scholarly journals Incorporating genetic selection into individual-based models (IBMs) of malaria and other infectious diseases

2019 ◽  
Author(s):  
Ian M. Hastings ◽  
Raman Sharma
Keyword(s):  
Control Strategies ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Wait Time ◽  
Antimicrobial Drug Resistance ◽  
Infinite Population ◽  
Individual Based Models ◽  
Population Sizes ◽  
Human Infections ◽  
The Impact

AbstractOptimal control strategies for human infections are often investigated by computational approaches using individual-based models (IBMs). These typically track humans and evaluate the impact of control interventions in terms of human deaths, clinical cases averted, interruption of transmission etc. Genetic selection can be incorporated into these IBMs and used to track the spread of mutations whose origin and spread are often driven by the intervention, and which subsequently undermine the control strategy; for example, mutations which encode antimicrobial drug resistance or diagnosis- or vaccine-escape phenotypes. Basic population genetic descriptions of selection are based on infinite population sizes (so that chance fluctuations in allele frequency are absent) but IBMs track finite population sizes. We describe how the finite sizes of IBMs affect simulating the dynamics of genetic selection and how best to incorporate genetic selection into these models. We use the OpenMalaria IBM of malaria as an example, but the same principles apply to IBMs of other diseases. We identify four strategies to incorporate selection into IBMs and make the following four recommendations. Firstly, calculate and report the selection coefficients, s, of the advantageous allele as the key genetic parameter. Secondly, use these values of ‘s’ to calculate the wait-time until a mutation successful establishes itself in the population. The wait time for the mutation can be added to speed of selection, s, to calculate when the mutation will reach significant, operationally important levels. Thirdly, quantify the ability of the IBM to robustly estimate small selection coefficients. Fourthly, optimise computational efficacy: when ‘s’ is small it is plausible that fewer replicates of larger IBMs will be more efficient than a larger number of replicates of smaller size.

scholarly journals Genome-Wide Linkage Disequilibrium and the Extent of Effective Population Sizes in Six Chinese Goat Populations Using a 50K Single Nucleotide Polymorphism Panel

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 350 ◽  
Author(s):  
Haile Berihulay ◽  
Rabiul Islam ◽  
Lin Jiang ◽  
Yuehui Ma
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Parameter ◽  
Genetic Selection ◽  
Chromosome 1 ◽  
Effective Population ◽  
Genome Wide ◽  
Population Sizes ◽  
Trait Locus ◽  
D Values ◽  
Genome Wide Linkage Disequilibrium

Genome-wide linkage disequilibrium is a useful parameter to study quantitative trait locus (QTL) mapping and genetic selection. In many genomic methodologies, effective population size is an important genetic parameter because of its relationship to the loss of genetic variation, increases in inbreeding, the accumulation of mutations, and the effectiveness of selection. In this study, a total of 193 individuals were genotyped to assess the extent of LD and Ne in six Chinese goat populations using the SNP 50K BeadChip. Across the determined autosomal chromosomes, we found an average of 0.02 and 0.23 for r2 and D’ values, respectively. The average r2 between all the populations varied little and ranged from 0.055 r2 for the Jining Grey to 0.128 r2 for the Guangfeng, with an overall mean of 0.083. Across the 29 autosomal chromosomes, minor allele frequency (MAF) was highest on chromosome 1 (0.321) and lowest on chromosome 25 (0.309), with an average MAF of 0.317, and showing the lowest (25.5% for Louping) and highest (28.8% for Qingeda) SNP proportions at MAF values > 0.3. The inbreeding coefficient ranged from 0.064 to 0.085, with a mean of 0.075 for all the autosomes. The Jining Grey and Qingeda populations showed higher Ne estimates, highlighting that these animals could have been influenced by artificial selection. Furthermore, a declining recent Ne was distinguished for the Arbas Cashmere and Guangfeng populations, and their estimated values were closer to 64 and 95, respectively, 13 generations ago, which indicates that these breeds were exposed to strong selection. This study provides an insight into valuable genetic information and will open up the opportunity for further genomic selection analysis of Chinese goat populations.

scholarly journals COVID-19: A scoping review

2020 ◽  
Author(s):  
Brhane Berhe ◽  
Haftom Legese ◽  
Hagos Degefa ◽  
Gebre Adhanom ◽  
Aderajew Gebrewahd ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Scoping Review ◽  
English Language ◽  
Control Strategies ◽  
Grey Literature ◽  
Published Data ◽  
Control And Prevention ◽  
Novel Coronavirus ◽  
Human Infections ◽  
The Impact

