Showing items 41 - 60 of 304

Your selections:

Establishment of “The South African Bioinformatics Student Council” and activity highlights:

  • Authors: Rafael, Candice Nancy , Ambler, Jon , Niehaus, Antoinette , Ross, James , Tastan Bishop, Özlem
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/148250 , vital:38723 , https://doi.org/10.14806/ej.23.0.903
  • Description: The South African Society for Bioinformatics1 (SASBi) was officially formed in September 2012 during a joint Congress with the South African Genetics Society (SAGS). Prior to this there was no official body to represent bioinformatic researchers and students in the country. The establishment of SASBi also led to the establishment of the Student Society as a platform for students to meet and discuss their research activities, but also to socialise and broaden their network of knowledge and friendships. A small group of students joined as volunteers to pioneer and set up a SASBi Student Council (SASBiSC). As a first step, one representative, selected from the attendees present at the first Joint Congress of SASBi and SAGS, was elected to the main SASBi Council.
  • Full Text:
  • Date Issued: 2018

General features and kinetic analysis of thermoluminescence from annealed natural quartz

  • Authors: Thomas, Sunil , Chithambo, Makaiko L
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/112885 , vital:33670 , https://doi.org/10.1016/j.jlumin.2018.02.003
  • Description: The aim of this study is to explore the thermoluminescence properties of beta irradiated natural quartz annealed at 900 °C, that is, beyond its second phase inversion temperature of 867 °C. The sample was annealed to improve its sensitivity and to deplete any residual charge from electron traps. The glow-curve corresponding to 10 Gy shows three peaks when measured at 1 °C/s; a dominant one at 71 °C, the subject of this report, and two other ones at 125 and 177 °C. The dose response of the main peak was studied in the range 1–300 Gy. The activation energy of the main glow-peak was evaluated as ~1 eV. Kinetic analyses using various methods show that the main glow-peak follows first order kinetics.
  • Full Text: false
  • Date Issued: 2018

Hybrid Sensor Simulation within an ICS Testbed

  • Authors: Shaw, Brent , Irwin, Barry V W
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/427713 , vital:72457 , https://www.researchgate.net/profile/Barry-Ir-win/publication/327624204_Hybrid_Sensor_Simulation_within_an_ICS_Testbed/links/5b9a50d8299bf14ad4d79587/Hybrid-Sensor-Simulation-within-an-ICS-Testbed.pdf
  • Description: Industrial Control Systems (ICS) are responsible for managing factories, power-grids and water treatment facilities, and play a key role in running and controlling national Critical Information Infrastructure (CII). The integrity and availability of these systems are paramount, and the threat of cyberphysical attacks on these systems warrant thorough research into ensuring their security. The increasing interconnectivity seen in both the domestic and industrial sectors exposes numerous devices and systems to the Internet. These devices are exposed to malware and advanced persistent threats, that can affect CII through the attack of ICS. While simulations provide insights into how systems might react to certain changes, they generally lack the ability to be integrated into existing hardware systems. Hybrid testbeds could provide a platform for testing hardware and software components, enabling researchers to examine the interactions between various different networking through exploratory research and investigation in a controlled environment. This work presents an approach to traffic generation for use within ICS/IoT testbeds, through the production of Docker-based simulation nodes that are constructed based on the configuration of the system.
  • Full Text:
  • Date Issued: 2018

Influence of annealing on thermoluminescence of natural quartz: kinetic analysis and experimental study of apparent inverse thermal quenching

