36 results on '"Delport, D"'
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2. Keeping kids in school: modelling school-based testing and quarantine strategies during the COVID-19 pandemic in Australia
- Author
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Abeysuriya, RG, Sacks-Davis, R, Heath, K, Delport, D, Russell, FM, Danchin, M, Hellard, M, McVernon, J, Scott, N, Abeysuriya, RG, Sacks-Davis, R, Heath, K, Delport, D, Russell, FM, Danchin, M, Hellard, M, McVernon, J, and Scott, N
- Abstract
BACKGROUND: In 2021, the Australian Government Department of Health commissioned a consortium of modelling groups to generate evidence assisting the transition from a goal of no community COVID-19 transmission to 'living with COVID-19', with adverse health and social consequences limited by vaccination and other measures. Due to the extended school closures over 2020-21, maximizing face-to-face teaching was a major objective during this transition. The consortium was tasked with informing school surveillance and contact management strategies to minimize infections and support this goal. METHODS: Outcomes considered were infections and days of face-to-face teaching lost in the 45 days following an outbreak within an otherwise COVID-naïve school setting. A stochastic agent-based model of COVID-19 transmission was used to evaluate a 'test-to-stay' strategy using daily rapid antigen tests (RATs) for close contacts of a case for 7 days compared with home quarantine; and an asymptomatic surveillance strategy involving twice-weekly screening of all students and/or teachers using RATs. FINDINGS: Test-to-stay had similar effectiveness for reducing school infections as extended home quarantine, without the associated days of face-to-face teaching lost. Asymptomatic screening was beneficial in reducing both infections and days of face-to-face teaching lost and was most beneficial when community prevalence was high. INTERPRETATION: Use of RATs in school settings for surveillance and contact management can help to maximize face-to-face teaching and minimize outbreaks. This evidence supported the implementation of surveillance testing in schools in several Australian jurisdictions from January 2022.
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- 2023
3. Health and economic benefits of achieving contraceptive and maternal health targets in Small Island Developing States in the Pacific and Caribbean.
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Kelly, SL, Walsh, T, Delport, D, Ten Brink, D, Martin-Hughes, R, Homer, CS, Butler, J, Adedeji, O, De Beni, D, Maurizio, F, Friedman, HS, Di Marco, D, Tobar, F, de la Corte Molina, MP, Richards, AS, Scott, N, Kelly, SL, Walsh, T, Delport, D, Ten Brink, D, Martin-Hughes, R, Homer, CS, Butler, J, Adedeji, O, De Beni, D, Maurizio, F, Friedman, HS, Di Marco, D, Tobar, F, de la Corte Molina, MP, Richards, AS, and Scott, N
- Abstract
INTRODUCTION: Reducing unmet need for modern contraception and expanding access to quality maternal health (MH) services are priorities for improving women's health and economic empowerment. To support investment decisions, we estimated the additional cost and expected health and economic benefits of achieving the United Nations targets of zero unmet need for modern contraceptive choices and 95% coverage of MH services by 2030 in select Small Island Developing States. METHODS: Five Pacific (Kiribati, Samoa, Solomon Islands, Tonga and Vanuatu) and four Caribbean (Barbados, Guyana, Jamaica and Saint Lucia) countries were considered based on population survey data availability. For each country, the Lives Saved Tool was used to model costs, health outcomes and economic benefits for two scenarios: business-as-usual (BAU) (coverage maintained) and coverage-targets-achieved, which scaled linearly from 2022 (following COVID-19 disruptions) coverage of evidence-based family planning and MH interventions to reach United Nations targets, including modern contraceptive methods and access to complete antenatal, delivery and emergency care. Unintended pregnancies, maternal deaths, stillbirths and newborn deaths averted by the coverage-targets-achieved scenario were converted to workforce, education and social economic benefits; and benefit-cost ratios were calculated. RESULTS: The coverage-targets-achieved scenario required an additional US$12.6M (US$10.8M-US$15.9M) over 2020-2030 for the five Pacific countries (15% more than US$82.4M to maintain BAU). This additional investment was estimated to avert 126 000 (40%) unintended pregnancies, 2200 (28%) stillbirths and 121 (29%) maternal deaths and lead to a 15-fold economic benefit of US$190.6M (US$67.0M-US$304.5M) by 2050. For the four Caribbean countries, an additional US$17.8M (US$15.3M-US$22.4M) was needed to reach the targets (4% more than US$405.4M to maintain BAU). This was estimated to avert 127 000 (23%) unintended pregnan
- Published
- 2023
4. Preventing a cluster from becoming a new wave in settings with zero community COVID-19 cases.
- Author
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Abeysuriya, RG, Delport, D, Stuart, RM, Sacks-Davis, R, Kerr, CC, Mistry, D, Klein, DJ, Hellard, M, Scott, N, Abeysuriya, RG, Delport, D, Stuart, RM, Sacks-Davis, R, Kerr, CC, Mistry, D, Klein, DJ, Hellard, M, and Scott, N
- Abstract
BACKGROUND: In settings with zero community transmission, any new SARS-CoV-2 outbreaks are likely to be the result of random incursions. The level of restrictions in place at the time of the incursion is likely to considerably affect possible outbreak trajectories, but the probability that a large outbreak eventuates is not known. METHODS: We used an agent-based model to investigate the relationship between ongoing restrictions and behavioural factors, and the probability of an incursion causing an outbreak and the resulting growth rate. We applied our model to the state of Victoria, Australia, which has reached zero community transmission as of November 2020. RESULTS: We found that a future incursion has a 45% probability of causing an outbreak (defined as a 7-day average of > 5 new cases per day within 60 days) if no restrictions were in place, decreasing to 23% with a mandatory masks policy, density restrictions on venues such as restaurants, and if employees worked from home where possible. A drop in community symptomatic testing rates was associated with up to a 10-percentage point increase in outbreak probability, highlighting the importance of maintaining high testing rates as part of a suppression strategy. CONCLUSIONS: Because the chance of an incursion occurring is closely related to border controls, outbreak risk management strategies require an integrated approaching spanning border controls, ongoing restrictions, and plans for response. Each individual restriction or control strategy reduces the risk of an outbreak. They can be traded off against each other, but if too many are removed there is a danger of accumulating an unsafe level of risk. The outbreak probabilities estimated in this study are of particular relevance in assessing the downstream risks associated with increased international travel.
