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.
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...
Klossiella equi Infecting Kidneys of Ontario Horses: Life Cycle Features and Multilocus Sequence-Based Genotyping Confirm the Genus Klossiella Belongs In the Adeleorina (Apicomplexa: Coccidia). Species in the genus Klossiella Smith and Johnson, 1902 are unique among the suborder Adeleorina because they are monoxenous in mammals exclusively, whereas all other reported members of the Adeleorina use invertebrates as definitive hosts. Unlike other coccidia, all members of the Adeleorina undergo syzygy, the association of microgamonts and macrogamonts before maturation to gametes and syngamy. After fertilization, many members of the Adeleorina produce thin-walled polysporocystic oocysts. Despite being biologically similar to other members of the Adeleorina, the phylogenetic placement of t...
Modelling of oscillatory cortisol response in horses using a Bayesian population approach for evaluation of dexamethasone suppression test protocols. Cortisol is a steroid hormone relevant to immune function in horses and other species and shows a circadian rhythm. The glucocorticoid dexamethasone suppresses cortisol in horses. Pituitary pars intermedia dysfunction (PPID) is a disease in which the cortisol suppression mechanism through dexamethasone is challenged. Overnight dexamethasone suppression test (DST) protocols are used to test the functioning of this mechanism and to establish a diagnosis for PPID. However, existing DST protocols have been recognized to perform poorly in previous experimental studies, often indicating presence of ...
Surveillance of animal diseases through implementation of a Bayesian spatio-temporal model: A simulation example with neurological syndromes in horses and West Nile Virus. A potentially sensitive way to detect disease outbreaks is syndromic surveillance, i.e. monitoring the number of syndromes reported in the population of interest, comparing it to the baseline rate, and drawing conclusions about outbreaks using statistical methods. A decision maker may use the results to take disease control actions or to initiate enhanced epidemiological investigations. In addition to the total count of syndromes there are often additional pieces of information to consider when assessing the probability of an outbreak. This includes clustering of syndromes in space and time as...
Resistance to pyrantel embonate and efficacy of fenbendazole in Parascaris univalens on Swedish stud farms. The aims of this study were to determine the species of Parascaris present in foals in Sweden and to establish whether anthelmintic resistance to pyrantel and fenbendazole is present on Swedish stud farms. Ascarid eggs collected from different regions in Sweden were karyotyped and were all identified as Parascaris univalens, characterized by one chromosomal pair. Faecal egg count reduction tests were performed on a total of 142 foals on 9 farms between September 2016 and May 2017. Healthy foals with at least 150 eggs per gram faeces (EPG) were included in the study and treated with oral pastes...
Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives. The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski's horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breed...
GWAS by GBLUP: Single and Multimarker EMMAX and Bayes Factors, with an Example in Detection of a Major Gene for Horse Gait. Bayesian models for genomic prediction and association mapping are being increasingly used in genetics analysis of quantitative traits. Given a point estimate of variance components, the popular methods SNP-BLUP and GBLUP result in joint estimates of the effect of all markers on the analyzed trait; single and multiple marker frequentist tests (EMMAX) can be constructed from these estimates. Indeed, BLUP methods can be seen simultaneously as Bayesian or frequentist methods. So far there is no formal method to produce Bayesian statistics from GBLUP. Here we show that the Bayes Factor, a commonly...
A comparison of methods for estimating substitution rates from ancient DNA sequence data. Phylogenetic analysis of DNA from modern and ancient samples allows the reconstruction of important demographic and evolutionary processes. A critical component of these analyses is the estimation of evolutionary rates, which can be calibrated using information about the ages of the samples. However, the reliability of these rate estimates can be negatively affected by among-lineage rate variation and non-random sampling. Using a simulation study, we compared the performance of three phylogenetic methods for inferring evolutionary rates from time-structured data sets: regression of root-to-tip...
