scholarly journals Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction

2021 ◽  
Author(s):  
Henrik Schiøler ◽  
Torben Knudsen ◽  
Rasmus Froberg Brøndum ◽  
Jakob Stoustrup ◽  
Martin Bøgsted
Keyword(s):  
Mathematical Modelling ◽  
South African ◽  
Hidden Markov ◽  
Large Animal ◽  
Affected Area ◽  
Animal Virus ◽  
Fast Spreading ◽  
Long Time ◽  
Containment Strategy ◽  
Probability Of Extinction

When a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading sub- types, as was the case for the Danish Cluster-5 mink, the British B.1.1.7, and the South African 501Y.V2 variants of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.

scholarly journals Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Henrik Schiøler ◽  
Torben Knudsen ◽  
Rasmus Froberg Brøndum ◽  
Jakob Stoustrup ◽  
Martin Bøgsted
Keyword(s):  
Mathematical Modelling ◽  
South African ◽  
Hidden Markov ◽  
Large Animal ◽  
Affected Area ◽  
Animal Virus ◽  
Fast Spreading ◽  
Long Time ◽  
Containment Strategy ◽  
Probability Of Extinction

AbstractWhen a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading lineages, as was the case for the Danish Cluster-5 mink variant (belonging to the B.1.1.298 lineage), the British B.1.1.7 lineage, and the South African B.1.351 lineage of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.

A Nonstationary Hidden Markov Model with Approximately Infinitely-Long Time-Dependencies

2016 ◽  
Vol 25 (05) ◽  
pp. 1640001 ◽  
Author(s):  
Sotirios Chatzis ◽  
Dimitrios Kosmopoulos ◽  
George Papadourakis
Keyword(s):  
Markov Models ◽  
Hidden Markov ◽  
Mean Field ◽  
Sequential Data ◽  
First Order ◽  
Order Markov Chain ◽  
Inference Algorithms ◽  
Unrealistic Assumption ◽  
Long Time ◽  
Time Dependencies

Hidden Markov models (HMMs) are a popular approach for modeling sequential data, typically based on the assumption of a first-order Markov chain. In other words, only one-step back dependencies are modeled which is a rather unrealistic assumption in most applications. In this paper, we propose a method for postulating HMMs with approximately infinitely-long time-dependencies. Our approach considers the whole history of model states in the postulated dependencies, by making use of a recently proposed nonparametric Bayesian method for modeling label sequences with infinitely-long time dependencies, namely the sequence memoizer. We manage to derive training and inference algorithms for our model with computational costs identical to simple first-order HMMs, despite its entailed infinitely-long time-dependencies, by employing a mean-field-like approximation. The efficacy of our proposed model is experimentally demonstrated.

Bona fides and ubuntu – A response to Dale Hutchison

Acta Juridica ◽  
2021 ◽  
Vol 2021 ◽  
pp. 85-106
Author(s):  
J Barnard-Naudé
Keyword(s):  
South African ◽  
Common Law ◽  
Standard Form ◽  
Contract Law ◽  
Law School ◽  
Point Of View ◽  
Long Time ◽  
School Faculty ◽  
The Common ◽  
Faculty Meeting

This paper is a response to Dale Hutchison’s recent arguments about the role of fairness in contract law after the Constitution. From the point of view of transformative constitutionalism, the paper argues that the fairness ‘debate’ in the South African law of contract should be approached as what it so patently is, namely, as evidence of a deep ideological conflict that has existed in our law of contract for a very long time, and that this debate now exists within the context of a larger debate about the appropriate transformative reach of the Constitution. The argument takes the form of two ‘dangerous supplements’ to Hutchison’s discourse. The first of these supplements contends that indeterminacy is a symptom of the common law itself, rather than a result of contract law’s contact with the Constitution. The second dangerous supplement suggests a responsible judicial engagement with bona fides and ubuntu, one that can exploit the strengths of both the common law and the Constitution and that understands good faith and ubuntu to be ‘inter-linking’ constitutional values that should be enlisted in unison or at least in resonance when it comes to the question of fairness in our contemporary law of contract. In conclusion, I offer a reading of Hutchison’s own politics of contract law and contend that his is an altruistic politics committed to the standard form. I contend that this politics of contract law is consistent with a transformative understanding of the post-apartheid legal order. ‘Law, like every other cultural institution, is a place where we tell one another stories about our relationships with ourselves, one another, and authority. In this, law is no different from the Boston Globe, the CBS evening news, Mother Jones, or a law school faculty meeting. When we tell one another stories, we use languages and themes that different pieces of the culture make available to us, and that limit the stories we can tell. Since our stories influence how we imagine, as well as how we describe, our relationships, our stories also limit who we can be’.