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- 2022
5. Characterisation of Spheroidised tungsten carbide metco 32c powder using radio frequency plasma
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Dire, RM, primary, Bissett, H, additional, Delport, D, additional, and Premlall, K, additional
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- 2022
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6. Students’ perceptions towards instructor-developed screencasts as a stand-alone method of instruction on WhatsApp in an introductory statistics course during COVID-19
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Delport, D. H., primary
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- 2022
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7. The effect of decarburization on the fatigue life of overhead line hardware
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Calitz, J., primary, Kok, S., additional, and Delport, D., additional
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- 2021
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8. Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission
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Scott, N, Palmer, A, Delport, D, Abeysuriya, R, Stuart, RM, Kerr, CC, Mistry, D, Klein, DJ, Sacks-Davis, R, Heath, K, Hainsworth, SW, Pedrana, A, Stoove, M, Wilson, D, Hellard, ME, Scott, N, Palmer, A, Delport, D, Abeysuriya, R, Stuart, RM, Kerr, CC, Mistry, D, Klein, DJ, Sacks-Davis, R, Heath, K, Hainsworth, SW, Pedrana, A, Stoove, M, Wilson, D, and Hellard, ME
- Abstract
OBJECTIVES: To assess the risks associated with relaxing coronavirus disease 2019 (COVID-19)-related physical distancing restrictions and lockdown policies during a period of low viral transmission. DESIGN: Network-based viral transmission risks in households, schools, workplaces, and a variety of community spaces and activities were simulated in an agent-based model, Covasim. SETTING: The model was calibrated for a baseline scenario reflecting the epidemiological and policy environment in Victoria during March-May 2020, a period of low community viral transmission. INTERVENTION: Policy changes for easing COVID-19-related restrictions from May 2020 were simulated in the context of interventions that included testing, contact tracing (including with a smartphone app), and quarantine. MAIN OUTCOME MEASURE: Increase in detected COVID-19 cases following relaxation of restrictions. RESULTS: Policy changes that facilitate contact of individuals with large numbers of unknown people (eg, opening bars, increased public transport use) were associated with the greatest risk of COVID-19 case numbers increasing; changes leading to smaller, structured gatherings with known contacts (eg, small social gatherings, opening schools) were associated with lower risks. In our model, the rise in case numbers following some policy changes was notable only two months after their implementation. CONCLUSIONS: Removing several COVID-19-related restrictions within a short period of time should be undertaken with care, as the consequences may not be apparent for more than two months. Our findings support continuation of work from home policies (to reduce public transport use) and strategies that mitigate the risk associated with re-opening of social venues.
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- 2021
9. Evaluation of spheroidized tungsten carbide powder produced by induction plasma melting
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Dire, R.M., primary, Bissett, H., additional, Delport, D., additional, and Premlall, K., additional
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- 2021
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10. Characterization of sulphate-reducing bacteria as a function of time on buried pipeline steel under cathodic protection
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Khoele, K, primary, Ama, O M, additional, and Delport, D J, additional
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- 2021
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11. Ending malnutrition in all its forms requires scaling up proven nutrition interventions and much more: a 129-country analysis.
- Author
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Scott, N, Delport, D, Hainsworth, S, Pearson, R, Morgan, C, Huang, S, Akuoku, JK, Piwoz, E, Shekar, M, Levin, C, Toole, M, Homer, CS, Scott, N, Delport, D, Hainsworth, S, Pearson, R, Morgan, C, Huang, S, Akuoku, JK, Piwoz, E, Shekar, M, Levin, C, Toole, M, and Homer, CS
- Abstract
Background
Sustainable Development Goal (SDG) 2.2 calls for an end to all forms of malnutrition, with 2025 targets of a 40% reduction in stunting (relative to 2012), for wasting to occur in less than 5% of children, and for a 50% reduction in anaemia in women (15-49 years). We assessed the likelihood of countries reaching these targets by scaling up proven interventions and identified priority interventions, based on cost-effectiveness.Methods
For 129 countries, the Optima Nutrition model was used to compare 2019-2030 nutrition outcomes between a status quo (maintained intervention coverage) scenario and a scenario where outcome-specific interventions were scaled up to 95% coverage over 5 years. The average cost-effectiveness of each intervention was calculated as it was added to an expanding package of interventions.Results
Of the 129 countries modelled, 46 (36%), 66 (51%) and 0 (0%) were on track to achieve the stunting, wasting and anaemia targets respectively. Scaling up 18 nutrition interventions increased the number of countries reaching the SDG 2.2 targets to 50 (39%), 83 (64%) and 7 (5%) respectively. Intermittent preventative treatment of malaria during pregnancy (IPTp), infant and young child feeding education, vitamin A supplementation and lipid-based nutrition supplements for children produced 88% of the total impact on stunting, with average costs per case averted of US$103, US$267, US$556 and US$1795 when interventions were consecutively scaled up, respectively. Vitamin A supplementation and cash transfers produced 100% of the total global impact on prevention of wasting, with average costs per case averted of US$1989 and US$19,427, respectively. IPTp, iron and folic acid supplementation for non-pregnant women, and multiple micronutrient supplementation for pregnant women produced 85% of the total impact on anaemia prevalence, with average costs per case averted of US$9, US$35 and US$47, respectively.Conclusions
Prioriti- Published
- 2020
12. NUMERACY STUDENTS' PERSPECTIVES ON A NEW DIGITAL LEARNING TOOL AT A SOUTH AFRICAN UNIVERSITY.
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Delport, D. H.
- Subjects
STUDENT attitudes ,NUMERACY ,SOUTH Africans ,UNIVERSITIES & colleges - Abstract
Students thrive in learning environments where they are able to remain engaged, interested and motivated. A new digital learning tool, MindTap Math Foundations, claims to transform learning by bringing elements from the interactive, gamified world so that students stay engaged, persist through challenges, feel more supported and connected with instructors, other students and their own learning experience. A South African university was the first higher education institution in South Africa to make use of this personalised learning system. A survey was employed to assess the effectiveness of MindTap Math Foundations as a digital learning tool. The focus of the article is on the analysis of the open-ended questions in the survey. The findings of this research support the claims Cengage make regarding the platform's benefits. Participants' responses revealed that the new digital learning tool is generally perceived as positive and beneficial for learning numeracy. Students' feedback also provided ideas and proposals for potential enhancement. Through students' experiences shared it was possible to pinpoint the strengths and challenges regarding aspects needing consideration and improvement. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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13. Core histone genes of Giardia intestinalis: genomic organization, promoter structure and expression.