Diagnostic accuracy of blood sucrose as a screening test for equine gastric ulcer syndrome (EGUS) in weanling foals. Equine gastric ulcer syndrome is an important cause of morbidity in weanling foals. Many foals are asymptomatic, and the development of an inexpensive screening test to ensure an early diagnosis is desirable. The objective of this study was to determine the diagnostic accuracy of blood sucrose for diagnosis of EGUS in weanling foals. Results: 45 foals were studied 7Â days before and 14Â days after weaning. The diagnostic accuracy of blood sucrose for diagnosis of gastric lesions (GL); glandular lesions (GDL); squamous lesions (SQL) and clinically significant gastric lesions (CSL) at 45 and 90Â...
Comparison of Tracheal Wash and Bronchoalveolar Lavage Cytology in 154 Horses With and Without Respiratory Signs in a Referral Hospital Over 2009-2015. Most equine lower respiratory diseases present as increased airway neutrophilia, which can be detected in tracheal wash (TW) or bronchoalveolar lavage fluid (BALF) cytology samples. The aim was to compare the TW and BALF results in a population of client-owned horses with and without clinical respiratory disease signs. A secondary aim was to determine the sensitivity (Se) and specificity (Sp) of TW and BALF neutrophilia in detecting respiratory disease. The cutoff values for neutrophils were also evaluated. Retrospective data from 154 horses of various breeds that had been subject to both TW a...
Clinical effect of corticosteroids in asthma-affected horses: A quantitative synthesis. There are limited findings from low-powered studies based on few number of subjects with equine asthma. Furthermore, no studies have been performed to assess a meaningful clinically detectable impact of corticosteroids in equine asthma. Objective: To assess and compare the clinical effect of inhaled and systemic corticosteroids in equine asthma and identify a quantitative clinical score suitable to assess the Minimal Important Difference (MID), expressed as the Minimally Clinically Detectable Difference (MCDD). Methods: Pair-wise and network meta-analysis. Methods: Literature searches for stud...
Proximal suspensory desmopathy in hindlimbs: Magnetic resonance imaging, gross post-mortem and histological study. There have been no previous studies correlating high-field magnetic resonance imaging (MRI) findings with gross and histological post-mortem examination in horses with hindlimb proximal suspensory desmopathy (PSD). Objective: To determine if adhesions between the suspensory ligament (SL) and adjacent tissues could be detected using high-field MRI and if collagen, adipose tissue and muscle pathology could be differentiated. Methods: Retrospective study. Methods: Nineteen horses with hindlimb PSD were humanely destroyed; 12 limbs of 11 horses with PSD underwent high-field MRI. All lame limbs wer...
Cheek tooth morphology and ancient mitochondrial DNA of late Pleistocene horses from the western interior of North America: Implications for the taxonomy of North American Late Pleistocene Equus. Horses were a dominant component of North American Pleistocene land mammal communities and their remains are well represented in the fossil record. Despite the abundant material available for study, there is still considerable disagreement over the number of species of Equus that inhabited the different regions of the continent and on their taxonomic nomenclature. In this study, we investigated cheek tooth morphology and ancient mtDNA of late Pleistocene Equus specimens from the Western Interior of North America, with the objective of clarifying the species that lived in this region prior to t...
A case-control study developing a model for predicting risk factors for high SeM-specific antibody titers after natural outbreaks of Streptococcus equi subsp equi infection in horses. OBJECTIVE To develop a risk prediction model for factors associated with an SeM-specific antibody titer ≥ 3,200 in horses after naturally occurring outbreaks of Streptococcus equi subsp equi infection and to validate this model. DESIGN Case-control study. ANIMALS 245 horses: 57 horses involved in strangles outbreaks (case horses) and 188 healthy horses (control horses). PROCEDURES Serum samples were obtained from the 57 cases over a 27.5-month period after the start of outbreaks; serum samples were obtained once from the 188 controls. A Bayesian mixed-effects logistic regression model was us...
Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics. The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis method...