  • Authors: Folley, Damilola E , Chithambo, Makaiko L
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/109996 , vital:33212 , https://doi.org/10.1016/j.radmeas.2018.04.010
  • Description: The influence of annealing on the main thermoluminescence glow-peak of natural quartz is reported. For comparison, results from un-annealed quartz are included. The glow-curve measured at 1 °Cs−1 after beta irradiation to 50 Gy revealed six peaks each for quartz annealed at 800 °C for 1 h and the un-annealed sample. The main peak in both quartzes was observed at 72 °C. This report focusses on kinetic analysis of the main peak. The analysis was carried out using various methods consisting of the initial rise, whole glow-peak, peak shape, variable heating rate and phosphorescence-based methods. The activation energy obtained using the various methods ranges between and for the annealed sample and between and for the un-annealed sample. The result suggests that annealing has little effect on the activation energy. The luminescence intensity decreased with heating rate in the un-annealed sample in a manner suggestive of thermal quenching. In contrast, the dependence of intensity on heating rate in the annealed sample is influenced by the dose the sample is irradiated to. Whereas thermal quenching was noted for a dose of 50 Gy in the un-annealed sample, the annealed sample showed evidence of thermal quenching at a low dose of 3 Gy with the opposite effect when irradiated to 50 Gy. The activation energies of thermal quenching were found as and for the un-annealed and annealed samples respectively. We ascribe the apparent dependence of thermal quenching on dose in the annealed sample to competition between radiative and non-radiative transitions at the recombination centre.
  • Full Text: false
  • Date Issued: 2018

Offline-First Design for Fault Tolerant Applications.

  • Authors: Linklater, Gregory , Marais, Craig , Herbert, Alan , Irwin, Barry V W
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/427683 , vital:72455 , https://www.researchgate.net/profile/Barry-Irwin/publication/327624337_Offline-First_Design_for_Fault_Tolerant_Applications/links/5b9a50a1458515310584ebbe/Offline-First-Design-for-Fault-Tolerant-Applications.pdf
  • Description: Faults are inevitable and frustrating, as we increasingly depend on network access and the chain of services that provides it, we suffer a greater loss in productivity when any of those services fail and service delivery is suspended. This research explores connectivity and infrastructure fault tolerance through offline-first application design using techniques such as CQRS and event sourcing. To apply these techniques, this research details the design, and implementation of LOYALTY TRACKER; an offline-first, PoS system for the Android platform that was built to operate in the context of a small pub where faults are commonplace. The application demonstrates data consistency and integrity and a complete feature set that continues to operate while offline but is limited by scalability. The application successfully achieves it’s goals in the limited capacity for which it was designed.
  • Full Text:
  • Date Issued: 2018

Phototransferred thermoluminescence and thermally-assisted optically stimulated luminescence dosimetry using α-Al2O3:C,Mg annealed at 1200°C

  • Authors: Kalita, Jitumani M , Chithambo, Makaiko L
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/105422 , vital:32511 , https://doi.org/10.1016/j.jlumin.2018.08.085
  • Description: We report phototransferred thermoluminescence (PTTL) and thermally-assisted optically stimulated luminescence (TA-OSL) of α-Al2O3:C,Mg annealed at 1200 °C. PTTL is TL measured from an irradiated phosphor after its exposure to light. The other theme of this study, TA-OSL is the additional amount of luminescence optically stimulated from a sample over and above the amount that would be measured at room temperature. A sample irradiated to 10 Gy and preheated to 230 °C at 1 °C/s followed by illumination by 470 nm blue light produced four PTTL peaks at 53, 80, 102 and 173 °C. The PTTL peaks occur at the same positions as the corresponding conventional TL peaks. Their kinetic parameters are also similar. The intensity of the PTTL peaks increased with duration of illumination to a maximum within 200 s for doses between 1 Gy and 10 Gy. The dose response of each of the PTTL peaks at 80, 102 and 173 °C is linear within 1–15 Gy. The rate of fading is low and the peaks are reproducible. When the irradiated sample is optically stimulated at temperatures between 30 °C and 300 °C, after preheating to 500 °C, the intensity of its TA-OSL goes through a peak with temperature at 200 °C. Using the rising edge of the plot, activation energy of thermal assistance for a deep electron trap was estimated as (0.21 ± 0.02) eV. The TA-OSL dose response is sublinear from 10–250 Gy and saturates thereafter. The PTTL and TA-OSL analyses signify that the concentration of deep traps in α-Al2O3:C,Mg increased after annealing at 1200 °C. As a result, the sample produced better PTTL and TA-OSL response than when annealed at lower temperature.
  • Full Text: false
  • Date Issued: 2018