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Trent University, Canada - Department of Biological and Chemistry, Yee J., Tang A., Lau WL., Ritter H., Delport D., Page, Melissa, Adam, RD., Müller, M., Wu, G., Trent University, Canada - Department of Biological and Chemistry, Yee J., Tang A., Lau WL., Ritter H., Delport D., Page, Melissa, Adam, RD., Müller, M., and Wu, G.
- Abstract
BACKGROUND: Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones. RESULTS: We identified two copies each of the core histone H2a, H2b and H3 genes, and three copies of the H4 gene, at separate locations on chromosomes 3, 4 and 5 within the genome of Giardia intestinalis, but no gene encoding a H1 linker histone could be recognized. The copies of each gene share extensive DNA sequence identities throughout their coding and 5' noncoding regions, which suggests these copies have arisen from relatively recent gene duplications or gene conversions. The transcription start sites are at triplet A sequences 1-27 nucleotides upstream of the translation start codon for each gene. We determined that a 50 bp region upstream from the start of the histone H4 coding region is the minimal promoter, and a highly conserved 15 bp sequence called the histone motif (him) is essential for its activity. The Giardia core histone genes are constitutively expressed at approximately equivalent levels and their mRNAs are polyadenylated. Competition gel-shift experiments suggest that a factor within the protein complex that binds him may also be a part of the protein complexes that bind other promoter elements described previously in Giardia. CONCLUSION: In contrast to other eukaryotes, the Giardia genome has only a single class of core histone genes that encode replication-independent histones. Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome.
- Published
- 2008
14. SASOP Biological Psychiatry Congress 2013 Abstracts
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Allers, E, primary, Allers, E, additional, Betancourt, O A, additional, Benson-Martin, J, additional, Buckley, P, additional, Chetty, I, additional, Chiliza, B, additional, Cilliers, P, additional, Clark, H, additional, Cowen, P, additional, Dannatt, L, additional, Domingo, A K, additional, Domschke, K, additional, Du Plessis, S, additional, Haddad, P, additional, Hemmings, S, additional, Henderson, D C, additional, Hitzeroth, V, additional, Janse van Rensburg, B, additional, Janse van Rensburg, S, additional, Jordaan, G, additional, Kramer, L, additional, Lachman, A, additional, Latecki, B, additional, Macqueen, P, additional, McGregor, N, additional, Moodley, A, additional, Moosa, Z M, additional, Mubaiwa, L, additional, Nagdee, M, additional, Nemeroff, C, additional, Nortje, G, additional, Ojagbemi, A, additional, Peter, E, additional, Phahladira, L, additional, Pienaar, W, additional, Ramlall, S, additional, Rataemane, S, additional, Roos, A, additional, Rosenstein, D, additional, Roux, J, additional, Schumann, C, additional, Solms, M, additional, Spies, G, additional, Subramaney, U, additional, Suliman, S, additional, Suomi, S, additional, Szabo, C, additional, Uys, H, additional, Van Tonder, J, additional, Zohar, J, additional, Bakelaar, S, additional, Breet, E, additional, Bronkhorst, A, additional, Davis, W, additional, De Klerk, D, additional, Delport, D, additional, Drögemöller, B, additional, Du Toit, E, additional, and Fouche, J P, additional
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- 2013
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15. Die ontwikkeling van ’n korrosiebestande langpadlengte-infrarooisel Deel I: Konstruksieparameters en -oorwegings
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Delport, D. J., primary, Potgieter, J. H., additional, Augustyn, W. G., additional, and Prior, J. H., additional
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- 2003
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16. 122 Developmental dyslexias: Retrospective analysis of 272 cases
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Cheminal, R., primary, Arnaud, C., additional, Crepin, S., additional, Davin, S., additional, Delport, D., additional, Klemm, P., additional, Sirmain, S., additional, Issert, B., additional, and Echenne, B., additional
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- 1999
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17. Analyse et prise en charge des difficultes scolaires en neuropediatrie
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Cheminal, R., primary, Delport, D., additional, Klemm, P., additional, Rivier, F., additional, and Echenne, B., additional
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- 1996
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18. Chloride-binding Effect of Blast Furnace Slag in Cement Pastes Containing Added Chlorides.
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Potgieter, J. H., Delport, D. J., Verryn, S., and Potgieter-Vermaak, S. S.
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SLAG , *BLAST furnaces , *PERMEABILITY , *CORROSION & anti-corrosives , *FLY ash - Abstract
Corrosion of rebar in concrete is commonly associated with, and to a large degree influenced by, the free chloride concentration in the pore water. It is standard industry practice to add various mineral admixtures such as pulverised fuel ash (PFA), or fly ash, ground granulated blast furnace slag (GGBS) and silica fume (SF), to concrete mixtures to increase the corrosion resistance of the reinforcement in the matrix and its subsequent design life span. Various investigations have reported on the effect of mineral admixtures and additions on chloride binding in cementitious matrices, and the current study contributes further to knowledge in this field. Unlike previous investigations, this study attempted to make a clear distinction between the contributions of the two components in a blended cement consisting of ordinary Portland cement (OPC) and ground blast furnace slag (BFS). These contributions of each component have been quantified. Relationships between the total amount of chloride bound, the level of BFS additions, and the levels of initial chloride content present in the matrix were determined. It was found that the OPC/BFS blended cement with partial BFS replacements of up to 50%displayed a lower binding capacity than that of the OPC on its own. This observation was derived based on the assumption that the OPC and slag reactions were treated as competing and equivalent and did not take any potential time delays into account, nor the degree of cement hydration. The chloride-binding efficiency by the BFS is dependent on both the BFS partial replacement addition level as well as the initial amount of chloride present in the matrix. It is shown that both the OPC and BFS contribute to chloride binding in cement pastes, depending on the amount of BFS that replace the OPC component in the matrix. [ABSTRACT FROM AUTHOR]
- Published
- 2011
19. Potentiometric Determination of Free Chloride in Cement Paste - an Alternative Method for Low-Budget Laboratories.
- Author
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Delport, D. J., Potgieter-Vermaak, S. S., McCrindle, R. I., and Potgieter, J. H.
