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AMADAR: a python-based package for large scale prediction of Diels–Alder transition state geometries and IRC path analysis

  • Authors: Isamura, Bienfait K , Lobb, Kevin A
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/453143 , vital:75226 , xlink:href="https://link.springer.com/article/10.1186/s13321-022-00618-3"
  • Description: Predicting transition state geometries is one of the most challenging tasks in computational chemistry, which often requires expert-based knowledge and permanent human intervention. This short communication reports technical details and preliminary results of a python-based tool (AMADAR) designed to generate any Diels–Alder (DA) transition state geometry (TS) and analyze determined IRC paths in a (quasi-)automated fashion, given the product SMILES. Two modules of the package are devoted to performing, from IRC paths, reaction force analyses (RFA) and atomic (fragment) decompositions of the reaction force F and reaction force constant κ. The performance of the protocol has been assessed using a dataset of 2000 DA cycloadducts retrieved from the ZINC database. The sequential location of the corresponding TSs was achieved with a success rate of 95%. RFA plots confrmed the reaction force constant κ to be a good indicator of the (non)synchronicity of the associated DA reactions. Moreover, the atomic decomposition of κ allows for the rationalization of the (a)synchronicity of each DA reaction in terms of contributions stemming from pairs of interacting atoms. The source code of the AMADAR tool is available on GitHub [CMCDD/AMADAR(github. com)] and can be used directly with minor customizations, mostly regarding the local working environment of the user.
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  • Date Issued: 2022

AMANZI For Food

An assessment of the medium-term reproductive success of an extralimital white rhinoceros population

  • Authors: Truter, Anja , Mgqatsa, Nokubonga , Parker, Daniel M
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/462570 , vital:76315 , xlink:href="https://doi.org/10.1080/15627020.2022.2132120"
  • Description: The white rhinoceros (Ceratotherium simum) is threatened primarily due to continued poaching for its horns. In South Africa, partly to promote the conservation of the species, white rhinos have been introduced into areas where they did not occur historically (i.e. where they are considered extralimital). Few studies have investigated the conservation contribution of extralimital white rhinos to the overall national herd. We aimed to determine whether the white rhinos introduced to a private game reserve in the Eastern Cape province have been successful from a reproductive perspective. We calculated inter-calving intervals, age at first calving, sex ratios of calves, and recruitment rates for white rhinos at a single site between 1992 and 2019. The average net annual population growth rate for the population was 10%, which is higher than the recommended 5% by the Biodiversity Management Plan for white rhinos. Trends in density-dependent parameters such as age at first calving and inter-calving intervals also indicated that the study population is still well below the density at which ecological constraints may manifest. We demonstrate that an extralimital white rhino population in the Eastern Cape can be successful from a reproductive perspective.
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  • Date Issued: 2022

An evaluation of hand-based algorithms for sign language recognition

  • Authors: Marais, Marc , Brown, Dane L , Connan, James , Boby, Alden
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/465124 , vital:76575 , xlink:href="https://ieeexplore.ieee.org/abstract/document/9856310"
  • Description: Sign language recognition is an evolving research field in computer vision, assisting communication between hearing disabled people. Hand gestures contain the majority of the information when signing. Focusing on feature extraction methods to obtain the information stored in hand data in sign language recognition may improve classification accuracy. Pose estimation is a popular method for extracting body and hand landmarks. We implement and compare different feature extraction and segmentation algorithms, focusing on the hands only on the LSA64 dataset. To extract hand landmark coordinates, MediaPipe Holistic is implemented on the sign images. Classification is performed using poplar CNN architectures, namely ResNet and a Pruned VGG network. A separate 1D-CNN is utilised to classify hand landmark coordinates extracted using MediaPipe. The best performance was achieved on the unprocessed raw images using a Pruned VGG network with an accuracy of 95.50%. However, the more computationally efficient model using the hand landmark data and 1D-CNN for classification achieved an accuracy of 94.91%.
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  • Date Issued: 2022

Analysing the Impact of Extended Curriculum Programmes: Implications for Theory, Design and Practice