Abstract Background: Globally, the novel coronavirus is a pandemic disease causing severe human infections. The severe acute respiratory syndrome 2 is causing severe and life-threatening complications. Methods: A scoping review was conducted following the methodological framework. In this scoping review, 70 records as of May 21, 2020, were included and discussed to better understand the current updates of the virus. PubMed, BioRxiv, MedRxiv, Global Health and google scholars were searched comprehensively for articles, preprints, grey literature, reports, conference proceedings and expert information. Studies conducted in human and published in the English language were included in the review. All the findings and statements of the review regarding the outbreak are based on published data.Results: We identified 408 records, of which 70 studies met the inclusion criteria. We synthesized the data from the included records and deep insights were extracted. The impact of the outbreak is worsening due to overcrowding, presence of asymptomatic carriers, scarcity of test kits, the immune escaping ability of the virus and lack of community awareness.Conclusions and recommendations: Due to the fast-spreading nature of the severe acute respiratory syndrome 2 the prevention and control strategies become challenging. It is imposing social, psychological, and socio-economic impacts. Adherence to physical distancing, quarantining suspects, using personal protective equipment, health education and introducing appropriate handwashing practices, avoiding contact with animals, improved control, and prevention strategies are recommended.

Characterizing the impact of recovering sea otters on commercially important crabs in California estuaries

2020 ◽  
Vol 655 ◽  
pp. 123-137
Author(s):  
TM Grimes ◽  
MT Tinker ◽  
BB Hughes ◽  
KE Boyer ◽  
L Needles ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Sea Otter ◽  
Dungeness Crab ◽  
Sea Otters ◽  
Elkhorn Slough ◽  
Enhydra Lutris Nereis ◽  
Crab Abundance ◽  
Population Sizes ◽  
Commercially Important ◽  
The Impact

Protective legislation and management have led to an increase in California’s sea otter Enhydra lutris nereis population. While sea otter recovery has been linked to ecosystem benefits, sea otter predation may negatively affect commercially valuable species. Understanding the potential influence of sea otters is of particular importance as their range expands into estuaries that function as nurseries for commercially valuable species like Dungeness crab Metacarcinus magister. We consider how sea otter predation has affected the abundance and size of juvenile Dungeness crab in Elkhorn Slough, California, USA, and analyzed cancrid crab abundance and size across 4 California estuaries with and without sea otters to understand how biotic and abiotic factors contribute to observed variation in crab size and abundance. We compared trends in southern sea otters relative to Dungeness crab landings in California to assess whether increasing sea otter abundance have negatively impacted landings. In Elkhorn Slough, juvenile Dungeness crab abundance and size have declined since 2012, coinciding with sea otter population growth. However, the impact of sea otters on juvenile Dungeness crab size was habitat-specific and only significant in unvegetated habitat. Across estuaries, we found that cancrid crab abundance and size were negatively associated with sea otter presence. While abiotic factors varied among estuaries, these factors explained little of the observed variation in crab abundance or size. Although we found evidence that sea otters can have localized effects on cancrid crab populations within estuaries, we found no evidence that southern sea otters, at recent population sizes, have negatively impacted Dungeness crab landings in California from 2000-2014.

scholarly journals Power Hardware-in-the-Loop-Based Performance Analysis of Different Converter Controllers for Fast Active Power Regulation in Low-Inertia Power Systems

Energies ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 3274
Author(s):  
Jose Rueda Torres ◽  
Zameer Ahmad ◽  
Nidarshan Veera Kumar ◽  
Elyas Rakhshani ◽  
Ebrahim Adabi ◽  
...  
Keyword(s):  
Performance Evaluation ◽  
Power Systems ◽  
Real Time ◽  
Control Strategies ◽  
Active Power ◽  
Power Electronic ◽  
Hardware In The Loop ◽  
Digital Controllers ◽  
Power Regulation ◽  
The Impact