- Subjects
- *
REINFORCING bars , *CORROSION & anti-corrosives , *POTENTIOMETRY , *ELECTROCHEMICAL analysis , *CEMENT research - Abstract
Corrosion of rebar in concrete is commonly associated with, and to a large degree influenced by, the free chloride concentration in the pore water. The amount of chloride in concrete is important because chloride can promote corrosion of steel reinforcement when moisture and oxygen are present. A potentiometric procedure that makes use of direct measurement with a chloride ion selective electrode has been developed to analyze free chloride in the pore water extracted from cement paste. The accuracy and reliability of this analytical technique has been checked against a certified reference material, Merck sodium chloride solution. Confidence levels (CL0.95), of 0.03 and relative standard deviations of 0.2 % for chloride were determined for ordinary Portland cement (OPC) chloride binding capacity. [ABSTRACT FROM AUTHOR]
- Published
- 2011
20. Chloride-binding effect of blast furnace slag in cement pastes containing added chlorides
- Author
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Potgieter, J. H., Delport, D. J., Verryn, S., and Sanja Potgieter-Vermaak
- Subjects
Chloride binding ,granulated blast furnace slag ,pore solution ,permeability ,corrosion - Abstract
Corrosion of rebar in concrete is commonly associated with, and to a large degree influenced by, the free chloride concentration in the pore water. It is standard industry practice to add various mineral admixtures such as pulverised fuel ash (PFA), or fly ash, ground granulated blast furnace slag (GGBS) and silica fume (SF), to concrete mixtures to increase the corrosion resistance of the reinforcement in the matrix and its subsequent design life span. Various investigations have reported on the effect of mineral admixtures and additions on chloride binding in cementitious matrices, and the current study contributes further to knowledge in this field. Unlike previous investigations, this study attempted to make a clear distinction between the contributions of the two components in a blended cement consisting of ordinary Portland cement (OPC) and ground blast furnace slag (BFS). These contributions of each component have been quantified. Relationships between the total amount of chloride bound, the level ofBFS additions, and the levels of initial chloride content present in the matrix were determined. It was found that the OPC/BFS blended cement with partial BFS replacements of up to 50% displayed a lower binding capacity than that of the OPC on its own. This observation was derived based on the assumption that the OPC and slag reactions were treated as competing and equivalent and did not take any potential time delays into account, nor the degree of cement hydration. The chloride-binding efficiency by the BFS is dependent on both the BFS partial replacement addition level as well as the initial amount of chloride present in the matrix. It is shown that both the OPC and BFS contribute to chloride binding in cement pastes, depending on the amount of BFS that replace the OPC component in the matrix.Keywords: Chloride binding, granulated blast furnace slag, pore solution, permeability, corrosion
21. Potentiometric determination of free chloride in cement paste - An alternative method for low-budget laboratories
- Author
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Delport, D. J., Sanja Potgieter-Vermaak, Mccrindle, R. I., and Potgieter, J. H.
- Subjects
free chloride ,potentiometry ,OPC - Abstract
Corrosion of rebar in concrete is commonly associated with, and to a large degree influenced by, the free chloride concentration in the pore water. The amount of chloride in concrete is important because chloride can promote corrosion of steel reinforcement when moisture and oxygen are present. A potentiometric procedure that makes use of direct measurement with a chloride ion selective electrode has been developed to analyze free chloride in the pore water extracted from cement paste.16 The accuracy and reliability of this analytical technique has been checked against a certified reference material, Merck sodium chloride solution. Confidence levels (CL0.95), of 0.03 and relative standard deviations of 0.2 % for chloride were determined for ordinary Portland cement (OPC) chloride binding capacity.Keywords: OPC, free chloride, potentiometry
22. COVID-19 outbreaks in residential aged care facilities: an agent-based modeling study.
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McAndrew F, Sacks-Davis R, Abeysuriya RG, Delport D, West D, Parta I, Majumdar S, Hellard M, and Scott N
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- Humans, Victoria epidemiology, Aged, SARS-CoV-2, Vaccination statistics & numerical data, Systems Analysis, COVID-19 epidemiology, COVID-19 prevention & control, COVID-19 mortality, Homes for the Aged statistics & numerical data, Disease Outbreaks prevention & control, Disease Outbreaks statistics & numerical data
- Abstract
Introduction: A disproportionate number of COVID-19 deaths occur in Residential Aged Care Facilities (RACFs), where better evidence is needed to target COVID-19 interventions to prevent mortality. This study used an agent-based model to assess the role of community prevalence, vaccination strategies, and non-pharmaceutical interventions (NPIs) on COVID-19 outcomes in RACFs in Victoria, Australia., Methods: The model simulated outbreaks in RACFs over time, and was calibrated to distributions for outbreak size, outbreak duration, and case fatality rate in Victorian RACFs over 2022. The number of incursions to RACFs per day were estimated to fit total deaths and diagnoses over time and community prevalence.Total infections, diagnoses, and deaths in RACFs were estimated over July 2023-June 2024 under scenarios of different: community epidemic wave assumptions (magnitude and frequency); RACF vaccination strategies (6-monthly, 12-monthly, no further vaccines); additional non-pharmaceutical interventions (10, 25, 50% efficacy); and reduction in incursions (30% or 60%)., Results: Total RACF outcomes were proportional to cumulative community infections and incursion rates, suggesting potential for strategic visitation/staff policies or community-based interventions to reduce deaths. Recency of vaccination when epidemic waves occurred was critical; compared with 6-monthly boosters, 12-monthly boosters had approximately 1.2 times more deaths and no further boosters had approximately 1.6 times more deaths over July 2023-June 2024. Additional NPIs, even with only 10-25% efficacy, could lead to a 13-31% reduction in deaths in RACFs., Conclusion: Future community epidemic wave patterns are unknown but will be major drivers of outcomes in RACFs. Maintaining high coverage of recent vaccination, minimizing incursions, and increasing NPIs can have a major impact on cumulative infections and deaths., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 McAndrew, Sacks-Davis, Abeysuriya, Delport, West, Parta, Majumdar, Hellard and Scott.)
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- 2024
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23. A Framework for Assessing the Impact of Outbreak Response Immunization Programs.