Project CrayOn: Back to the future for a more General-Purpose GPU

  • Authors: Machanick, Philip
  • Date: 2018
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/439353 , vital:73569 , http://wp3workshop.website/pdfs/WP3_machanick.pdf
  • Description: General purpose of use graphics processing units (GPGPU) recapitulates many of the lessons of the early generations of supercomputers. To what extent have we learnt those lessons, rather than repeating the mistakes? To answer that question, I review why the Cray-1 design ushered in a succession of successful supercomputer designs, while more exotic modes of parallelism failed to gain traction. In the light of this review, I propose that new packaging breakthroughs create an opening for revisiting our approach to GPUs and hence GPGPU. If we do not do so now, the GPU endpoint–when no GPU enhancement will be perceptible to human senses–will in any case remove the economic incentive to build ever-faster GPUs and hence the economy of scale incentive for GPGPU. Anticipating this change now makes sense when new 3D packaging options are opening up; I propose one such option inspired by packaging of the Cray-1.
  • Full Text:
  • Date Issued: 2018

Real-time geotagging and filtering of network data using a heterogeneous NPU-CPU architecture

  • Authors: Pennefather, Sean , Bradshaw, Karen L , Irwin, Barry V W
  • Date: 2018
  • Subjects: To be catalogued
  • Language: English
  • Type: text , book
  • Identifier: http://hdl.handle.net/10962/460603 , vital:75968 , ISBN 9780620810227
  • Description: In this paper, we present the design and implementation of a NPU-CPU heterogeneous network monitoring application. This application allows for both filtering and monitoring operations to be performed on network traffic based on country of origin or destination of IP traffic in real-time at wire speeds up to 1 Gbit/s. This is achievable by distributing the application components to the relevant candidate architectures, leveraging the strengths of each. Communication between architectures is handled at runtime by a low latency synchronous message passing library. Testing of the implemented application indicates that the system can perform geolocation lookups on network traffic in real-time without impacting network throughput.
  • Full Text:
  • Date Issued: 2018

Spermatophore dimorphism in the chokka squid Loligo reynaudii associated with alternative mating tactics

  • Authors: Sato, Noriyosi , Iwata, Yoko , Shaw, Paul W , Sauer, Warwick H H
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/127070 , vital:35952 , https://doi.10.1093/mollus/eyy002
  • Description: Chokka squid (Loligo reynaudii) have characteristic alternative mating tactics: ‘consort’ males temporarily pair with and guard a female and transfer spermatophores onto her oviduct opening inside the mantle cavity, whereas ‘sneaker’ males rush towards a mating pair and transfer spermatophores onto the female’s buccal membrane near her sperm storage organ. Differences in mating behaviours and their related sperm-storage sites clearly constrain the fertilization process and can drive dimorphism between consort and sneaker males. The presence and character of male dimorphism has not yet been fully examined in this species, but consort males are commonly much larger than sneaker males. We observed clear dimorphism in spermatangia (the sperm mass ejaculated from the spermatophore), consistently associated with the two alternative sperm storage sites on the female’s body. Observations of spermatophores stored in the Needham’s sac of mature males confirmed that small males produce ‘sneaker-type’ spermatangia whereas larger males produce ‘consort-type’ spermatangia, and no individuals possessed both types. Therefore, by association, the mating tactic adopted (including the sperm deposition site used) by individual males can be determined from observation of their spermatangial type, without requiring direct behavioural observation of mating. This ability to infer information about mating tactic will improve our understanding of the reproductive system and mating dynamics in this species.
  • Full Text:
  • Date Issued: 2018

The effect of annealing and beta irradiation on thermoluminescence spectra of α-Al2O3: C, Mg

  • Authors: Kalita, Jitumani M , Chithambo, Makaiko L
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/112875 , vital:33669 , https://doi.org/10.1016/j.jlumin.2017.12.036
  • Description: The effect of annealing on thermoluminescence spectra of beta irradiated α-Al2O3:C,Mg has been studied. Measurements were made on an un-annealed sample and samples annealed at 600, 700 and 900 °C. A glow curve measured at 1 °C/s from samples irradiated to 1 Gy shows a high intensity peak at 163 °C and six secondary peaks of weaker intensity at 43, 73, 195, 280, 329 and 370 °C. When the samples are annealed at 700 or 900 °C, an additional secondary peak appears at 100 °C. The thermoluminescence spectrum of an un-annealed sample measured at 1 °C/s between 300 and 700 nm shows the main emission band at ~ 410 nm and subsidiary emission bands at ~ 325 and 485 nm. The emission from samples annealed at 700 and 900 °C show similar bands except for a decrease in intensity of the emission at 485 nm. The emission bands at 325, 410 and 485 nm are attributed to F+, F and F22+(2Mg) -centres respectively. The decrease of the emission band at 485 nm is deduced to be due to the destruction of the F22+(2Mg) centre at 700 °C. The emission bands are unaffected by irradiation dose between 10 and 320 Gy. However, when the sample is annealed at or beyond 700 °C, any effects on the F+ and F centres emission can be easier distinguished particularly for doses greater than 10 Gy.
  • Full Text: false
  • Date Issued: 2018