  • Authors: Boughey, Chrissie
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , book chapter
  • Identifier: http://hdl.handle.net/10962/434453 , vital:73063 , ISBN 9781991201737 , https://africansunmedia.store.it.si/ZA/book/extended-curriculum-programmes-challenges-and-opportunities/1199327
  • Description: The introduction of ECPs in South African Universities is seen by many as South Africa’s key strategy for addressing the problem of poor patterns of student success and has its basis on the uncontested acceptance that an extended study duration may be necessary to bring some categories of learners to a level of parity with the readiness expectations of their course of study. Even so, this transformative strategic imperative has been plagued by a range of challenges that include poor systems readiness; poor selection mechanisms in the identification of ECP students; poor numeracy and literacy amongst students, and indifferent teacher involvement in ECPs. This volume offers a rare insight into many of the above-recognised challenges and in so doing provides critical matter for thought for educators within the higher education sector.
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  • Date Issued: 2022

Application of gold and palladium nanoparticles supported on polymelamine microspheres in the oxidation of 1-phenylethanol and some other phenyl substituted alcohols

  • Authors: Storm, Ené , Maggott, Emile D , Mashazi, Philani N , Nyokong, Tebello , Malgas-Enus, Rehana , Mapolie, Selwyn F
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/299824 , vital:57858 , xlink:href="https://doi.org/10.1016/j.mcat.2022.112456"
  • Description: Melamine formaldehyde and melamine resorcinol formaldehyde microspheres were decorated with Au and Pd nanoparticles and applied as heterogeneous catalysts in the oxidation of 1-phenylethanol. The catalysts showed similar activities irrespective of the support employed. Moderate conversion activities of 48–50% were achieved when using acetonitrile as solvent; however, when employing water as solvent, the supported catalysts formed a three-phase, emulsion system which facilitated the catalytic conversion of 1-phenylethanol to acetophenone at much higher conversions of around 83%. The oxidant, TBHP, decomposed rapidly in acetonitrile, whilst it remained stable in aqueous solution, leading to the enhanced activities observed when using water as solvent. These systems also proved to be recyclable for up to five cycles, with only slight loss of activity observed; this can be attributed to the physical loss of catalyst during the workup procedure conducted between each cycle.
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  • Date Issued: 2022

Aptamer versus antibody as probes for the impedimetric biosensor for human epidermal growth factor receptor

  • Authors: Centane, Sixolile , Nyokong, Tebello
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/229884 , vital:49720 , xlink:href="https://doi.org/10.1016/j.jinorgbio.2022.111764"
  • Description: In the present work, the performance of aptamer and antibody bioreceptors for the detection of the human epidermal growth factor receptor (HER2) cancer biomarker on a glassy carbon electrode is reported. The carboxylic acid group rich graphene quantum dots (GQDs) modified with gold nanoparticles and a porphyrin binuclear framework (CoP-BNF) were used to modify the glassy carbon electrode. The aptamer and antibody were both amine functionalized and attached to GQDs and CoP-BNF through an amide bond. The designed immunosensors and aptasensors in this work were characterized using electrochemical impedance spectroscopy. The aptasensors, compared to the immunosensors gave better limit of detection values. The aptasensor outperforms the immunosensor in terms of its reusability and storability, while the immunosensor could not be regenerated for subsequent experiments. The potential applicability of all sensors in this work was also investigated, by detection of HER2 in spiked human serum with acceptable results.
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  • Date Issued: 2022

Artisanal mining versus sustainability of agricultural food supply chains: effects of the conflicts in Southern Zimbabwe

  • Authors: Chari, Felix , Novukela, Cawe , Ngcamu , Bethuel Sibongiseni
  • Date: 2022
  • Subjects: Traditional farming Small Scale mining Great Zimbabwe Article
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/11260/7082 , vital:52810 , xlink:href="https://doi.org/10.1080/23311886.2021.2002542"
  • Description: This article seeks to establish the social and environmental consequences of artisanal mining on economic sustainability of agricultural food supply chains in Zimbabwe. Following a descriptive research design, interviews were conducted with 36 farmers. Interviewees were purposively sampled from potential respondents in Southern Zimbabwe. Interview results were triangulated with data from published reports and newspaper articles. Data was analysed using NVivo application version 12 and presented in vignettes. The results of this study are useful to artisanal miners, farmers, and government. Recommendations for further studies are given. KEYWORDS: Artisanal mining farmers food supply chains Zimbabwe sustainability
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  • Date Issued: 2022

Assessing climate risk to support urban forests in a changing climate

Assessing the electrocatalytic activity of a localized push-pull system in cobalt phthalocyanine/graphene quantum dot hybrids