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Delport D, Sanderson B, Sacks-Davis R, Vaccher S, Dalton M, Martin-Hughes R, Mengistu T, Hogan D, Abeysuriya R, and Scott N
- Abstract
The impact of outbreak response immunization (ORI) can be estimated by comparing observed outcomes to modelled counterfactual scenarios without ORI, but the most appropriate metrics depend on stakeholder needs and data availability. This study developed a framework for using mathematical models to assess the impact of ORI for vaccine-preventable diseases. Framework development involved (1) the assessment of impact metrics based on stakeholder interviews and literature reviews determining data availability and capacity to capture as model outcomes; (2) mapping investment in ORI elements to model parameters to define scenarios; (3) developing a system for engaging stakeholders and formulating model questions, performing analyses, and interpreting results; and (4) example applications for different settings and pathogens. The metrics identified as most useful were health impacts, economic impacts, and the risk of severe outbreaks. Scenario categories included investment in the response scale, response speed, and vaccine targeting. The framework defines four phases: (1) problem framing and data sourcing (identification of stakeholder needs, metrics, and scenarios); (2) model choice; (3) model implementation; and (4) interpretation and communication. The use of the framework is demonstrated by application to two outbreaks, measles in Papua New Guinea and Ebola in the Democratic Republic of the Congo. The framework is a systematic way to engage with stakeholders and ensure that an analysis is fit for purpose, makes the best use of available data, and uses suitable modelling methodology.
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- 2024
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24. Keeping kids in school: modelling school-based testing and quarantine strategies during the COVID-19 pandemic in Australia.
- Author
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Abeysuriya RG, Sacks-Davis R, Heath K, Delport D, Russell FM, Danchin M, Hellard M, McVernon J, and Scott N
- Subjects
- Humans, Quarantine, SARS-CoV-2, Pandemics prevention & control, Australia epidemiology, COVID-19 epidemiology, COVID-19 prevention & control
- Abstract
Background: In 2021, the Australian Government Department of Health commissioned a consortium of modelling groups to generate evidence assisting the transition from a goal of no community COVID-19 transmission to 'living with COVID-19', with adverse health and social consequences limited by vaccination and other measures. Due to the extended school closures over 2020-21, maximizing face-to-face teaching was a major objective during this transition. The consortium was tasked with informing school surveillance and contact management strategies to minimize infections and support this goal., Methods: Outcomes considered were infections and days of face-to-face teaching lost in the 45 days following an outbreak within an otherwise COVID-naïve school setting. A stochastic agent-based model of COVID-19 transmission was used to evaluate a 'test-to-stay' strategy using daily rapid antigen tests (RATs) for close contacts of a case for 7 days compared with home quarantine; and an asymptomatic surveillance strategy involving twice-weekly screening of all students and/or teachers using RATs., Findings: Test-to-stay had similar effectiveness for reducing school infections as extended home quarantine, without the associated days of face-to-face teaching lost. Asymptomatic screening was beneficial in reducing both infections and days of face-to-face teaching lost and was most beneficial when community prevalence was high., Interpretation: Use of RATs in school settings for surveillance and contact management can help to maximize face-to-face teaching and minimize outbreaks. This evidence supported the implementation of surveillance testing in schools in several Australian jurisdictions from January 2022., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Abeysuriya, Sacks-Davis, Heath, Delport, Russell, Danchin, Hellard, McVernon and Scott.)
- Published
- 2023
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25. COVID-19 epidemic modelling for policy decision support in Victoria, Australia 2020-2021.
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Scott N, Abeysuriya RG, Delport D, Sacks-Davis R, Nolan J, West D, Sutton B, Wallace EM, and Hellard M
- Subjects
- Humans, Victoria epidemiology, SARS-CoV-2, Communicable Disease Control, Policy, COVID-19 epidemiology
- Abstract
Background: Policy responses to COVID-19 in Victoria, Australia over 2020-2021 have been supported by evidence generated through mathematical modelling. This study describes the design, key findings, and process for policy translation of a series of modelling studies conducted for the Victorian Department of Health COVID-19 response team during this period., Methods: An agent-based model, Covasim, was used to simulate the impact of policy interventions on COVID-19 outbreaks and epidemic waves. The model was continually adapted to enable scenario analysis of settings or policies being considered at the time (e.g. elimination of community transmission versus disease control). Model scenarios were co-designed with government, to fill evidence gaps prior to key decisions., Results: Understanding outbreak risk following incursions was critical to eliminating community COVID-19 transmission. Analyses showed risk depended on whether the first detected case was the index case, a primary contact of the index case, or a 'mystery case'. There were benefits of early lockdown on first case detection and gradual easing of restrictions to minimise resurgence risk from undetected cases. As vaccination coverage increased and the focus shifted to controlling rather than eliminating community transmission, understanding health system demand was critical. Analyses showed that vaccines alone could not protect health systems and need to be complemented with other public health measures., Conclusions: Model evidence offered the greatest value when decisions needed to be made pre-emptively, or for questions that could not be answered with empiric data and data analysis alone. Co-designing scenarios with policy-makers ensured relevance and increased policy translation., (© 2023. The Author(s).)
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- 2023
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26. Health and economic benefits of achieving contraceptive and maternal health targets in Small Island Developing States in the Pacific and Caribbean.
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Kelly SL, Walsh T, Delport D, Ten Brink D, Martin-Hughes R, Homer CS, Butler J, Adedeji O, De Beni D, Maurizio F, Friedman HS, Di Marco D, Tobar F, de la Corte Molina MP, Richards AS, and Scott N
- Subjects
- Infant, Newborn, Female, Pregnancy, Humans, Contraceptive Agents, Stillbirth epidemiology, Maternal Health, Caribbean Region, Maternal Death, COVID-19
- Abstract
Introduction: Reducing unmet need for modern contraception and expanding access to quality maternal health (MH) services are priorities for improving women's health and economic empowerment. To support investment decisions, we estimated the additional cost and expected health and economic benefits of achieving the United Nations targets of zero unmet need for modern contraceptive choices and 95% coverage of MH services by 2030 in select Small Island Developing States., Methods: Five Pacific (Kiribati, Samoa, Solomon Islands, Tonga and Vanuatu) and four Caribbean (Barbados, Guyana, Jamaica and Saint Lucia) countries were considered based on population survey data availability. For each country, the Lives Saved Tool was used to model costs, health outcomes and economic benefits for two scenarios: business-as-usual (BAU) (coverage maintained) and coverage-targets-achieved, which scaled linearly from 2022 (following COVID-19 disruptions) coverage of evidence-based family planning and MH interventions to reach United Nations targets, including modern contraceptive methods and access to complete antenatal, delivery and emergency care. Unintended pregnancies, maternal deaths, stillbirths and newborn deaths averted by the coverage-targets-achieved scenario were converted to workforce, education and social economic benefits; and benefit-cost ratios were calculated., Results: The coverage-targets-achieved scenario required an additional US$12.6M (US$10.8M-US$15.9M) over 2020-2030 for the five Pacific countries (15% more than US$82.4M to maintain BAU). This additional investment was estimated to avert 126 000 (40%) unintended pregnancies, 2200 (28%) stillbirths and 121 (29%) maternal deaths and lead to a 15-fold economic benefit of US$190.6M (US$67.0M-US$304.5M) by 2050. For the four Caribbean countries, an additional US$17.8M (US$15.3M-US$22.4M) was needed to reach the targets (4% more than US$405.4M to maintain BAU). This was estimated to avert 127 000 (23%) unintended pregnancies, 3600 (23%) stillbirths and 221 (25%) maternal deaths and lead to a 24-fold economic benefit of US$426.2M (US$138.6M-US$745.7M) by 2050., Conclusion: Achieving full coverage of contraceptive and MH services in the Pacific and Caribbean is likely to have a high return on investment., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2023
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27. Frequent and unpredictable changes in COVID-19 policies and restrictions reduce the accuracy of model forecasts.