Thermoluminescence of annealed synthetic quartz: the influence of annealing on kinetic parameters and thermal quenching

  • Authors: Dawam, Robert R , Chithambo, Makaiko L
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/110050 , vital:33218 , https://doi.org/10.1016/j.radmeas.2018.06.004
  • Description: The thermoluminescence of synthetic quartz annealed at various temperatures up to 900 °C is reported. Glow curves measured at 1 oCs−1 following beta irradiation to 40 Gy from a sample annealed at 500 °C and from an unannealed one consist of a prominent peak at 70 °C and secondary peaks at 110, 180 and 310 °C. In comparison, the glow peak from the sample annealed at 900 °C consists of three peaks but with the main peak at 86 °C and other lower intensity peaks at 170 and 310 °C. Kinetic analysis was carried out on the main peak only in each case. The order of kinetics of this peak was determined to be first order using various methods. The activation energy was evaluated as an average of 0.90±0.02eV for the unannealed sample and the one annealed at 500 °C. However, when the synthetic quartz is annealed at 900 °C, the activation energy decreases to 0.65±0.02eV. The main point of interest however concerns thermal quenching. It was noted that for the sample annealed at 500 °C as well as the unannealed one, the maximum intensity of the main peak decreases with heating rate. This phenomenon is associated with thermal quenching. When the same experiment is carried out using quartz annealed at 900 °C and irradiated to the same dose, namely 40 Gy, the intensity increases with heating rate. This would imply that this sample is not affected by thermal quenching. Using the notion that the radiative and non-radiative recombination routes are competitive, we repeated the experiment using a low dose of 3 Gy. In this case, the intensity decreased with heating rate showing that the process can be tuned. The activation energy for thermal quenching for the samples annealed at 900 °C, 500 °C and unnannealed one was found as 0.65±0.02eV, 0.82±0.02eV and 0.95±0.06eV. Evidently, annealing affects recombination processes in synthetic quartz.
  • Full Text: false
  • Date Issued: 2018

Towards Enhanced Threat Intelligence Through NetFlow Distillation

  • Authors: Herbert, Alan , Irwin, Barry V W
  • Date: 2018
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/427699 , vital:72456 , https://www.researchgate.net/profile/Barry-Ir-win/publication/327624198_Towards_Enhanced_Threat_Intelligence_Through_NetFlow_Distillation/links/5b9a501fa6fdcc59bf8ee8ea/Towards-Enhanced-Threat-Intelligence-Through-NetFlow-Distillation.pdf
  • Description: Bolvedere is a hardware-accelerated NetFlow analysis platform intended to discern and distribute NetFlow records in a requested format by a user. This functionality removes the need for a user to deal with the NetFlow protocol directly, and also reduces the requirement of CPU resources as data would be passed on to a host in the known requested format.
  • Full Text:
  • Date Issued: 2018

Violations of good security practices in graphical passwords schemes: Enterprise constraints on scheme-design

  • Authors: Vorster, Johannes , Irwin, Barry V W , van Heerden, Renier P
  • Date: 2018
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/430324 , vital:72683 , https://researchspace.csir.co.za/dspace/bitstream/handle/10204/10919/Vorster_22337_2018.pdf?sequence=1isAllowed=y
  • Description: During the past decade, the sophistication and maturity of Enterprise-level Information Security (EIS) Standards and Systems has increased significantly. This maturity, particularly in the handling of enterprise-wide capability models, has led to a set of standards – e.g. ISO/IEC 27001, NIST 800-53, ISO/IEC 27789 and CSA CCM – that propose controls applicable to the implementation of an Information Security Manage-ment System (ISMS). By nature, the academic community is fruitful in its endeavour to propose new password schemes; and Graphical Passwords (GPs) have had many proposals for schemes. In this paper, we explore the impact of good security standards and lessons-learnt over the past decade of EID as a model of constraint on GPs schemes. The paper focuses on a number of GP schemes and points out the var-ious security constraints and limitations, if such schemes are to be im-plemented at the enterprise level.
  • Full Text:
  • Date Issued: 2018

