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Topic:Cluster Analysis
Cluster analysis is a statistical method used to group objects, such as horses, into clusters based on similarities in their characteristics or behaviors. In equine research, cluster analysis can help identify patterns and relationships within large datasets, such as genetic information, performance metrics, or health parameters. This technique is valuable for categorizing horses into distinct groups for further analysis, such as distinguishing between different breeds, identifying common traits in performance horses, or assessing health risks. This page aggregates peer-reviewed research studies and scholarly articles that explore the application, methodologies, and findings of cluster analysis in various aspects of equine science.
Transmission of Salmonella clones between different animal species in a horse and cattle breeding region in Japan. Sequence type 34 (ST34) Salmonella enterica serovar Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are the most prevalent clones among humans and animals worldwide, including in Japan. Although cross-species transmission may have occurred in the background of global spread, the matter remains unresolved. Here, we conducted high-resolution phylogenetic analysis using whole-genome sequencing data of Salmonella Typhimurium and 4,[5],12:i:- obtained from a horse and cattle breeding district in Japan and identified cases of cross-species transmission of ST34 Salmonella 4,[5],12:i:...
Friends, forage, freedom: A cluster analysis investigating horse management styles and welfare in the UK and Ireland. This study aims to improve the welfare and management of recreational horses by identifying how different management styles affect horse health and behaviour. We examined the management styles of recreational horse owners in the UK and Ireland, focusing on social interaction (friends), access to suitable forage (forage), and unrestricted movement (freedom). We collected 1,501 survey responses, distributed via social media, and summarised the characteristics and management choices of the respondents. Using the Divisive ANAlysis cluster package in R, three distinct management styles were identif...
“Synthetic gp90 peptide ELISA for equine infectious anemia virus: Improved sensitivity and risk factor insights”. Equine infectious anemia virus (EIAV) is a globally significant equine pathogen, and its control relies on effective serological surveillance. The agar gel immunodiffusion (AGID) test, the WOAH-prescribed method, has limitations in sensitivity. This study developed and validated an indirect ELISA using a synthetic peptide derived from a conserved region of the EIAV gp90 surface glycoprotein. The assay was evaluated using 773 horse sera from the Metropolitan Zone of the Valley of Mexico and compared to the AGID test. The gp90-EIAV ELISA demonstrated a sensitivity of 85.3 % and a specificity o...
Spatiotemporal patterns in British racing and equestrian sports: Implications for pathogen transmission. The widespread assumption that there is minimal potential for pathogen transmission between British racehorse and sport horse populations remains unverified by empirical evidence. Objective: To characterise spatiotemporal patterns of horse attendance at racing and other sport events in Great Britain in 2018. Methods: Spatiotemporal analysis. Methods: Publicly available data from British Horseracing Authority, British Dressage, British Eventing, Endurance GB, and British Showjumping events in Great Britain during 2018 were analysed. Horse attendance was summarised by discipline, month, and seas...
Analysis of Genetic Diversity and Race Genetic Structure of Major Horse Breeds in Xinjiang, China. The study of horse genetic diversity is imperative for informing conservation strategies, safeguarding ancestral lineages, and enhancing breed adaptability to environmental and disease pressures. This study employed 13 microsatellite markers with fluorescent-labeled capillary electrophoresis to analyze the genetic diversity of the Kyrgyz horse ( = 30) and Barkol horse ( = 30) for the first time, comparing them with three other indigenous horse breeds ( = 30 per breed) from Xinjiang, China. A total of 208 alleles were detected. The Polymorphic Information Content (PIC) results from GenAlEx 6.51...
Insights into Genomic Patterns of Homozygosity in the Endangered Dülmen Wild Horse Population. Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with...
Morphometric characteristics of quarter horses in barrel racing events: impacts on performance and competitive success. This study investigated the influence of morphometric characteristics on performance in Quarter Horses competing in barrel racing. Methods: A total of 125 horses were assessed using 28 linear and angular body measurements derived from standardized left-side photographs captured via smartphone and analyzed with open-source software. Results: Measurements were subjected to exploratory factor analysis, extracting six principal components (forequarters, hindquarters, midsection, posterior angles, scapular traits, age and weight), which together explained 83.0 % of the morphological variance. Foreq...
Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population. Strangles (Streptococcus equi infection) remains endemic in the UK, with ~300 laboratory diagnoses annually. Sub-clinically infected long-term carriers are considered a key driver of endemicity. Analysing genomes of circulating strains could provide valuable transmission insights of this pathogen. Objective: To determine the population structure and diversity of UK S. equi isolates and to model transmission using epidemiological and whole genome sequencing data. Methods: Retrospective cross-sectional epidemiological and genomic surveillance. Methods: A dated phylogenetic tree derived from 511...
Measurement of eco-efficiency in the horse industry, spatiotemporal evolution and convergence analysis. The horse industry constitutes a vital economic sector in Xinjiang, China. This study quantitatively assesses the sector's sustainable development through eco-efficiency analysis across northern Xinjiang counties from 2001 to 2021. The research employs four analytical methods: the S-SBM model for efficiency measurement, kernel density estimation for distribution analysis, Moran's index for spatial autocorrelation examination, and convergence tests for long-term trend assessment. Results demonstrate a consistent decline in eco-efficiency, decreasing from 0.821 in 2001 to 0.444 in 2021, with an ...
Clusters of high transmission risk and time series for Equine Infectious Anemia in Brazil. This study identifies high-risk areas for Equine Infectious Anemia (EIA) in Brazil and analyzes the temporal trend of the disease across regions and Federative Units over an 18-year period (2006-2023), using data from the National Animal Health Information System (SIZ). During the analyzed period, 111,826 cases of EIA were reported in Brazil, with a predominance in the Northeast (39.75 %), Central-West (27.56 %), and North (20.95 %) regions. The state of Mato Grosso recorded the highest number of cases (17.02 %), while Sergipe had the lowest (0.36 %). In the incidence risk analysis, the s...
Selection of density standard and X-ray tube settings for computed digital absorptiometry in horses using the k-means clustering algorithm. In veterinary medicine, conventional radiography is the first-choice method for most diagnostic imaging applications in both small animal and equine practice. One direction in its development is the integration of bone density evaluation and artificial intelligence-assisted clinical decision-making, which is expected to enhance and streamline veterinarians' daily practices. One such decision-support method is k-means clustering, a machine learning and data mining technique that can be used clinically to classify radiographic signs into healthy or affected clusters. The study aims to investigat...
Predictors and barriers for biosecurity uptake and risk understanding among Ontario horse owners. This study aimed to describe implementation of biosecurity practices by Ontario horse owners and investigate whether biosecurity implementation was associated with horse-owner demographic characteristics and personality traits. Unassigned: A cross-sectional questionnaire was administered to a convenience sample of horse owners in Ontario to collect data on demographics, personality traits, risk comprehension, and biosecurity practices. Hierarchical cluster analysis was used to identify clusters of participants with shared personality traits, and univariable associations between clusters and de...
Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. The Rhenish German draught horse is an endangered German horse breed, originally used as working horse in agriculture. Therefore, the objective of this study was to evaluate the breed's genetic diversity using pedigree and genomic data in order to analyze classical and ancestral pedigree-based inbreeding, runs of homozygosity, ROH islands, and consensus ROH. Methods: We studied the genome-wide genotype data of 675 Rhenish German draught horses and collated pedigree-based inbreeding coefficients for these horses. The final dataset contained 64,737 autosomal SNPs. Results: The average number of ...
Identifying Novel Emotions and Wellbeing of Horses from Videos Through Unsupervised Learning. This research applies unsupervised learning on a large original dataset of horses in the wild to identify previously unidentified horse emotions. We construct a novel, high-quality, diverse dataset of 3929 images consisting of five wild horse breeds worldwide at different geographical locations. We base our analysis on the seven Panksepp emotions of mammals "Exploring", "Sadness", "Playing", "Rage", "Fear", "Affectionate" and "Lust", along with one additional emotion "Pain" which has been shown to be highly relevant for horses. We apply the contrastive learning framework MoCo (Momentum Contras...