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Houdroge F, Palmer A, Delport D, Walsh T, Kelly SL, Hainsworth SW, Abeysuriya R, Stuart RM, Kerr CC, Coplan P, Wilson DP, and Scott N
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- Humans, Policy, Forecasting, Regression Analysis, COVID-19 epidemiology
- Abstract
Between June and August 2020, an agent-based model was used to project rates of COVID-19 infection incidence and cases diagnosed as positive from 15 September to 31 October 2020 for 72 geographic settings. Five scenarios were modelled: a baseline scenario where no future changes were made to existing restrictions, and four scenarios representing small or moderate changes in restrictions at two intervals. Post hoc, upper and lower bounds for number of diagnosed Covid-19 cases were compared with actual data collected during the prediction window. A regression analysis with 17 covariates was performed to determine correlates of accurate projections. It was found that the actual data fell within the lower and upper bounds in 27 settings and out of bounds in 45 settings. The only statistically significant predictor of actual data within the predicted bounds was correct assumptions about future policy changes (OR 15.04; 95% CI 2.20-208.70; p = 0.016). Frequent changes in restrictions implemented by governments, which the modelling team was not always able to predict, in part explains why the majority of model projections were inaccurate compared with actual outcomes and supports revision of projections when policies are changed as well as the importance of modelling teams collaborating with policy experts., (© 2023. The Author(s).)
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- 2023
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28. Cost optimisation analysis of the expanded programme for immunisation: balancing equity and coverage in Pakistan.
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Houdroge F, Yunus H, Delport D, Stearns E, Palmer A, Naim A, Kashif A, Pyne HH, Scott N, Oelrichs R, and Wilson D
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- Child, Child, Preschool, Costs and Cost Analysis, Humans, Pakistan, Vaccination, Immunization, Vaccination Coverage
- Abstract
Introduction: With limited resources, attaining maximal average health service coverage can be at odds with maximising equity which attempts to promote greater reach among underserved populations. In this study, we examined the trade-offs in immunisation coverage levels and equity for children under 5 years of age in Pakistan across various subpopulations who can be targeted with different combinations of immunisation service modalities., Methods: We conducted a detailed costing exercise across 16 geographically and demographically diverse districts in Pakistan. These data were the basis for (a) technical efficiency benchmarking via Data Envelopment Analysis to identify potential efficiency gains by location, delivery model and cost ingredient; (b) allocative efficiency optimisation modelling to understand how resource allocations could be optimised and to devise recommended budget allocations and operational metrics. Finally, the hypothetical overall efficiency gains attainable were estimated if available resources were allocated with the optimal emphases, and if service delivery models operated at productivity levels at the benchmarked frontier of efficiency., Results: Benchmarking suggests that ~44% of delivery models are running efficiently and 37% are highly inefficient. While coverage and equity are usually at odds, surprisingly, the optimisation modelling revealed that substantial improvements in equity between subpopulations does not necessarily cost very much in overall immunisation coverage: theoretically, equity can be achieved while still attaining close to maximal immunisation coverage. Overall, analyses suggest greater emphases should be placed on outreach delivery models which particularly target rural areas and slum populations., Conclusion: The unit cost differentials within districts are not sufficiently large for there to be a large reduction in potential Fully Immunised Children coverage if one focuses on maximising equity. However, reallocations of programme budgets can have a significant impact on equity outcomes, particularly at current low spending amounts. Therefore, it is recommended to address equity as the key objective in national immunisation programming., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
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- 2022
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29. Preventing a cluster from becoming a new wave in settings with zero community COVID-19 cases.
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Abeysuriya RG, Delport D, Stuart RM, Sacks-Davis R, Kerr CC, Mistry D, Klein DJ, Hellard M, and Scott N
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- Disease Outbreaks prevention & control, Humans, Longitudinal Studies, SARS-CoV-2, Victoria epidemiology, COVID-19 epidemiology, COVID-19 prevention & control
- Abstract
Background: In settings with zero community transmission, any new SARS-CoV-2 outbreaks are likely to be the result of random incursions. The level of restrictions in place at the time of the incursion is likely to considerably affect possible outbreak trajectories, but the probability that a large outbreak eventuates is not known., Methods: We used an agent-based model to investigate the relationship between ongoing restrictions and behavioural factors, and the probability of an incursion causing an outbreak and the resulting growth rate. We applied our model to the state of Victoria, Australia, which has reached zero community transmission as of November 2020., Results: We found that a future incursion has a 45% probability of causing an outbreak (defined as a 7-day average of > 5 new cases per day within 60 days) if no restrictions were in place, decreasing to 23% with a mandatory masks policy, density restrictions on venues such as restaurants, and if employees worked from home where possible. A drop in community symptomatic testing rates was associated with up to a 10-percentage point increase in outbreak probability, highlighting the importance of maintaining high testing rates as part of a suppression strategy., Conclusions: Because the chance of an incursion occurring is closely related to border controls, outbreak risk management strategies require an integrated approaching spanning border controls, ongoing restrictions, and plans for response. Each individual restriction or control strategy reduces the risk of an outbreak. They can be traded off against each other, but if too many are removed there is a danger of accumulating an unsafe level of risk. The outbreak probabilities estimated in this study are of particular relevance in assessing the downstream risks associated with increased international travel., (© 2022. The Author(s).)
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- 2022
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30. Covasim: An agent-based model of COVID-19 dynamics and interventions.