Calcium supplementation commencing before or early in pregnancy, or food fortification with calcium, for preventing hypertensive disorders of pregnancy

  • Authors: Hofmeyr, Georges Justus , Manyame, S
  • Date: 2017
  • Subjects: South Africa Pregnancy Computer File
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/11260/6215 , vital:45282 , "https://DOI:10.1002/14651858.CD011192.pub2"
  • Description: Background Pre-eclampsia is considerably more prevalent in low- than high-income countries. One possible explanation for this discrepancy is dietary diKerences, particularly calcium deficiency. Calcium supplementation in the second half of pregnancy reduces the serious consequences of pre-eclampsia and is recommended by the WorldHealthOrganization (WHO) for women with low dietary calcium intake, but has limited eKect on the overallrisk of pre-eclampsia. It is important to establish whether calcium supplementation before and in early pregnancy has added benefit. Such evidence would be justification for population-level fortification of staple foods with calcium. Objectives To determine the eKect of calcium supplementation or food fortification with calcium, commenced before or early in pregnancy and continued at least until mid-pregnancy, on pre-eclampsia and other hypertensive disorders, maternal morbidity and mortality, as well as fetal and neonatal outcomes. Search methods We searched the Cochrane Pregnancy and Childbirth Trials Register (10 August 2017), PubMed (29 June 2017), ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (ICTRP) (10 August 2017) and reference lists of retrieved studies. Selection criteria Randomised controlled trials of calcium supplementation orfood fortification which include women of child bearing age not yet pregnant, or in early pregnancy. Cluster-RCTs, quasi-RCTs and trials published in abstract form only would have been eligible for inclusion in this review but none were identified. Cross-over designs are not appropriate for this intervention. The scope of this review is to consider interventions including calcium supplementation with or without additional supplements or treatments, compared with placebo or no intervention. Data collection and analysis Two review authors independently assessed trials for inclusion and risk of bias, extracted data and checked them for accuracy. Main results This review is based on one RCT (involving 60 women) which looked at calcium plus additional supplements versus control. The women (who had lowantioxidant status)were in the early stages of pregnancy.We did notidentify any studieswhere supplementation commenced pre-pregnancy. Another RCT comparing calcium versus placebo is ongoing but not yet complete. We did not identify any studies looking at any of our other planned comparisons. Calcium plus antioxidants and other supplements versus placebo We included one small study (involving 60 women with low antioxidantlevels) which was conducted in an academic hospital in Indondesia. The study was at low risk of bias for all domains with the exception of selective reporting, for which it was unclear. Women in the intervention group received calcium (800 mg) plus N-acetylcysteine (200 mg), Cu (2 mg), Zn (15 mg), Mn (0.5 mg) and selenium (100 mcg) and vitamins A (1000 IU), B6 (2.2 mg), B12 (2.2 mcg), C (200 mg), and E (400 IU) versus the placebo control group of women who received similar looking tablets containing iron and folic acid. Both groups received iron (30 mg) and folic acid (400 mcg). Tablets were taken twice daily from eight to 12 weeks of gestation and then throughout pregnancy. The included study found that calcium supplementation plus antioxidants and other supplements may slightly reduce pre-eclampsia (gestational hypertension and proteinuria) (risk ratio (RR) 0.24, 95% confidence interval (CI) 0.06 to 1.01; low-quality evidence), but this is uncertain due to wide confidence intervals just crossing the line of no eKect, and small sample size. It appears that earlypregnancy loss before 20 weeks' gestation (RR 0.06, 95% CI 0.00 to 1.04; moderate-quality evidence) may be slightly reduced by calcium plus antioxidants and other supplements, but this outcome also has wide confidence intervals, which just cross the line of no eKect. Very few events were reported under the composite outcome, severe maternal morbidity and mortality index and no clear diKerence was seen between groups (RR 0.36, 95% CI 0.04 to 3.23; low-quality evidence). However, the included study observed a reduction in the composite outcome pre-eclampsia and/or pregnancy loss at any gestational age (RR 0.13, 95% CI 0.03 to 0.50; moderate-quality evidence), and pregnancy loss/stillbirth at any gestational age (RR 0.06, 95% CI 0.00 to 0.92;moderate-quality evidence)in the calcium plus antioxidant/supplement group. Other outcomes reported (placental abruption, severe pre-eclampsia and preterm birth (less than 37 weeks' gestation)) were too infrequent for meaningful analysis. No data were reported for the outcomes caesarean section, birthweight less 2500 g, Apgar score less than seven at five minutes, death or admission to neonatal intensive care unit (ICU), or pregnancy loss, stillbirth or neonatal death before discharge from hospital. Authors' conclusions The results of this review are based on one small study in which the calcium intervention group also received antioxidants and other supplements. Therefore, we are uncertain whether any of the eKects observed in the study were due to calcium supplementation or not. The evidence in this review was graded low to moderate due to imprecision. There is insuKicient evidence on the eKectiveness or otherwise of pre- or early-pregnancy calcium supplementation, or food fortification for preventing hypertensive disorders of pregnancy. Furtherresearch is needed to determine whether pre- or early-pregnancy supplementation, orfood fortification with calcium is associated with a reduction in adverse pregnancy outcomes such as pre-eclampsia and pregnancy loss. Such studies should be adequately powered, limited to calcium supplementation, placebo-controlled, and include relevant outcomes such as those chosen for this review. There is one ongoing study of calcium supplementation alone versus placebo and this may provide additional evidence in future updates
  • Full Text:
  • Date Issued: 2017