An Equine Protein Atlas Highlights Synovial Fluid Proteome Dynamics during Experimentally LPS-Induced Arthritis. In human proteomics, substantial efforts are ongoing to leverage large collections of mass spectrometry (MS) fragment ion spectra into extensive spectral libraries (SL) as a resource for data independent acquisition (DIA) analysis. Currently, such initiatives in equine research are still missing. Here we present a large-scale equine SL, comprising 6394 canonical proteins and 89,329 unique peptides, based on data dependent acquisition analysis of 75 tissue and body fluid samples from horses. The SL enabled large-scale DIA-MS based quantification of the same samples to generate a quantitative eq...
Influence of Sires on Population Substructure in Dülmen Wild Horses. The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185...
Characterisation of phenotypic patterns in equine exercise-associated myopathies. Equine exercise-associated myopathies are prevalent, clinically heterogeneous, generally idiopathic disorders characterised by episodes of myofibre damage that occur in association with exercise. Episodes are intermittent and vary within and between affected horses and across breeds. The aetiopathogenesis is often unclear; there might be multiple causes. Poor phenotypic characterisation hinders genetic and other disease analyses. Objective: The aim of this study was to characterise phenotypic patterns across exercise-associated myopathies in horses. Methods: Historical cross-sectional study, w...
Mitochondrial DNA and Y chromosome reveal the genetic structure of the native Polish Konik horse population. Polish Konik remains one of the most important horse breeds in Poland. The primitive, native horses with a stocky body and mouse-like coat color are protected by a conservation program, while their Polish population consists of about 3,480 individuals, representing 16 dam and six sire lines. To define the population's genetic structure, mitochondrial DNA and Y chromosome sequence variables were identified. The mtDNA whole hypervariable region analysis was carried out using the Sanger sequencing method on 233 Polish Koniks belonging to all dam lines, while the Y chromosome analysis was performe...
Three-Dimensional Segmentation of Equine Paranasal Sinuses in Multidetector Computed Tomography Datasets: Preliminary Morphometric Assessment Assisted with Clustering Analysis. The paranasal sinuses, a bilaterally symmetrical system of eight air-filled cavities, represent one of the most complex parts of the equine body. This study aimed to extract morphometric measures from computed tomography (CT) images of the equine head and to implement a clustering analysis for the computer-aided identification of age-related variations. Heads of 18 cadaver horses, aged 2-25 years, were CT-imaged and segmented to extract their volume, surface area, and relative density from the frontal sinus (FS), dorsal conchal sinus (DCS), ventral conchal sinus (VCS), rostral maxillary sinus ...
Feeding behaviour related to different feeding devices. Slow feeding devices (SFDs) are useful tools in order to improve the horse well-being and to reduce wastage, but their use may result in unnatural posture during feeding and frustration behaviours. Moreover, it may be important to evaluate the laterality during feeding. The aim of the study was to investigate ponies' feeding behaviour (i.e., lateralisation, frustration, postural eating style) with different hay feeding methods: on the ground (G), a fully filled hay net (HF), a partially filled hay net (HL), and a slow feeder hay box (HB). Nine ponies of two different breed types (Shetland and ...
Genome-wide search reveals the uniqueness of DNA regions associated with coat color and innate immunity in Hokkaido Native Horse. Hokkaido Native Horse (HKD) is a horse breed native to Hokkaido in Japan known for the traits such as coat color with no white spots and adaptability to the local cold climate. To examine whether those traits of HKD are conferred at the DNA level, we attempted to identify fixed DNA regions in HKD individuals, that is, the selection signatures of HKD. A comparison of genome-wide single nucleotide polymorphism genotypes in 58 HKD individuals by principal component analysis, and cluster analysis between breeds, including HKD, and within the HKD individuals indicated the genetic independence of HK...