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Kerr CC, Stuart RM, Mistry D, Abeysuriya RG, Rosenfeld K, Hart GR, Núñez RC, Cohen JA, Selvaraj P, Hagedorn B, George L, Jastrzębski M, Izzo AS, Fowler G, Palmer A, Delport D, Scott N, Kelly SL, Bennette CS, Wagner BG, Chang ST, Oron AP, Wenger EA, Panovska-Griffiths J, Famulare M, and Klein DJ
- Subjects
- Basic Reproduction Number, COVID-19 Testing, COVID-19 Vaccines, Computational Biology, Computer Simulation, Contact Tracing, Disease Progression, Hand Disinfection, Host Microbial Interactions, Humans, Masks, Mathematical Concepts, Pandemics, Physical Distancing, Quarantine, Software, COVID-19 etiology, COVID-19 prevention & control, COVID-19 transmission, Models, Biological, SARS-CoV-2, Systems Analysis
- Abstract
The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), an open-source model developed to help address these questions. Covasim includes country-specific demographic information on age structure and population size; realistic transmission networks in different social layers, including households, schools, workplaces, long-term care facilities, and communities; age-specific disease outcomes; and intrahost viral dynamics, including viral-load-based transmissibility. Covasim also supports an extensive set of interventions, including non-pharmaceutical interventions, such as physical distancing and protective equipment; pharmaceutical interventions, including vaccination; and testing interventions, such as symptomatic and asymptomatic testing, isolation, contact tracing, and quarantine. These interventions can incorporate the effects of delays, loss-to-follow-up, micro-targeting, and other factors. Implemented in pure Python, Covasim has been designed with equal emphasis on performance, ease of use, and flexibility: realistic and highly customized scenarios can be run on a standard laptop in under a minute. In collaboration with local health agencies and policymakers, Covasim has already been applied to examine epidemic dynamics and inform policy decisions in more than a dozen countries in Africa, Asia-Pacific, Europe, and North America., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2021
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31. Modelling the impact of relaxing COVID-19 control measures during a period of low viral transmission.
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Scott N, Palmer A, Delport D, Abeysuriya R, Stuart RM, Kerr CC, Mistry D, Klein DJ, Sacks-Davis R, Heath K, Hainsworth SW, Pedrana A, Stoove M, Wilson D, and Hellard ME
- Subjects
- Contact Tracing methods, Humans, Mobile Applications, Risk Assessment, SARS-CoV-2, Smartphone, Victoria epidemiology, COVID-19 prevention & control, COVID-19 transmission, Epidemiological Monitoring, Health Policy, Models, Theoretical, Physical Distancing, Quarantine
- Abstract
Objectives: To assess the risks associated with relaxing coronavirus disease 2019 (COVID-19)-related physical distancing restrictions and lockdown policies during a period of low viral transmission., Design: Network-based viral transmission risks in households, schools, workplaces, and a variety of community spaces and activities were simulated in an agent-based model, Covasim., Setting: The model was calibrated for a baseline scenario reflecting the epidemiological and policy environment in Victoria during March-May 2020, a period of low community viral transmission., Intervention: Policy changes for easing COVID-19-related restrictions from May 2020 were simulated in the context of interventions that included testing, contact tracing (including with a smartphone app), and quarantine., Main Outcome Measure: Increase in detected COVID-19 cases following relaxation of restrictions., Results: Policy changes that facilitate contact of individuals with large numbers of unknown people (eg, opening bars, increased public transport use) were associated with the greatest risk of COVID-19 case numbers increasing; changes leading to smaller, structured gatherings with known contacts (eg, small social gatherings, opening schools) were associated with lower risks. In our model, the rise in case numbers following some policy changes was notable only two months after their implementation., Conclusions: Removing several COVID-19-related restrictions within a short period of time should be undertaken with care, as the consequences may not be apparent for more than two months. Our findings support continuation of work from home policies (to reduce public transport use) and strategies that mitigate the risk associated with re-opening of social venues., (© 2020 The Authors. Medical Journal of Australia published by John Wiley & Sons Australia, Ltd on behalf of AMPCo Pty Ltd.)
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- 2021
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32. Nursing and paramedicine student and academic perceptions of the two phase debrief model: A thematic analysis.
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Colleen R, Shannon D, Patricia C, Penny H, and Tracey S
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- Australia, Clinical Competence, Humans, Learning, Perception, Education, Nursing, Baccalaureate, Students, Nursing
- Abstract
Simulation debriefing standards and models recommend simulation facilitators spend time debriefing learner feelings and clinical reasoning following the simulation scenario. Many debriefing models are available, more so in nursing than in paramedicine, however few models combine specific frameworks to debrief learner feelings and unpack cognitive decisions. The Two Phase Debrief model was designed to support debriefers to spend equal amounts of time debriefing learner felt reactions and clinical decision making, guided by specific tools and skills for each phase. Australian nursing and paramedicine students (n = 19) and academics (n = 9) evaluated the Two Phase Debrief model using a qualitative descriptive design. Analysis of focus group data revealed three themes: Valuing time for debrief, Valuing skills for debrief and Valuing emotions. Across the two disciplines, academics agreed learners would benefit from debriefing using Two Phase Debrief model but considered time a barrier. Nursing and paramedicine students felt the equal time spent exploring emotions and clinical reasoning contributed to a positive learning experience and that expert debriefers may not need disciplinary specific content knowledge. These and other findings discussed indicate there is more work needed to understand the appetite for and required skills of expert cross disciplinary simulation debriefing teams., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
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- 2021
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33. Ending malnutrition in all its forms requires scaling up proven nutrition interventions and much more: a 129-country analysis.