  • Authors: Nkhahle, Reitumetse , Nyokong, Tebello
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/229909 , vital:49722 , xlink:href="https://doi.org/10.1016/j.matchemphys.2022.125842"
  • Description: In this study, two cobalt phthalocyanines (asymmetric complex 1) and symmetric (complex 2) were synthesized and conjugated to nitrogen-doped graphene quantum dots (NGQDs) through covalent and non-covalent means to create Co phthalocyanine (CoPc)-NGQDs hybrid systems. The CoPcs and conjugates were applied as electrode modifiers on a glassy carbon electrode in the electrochemical sensing of nitrite. Of the CoPcs alone, complex 1 performed better than complex 2 regarding the limits of detection (LoD) recorded (5.74 μM for 1 and 15.1 μM for 2). Regarding the conjugates/nanocomposites, the π-π stacked conjugate derived from complex 2 (2πNGQDs) demonstrated highly favourable electrochemical potential with an LoD value of 0.70 μM. The nanocomposites fashioned from complex 1 were marred by a reduced loading which rendered the conjugates poor electrochemical sensors. These observations however do not disqualify GQDs as complementary nanomaterials to phthalocyanines but rather shed light on seeking alternative routes to increasing the Pc loading in conjugates (more so in π-π stacked conjugates).
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  • Date Issued: 2022

Assessing the Impact of DNS Configuration on Low Bandwidth Networks

  • Authors: Okuthe, J A , Terzoli, Alfredo
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/430903 , vital:72726 , https://doi.org/10.1007/978-3-031-34896-9_6
  • Description: Domain name system (DNS) is an essential enabler for connecting us-ers and services on the Internet. DNS translates human readable do-main names into IP addresses and precedes client connection to a server via a domain name. DNS service is therefore expected to con-sume network bandwidth even though it offers no direct benefit to the user. Having observed the large component of DNS traffic on the com-munity network local loop in our previous study, we migrated the DNS service from a server on the LAN to the gateway router and reconfig-ured the cache time-to-live. Results from the analysis of network traffic captured from the gateway router interface show a 26% decrease in the downlink bandwidth utilization and 46% decline in the uplink bandwidth utilization. The DNS component of the local loop traffic reduces from 45.28% to 4.11%. On the other hand, the Web component of the local loop traffic increases from 49.42% to 95.49%. Data collected from a mirroring port on the LAN switch indicate a decrease in the DNS portion of the internal traffic from 0.38% to 0.18%. Although the DNS reconfigu-ration helps alleviate network bandwidth constraints and reduces DNS component of the traffic, the Web portion increases. The implementa-tion of effective, efficient and sustainable Web traffic management is therefore required.
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  • Date Issued: 2022

Asymmetrical zinc (II) phthalocyanines conjugated to metal tungstate nanoparticles for photoinactivation of Staphylococcus aureus

  • Authors: Mgidlana, Sithi , Managa, Muthumuni , Nyokong, Tebello
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/295718 , vital:57372 , xlink:href="https://doi.org/10.1080/00958972.2022.2090837"
  • Description: In this study, we report for the first time on the photodynamic antimicrobial chemotherapy (PACT) of asymmetrical zinc(II) phthalocyanines and their conjugates with nickel tungstate (NiWO4), cobalt tungstate (CoWO4) and bismuth tungstate (Bi2WO6) nanoparticles. CoWO4, NiWO4 and Bi2WO6 were capped with glutathione and covalently linked to three asymmetrical zinc(II) phthalocyanines for PACT. The plate count method was used to investigate the effect of covalently linking asymmetrical zinc(II) phthalocyanines to nanoparticles under light (for PACT against Staphylococcus aureus) and in the dark. Both Pc complexes and the conjugates indicated minimum dark-toxicity. The conjugates showed greater antimicrobial activity against a gram-positive and drug resistant bacteria, Staphylococcus aureus, than Pc complexes alone.
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  • Date Issued: 2022

