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Topic:Bayesian Analysis
Bayesian analysis is a statistical method that applies Bayes' theorem to update the probability of a hypothesis as more evidence or information becomes available. In equine research, Bayesian analysis can be used to interpret data and make probabilistic inferences about various aspects of horse health, behavior, and performance. This approach allows researchers to incorporate prior knowledge or expert opinion into the analysis, providing a flexible framework for dealing with complex datasets and uncertainty. Applications of Bayesian analysis in equine studies may include genetic evaluations, disease prevalence estimation, and performance prediction. This page compiles peer-reviewed research studies and scholarly articles that explore the application, methodology, and outcomes of Bayesian analysis in the context of equine science.
The Relevance of the Expected Value of the Proportion of Arabian Genes in Genetic Evaluations for Eventing Competitions. The Arabian horse is a generally reliable sport horse, and continues to be a remarkable endurance horse, so the relevance of the expected value of the proportion of Arabian genes (EV%AG) in horses participating in eventing could be a relevant factor. A total of 1089 horses participating in eventing (8866 records) were used. A GLM revealed that the EV%AG was significant in dressage, show jumping and cross-country. A BLUP genetic evaluation was computed with five genetic models (without the EV%AG (0) using as a covariate (A), as a fixed effect (B), with variance heterogeneity, and in genetic gro...
Prevalence and genetic diversity of Theileria equi from horses in Xinjiang Uygur Autonomous region, China. Theileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence...
Estimating Temporally Variable Selection Intensity from Ancient DNA Data. Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes ...
Molecular Features and Antimicrobial Susceptibilities of Streptococcus equi ssp. equi Isolates from Strangles Cases in Indonesia. Strangles, caused by ssp. (), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobi...
Bayesian accuracy estimates and fit for purpose thresholds of cytology and culture of endometrial swab samples for detecting endometritis in mares. The overall aim of this work was to identify the potential impact of misclassification errors associated with routine screening and diagnostic testing for endometritis in mares. Using Bayesian latent class models (BLCM), specific objectives were to: 1) estimate the diagnostic accuracy of cytology and culture of endometrial swab samples to detect endometritis in mares; 2) assess the impact of different cytology thresholds on test accuracy and misclassification costs; and 3) assess the sensitivity (Se) and specificity (Sp) of a diagnostic strategy including both tests interpreted in series and p...
Anthelmintic resistance of horse strongyle nematodes to fenbendazole in Lithuania. Control of strongyle infections presents a global challenge for horse practitioners due to the development of anthelmintic resistance (AR), however comprehensive information on AR in Lithuania is still lacking. The aim of this study was to assess the current situation of fenbendazole (FBZ) AR in horses at stable level in Lithuania. Results: Faecal samples from 121 horses from six stables were examined using the Mini-FLOTAC method. Of these, 89 horses met the inclusion criteria that included strongyle faecal egg counts (FEC) exceeding 200 eggs per gram (EPG). Faecal egg count reduction tests (F...
Morpho-Functional Traits in Pura Raza Menorquina Horses: Genetic Parameters and Relationship with Coat Color Variables. The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animal...
Occurrence of Equine Foamy Virus Infection in Horses from Poland. Equine foamy virus (EFVeca) is a foamy virus of non-primate origin and among the least-studied members of this retroviral subfamily. By sequence comparison, EFVeca shows the highest similarity to bovine foamy virus. In contrast to simian, bovine or feline foamy viruses, knowledge about the epidemiology of EFVeca is still limited. Since preliminary studies suggested EFVeca infections among horses in Poland, we aimed to expand the diagnostics of EFVeca infections by developing specific diagnostic tools and apply them to investigate its prevalence. An ELISA test based on recombinant EFVeca Gag pr...
Population structure and genomic footprints of selection in five major Iranian horse breeds. The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, thre...
Phylogenetic and Mutation Analysis of the Venezuelan Equine Encephalitis Virus Sequence Isolated in Costa Rica from a Mare with Encephalitis. Venezuelan Equine Encephalitis virus (VEEV) is an arboviral pathogen in tropical America that causes lethal encephalitis in horses and humans. VEEV is classified into six subtypes (I to VI). Subtype I viruses are divided into epizootic (IAB and IC) and endemic strains (ID and IE) that can produce outbreaks or sporadic diseases, respectively. The objective of this study was to reconstruct the phylogeny and the molecular clock of sequences of VEEV subtype I complex and identify mutations within sequences belonging to epizootic or enzootic subtypes focusing on a sequence isolated from a mare in C...