Future electrical power systems will be dominated by power electronic converters, which are deployed for the integration of renewable power plants, responsive demand, and different types of storage systems. The stability of such systems will strongly depend on the control strategies attached to the converters. In this context, laboratory-scale setups are becoming the key tools for prototyping and evaluating the performance and robustness of different converter technologies and control strategies. The performance evaluation of control strategies for dynamic frequency support using fast active power regulation (FAPR) requires the urgent development of a suitable power hardware-in-the-loop (PHIL) setup. In this paper, the most prominent emerging types of FAPR are selected and studied: droop-based FAPR, droop derivative-based FAPR, and virtual synchronous power (VSP)-based FAPR. A novel setup for PHIL-based performance evaluation of these strategies is proposed. The setup combines the advanced modeling and simulation functions of a real-time digital simulation platform (RTDS), an external programmable unit to implement the studied FAPR control strategies as digital controllers, and actual hardware. The hardware setup consists of a grid emulator to recreate the dynamic response as seen from the interface bus of the grid side converter of a power electronic-interfaced device (e.g., type-IV wind turbines), and a mockup voltage source converter (VSC, i.e., a device under test (DUT)). The DUT is virtually interfaced to one high-voltage bus of the electromagnetic transient (EMT) representation of a variant of the IEEE 9 bus test system, which has been modified to consider an operating condition with 52% of the total supply provided by wind power generation. The selected and programmed FAPR strategies are applied to the DUT, with the ultimate goal of ascertaining its feasibility and effectiveness with respect to the pure software-based EMT representation performed in real time. Particularly, the time-varying response of the active power injection by each FAPR control strategy and the impact on the instantaneous frequency excursions occurring in the frequency containment periods are analyzed. The performed tests show the degree of improvements on both the rate-of-change-of-frequency (RoCoF) and the maximum frequency excursion (e.g., nadir).

scholarly journals The Impact of Health Policies and Sociodemographic Factors on Doubling Time of the COVID-19 Pandemic in Mexico

2021 ◽  
Vol 18 (5) ◽  
pp. 2354
Author(s):  
Lina Díaz-Castro ◽  
Héctor Cabello-Rangel ◽  
Kurt Hoffman
Keyword(s):  
Population Density ◽  
Doubling Time ◽  
Sociodemographic Factors ◽  
Health Policies ◽  
Government Response ◽  
University Of Oxford ◽  
Negative Effect ◽  
Population Sizes ◽  
The University ◽  
The Impact

Background. The doubling time is the best indicator of the course of the current COVID-19 pandemic. The aim of the present investigation was to determine the impact of policies and several sociodemographic factors on the COVID-19 doubling time in Mexico. Methods. A retrospective longitudinal study was carried out across March–August, 2020. Policies issued by each of the 32 Mexican states during each week of this period were classified according to the University of Oxford Coronavirus Government Response Tracker (OxCGRT), and the doubling time of COVID-19 cases was calculated. Additionally, variables such as population size and density, poverty and mobility were included. A panel data model was applied to measure the effect of these variables on doubling time. Results. States with larger population sizes issued a larger number of policies. Delay in the issuance of policies was associated with accelerated propagation. The policy index (coefficient 0.60, p < 0.01) and the income per capita (coefficient 3.36, p < 0.01) had a positive effect on doubling time; by contrast, the population density (coefficient −0.012, p < 0.05), the mobility in parks (coefficient −1.10, p < 0.01) and the residential mobility (coefficient −4.14, p < 0.01) had a negative effect. Conclusions. Health policies had an effect on slowing the pandemic’s propagation, but population density and mobility played a fundamental role. Therefore, it is necessary to implement policies that consider these variables.

scholarly journals Estimating asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan: a mathematical modeling study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xi Huo ◽  
Jing Chen ◽  
Shigui Ruan
Keyword(s):  
Disease Transmission ◽  
Large Scale ◽  
Transmission Rate ◽  
Control Strategies ◽  
Herd Immunity ◽  
Antibody Prevalence ◽  
Screening Process ◽  
Vaccination Programs ◽  
Prevalence Level ◽  
The Impact

Abstract Background The COVID-19 outbreak in Wuhan started in December 2019 and was under control by the end of March 2020 with a total of 50,006 confirmed cases by the implementation of a series of nonpharmaceutical interventions (NPIs) including unprecedented lockdown of the city. This study analyzes the complete outbreak data from Wuhan, assesses the impact of these public health interventions, and estimates the asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan. Methods By taking different stages of the outbreak into account, we developed a time-dependent compartmental model to describe the dynamics of disease transmission and case detection and reporting. Model coefficients were parameterized by using the reported cases and following key events and escalated control strategies. Then the model was used to calibrate the complete outbreak data by using the Monte Carlo Markov Chain (MCMC) method. Finally we used the model to estimate asymptomatic and undetected cases and approximate the overall antibody prevalence level. Results We found that the transmission rate between Jan 24 and Feb 1, 2020, was twice as large as that before the lockdown on Jan 23 and 67.6% (95% CI [0.584,0.759]) of detectable infections occurred during this period. Based on the reported estimates that around 20% of infections were asymptomatic and their transmission ability was about 70% of symptomatic ones, we estimated that there were about 14,448 asymptomatic and undetected cases (95% CI [12,364,23,254]), which yields an estimate of a total of 64,454 infected cases (95% CI [62,370,73,260]), and the overall antibody prevalence level in the population of Wuhan was 0.745% (95% CI [0.693%,0.814%]) by March 31, 2020. Conclusions We conclude that the control of the COVID-19 outbreak in Wuhan was achieved via the enforcement of a combination of multiple NPIs: the lockdown on Jan 23, the stay-at-home order on Feb 2, the massive isolation of all symptomatic individuals via newly constructed special shelter hospitals on Feb 6, and the large scale screening process on Feb 18. Our results indicate that the population in Wuhan is far away from establishing herd immunity and provide insights for other affected countries and regions in designing control strategies and planing vaccination programs.