Cape White-eyes in the Eastern Cape: plumage characters, survival, and movements

  • Authors: Craig, Adrian J F K , Galpin, Mark D , Hulley, Patrick E , Tree, Anthony J
  • Date: 2017
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/465358 , vital:76597 , https://journals.uct.ac.za/index.php/BO/article/view/423/464
  • Description: Almost all our records of green-bellied Cape White-eyes are outside the breeding season, with a peak in winter. They possibly come from localities to the east of Grahamstown, Bathurst and Port Alfred, but we have no direct evidence of such movement, nor of altitudinal migration between coastal and inland sites. The higher frequency of green-bellied birds at the coastal ringing sites may suggest local movements within the coastal belt, or occasional coastwards movement by adjoining populations, which could also account for the diversity of flank colours recorded in a small proportion of the birds.
  • Full Text:
  • Date Issued: 2017

Challenges with modelling transcription factor binding

  • Authors: Machanick, Philip , Kibet, Caleb K
  • Date: 2017
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/439158 , vital:73551 , 10.1109/NEXTCOMP.2017.8016178
  • Description: Modelling transcription factor binding presents a number of challenges. In its simplest form, binding can be modelled by a consensus sequence but a number of factors including degeneracy of binding sites, alternative modes of binding and differences between artificially-constructed and in vivo DNA make modelling binding complex. In this paper we outline difficulties and report on progress with improving modelling of binding. We focus on improving measurement of binding models, a necessary prerequisite for finding better models.
  • Full Text:
  • Date Issued: 2017

Comparative perch selection in Southern Fiscal Lanius collaris and Fiscal Flycatcher Sigelus silens at Amakhala Game Reserve, South Africa

  • Authors: Daniels, Ryan J , Hulley, Patrick E , Craig, Adrian J F K
  • Date: 2017
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/449294 , vital:74809 , https://doi.org/10.2989/00306525.2016.1264496
  • Description: The Southern Fiscal Lanius collaris and the Fiscal Flycatcher Sigelus silens are common, widespread and sympatric in much of southern Africa. They are similar in plumage and ecology, which may predispose them to competition and interspecific territorial aggression but this has not been tested to date. Here we tested for evidence of competition for perch space. At Amakhala Private Game Reserve, Eastern Cape, South Africa we monitored the occurrence and perch use of both species along transects. The birds do co-occur locally but there is evidence of small-scale spatial separation possibly a result of interspecific territoriality. Perch selection differed in respect of perch type but not perch height. Both species perched prominently in the majority of observations. Southern Fiscals make greater use of Searsia and Gymnosporia trees, whereas the Fiscal Flycatcher makes near-equal use of Vachellia karroo, Searsia and Gymnosporia trees. This may be an example of niche partitioning, though it remains unclear whether the birds actively compete for perch space, or if the separation is a product of different perch preferences, territoriality and the local plant community.
  • Full Text:
  • Date Issued: 2017