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Scott N, Delport D, Hainsworth S, Pearson R, Morgan C, Huang S, Akuoku JK, Piwoz E, Shekar M, Levin C, Toole M, and Homer CS
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- Adolescent, Adult, Dietary Supplements, Female, Humans, Male, Middle Aged, Sustainable Development, Young Adult, Malnutrition prevention & control, Nutritional Support methods
- Abstract
Background: Sustainable Development Goal (SDG) 2.2 calls for an end to all forms of malnutrition, with 2025 targets of a 40% reduction in stunting (relative to 2012), for wasting to occur in less than 5% of children, and for a 50% reduction in anaemia in women (15-49 years). We assessed the likelihood of countries reaching these targets by scaling up proven interventions and identified priority interventions, based on cost-effectiveness., Methods: For 129 countries, the Optima Nutrition model was used to compare 2019-2030 nutrition outcomes between a status quo (maintained intervention coverage) scenario and a scenario where outcome-specific interventions were scaled up to 95% coverage over 5 years. The average cost-effectiveness of each intervention was calculated as it was added to an expanding package of interventions., Results: Of the 129 countries modelled, 46 (36%), 66 (51%) and 0 (0%) were on track to achieve the stunting, wasting and anaemia targets respectively. Scaling up 18 nutrition interventions increased the number of countries reaching the SDG 2.2 targets to 50 (39%), 83 (64%) and 7 (5%) respectively. Intermittent preventative treatment of malaria during pregnancy (IPTp), infant and young child feeding education, vitamin A supplementation and lipid-based nutrition supplements for children produced 88% of the total impact on stunting, with average costs per case averted of US$103, US$267, US$556 and US$1795 when interventions were consecutively scaled up, respectively. Vitamin A supplementation and cash transfers produced 100% of the total global impact on prevention of wasting, with average costs per case averted of US$1989 and US$19,427, respectively. IPTp, iron and folic acid supplementation for non-pregnant women, and multiple micronutrient supplementation for pregnant women produced 85% of the total impact on anaemia prevalence, with average costs per case averted of US$9, US$35 and US$47, respectively., Conclusions: Prioritising nutrition investment to the most cost-effective interventions within the country context can maximise the impact of funding. A greater focus on complementing nutrition-specific interventions with nutrition-sensitive ones that address the social determinants of health is critical to reach the SDG targets.
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- 2020
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34. [Simulation for the announcement of health care-associated harm].
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Cluzel F, Lopes R, Guévara F, and Delport D
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- Health Personnel psychology, Humans, Communication, Health Personnel education, Medical Errors, Simulation Training
- Abstract
A participative pedagogical tool, simulation aids the transfer of competencies in relation to the complex situation of announcing health care-associated harm. The aim is to reinforce patient safety and to improve the quality of communication with patients and between health professionals., (Copyright © 2017 Elsevier Masson SAS. All rights reserved.)
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- 2017
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35. Significance of dietary folate intake, homocysteine levels and MTHFR 677 C>T genotyping in South African patients diagnosed with depression: test development for clinical application.
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Delport D, Schoeman R, van der Merwe N, van der Merwe L, Fisher LR, Geiger D, and Kotze MJ
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- Adult, Biomarkers blood, Depressive Disorder, Major blood, Depressive Disorder, Major diet therapy, Diet adverse effects, Female, Humans, Male, Middle Aged, South Africa epidemiology, Depressive Disorder, Major genetics, Folic Acid administration & dosage, Genotype, Homocysteine blood, Methylenetetrahydrofolate Reductase (NADPH2) genetics, Surveys and Questionnaires standards
- Abstract
Low folate intake in the presence of the functional MTHFR 677 C > T (rs1801133) polymorphism is an important cause of elevated homocysteine levels previously implicated in major depressive disorder (MDD) and many other chronic diseases. In this study the clinical relevance and inter-relationship of these aspects were evaluated in 86 South African patients diagnosed with MDD and 97 population-matched controls participating in a chronic diseases screening program. A questionnaire-based clinical and nutrition assessment was performed, homocysteine levels determined, and all study participants genotyped for MTHFR 677 C > T (rs1801133) using allele-specific TaqMan technology. The folate score was found to be significantly lower in the patient group compared to controls (p = 0.003) and correlated with increased body mass index (BMI), particularly in females with MDD (p = 0.009). BMI was significantly higher in the MDD patients compared with controls after adjustment for age and sex (p = 0.015), but this association was no longer significant after further adjustment for the level of folate intake in the diet. In MDD patients but not controls, the minor T-allele of MTHFR 677 C > T was associated with increased BMI (p = 0.032), which in turn correlated significantly with increased homocysteine levels. The significant association between BMI and homocysteine levels was observed in both the MDD patient (p = 0.049) and control (p = 0.018) study groups. The significantly higher homocysteine levels observed in MDD patients compared to controls after adjustment for age and sex (p = 0.030), therefore appears to be mediated by the effects of MTHFR 677 C > T and low folate intake on BMI. Detection of the low-penetrance MTHFR 677 C > T mutation reinforces the importance of folate intake above the recommended daily dose to prevent or restore dysfunction of the methylation pathway.
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- 2014
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36. Core histone genes of Giardia intestinalis: genomic organization, promoter structure, and expression.
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Yee J, Tang A, Lau WL, Ritter H, Delport D, Page M, Adam RD, Müller M, and Wu G
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- Animals, Base Sequence, Conserved Sequence, Gene Dosage, Molecular Sequence Data, Protein Binding, Transcription Initiation Site, Gene Expression Regulation genetics, Genes, Protozoan genetics, Genome, Protozoan genetics, Giardia lamblia genetics, Histones genetics, Promoter Regions, Genetic genetics
- Abstract
Background: Giardia intestinalis is a protist found in freshwaters worldwide, and is the most common cause of parasitic diarrhea in humans. The phylogenetic position of this parasite is still much debated. Histones are small, highly conserved proteins that associate tightly with DNA to form chromatin within the nucleus. There are two classes of core histone genes in higher eukaryotes: DNA replication-independent histones and DNA replication-dependent ones., Results: We identified two copies each of the core histone H2a, H2b and H3 genes, and three copies of the H4 gene, at separate locations on chromosomes 3, 4 and 5 within the genome of Giardia intestinalis, but no gene encoding a H1 linker histone could be recognized. The copies of each gene share extensive DNA sequence identities throughout their coding and 5' noncoding regions, which suggests these copies have arisen from relatively recent gene duplications or gene conversions. The transcription start sites are at triplet A sequences 1-27 nucleotides upstream of the translation start codon for each gene. We determined that a 50 bp region upstream from the start of the histone H4 coding region is the minimal promoter, and a highly conserved 15 bp sequence called the histone motif (him) is essential for its activity. The Giardia core histone genes are constitutively expressed at approximately equivalent levels and their mRNAs are polyadenylated. Competition gel-shift experiments suggest that a factor within the protein complex that binds him may also be a part of the protein complexes that bind other promoter elements described previously in Giardia., Conclusion: In contrast to other eukaryotes, the Giardia genome has only a single class of core histone genes that encode replication-independent histones. Our inability to locate a gene encoding the linker histone H1 leads us to speculate that the H1 protein may not be required for the compaction of Giardia's small and gene-rich genome.
- Published
- 2007
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