scholarly journals MATHEMATICAL MODELLING OF WATER-QUALITY FOR LONG TIME PERIODS

1984 ◽  
Vol 1 (19) ◽  
pp. 207
Author(s):  
P. Huizinga
Keyword(s):  
Water Quality ◽  
Mathematical Modelling ◽  
Test Cases ◽  
Quality Model ◽  
One Dimensional ◽  
Long Time ◽  
Time Periods ◽  
Theoretical Test ◽  
Modelling Of Water Quality

This paper presents a one-dimensional dynamic water-quality model suitable for long-term application to estuaries. The computation techniques used in the model are very simple, but very good results have been obtained both for theoretical test cases and from applications to estuaries when compared with prototype measurements.

scholarly journals Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study

2021 ◽  
Vol 17 (12) ◽  
pp. e1009680
Author(s):  
Deus Thindwa ◽  
Nicole Wolter ◽  
Amy Pinsent ◽  
Maimuna Carrim ◽  
John Ojal ◽  
...  
Keyword(s):  
South African ◽  
Hidden Markov ◽  
Age Groups ◽  
Hiv Status ◽  
Older Children ◽  
Markov Modelling ◽  
Household Transmission ◽  
Pneumococcal Carriage ◽  
Immunodeficiency Virus ◽  
Infected Adult

Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant’s age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (≥18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9–80.5%) than older children (5–17 years-old) (31.7–50.0%) or adults (11.5–23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7–15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91–1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2–12.8 vs 6.0 days, 95%CI: 5.6–6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507–714 vs 389, 95%CI: 311.1–435.5) were estimated in HIV-infected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.

scholarly journals CHALLENGES IN FORENSIC DETECTION OF FORGERY BY DISAPPEARING INK

2020 ◽  
pp. 1-2
Author(s):  
Sujay Saha ◽  
Ashok Kumar Barik ◽  
Kananbala Jena
Keyword(s):  
Public Trust ◽  
Market Survey ◽  
Common People ◽  
Affected Area ◽  
Security Feature ◽  
Different Types ◽  
Long Time ◽  
Normal Light ◽  
Physical And Chemical

Common People have used ink and paper for making notes for a long time. Due to public trust on permanency and authenticity of records written in ink, handwritten entries on different types of printed banking instruments has enjoyed confidence of both banks and customers for a long time. But, ink writings could be manipulated to achieve intentions of fraudsters without knowledge of the writer. Fraudsters first erase the ink writing by different methods and cover the area with new writings. Common methods to erase writings are physical and chemical erasures. In the cases where physical erasures are done, either traces of ink left on the paper or the signs of abrasion on the paper attracts the attention of examiner. Chemical erasures mostly lead to change in tint of the surface in the affected area. Both chemical and physical erasure leads to loss of micro printing done as a security feature in the area. Recently, we came across a case where earlier writings were changed without any easily detectable changes in normal light. Market survey reveals that disappearing ink pens are commercially available which can disappear after writing on paper in matter of hours. Since no physical abrasion is required or chemicals were used to erase the same, no tell tale signs of either kind of erasure is readily detected. This paper discusses how one such case could be detected and suggests directions to design a module so that these types of cases do not go undetected.

scholarly journals Reimagining pedagogy for theological education at a South African University: An ethnographic exploration

2021 ◽  
Vol 42 (1) ◽  
Author(s):  
Lindie Denny ◽  
Cas Wepener
Keyword(s):  
Higher Education ◽  
South Africa ◽  
South African ◽  
Practical Theology ◽  
Theological Education ◽  
Cultural Anthropology ◽  
Special Focus ◽  
South African Universities ◽  
Long Time ◽  
Curriculum Transformation