Evaluation of factors associated with surgical site infection in equine proximal interphalangeal joint arthrodesis: 54 cases (2010-2019). The frequency of surgical site infection (SSI) following orthopaedic implant placement in horses has been reported but not compared with respect to specific antibiotic protocols administered. To determine factors associated with SSI in horses undergoing proximal interphalangeal joint (PIPJ) arthrodesis including perioperative antibiotic protocols. Records were evaluated (2010-2019), and horses undergoing PIPJ arthrodesis were identified. Patient signalment, supervising surgeon, reason for surgery, limb, implants placed, anaesthetic time, duration casting/coaptation postoperatively, antibiotic ...
How far away do you keep your equines? Estimation of the equine population’s spatial distribution in France. It is essential to have an accurate picture of the spatial distribution of equines to be able to monitor equine health events effectively. In France, this information is only available for certain categories of live equines kept in professional structures and for dead equines removed by renderers. This limits the surveillance, prevention and control methods able to be used to prevent the spread of equine diseases. Our study aimed to provide a realistic estimate of the spatial distribution of the French equine population at the detailed scale of the French commune (France's smallest administrat...
Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US ...
Reduced rank analysis of morphometric and functional traits in Campolina horses. Multitrait models can increase the accuracy of breeding value prediction and reduce bias due to selection by using traits measured before and after it has occurred. However, as the number of traits grows, a similar trend is expected for the number of parameters to be estimated, which directly affects the computing power and the amount of data required. The aim of the present study was to apply reduced rank (principal components model-PCM) and factor analytical models (FAM), to estimate (co)variance components for nineteen traits, jointly evaluated in a single analysis in Campolina horses. A to...
Tooth Elongation of Maxillary Second Premolars and Mandibular Third Molars and Associated Periodontal Disease in Horses: A Retrospective Study. Periodontal disease has been identified in horses and donkeys through the millennia at a prevalence of up to 75% and is a leading cause of tooth loss in horses. We hypothesize that there is a correlation between tooth elongations and periodontal disease. Dental records of all client owned horses examined by a single AVDC/equine board certified practitioner in 2016-2018 were analyzed. Inclusion criteria consisted of the examination finding of tooth elongation of one of the following teeth pairs 106/107, 206/207, 310/311, or 410-411. The included cases were then examined for the finding of perio...
Genetic diversity and population genetic structure in native Ethiopian donkeys (Equus asinus) inferred from equine microsatellite markers. We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respective...
Apparent Breed Predilection for Equid Herpesvirus-1-Associated Myeloencephalopathy (EHM) in a Multiple-Breed Herd. Equid herpesvirus type 1 (EHV-1) causes several outbreaks of abortion and/or equid herpesvirus-associated myeloencephalopathy (EHM) worldwide each year. EHM is of great concern, as permanent neurological gait anomalies can leave a horse unfit for future use. The study assesses the risk factors associated with the occurrence of EHM. During an unmitigated outbreak, 141 adult horses/ponies of several distinct breeds were evaluated-using multiple Bayesian logistic regression calculating the odds ratios for breed, age, and sex. In total, 33 of the 141 horses showed signs of EHM. Fjord horses and wa...
Genomic characterisation of bovine papillomavirus types 1 and 2 identified in equine sarcoids in Japan. Bovine papillomavirus types 1 and 2 (BPV1/2) infection in horses has been associated with the development of equine sarcoids. Previous findings revealed the presence of sarcoid-associated BPV sequence variants that have been proposed as a key factor of cross-species infection in horses. To verify this hypothesis, sarcoid-associated BPV variants should be identified regardless of geographic location. Objective: Sequence analyses of BPV1/2 derived from both horses and cattle were conducted to clarify the sarcoid-associated sequence variants. The aim of this study was to clarify the correlation b...
Bayesian-based withdrawal estimates using pharmacokinetic parameters for two capsaicinoid-containing products administered to horses. Capsaicinoids deter horses from chewing on bandages and are applied topically to provide analgesia to musculoskeletal injuries. They are banned during competition due to their nerve blocking properties. The pharmacokinetics of oral (PO) and direct gastric administration via nasogastric tube (NG), or topical (TOP) administration of two capsaicinoid-containing products were investigated, and the withdrawal times required prior to competition were estimated. Capsaicin (CAP) and dihydrocapsaicin (DCAP) were quantified in plasma, and both compounds were best described by a delayed absorption two co...
Towards compound identification of synthetic opioids in nontargeted screening using machine learning techniques. The constant evolution of the illicit drug market makes the identification of unknown compounds problematic. Obtaining certified reference materials for a broad array of new analogues can be difficult and cost prohibitive. Machine learning provides a promising avenue to putatively identify a compound before confirmation against a standard. In this study, machine learning approaches were used to develop class prediction and retention time prediction models. The developed class prediction model used a naïve Bayes architecture to classify opioids as belonging to either the fentanyl analogues, AH...