Design of a Message Passing Model for Use in a Heterogeneous CPU-NFP Framework for Network Analytics. Southern Africa Telecommunication Networks and Applications Conference (SATNAC) 2017, 3-10 September 2017

  • Authors: Pennefather, Sean , Bradshaw, Karen L , Irwin, Barry V W
  • Date: 2017
  • Subjects: To be catalogued
  • Language: English
  • Type: text , book
  • Identifier: http://hdl.handle.net/10962/460011 , vital:75884 , ISBN 9780620767569 , http://dx.doi.org/10.18489/sacj.v31i2.692
  • Description: Currently, network analytics requires direct access to network packets, normally through a third-party application, which means that obtaining realtime results is difficult. We propose the NFP-CPU heterogeneous framework to allow parts of applications written in the Go programming language to be executed on a Network Flow Processor (NFP) for enhanced performance. This paper explores the need and feasibility of implementing a message passing model for data transmission between the NFP and CPU, which is the crux of such a heterogeneous framework. Architectural differences between the two domains are highlighted within this context and we present a solution to bridging these differences.
  • Full Text:
  • Date Issued: 2017

Ferrocenyl and organic novobiocin derivatives: synthesis and their in vitro biological activity

  • Authors: Mbaba, Mziyanda , Mabhula, Amanda N , Boel, Natasha , Edkins, Adrienne L , Isaacs, Michelle , Hoppe, Heinrich C , Khanye, Setshaba D
  • Date: 2017
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/66189 , vital:28914 , https://doi.org/10.1016/j.jinorgbio.2017.04.014
  • Description: publisher version , A focused series of novobiocin derivatives containing a ferrocene unit together with their corresponding organic novobiocin analogues have been synthesized in modest to good yields. These compounds were screened for biological activity against a chloroquine-sensitive strain of Plasmodium falciparum (3D7) and human breast cancer cell line (HCC38). With the exception of compounds 5c and 5d, the general trend observed is that incorporation of the ferrocene moiety into novobiocin scaffold resulted in compounds 6a–d/6f showing enhanced activity compared to organic analogues 5a–b and 5e–f.
  • Full Text: false
  • Date Issued: 2017

Gill Memorial Medal Address 2014 Reviewing the Red Bishop: the bird that introduced me to ornithology

  • Authors: Craig, Adrian J F K
  • Date: 2017
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/449401 , vital:74818 , https://www.tandfonline.com/doi/pdf/10.2989/00306525.2017.1302754
  • Description: Euplectes (Craig 1992). Body mass, high at the start of the breeding season and then declining, increases again during this post-nuptial moult (Craig 1978). An initial analysis of the timing of moult estimated the duration of wing-moult at 110 d on the basis of birds recaptured during moult (Craig and Manson 1979a). Later, these data were reanalysed using new mathematical methods (Craig et al. 2001), which yielded a shorter estimate of 89 d for completion of wing-moult. Moult data from different regions of southern Africa, with samples of> 50 birds, showed striking differences with estimates of the duration of wing-moult ranging from 62 to 114 d (Oschadleus and Underhill 2006; Craig et al. 2010). However, the earlier conclusion that the start of moult in Zimbabwe was significantly later than in KwaZulu-Natal (Craig and Manson 1979a) was not supported when a larger sample of birds from the summer rainfall region was examined (Craig et al. 2010). Nine captive male Red Bishops kept under constant conditions of 14 h light: 10 h dark continued normal cycles of wing-moult, and showed cycles of testis enlargement and regression, but retained either partial or full nuptial plumage over a two-year period (Craig 1985). This suggests that circannual rhythms may play some role in the timing of moult, but further experimental investigations are required to confirm this idea.
  • Full Text:
  • Date Issued: 2017
  • Disclaimer
  • Privacy
  • Copyright
  • Contact