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.
Complex dynamic upper airway collapse: associations between abnormalities in 99 harness racehorses with one or more dynamic disorders. Many horses demonstrate dynamic collapse of more than one upper respiratory tract (URT) structure during high-speed treadmill videoendoscopy (HSTV). Objective: To report the frequency of complex dynamic URT collapse in harness racehorses and determine if an association exists between occurrence of certain disorders. Methods: Retrospective study of 99 Standardbreds and Coldblooded trotters that had one or more dynamic URT disorders identified during HSTV between 1998 and 2006. The horses underwent HSTV using a protocol that included periods of free head carriage and poll flexion until fully fat...
Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. The diversity of the equine fecal bacterial community was evaluated using pyrosequencing of 16S rRNA gene amplicons. Fecal samples were obtained from horses fed cool-season grass hay. Fecal bacteria were characterized by amplifying the V4 region of bacterial 16S rRNA gene. Of 5898 mean unique sequences, a mean of 1510 operational taxonomic units were identified in the four fecal samples. Equine fecal bacterial richness was higher than that reported in humans, but lower than that reported in either cattle feces or soil. Bacterial classified sequences were assigned to 16 phyla, of which 10 were ...
Assessment of endogenous growth hormone pulsatility in gelded yearling horses using deconvolution analysis. Defining normal Growth Hormone (GH) secretory dynamics in the horse is necessary to understand altered GH dynamics related to issues like welfare and disease. Methods: Twelve healthy yearlings and two mature Standardbreds were used to quantify GH secretion. Endogenous GH half-life was determined after administration of 1.0 µg/kg BW GH releasing hormone (GHRH). Exogenous GH half-life was determined after administration of 20 µg/kg BW recombinant equine GH (reGH) with and without suppression of endogenous GH secretion by somatostatin infusion (50 µg/m(2)/h). Pulse detection algorithm (C...
Isolation and phylogenetic grouping of equine encephalosis virus in Israel. During 2008-2009 in Israel, equine encephalosis virus (EEV) caused febrile outbreaks in horses. Phylogenetic analysis of segment 10 of the virus strains showed that they form a new cluster; analysis of segment 2 showed ≈92% sequence identity to EEV-3, the reference isolate. Thus, the source of this emerging EEV remains uncertain.
Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers. Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a ...
Attack risk on infected properties during the 2007 equine influenza outbreak in New South Wales, Australia. The aim of this preliminary study was to estimate the proportions of seropositive horses on infected premises (IPs) in order to assess the attack risk of the disease. Logistic regression analyses were conducted to evaluate the differences in attack risks between enterprise sizes and predefined spatial clusters/regions. The average attack risk experienced during the outbreak was 96.88% (median 100%), but it differed according to the size of the enterprise and other geographic and demographic conditions. The highest attack risks were observed in the Dubbo cluster/region and the lowest in the Nar...
The role of working equines to livelihoods in current day campesino hill-slope communities in central Mexico. Small-holder campesino agriculture is based on the diversified use of resources and off-farm work. Working equines have a multifunctional character and sustain the diversification of livelihoods having different values as assets or providing services. The objective was to identify the role of working equines in current diversification strategies in the livelihoods of campesino families in a hill-slope community in central Mexico within livelihoods analysis. Thirty-one variables related to ownership and use of working equines were analysed by cluster analysis and descriptive statistics contrast...
Identifying equine premises at high risk of introduction of vector-borne diseases using geo-statistical and space-time analyses. The identification of premises that may play an important role in the introduction or spread of animal diseases is fundamental to the development of risk-based surveillance and control programs. A combination of geo-statistical and cluster analysis methods was used to identify geographical areas and periods of time at highest risk for introduction of the African horse sickness virus (AHSV) into the Castile and Leon (CyL) region of Spain. Risk was estimated based on the predicted premises-specific abundance of Culicoides spp., a vector for AHSV, and on the frequency of equine introductions from...
Target Group Segmentation in the Horse Buyers’ Market against the Background of Equestrian Experience. Whereas in former times horses were reserved primarily for people involved in agriculture, elite equestrians or the military, nowadays equestrian sport has become an activity for people with a wide variety of backgrounds. However, as more and more people become involved with equestrian sport today, the knowledge concerning animal husbandry in general is diminishing due to an alienation from agricultural themes in modern societies. As a consequence, this development affects both riding ability and the appraisal of horses, especially with respect to the purchase of horses. In order to analyse wh...
