, Tawanda, Nyokong, Tebello
- Authors: Nyoni, Stephen , Mugadza, Tawanda , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/193813 , vital:45398 , xlink:href="https://doi.org/10.1016/j.electacta.2013.10.023"
- Description: Voltammetry, chronoamperometry, scanning electrochemical microscopy and electrochemical impedance spectroscopy methods are used for characterization of a glassy carbon electrode modified with multi-walled carbon nanotubes (MWCNTs)–cobalt tetraaminophthalocyanine (CoTAPc) mixture or sequential drop dry modification technique whereby the MWCNTs are first placed on to the electrode followed by CoTAPc. The sequential drop dry CoTAPc–MWCNTs modified surface gave better catalytic responses with a catalytic rate constant of 2.2 × 105 M−1 s−1, apparent electron transfer rate constant of 0.073 cm s−1, and a limit of detection of 2.8 × 10−7 M. Scanning electrochemical microscopy (SECM) surface characterization (topography and reactivity) further gave proof the better catalytic perfomance of the sequential drop dry CoTAPc–MWCNTs modified surface.
- Full Text:
- Authors: Nyoni, Stephen , Mugadza, Tawanda , Nyokong, Tebello
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/193813 , vital:45398 , xlink:href="https://doi.org/10.1016/j.electacta.2013.10.023"
- Description: Voltammetry, chronoamperometry, scanning electrochemical microscopy and electrochemical impedance spectroscopy methods are used for characterization of a glassy carbon electrode modified with multi-walled carbon nanotubes (MWCNTs)–cobalt tetraaminophthalocyanine (CoTAPc) mixture or sequential drop dry modification technique whereby the MWCNTs are first placed on to the electrode followed by CoTAPc. The sequential drop dry CoTAPc–MWCNTs modified surface gave better catalytic responses with a catalytic rate constant of 2.2 × 105 M−1 s−1, apparent electron transfer rate constant of 0.073 cm s−1, and a limit of detection of 2.8 × 10−7 M. Scanning electrochemical microscopy (SECM) surface characterization (topography and reactivity) further gave proof the better catalytic perfomance of the sequential drop dry CoTAPc–MWCNTs modified surface.
- Full Text:
Selective modulation of plasmodial Hsp70s by small molecules with antimalarial activity
- Cockburn, Ingrid L, Boshoff, Aileen, Pesce, Eva-Rachele, Blatch, Gregory L
- Authors: Cockburn, Ingrid L , Boshoff, Aileen , Pesce, Eva-Rachele , Blatch, Gregory L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/431192 , vital:72752 , xlink:href="https://doi.org/10.1515/hsz-2014-0138"
- Description: Plasmodial heat shock protein 70 (Hsp70) chaperones represent a promising new class of antimalarial drug targets because of the important roles they play in the survival and pathogenesis of the malaria parasite Plasmodium falciparum. This study assessed a set of small molecules (lapachol, bromo-β-lapachona and malonganenones A, B and C) as potential modulators of two biologically important plasmodial Hsp70s, the parasite-resident PfHsp70-1 and the exported PfHsp70-x. Compounds of interest were assessed for modulatory effects on the steady-state basal and heat shock protein 40 (Hsp40)-stimulated ATPase activities of PfHsp70-1, PfHsp70-x and human Hsp70, as well as on the protein aggregation suppression activity of PfHsp70-x. The antimalarial marine alkaloid malonganenone A was of particular interest, as it was found to have limited cytotoxicity to mammalian cell lines and exhibited the desired properties of an effective plasmodial Hsp70 modulator. This compound was found to inhibit plasmodial and not human Hsp70 ATPase activity (Hsp40-stimulated), and hindered the aggregation suppression activity of PfHsp70-x. Furthermore, malonganenone A was shown to disrupt the interaction between PfHsp70-x and Hsp40. This is the first report to show that PfHsp70-x has chaperone activity, is stimulated by Hsp40 and can be specifically modulated by small molecule compounds.