Pilot study of locomotor asymmetry in horses walking in circles with and without a rider. Horses commonly show asymmetries that manifest as left (L)-right (R) differences in vertical excursion of axial body segments. Moving on a circle confounds inherent individual asymmetries. Our goals were to evaluate individual and group asymmetry patterns and compare objective data with subjective impressions of side preference/laterality in horses walking on L and R circles. Unassigned: Fifteen horses walked on L and R circles unridden and ridden on long and short reins. Optical motion capture (150 Hz) tracked skin-fixed markers. Variables were trunk horizontal angle; neck-to-trunk angle; ver...
Decoding the transcriptomic expression and genomic methylation patterns in the tendon proper and its peritenon region in the aging horse. Equine tendinopathies are challenging because of the poor healing capacity of tendons commonly resulting in high re-injury rates. Within the tendon, different regions - tendon proper (TP) and peritenon (PERI) - contribute to the tendon matrix in differing capacities during injury and aging. Aged tendons have decreased repair potential; the underlying transcriptional and epigenetic changes that occur in the TP and PERI regions are not well understood. The objective of this study was to assess TP and PERI regional differences in adolescent, midlife, and geriatric horses using RNA sequencing and ...
Comparative Analysis of Protein Digestion Characteristics in Human, Cow, Goat, Sheep, Mare, and Camel Milk under Simulated Infant Condition. An infant in vitro digestion model was utilized to investigate protein digestion characteristics in human and diverse mammalian milk (i.e., cow, goat, sheep, mare, and camel milk) using electrophoresis and chromatography. Digestive differences among milks were mainly manifested in the infant gastric phase, as evidenced by varying degrees of protein digestion. Notably, proteins (i.e., lactoferrin, serum albumin, and immunoglobulin G-heavy chain) remained partially intact in human milk, whereas these proteins in animal milk were exclusively degraded after gastrointestinal digestion. The peptide ...
Multi-Omic Temporal Landscape of Plasma and Synovial Fluid-Derived Extracellular Vesicles Using an Experimental Model of Equine Osteoarthritis. Extracellular vesicles (EVs) contribute to osteoarthritis pathogenesis through their release into joint tissues and synovial fluid. Synovial fluid-derived EVs have the potential to be direct biomarkers in the causal pathway of disease but also enable understanding of their role in disease progression. Utilizing a temporal model of osteoarthritis, we defined the changes in matched synovial fluid and plasma-derived EV small non-coding RNA and protein cargo using sequencing and mass spectrometry. Data exploration included time series clustering, factor analysis and gene enrichment interrogation. ...
Core genome multilocus sequence typing analysis of Finnish Taylorella equigenitalis isolates. In Finland, Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), was first detected in 1992. The aim of this study was to genotype Finnish T. equigenitalis isolates to investigate the epidemiology of the infection in the Finnish horse population. A total of 34 T. equigenitalis isolates from 24 horses obtained during 1992-2021 were subjected to whole genome sequencing (WGS) and subsequent local ad hoc core genome multi-locus sequence typing (cgMLST) targeting 1259 loci. Classical MLST profiles were extracted from the whole-genome sequence data. Three novel MLST ty...
Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of th...
Fecal Microbiota and Diet Composition of Buryatian Horses Grazing Warm- and Cold-Season Grass Pastures. The Buryatian horse is an ancient breed and, as an indigenous breed, they have unique adaptive abilities to use scarce pastures, graze in winter, and survive in harsh conditions with minimal human care. In this study, fecal microbiota of Buryatian horses grazing in the warm and cold seasons were investigated using NGS technology on the Illumina MiSeq platform. We hypothesized that the composition of microbial communities in the feces of horses maintained on pasture would change in the different seasons, depending on the grass availability and different plant diets. We conducted microhistologic...
Genomic Analysis of Clostridioides difficile Recovered from Horses in Western Australia. Clostridioides difficile poses an ongoing threat as a cause of gastrointestinal disease in humans and animals. Traditionally considered a human healthcare-related disease, increases in community-associated C. difficile infection (CDI) and growing evidence of inter-species transmission suggest a wider perspective is required for CDI control. In horses, C. difficile is a major cause of diarrhoea and life-threatening colitis. This study aimed to better understand the epidemiology of CDI in Australian horses and provide insights into the relationships between horse, human and environmental strains...
Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