scholarly journals The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time

2021 ◽  
Vol 9 (2) ◽  
pp. 221
Author(s):  
Ilaria Patuzzi ◽  
Massimiliano Orsini ◽  
Veronica Cibin ◽  
Sara Petrin ◽  
Eleonora Mastrorilli ◽  
...  
Keyword(s):  
Campylobacter Jejuni ◽  
Broiler Chickens ◽  
Control Strategies ◽  
Chicken Meat ◽  
Control Measures ◽  
Microbial Network ◽  
Gut Colonization ◽  
Commercial Broiler ◽  
Zoonotic Bacteria ◽  
Human Infections

Campylobacter is the most frequent foodborne zoonotic bacteria worldwide, with chicken meat being overwhelmingly the most important reservoir for human infections. Control measures implemented at the farm level (i.e., biosecurity or vaccination), which have been successfully applied to limit other pathogens, such as Salmonella, have not been effective in reducing Campylobacter occurrence. Thus, new approaches are needed to fully understand the ecological interactions of Campylobacter with host animals to effectively comprehend its epidemiology. The objective of this study was to analyse longitudinally the gut microbiota composition of Campylobacter-infected and non-infected farms to identify any difference that could potentially be indicative of gut colonization by Campylobacter spp. Differences in the colonization rate and timing were observed at the farms that became positive for Campylobacter jejuni over the investigated time points, even though in positive tests, the occurrence of Campylobacter jejuni gut colonization was not observed before the second week of the life of the birds. Significant differences were observed in the abundances of specific bacterial taxa between the microbiota of individuals belonging to farms that became Campylobacter positive during the study and those who remained negative with particular reference to Bacteroidales and Clostridiales, respectively. Moreover, Campylobacter colonization dramatically influenced the microbiota richness, although to a different extent depending on the infection timing. Finally, a key role of Faecalibacterium and Lactobacillus genera on the Campylobacter microbial network was observed. Understanding the ecology of the Campylobacter interaction with host microbiota during infection could support novel approaches for broiler microbial barrier restoration. Therefore, evidence obtained through this study can be used to identify options to reduce the incidence of infection at a primary production level based on the targeted influence of the intestinal microbiota, thus helping develop new control strategies in order to mitigate the risk of human exposure to Campylobacter by chicken meat consumption.

scholarly journals Prevalence of mastitis in Nigerian livestock: a Review

2020 ◽  
Vol 1 (1) ◽  
pp. 20-29
Author(s):  
Hussaini Ojagefu Adamu ◽  
Rahimat Oshuwa Hussaini ◽  
Cedric Obasuyi ◽  
Linus Irefo Anagha ◽  
Gabriel Oscy Okoduwa
Keyword(s):  
Control Strategies ◽  
Dairy Farms ◽  
Livestock Production ◽  
Sub Saharan Africa ◽  
Economic Losses ◽  
Ecological Development ◽  
Management Plans ◽  
Sub Saharan ◽  
Control And Management ◽  
The Impact

AbstractMastitis is a disease of livestock that directly impede livestock production and thus hindering the socio-ecological development of sub-Saharan Africa. Studies have estimated the prevalence of this disease in 30% of Africa countries, with Ethiopia having the highest prevalence. The coverage is low, despite the wide livestock and dairy farms distribution in Africa. Furthermore, estimated economic losses due to the impact of mastitis are lacking in Nigeria. The disease is endemic in Nigeria as indicated by the available data and there are no proposed management plans or control strategies. This review is thus presented to serve as a wakeup call to all parties involved to intensify efforts towards the diagnosis, control, and management of the disease in Nigeria.

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