- Full Text:
- Authors: Cockburn, Ingrid L , Boshoff, Aileen , Pesce, Eva-Rachele , Blatch, Gregory L
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/431192 , vital:72752 , xlink:href="https://doi.org/10.1515/hsz-2014-0138"
- Description: Plasmodial heat shock protein 70 (Hsp70) chaperones represent a promising new class of antimalarial drug targets because of the important roles they play in the survival and pathogenesis of the malaria parasite Plasmodium falciparum. This study assessed a set of small molecules (lapachol, bromo-β-lapachona and malonganenones A, B and C) as potential modulators of two biologically important plasmodial Hsp70s, the parasite-resident PfHsp70-1 and the exported PfHsp70-x. Compounds of interest were assessed for modulatory effects on the steady-state basal and heat shock protein 40 (Hsp40)-stimulated ATPase activities of PfHsp70-1, PfHsp70-x and human Hsp70, as well as on the protein aggregation suppression activity of PfHsp70-x. The antimalarial marine alkaloid malonganenone A was of particular interest, as it was found to have limited cytotoxicity to mammalian cell lines and exhibited the desired properties of an effective plasmodial Hsp70 modulator. This compound was found to inhibit plasmodial and not human Hsp70 ATPase activity (Hsp40-stimulated), and hindered the aggregation suppression activity of PfHsp70-x. Furthermore, malonganenone A was shown to disrupt the interaction between PfHsp70-x and Hsp40. This is the first report to show that PfHsp70-x has chaperone activity, is stimulated by Hsp40 and can be specifically modulated by small molecule compounds.
- Full Text:
Synthesis and MRSA PK inhibitory activity of thiazole containing deoxytopsentin analogues
- Veale, Clinton G L, Lobb, Kevin A, Zoraghi, Roya, Morrison, James P, Reiner, Neil E, Andersen, Raymond J, Davies-Coleman, Michael T
- Authors: Veale, Clinton G L , Lobb, Kevin A , Zoraghi, Roya , Morrison, James P , Reiner, Neil E , Andersen, Raymond J , Davies-Coleman, Michael T
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448028 , vital:74692 , xlink:href="https://doi.org/10.1016/j.tet.2014.09.007"
- Description: The public health care crisis caused by the emergence of drug resistant bacterial strains, e.g., methicillin resistant Staphylococcus aureus (MRSA) has underlined the urgent need to accelerate the discovery of new chemical entities active against antibiotic resistant bacteria. We report here the synthesis of a series thiazole containing deoxytopsentin analogues, which show moderate activity against a target MRSA pyruvate kinase enzyme: an evolutionary conserved hub protein critical for bacterial survival. A Hantzsch thiazole coupling between a-oxo-1H-indole-3-thioacetamides and 2-bromo-1-(1H-indol-3-yl)-ethanones provided facile access to the thiazole containing deoxytopsentin compounds.
- Full Text:
- Authors: Veale, Clinton G L , Lobb, Kevin A , Zoraghi, Roya , Morrison, James P , Reiner, Neil E , Andersen, Raymond J , Davies-Coleman, Michael T
- Date: 2014
- Subjects: To be catalogued
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/448028 , vital:74692 , xlink:href="https://doi.org/10.1016/j.tet.2014.09.007"
- Description: The public health care crisis caused by the emergence of drug resistant bacterial strains, e.g., methicillin resistant Staphylococcus aureus (MRSA) has underlined the urgent need to accelerate the discovery of new chemical entities active against antibiotic resistant bacteria. We report here the synthesis of a series thiazole containing deoxytopsentin analogues, which show moderate activity against a target MRSA pyruvate kinase enzyme: an evolutionary conserved hub protein critical for bacterial survival. A Hantzsch thiazole coupling between a-oxo-1H-indole-3-thioacetamides and 2-bromo-1-(1H-indol-3-yl)-ethanones provided facile access to the thiazole containing deoxytopsentin compounds.
- Full Text:
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