scholarly journals Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization

2021 ◽  
Vol 8 ◽  
Author(s):  
Víctor Lorente-Leal ◽  
Damien Farrell ◽  
Beatriz Romero ◽  
Julio Álvarez ◽  
Lucía de Juan ◽  
...  
Keyword(s):  
Real World ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Variant Calling ◽  
Pairwise Comparison ◽  
Tuberculosis Control ◽  
Animal Pathogens ◽  
Overall Performance ◽  
The Republic ◽  
Control And Eradication

Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In the context of the control of tuberculosis (TB) in livestock, mainly caused by Mycobacterium bovis, these tools offer a high-resolution alternative to traditional molecular methods in the study of herd breakdown events. However, despite the increased use and efforts in the standardization of WGS methods in human tuberculosis around the world, the application of these WGS-enabled approaches to control TB in livestock is still in early development. Our study pursued an initial evaluation of the performance and agreement of four publicly available pipelines for the analysis of M. bovis WGS data (vSNP, SNiPgenie, BovTB, and MTBseq) on a set of simulated Illumina reads generated from a real-world setting with high TB prevalence in cattle and wildlife in the Republic of Ireland. The overall performance of the evaluated pipelines was high, with recall and precision rates above 99% once repeat-rich and problematic regions were removed from the analyses. In addition, when the same filters were applied, distances between inferred phylogenetic trees were similar and pairwise comparison revealed that most of the differences were due to the positioning of polytomies. Hence, under the studied conditions, all pipelines offer similar performance for variant calling to underpin real-world studies of M. bovis transmission dynamics.

scholarly journals Population genetic structure of pedunculate oak (Quercus robur L.) in Belarus according to the analysis of chloroplast DNA

2021 ◽  
pp. 59-70
Author(s):  
Vladimir E. Padutov
Keyword(s):  
Genetic Structure ◽  
Chloroplast Dna ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Quercus Robur ◽  
Phylogenetic Trees ◽  
Rflp Analysis ◽  
Pedunculate Oak ◽  
Maximum Likelihood Methods ◽  
The Republic

Pedunculate oak (Quercus robur L.) is one of the main forest forming species in the Republic of Belarus. Its population genetic structure was formed under the influence of various migration processes. Six chloroplast DNA loci (µdt1, µdt3, µdt4, µcd4, µcd5 and µkk4) were used for the genogeographic study. The material for the analysis was collected in 100 oak forest stands (2325 samples); 18 allelic variants were identified, which are grouped into 17 different combinations (haplotypes). Five of them are widespread (the proportion of occurrence varies from 7 to 48 %, totalling 85 %). The remaining 12 are rare (the proportion of occurrence varies from 1 to 3 %, totalling 15 %). Phylogenetic trees constructed using the nearest neighbour and maximum likelihood methods show the presence of two groups (branches) of haplotypes. One of it comprises 8 variants including 2 dominant haplotypes and the other comprises 9 variants including 3 dominant haplotypes. PCR-RFLP analysis of chloroplast DNA showed that the pedunculate oak in Belarus originates from the Balkan refugium. Haplotype No. 1 (µdt189, µdt3123, µdt4142, µcd494, µcd574, µkk4109) is found almost everywhere in Belarus with the exception of the southwest and northeast, while haplotype No. 8 (µdt189, µdt3121, µdt4142, µcd494, µcd574, µkk4109) is mainly localised in the southwest and northeast. Haplotypes No. 3 (µdt189, µdt3120, µdt4141, µcd494, µcd575, µkk4109) and No. 7 (µdt189, µdt3122, µdt4142, µcd494, µcd574, µkk4109) predominantly found in the west of the country. Haplotype No. 2 (µdt190, µdt3120, µdt4141, µcd495, µcd574, µkk4109) is typical for the southeast.

scholarly journals Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution

2020 ◽  
Author(s):  
Christopher Kay ◽  
Tom A Williams ◽  
Wendy Gibson
Keyword(s):  
Molecular Evolution ◽  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Phylogenetic Trees ◽  
Nucleotide Composition ◽  
Sub Saharan Africa ◽  
African Trypanosomes ◽  
Animal Pathogens ◽  
Recent Emergence ◽  
The Impact

Abstract Background: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA (mtDNA). African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of trypanosome mtDNA to study the evolutionary history of trypanosomes and the molecular evolution of their mtDNAs.Results: We used long-read sequencing to completely assemble mtDNAs from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome mtDNAs from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. Whole mtDNA coding regions were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense .Conclusions: Our mtDNA data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum , major human and animal pathogens.

scholarly journals Benchmarking Analysis of Factors Influencing Container Traffic in the Port of Rijeka

Pomorstvo ◽  
2019 ◽  
Vol 33 (2) ◽  
pp. 119-129
Author(s):  
Antonija Petrlić ◽  
Nataša Pavletić
Keyword(s):  
Maritime Transportation ◽  
Eastern European ◽  
Competitive Advantages ◽  
The North ◽  
Overall Performance ◽  
The Republic ◽  
Eastern European Countries ◽  
The City ◽  
North Adriatic Sea ◽  
Economic Function