Study design synopsis: Battle in the stable: Bayesianism versus Frequentism. Frequentism dominates scientific practice although Bayesianism may provide an alternative, especially when analysing data from complex, high-dimensional models. The key differences between Bayesianism and Frequentism are highlighted in the introduction. Next, I review the different stages of Bayesian statistical reasoning in a research setting, explain the key concepts and illustrate them with toy examples taken in equine veterinary medicine. An extension to more complex models (Bayes network) is introduced and guidelines are offered as a conclusion.
Survey of Risk Factors and Genetic Characterization of Ewe Neck in a World Population of Pura Raza Español Horses. Ewe Neck is a relatively common morphological defect in Pura Raza Español (PRE) horses and other Baroque type horse breeds, which adversely affects the breeding industry; (1) objectives: to establish the within-breed prevalence, possible associated factors, and heritability of Ewe Neck in PRE horses; (2) methods: the database included evaluations of 35,267 PRE horses. The Ewe Neck defect, 16 morphological traits, and 4 body indices were recorded. A Bayesian genetic animal model included the following systematic effects: sex, age, coat color, geographical area of the stud, and birth stud size ...
Diagnostic performance of McMaster, Wisconsin, and automated egg counting techniques for enumeration of equine strongyle eggs in fecal samples. Fecal egg counts are the cornerstone of equine parasite control programs. Previous work led to the development of an automated, image-analysis-based parasite egg counting system. The system has been further developed to include an automated reagent dispenser unit and a custom camera (CC) unit that generates higher resolution images, as well as a particle shape analysis (PSA) algorithm and machine learning (ML) algorithm. The first aim of this study was to conduct a comprehensive comparison of method precision between the original smartphone (SP) unit with the PSA algorithm, CC/PSA, CC/ML, and ...
Modelling the probability and impact of false-positive serology for Borrelia burgdorferi sensu lato: A case study. Serological screening tests for Lyme borreliosis have poor specificity, with potential for misdiagnosis and unnecessary antimicrobial treatment. Objective: To evaluate the impact of Lyme borreliosis seroprevalence and serologic test characteristics on the probability of obtaining a false-positive result and impact on antimicrobial use. Methods: Cross-sectional serological survey and modelling. Methods: Sera from 303 horses in southern Belgium were analysed by enzyme-linked immunosorbent assay (ELISA). Apparent seroprevalence was derived from serological data and a Bayesian estimate of true ser...
GIBBSTHUR: Software for Estimating Variance Components and Predicting Breeding Values for Ranking Traits Based on a Thurstonian Model. (1) Background: Ranking traits are used commonly for breeding purposes in several equine populations; however, implementation is complex, because the position of a horse in a competition event is discontinuous and is influenced by the performance of its competitors. One approach to overcoming these limitations is to assume an underlying Gaussian liability that represents a horse's performance and dictates the observed classification in a competition event. That approach can be implemented using Montecarlo Markov Chain (McMC) techniques with a procedure known as the Thurstonian model. (2) Metho...
Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites. STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the his...
Accuracy of transcranial magnetic stimulation and a Bayesian latent class model for diagnosis of spinal cord dysfunction in horses. Spinal cord dysfunction/compression and ataxia are common in horses. Presumptive diagnosis is most commonly based on neurological examination and cervical radiography, but the interest into the diagnostic value of transcranial magnetic stimulation (TMS) with recording of magnetic motor evoked potentials has increased. The problem for the evaluation of diagnostic tests for spinal cord dysfunction is the absence of a gold standard in the living animal. Objective: To compare diagnostic accuracy of TMS, cervical radiography, and neurological examination. Methods: One hundred seventy-four horses ad...
Relationship between tracheobronchoscopic score and bronchoalveolar lavage red blood cell numbers in the diagnosis of exercise-induced pulmonary hemorrhage in horses. Exercise-induced pulmonary hemorrhage (EIPH) is diagnosed and its severity assessed by post-exercise tracheobronchoscopy, and enumeration of bronchoalveolar lavage fluid red blood cells (BALFRBC). Minimal information is available regarding the relationship of tracheobronchoscopy score to BALFRBC number. Objective: Evaluate the relationship between BALFRBC number and tracheobronchoscopy scores and determine their diagnostic sensitivities. Methods: Nine sedentary horses, 21 fit Thoroughbreds, 129 Barrel Racers. Methods: Normal BALFRBC number and the effect of bronchoalveolar lavage (BAL) on it w...
Genome-wide association study for insect bite hypersensitivity susceptibility in horses revealed novel associated loci on chromosome 1. Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) associated with equine IBH susceptibility. After quality control, 33,523 SNPs were included in a Bayesian genome-wide association study on 177 affected and 178 unaffected Icelandic horses. We report associated regio...
Comparing assignment-based approaches to breed identification within a large set of horses. Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highes...