Austral birds offer insightful complementary models in ecology and evolution

  • Authors: Theuerkauf, Jörn , Villavicencio, Camilla P , Adreani, Nicholas M , Attisano, Alfredo , Craig, Adrian J F K , D’Amelio, Pietro B , Gula, Roman , Lee, Alan T K , Mentesana, Lucia , Quillfeldt, Petra , Quirici, Veronica , Quispe, René , Vásquez, Rodrigo A , Wingfield, John C , Masello, Juan F
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/449097 , vital:74788 , https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(22)00114-8
  • Description: The Southern Hemisphere differs from the Northern Hemisphere in many aspects. However, most ecological and evolutionary research is conducted in the Northern Hemisphere and its conclusions are extrapolated to the entire globe. Therefore, unique organismal and evolutionary characteristics of the south are overlooked. We use ornithology to show the importance of including a southern perspective. We present examples of plumage pigmentation, brood-parasitic nestling ejection, flightlessness, female song, and female aggression modulated by progesterone as complementary models for investigating fundamental biological questions. More research in the Southern Hemisphere, together with increased cooperation among researchers across the hemispheres and within the Southern Hemisphere, will provide a greater global outlook into ecology and evolution.
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  • Date Issued: 2022

Award from the Women's Development Foundation, 2010

  • Date: 2022 , 2022-09-23
  • Subjects: Bam, Brigalia , Bam, Brigalia -- Awards
  • Language: English
  • Type: realia
  • Identifier: http://hdl.handle.net/10948/56595 , vital:56867
  • Description: Dr. Brigalia Bam received an award from The Women's Development Foundation in 2010 for repositioning the Foundation. , Donated/gifted to Nelson Mandela University Archives , Forms part of: Brigalia Bam collection
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  • Date Issued: 2022

Backpack carriage and musculoskeletal pain among primary school learners in King Williams Town, South Africa

  • Authors: Moni, Busisiwe
  • Date: 2022
  • Subjects: Backache -- Prevention , Pediatric rheumatology , Pain -- Treatment
  • Language: English
  • Type: Master's theses , text
  • Identifier: http://hdl.handle.net/10353/26984 , vital:66208
  • Description: BACKGROUND: There is rising concern that kids are walking to school with too much weight on their backs. The weight of schoolchildren's backpacks is a persistent and divisive topic in the fields of education and health. Children who carry heavy backpacks are more likely to have back discomfort and musculoskeletal pain, which raises their risk of developing chronic back pain as adults. There is little research on this topic among South African school-age youngsters. The goal of the study was to find out how common low back and other musculoskeletal complaints were among primary school students who used a school bag. RESEARCH AIM: The purpose of the study was to identify the prevalence and location of musculoskeletal discomfort in primary school students in King William's Town, South Africa, and describe their link with backpack use. METHOD: In King Williams Town, Eastern Cape, South Africa, a descriptive cross-sectional survey was conducted among elementary school students between the ages of 9 and 14 years old. A systematic questionnaire and the Cornell Musculoskeletal Questionnaire were used to gather the data (body chart). Age, gender, and schoolbag details (style of backpack, carrying technique, and carrying time) were collected. The learner's waist, hip, and bag circumferences were all measured. On the data, descriptive and interferential statistics were used. FINDINGS: The study's conclusions showed that students' musculoskeletal pain was brought on by the weight of their backpacks or school bags. The majority of the students (89.8percent) complain about the difficulty they experience when lugging their heavy backpacks to class. In addition, 83.4percent of the students had bags that weighed more than 10percent of their body weight. Additionally, a sizable percentage of students (89.8percent) carry a hefty bag to school every day and report feeling fatigued while doing so (90.8percent). 90percent of the students reported feeling discomfort before, during, or after carrying their schoolbags. This pain is related with carrying a schoolbag. The majority of students (53.5percent) felt that their daily pain interferes with their ability to study. In order of severity, the majority of students report having discomfort in their shoulders (82.7percent), lower back (59.9percent), neck (47.0percent), upper back (40.7percent), and upper arm (16.4percent). CONCLUSION: According to the study, there is a link between students' musculoskeletal pain and carrying hefty backpacks or school bags. The shoulders are where musculoskeletal discomfort is most frequently felt. The study supported the findings of the majority of studies cited in the literature that most schoolchildren suffer from musculoskeletal pain because the weight of their backpacks is excessive compared to their size, weight, and age. RECOMMENDATIONS: The study produced a number of recommendations, including that the Department of Basic Education inform teachers, students, parents, guardians, and other key stakeholders about the effects of heavy backpacks or schoolbags on students' musculoskeletal pain. For students' convenience and to lighten the load on their school bags, locker rooms should be available. Teachers, parents, and guardians should also pay attention to the school bags that students are using to make sure that the weight is appropriate for their age and body size. , Thesis (MPA) -- Faculty of Health Sciences, 2022
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  • Date Issued: 2022

Best of both worlds: The thermal physiology of Hydrellia egeriae, a biological control agent for the submerged aquatic weed, Egeria densa in South Africa