Curriculum transformation within Higher Education has been an ongoing process within South Africa Universities. For a long time, apartheid and the conception of race have shaped the education framework. Recently, decolonisation discourses have led to a rethinking about Curricula of Higher Education. Theological Education has been highlighted, as theological faculties within Universities perpetuate European epistemologies. In order to contribute towards curriculum transformation in South Africa, pedagogy for theological education within South African Universities is explored in this article, and a new praxis theory for a reimagined pedagogy is presented. This article presents only part of the research conducted within a South African University. A description and analysis of the empirical research are provided together with a reimagined pedagogy for theological education at a South African University.Intradisciplinary and/or interdisciplinary implications: The research was performed within the field of Practical Theology with a special focus on pedagogy; however, inter-disciplinary insights were gained from fields such as Education and History, and on an intra-disciplinary level, the research used qualitative methods from Cultural Anthropology and Rituals Studies to empirically study pedagogy as a practice.

scholarly journals Dawn of a new era for permanent life partners: from Volks v Robinson to Bwanya v Master of the High Court

De Jure ◽  
2020 ◽  
Vol 53 ◽  
Keyword(s):  
South Africa ◽  
South African ◽  
Positive Development ◽  
Court Case ◽  
Constitutional Court ◽  
Sex Partners ◽  
New Era ◽  
High Court ◽  
Long Time ◽  
Marital Union

SUMMARY The laws in South Africa pertaining to marital affairs have for a long time developed from a conservative form to a non-conservative one. This can be denoted from the passing of legislation such as the Recognition of Customary Marriages Act 120 of 1998, affording women in customary marriages the same protection as those in civil marriages as well as the Civil Union Act 17 of 2006, allowing same-sex partners to formalise their union. Since the advent of the Constitution it can therefore be concluded that the courts and legislature have worked relentlessly to ensure the equal enjoyment of rights to all South African people. Regardless of the immense efforts to develop this area of law, certain groups still remain unprotected and often rely on piece-meal protection often derived from court decisions. Such groups include heterosexual parties to a permanent life partnership. Although such permanent life partnerships are acknowledged in South Africa, there is no legislative protection with regards to maintenance or inheritance at the dissolution of the union. This is different to formalised unions such as marriage and civil unions with extensive legislation concerning the aftermath of such unions. A plethora of cases suggests that, this position has been challenged many times to no avail. In 2005, the Constitutional Court in Volks v Robinson, held that the distinction between married and unmarried couples could not be held to be unfair as a marriage encompassed legal reciprocal duties which were not present in a non-marital union. Effectively, permanent life partners could not claim maintenance or inheritance from the estate of their deceased partner. In a recent welcomed decision by the High Court, a heterosexual permanent life partner was permitted to inherit from the estate of her deceased partner. This article discusses the Constitutional Court case and the recent High Court case to elicit that South Africa is headed towards positive development with regard to marital unions and those akin to such unions.

scholarly journals Entrepreneurial networks: Findings from a South African study

2004 ◽  
Vol 7 (4) ◽  
pp. 589-600 ◽  
Author(s):  
BC Mitchell ◽  
MJ Co
Keyword(s):  
South Africa ◽  
Empirical Study ◽  
South African ◽  
Family Members ◽  
Network Ties ◽  
African Study ◽  
Entrepreneurial Networks ◽  
South Africans ◽  
Kwazulu Natal ◽  
Long Time

The purpose of the empirical study is to make intelligible how entrepreneurs use networks, as well as describe the characteristics of these networks. A survey of 325 entrepreneurs from the KwaZulu-Natal province of South Africa was conducted. Results indicate that although South African entrepreneurs have more contacts in their networks, they spend less time in developing and maintaining contacts when compared to their international counterparts. Results show that South Africans have established their network ties for a long time, although most of the contacts were met through the entrepreneur’s own effort rather than through referrals. Results also show that most of the network members are either friends or family members, which is different to international findings where most network members are business associates.

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