Traditionally, ports have been regarded as hubs responsible for the reception of ships and passengers, but nowadays they have a much wider economic function, being clusters of various activities directly or indirectly linked to maritime transportation and seaborne trade, among which container traffic is the most important segment. The Port of Rijeka as the largest Croatian cargo port, positioned in the North Adriatic Sea, has exceptional but not fully exploited opportunities for further economic development of importance not just for the port and the city but for the Republic of Croatia as well. In addition, its geostrategic position makes it an important international port for Central and South Eastern European countries. The aim of this paper is to investigate and identify the current position of the Port of Rijeka (hereinafter Rijeka) in relation to the container business and, using Benchmarking as the research method, to analyse the established five main factors that have to be taken into consideration where its efficiency is compared to the statistically proven “best container port” in the region – the Port of Koper (hereinafter Koper). The results show significant competitive advantages of the Port of Koper almost in any of the analysed factors. Therefore, recommendations are given for further actions and improvement according to the natural advantages that Rijeka has to utilize in order to enhance its competitiveness and overall performance.

scholarly journals Economic Losses’ Estimation of carcass and Organ Condemnations From Slaughter Cattle in Thailand, Pará State, Brazilian Amazon

2019 ◽  
Vol 7 (2) ◽  
pp. 75
Author(s):  
Gerlane Nunes Noronha ◽  
Marcos Antônio Souza dos Santos ◽  
Washington Luiz Assunção Pereira ◽  
Alexandre Do Rosário Casseb ◽  
Andréia Santana Bezerra ◽  
...  
Keyword(s):  
Disease Control ◽  
Bovine Tuberculosis ◽  
Economic Loss ◽  
Brazilian Amazon ◽  
Economic Losses ◽  
National Program ◽  
Tuberculosis Control ◽  
Slaughter Cattle ◽  
Control And Eradication

The article identifies the main pathologies found and estimates the economic losses generated in a slaughterhouse in the Thailand municipality, Pará, during the period from March 2010 to October 2014. 55,169 animals were slaughtered, with total economic losses of R$ 1,221,035.90 and ischemia was the most frequent lesion (41.86%). The most frequent condemnation organs were lungs (48.75%), kidneys (41.66%) and liver (3.61%), which produced economic loss of R$ 76,405.65 (6.26%). Tuberculosis was the main cause of carcass condemnation, responsible for R$ 872,783.64 of economic losses. The bovine tuberculosis control can begin in production, with examinations on the farm to slaughter lines, with careful carcass inspection, as advocated by the National Program for the Control and Eradication of Animal Brucellosis and Tuberculosis (PNCEBT), which increases disease control and minimizes condemnations and economic losses at slaughter.

011-PA10 Epidemiological tuberculosis control in the Republic of Belarus

1995 ◽  
Vol 76 ◽  
pp. 41
Author(s):  
V. Borschchevski ◽  
O. Kalechits ◽  
A. Bogomazova
Keyword(s):  
Tuberculosis Control ◽  
The Republic

The Image of Woman as Motherhood in Rabindranath Tagore’s Gora

2016 ◽  
Vol 6 (9) ◽  
pp. 1841
Author(s):  
Negin Karami ◽  
Sohila Faghfori ◽  
Esmaeil Zohdi
Keyword(s):  
Real World ◽  
Central Character ◽  
Rabindranath Tagore ◽  
The Real ◽  
The Family ◽  
The Republic ◽  
Women's Role ◽  
Divine Mother

This article evaluates the image of a traditional Indian motherhood in Gora written by Rabindranath Tagore. In Gora, Tagore portrays a divine mother and a goddess as well as the conception of the central character in relation to development of social, political, religious, and economical decisions of male. Yet, he insists that woman has the important roles in man’s life and she should make the best identity for her own life in the family or in the larger society. However, This essay can be read as the ideology of a feminine ideal that compares nature of India motherland with mother of everyone in all aspects of life but it examines distinctions between Tagore and Wollstonecraft concerning women’s role as mothers within the family because as a feminist she argues that the rights of women are demanded within the republic. In order to explore Rabindranath Tagore’s treatment of motherhood, Virginia Woolf’s perspective will be analyzed in respect to her feministic approach. So, disregarding how Tagore demonstrates the idea of words, Woolf realizes ideal of motherhood was essential in women’s life and develops a female atmosphere in which women portray their status in the real world and fight against their patriarchal mother.