  • Authors: Smith, Rosali , Coetzee, Julie A , Hill, Martin P
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/417913 , vital:71494 , xlink:href="https://doi.org/10.1007/s10526-022-10142-w"
  • Description: The submerged aquatic weed, Egeria densa Planch. (Hydrocharitaceae) or Brazilian waterweed, is a secondary invader of eutrophic freshwater systems in South Africa, following the successful management of floating aquatic weeds. In 2018, the leaf and stem-mining fly, Hydrellia egeriae Rodrigues-Júnior, Mathis and Hauser (Diptera: Ephydridae), was released against E. densa, the first agent released against a submerged aquatic weed in South Africa. During its life stages, the biological control agent is exposed to two environments, air and water. The thermal physiology of both life stages was investigated to optimize agent establishment through fine-tuned release strategies. The thermal physiological limits of H. egeriae encompassed its host plant’s optimal temperature range of 10 to 35 °C, with lower and upper critical temperatures of 2.6 to 47.0 °C, lower and upper lethal temperatures of − 5.6 and 40.6 °C for adults, and − 6.3 to 41.3 °C for larvae. Results from development time experiments and degree-day accumulation showed that the agent is capable of establishing at all E. densa sites in South Africa, with between 6.9 and 8.3 generations per year. However, cold temperatures (14 °C) prolonged the agent’s development time to three months, allowing it to only develop through one generation in winter. Predictions obtained from laboratory thermal physiology experiments corroborates field data, where the agent has established at all the sites it was released.
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  • Date Issued: 2022

Beyond epistemology: the challenge of reconceptualising knowledge in higher education

  • Authors: Luckett, Kathy , Blackie, Margaret A L
  • Date: 2022
  • Subjects: To be catalogued
  • Language: English
  • Type: text , article
  • Identifier: http://hdl.handle.net/10962/426598 , vital:72371 , xlink:href="https://doi.org/10.1080/13562517.2022.2111206"
  • Description: In this Point of Departure, we build on the scholarship of Suellen Shay. Shay explored the nature of higher education, examining assessment and the relation between curriculum and knowledge structures across several disciplines. She drew on the work of Bernstein and in her later work responded to the calls for decolonisation. We first contextualise the work of Basil Bernstein and explain its attraction for scholars of education development in the South African HE context. We then provide a brief summary of recent decolonial scholarship. On this basis, we speculate what a critique and caricature of the Bernsteinian tradition by the decolonial school might look like. In turn we offer a caricatured rebuttal by the Bernsteinian school to the decolonial critique. Finally, we pull our argument together and, by drawing on Bhaskar’s critical realism, assert the importance of an adequate theorisation of ontology.
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  • Date Issued: 2022

Big African clay pot, rust color with silver alloy patterns

  • Date: 2022 , 2022-10-10
  • Subjects: Bam, Brigalia , Pots
  • Language: English
  • Type: realia , 2022
  • Identifier: http://hdl.handle.net/10948/57015 , vital:57270
  • Description: African clay pot, rust color with silver alloy patterns. , Women have acquired amazing skills in making clay pots, mats, baskets, etc., to preserve African Women's Art. , Donated/gifted to Nelson Mandela University Archives , Forms part of: Brigalia Bam collection
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  • Date Issued: 2022

Black and white Xhosa beaded necklace with a woven insert pattern

  • Date: 2022 , 2022-09-22
  • Subjects: Bam, Brigalia , Beadwork, Xhosa
  • Language: English
  • Type: realia
  • Identifier: http://hdl.handle.net/10948/56515 , vital:56827
  • Description: Black and white Xhosa beaded necklace with a woven insert pattern. This was a gift to Dr. Brigalia Bam from Switzerland. , Donated/gifted to Nelson Mandela University Archives , Forms part of: Brigalia Bam collection
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  • Date Issued: 2022

Black, pink and blue beaded necklace

  • Date: 2022 , 2022-09-22
  • Subjects: Bam, Brigalia , Necklaces
  • Language: English
  • Type: realia
  • Identifier: http://hdl.handle.net/10948/56520 , vital:56832
  • Description: Black, pink and blue beaded necklace. This was a gift to Dr. Brigalia Bam from Switzerland. , Donated/gifted to Nelson Mandela University Archives , Forms part of: Brigalia Bam collection
  • Full Text: false
  • Date Issued: 2022
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