Infrared spectroscopy reveals both qualitative and quantitative differences in equine subchondral bone during maturation. The collagen phase in bone is known to undergo major changes during growth and maturation. The objective of this study is to clarify whether Fourier transform infrared (FTIR) microspectroscopy, coupled with cluster analysis, can detect quantitative and qualitative changes in the collagen matrix of subchondral bone in horses during maturation and growth. Equine subchondral bone samples (n = 29) from the proximal joint surface of the first phalanx are prepared from two sites subjected to different loading conditions. Three age groups are studied: newborn (0 days old), immature (5 to 11 months ol...
Evaluation of virulence factor profiling in the characterization of veterinary Escherichia coli isolates. Escherichia coli has been used as an indicator organism for fecal contamination of water and other environments and is often a commensal organism in healthy animals, yet a number of strains can cause disease in young or immunocompromised animals. In this study, 281 E. coli isolates from bovine, porcine, chicken, canine, equine, feline, and other veterinary sources were analyzed by BOXA1R PCR and by virulence factor profiling of 35 factors to determine whether they had utility in identifying the animal source of the isolates. The results of BOXA1R PCR analysis demonstrated a high degree of dive...
Geographic distribution modeling and spatial cluster analysis for equine piroplasms in Greece. Maximum entropy ecological niche modeling and spatial scan statistic were utilized to predict the geographic range and to investigate clusters of infections for equine piroplasms in Greece, using the Maxent and SaTScan programs, respectively. The eastern half of the country represented the culminating area with high probabilities (p>0.75) of presence of equine piroplasms and encompassed most regions with high concentration of equid host populations. The most important environmental factor that contributed to the ecological niche modeling was land cover followed by temperature. Significant c...
Severe anthrax outbreaks in Italy in 2004: considerations on factors involved in the spread of infection. Anthrax is a disease of humans and animals caused by the encapsulated, spore-forming Bacillus anthracis. In Italy, anthrax is normally a sporadic disease. During the summer 2004, anthrax broke out in the Basilicata, in southern Italy, a region with a low prevalence of anthrax in which vaccination had been suspended since 1998. The disease involved several animals in few weeks and in a large area. Over 41 days, 81 cattle died, as well as 15 sheep, 9 goats, 11 horses and 8 deer. The Multiple-locus Variable-Number Tandem Repeats Analysis (MLVA) showed that all the 53 isolates belonged to the Clus...
Genetic diversity and population structure in Brazilian Mangalarga Marchador horses. One hundred and fifteen unrelated Mangalarga Marchador horses were sampled from three geographically distinct regions of Minas Gerais State, Brazil (South, Southeast, and Northeast) and tested for 10 microsatellite loci. Genetic diversity and population structure parameters were estimated with ARLEQUIN 3.0, CERVUS 2.0, POPGENE 1.31, GENEPOP on the web, STRUCTURE 2.0, and SPAGEDI 1.2 software packages. Under Hardy-Weinberg assumptions, seven markers were at equilibrium (LEX014, LEX017, LEX019, SGCV23, TKY321, VHL20, and VIASH39), while two (ASB3 and LEX031) presented significant homozygote exce...
The impact of landscape disturbance on spatial genetic structure in the Guanacaste tree, Enterolobium cyclocarpum (Fabaceae). We examined spatial genetic structure (SGS) in Enterolobium cyclocarpum (the Guanacaste tree), a dominant tree of Central American dry forests in 4 sites in Guanacaste Province, Costa Rica. In disturbed dry forest sites (e.g., pastures), E. cyclocarpum is primarily dispersed by cattle and horses, whose movements are restricted by pasture boundaries. The study sites varied in tree densities and disturbance. Allozyme analyses of adult trees demonstrated significant levels of SGS in 3 of 4 sites. SGS was primarily due to clusters of young adults located along seasonal streams, rocky areas, and in...
Multivariate analysis for characteristics of heat tolerance in horses in Brazil. The environment in which the horse is reared affects its ability to maintain thermal balance which is in turn related to thermal characteristics and regulatory physiological mechanisms. In this study a multivariate analysis of physiological traits in relation to heat tolerance in horses was carried out in the Federal District, Brazil. The aim was to test the ability of these analyses to separate groups of animals and determine which physiological traits are most important in the adaptation to heat stress. Forty adult horses (4 to 13 years) were used, ten from each of four different genetic gro...
Different mechanisms of spinal fusion using equine bone protein extract, rhBMP-2 and autograft during the process of anterior lumbar interbody fusion. To elucidate the molecular mechanisms of spinal fusion with different graft materials during an anterior lumbar interbody fusion, we examined the gene-expression profiles after implantation of equine bone protein extract, rhBMP-2 and autograft using microarray technology and data analysis, including hierarchical clustering, self-organizing maps (SOM), KEGG pathway and Biological process GO analyses in a porcine model. The results suggest that equine bone protein extract exhibited a more similar expression pattern with autograft than that of rhBMP-2. rhBMP-2 recruits progenitor cells, prolifera...