Evaluating Supplier Involvement Using DEA and Piecewise Triangular Fuzzy AHP

2007 ◽  
Author(s):  
Shouhua Yuan ◽  
Yiliu Tu ◽  
Deyi Xue
Keyword(s):  
Decision Making ◽  
Fuzzy Ahp ◽  
Pairwise Comparison ◽  
Comparison Method ◽  
Data Envelopment ◽  
Novel Method ◽  
Overall Performance ◽  
Dea Method ◽  
The Individual ◽  
Hierarchy Process

Data Envelopment Analysis (DEA) has been widely applied in evaluating multi-criteria decision making problems which have multi-inputs and multi-outputs. However, the traditional DEA method does neither take the decision maker’s subjective preferences to the individual criteria into consideration, nor rank the selected options or decision making units (DMUs). On the other hand, Satty’s Analytical Hierarchy Process (AHP) was established to rank options or DMUs under multi-inputs and multi-outputs through pairwise comparisons. But in most cases, the AHP pairwise comparison method is not perfectly consistent, which may give rise to confusions in determining the appropriate priorities of each criterion to be considered. The inconsistency implicates the fuzziness in generating the relative important weight for each criterion. In this paper, a novel method which employs both DEA and AHP methods is proposed to evaluate the overall performance of suppliers’ involvement in the production of a manufacturing company. This method has been developed through modifying the DEA method into a weighting constrained DEA method by using a piecewise triangular weighting fuzzy set which is generated from the inconsistent AHP comparisons. A bias tolerance ratio (BTR) is introduced to represent the varying but restrained weighting values of each criterion. Accordingly, the BTR provides the decision maker a controllable parameter by tightening or loosening the range of the weighting values in evaluating the overall performance of available suppliers, which in hence, overcomes the two weaknesses of the traditional DEA method.

scholarly journals Triadic IBD coefficients and applications to estimating pairwise relatedness

2007 ◽  
Vol 89 (3) ◽  
pp. 135-153 ◽  
Author(s):  
JINLIANG WANG
Keyword(s):  
Genetic Relatedness ◽  
Mean Squared Error ◽  
Likelihood Method ◽  
Research Areas ◽  
Squared Error ◽  
Identical By Descent ◽  
Moment Estimators ◽  
Overall Performance ◽  
Methodological Studies

SummaryKnowledge of the genetic relatedness among individuals is essential in diverse research areas such as behavioural ecology, conservation biology, quantitative genetics and forensics. How to estimate relatedness accurately from genetic marker information has been explored recently by many methodological studies. In this investigation I propose a new likelihood method that uses the genotypes of a triad of individuals in estimating pairwise relatedness (r). The idea is to use a third individual as a control (reference) in estimating the r between two other individuals, thus reducing the chance of genes identical in state being mistakenly inferred as identical by descent. The new method allows for inbreeding and accounts for genotype errors in data. Analyses of both simulated and human microsatellite and SNP datasets show that the quality of r estimates (measured by the root mean squared error, RMSE) is generally improved substantially by the new triadic likelihood method (TL) over the dyadic likelihood method and five moment estimators. Simulations also show that genotyping errors/mutations, when ignored, result in underestimates of r for related dyads, and that incorporating a model of typing errors in the TL method improves r estimates for highly related dyads but impairs those for loosely related or unrelated dyads. The effects of inbreeding were also investigated through simulations. It is concluded that, because most dyads in a natural population are unrelated or only loosely related, the overall performance of the new triadic likelihood method is the best, offering r estimates with a RMSE that is substantially smaller than the five commonly used moment estimators and the dyadic likelihood method.

scholarly journals COMPARATIVE ANALYSIS OF DIFFERENT STRATEGIES FOR THE CONTROL OF CLASSICAL SWINE FEVER IN THE REPUBLIC OF SERBIA USING MONTE CARLO SIMULATION

2016 ◽  
Vol 9 (1) ◽  
pp. 43-59
Author(s):  
Slavoljub Stanojević ◽  
Miroslav Valčić ◽  
Sonja Radojičić ◽  
Slobodan Stanojević ◽  
Stevan Avramov ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Control Strategy ◽  
Classical Swine Fever ◽  
Direct Costs ◽  
Control Measures ◽  
Early Diagnostics ◽  
Restricted Movement ◽  
The Republic ◽  
Strong Control ◽  
Control And Eradication

Several diff erent strategies for control and eradication of Classical Swine Fever (CSF) were compared using a Monte Carlo method-based simulationmodel. Th e control strategy analyzed in this paper, in addition to other CSF control measures, includes application of biosecurity measures on pigfarms and rural backyard holdings. Elements of the control strategy are based on applicable regulations and include the simulation of detection ofthe disease, setting up the protected and surveillance zones, standstill of pig movements and restricted movement of animals, vehicles, equipment, and people with strong control measures in protection and surveillance zones, euthanasia of susceptible pigs, protective vaccination of pigs, compensation etc. During the simulation, diff erent output parameters were compared such as: duration of epizootic of a disease, number of aff ected holdings and animals, direct costs such as those for dead or culled animals, costs of surveillance, disposal of infectious materials, cleaning and disinfection.Depopulation of aff ected animals with early diagnostics and vaccination in protection and surveillance zone proved to be the most eff ective measures to stop spreading and eradication of the disease. However, during the simulation, systematic implementation of biosecurity measures in all pig production clusters demonstrated to be appropriate strategy for sustainable control of CSF and setting up a stable epizootiological situation.

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