Identification of sperm subpopulations in stallion ejaculates: changes after cryopreservation and comparison with traditional statistics. In an attempt to improve the information obtained after computer-assisted sperm analysis (CASA), data from five stallions (three ejaculates from each) were analysed before (fresh, extended semen) and after cryopreservation using traditional statistics as well as a cluster analysis. The data matrix consisted of 13 987 observations of individual spermatozoa for fresh, extended semen, and 8305 for frozen-thawed samples. As expected, freezing and thawing resulted in a marked decrease of CASA-derived variables of sperm kinematics. All sperm velocities were significantly lower in frozen-thawed sampl...
Preclinical animal models in single site cartilage defect testing: a systematic review. Review the literature for single site cartilage defect research and evaluate the respective strengths and weaknesses of different preclinical animal models. Methods: A literature search for animal models evaluating single site cartilage defects was performed. Variables tabulated and analyzed included animal species, age and number, defect depth and diameter and study duration. Cluster analyses were then used to separate animals with only distal femoral defects into similar groups based on defect dimensions. Representative human studies were included allowing comparison of common clinical lesio...
Evaluation of a multiplex PCR for detection of serotypes K1, K2 and K5 in Klebsiella sp. and comparison of isolates within these serotypes. A multiplex PCR using targets within the serotype-specific region of the capsular polysaccharide synthesis gene cluster of serotypes K1, K2 and K5 was evaluated using the 77 reference serotype strains of Klebsiella, and a panel of clinical isolates subjected previously to conventional serotyping. The PCR was highly specific for these serotypes, which are those most associated with virulence in humans and horses. PCR confirmed that isolates of the K5 serotype had cross-reacted with antiserum for other serotypes, particularly for K7. K5 isolates received by our laboratory were almost exclusively...
Developmental orthopaedic disease in limbs of foals: between-breed variations in the prevalence, location and severity at weaning. Developmental orthopaedic disease (DOD) affects all breeds and is a common cause of pain and lameness for horses in sports. A thorough knowledge of between-breed variations for the prevalence of DOD, for its distribution among the various joints and for its severity at earlier stages in the disease process is needed in order to improve the relevance and the cost-effectiveness of DOD screening protocols. However, no prevalence study for DOD simultaneously performed on several breeds with similar farming systems and based on radiographic findings (RF) on quite a large number of joints and views,...
A survey of horse owners in Great Britain regarding horses in their care. Part 1: Horse demographic characteristics and management. Information is scarce as to how horses are kept and managed in the general horse population of Great Britain. Objective: To characterise the demographics of horses in Great Britain and assess their care (with particular reference to the respiratory system). Methods: Horse owners were surveyed using a self-administered postal questionnaire. These owners were selected randomly, following geographical stratification, using 2-stage cluster sampling of veterinary practices and their clients. Results: The overall response proportion to the survey was 68.2%. An investigation of nonresponse bias detec...
Genetic relationships of five Indian horse breeds using microsatellite markers. The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's DA genetic distance of 0.071 and 0.186, respectively. In a Nei's DA genetic distances based neighbour joining...
A pattern recognition approach for the quantification of horse and rider interactions. Interactions of various systems were investigated in several studies of dynamic systems, but the interactions between horse and rider have not yet been documented. These interactions include the rider's ability to control the horse, adapt to the horse and maintain both participants' body position. An optimum interaction is also adapted to the individual nature of the horse. Objective: To identify rider-horse interactions by means of artificial neural nets analysing the time-continuous pattern. Methods: Fourteen horses were measured trotting on hand, and ridden at working trot with a profession...
Gait characterisation and classification in horses. Although a large number of foot-fall sequences are possible in quadrupeds, few sequences are routinely used. The aim of this paper is to characterise, by foot-fall pattern, the gaits used by horses and develop a novel technique to classify symmetric and asymmetric gaits using one common criterion. To achieve this speed and relative foot-fall, timings of all four limbs of eight Icelandic horses were measured using accelerometers. Linear discriminant analysis (LDA) was performed to find criteria that are optimal for discriminating between the different gaits. This also allowed us to evaluate whe...
Remote sensing based identification of environmental risk factors associated with West Nile disease in horses in Camargue, France. Geographic information system and remote sensing technologies were used to identify landscape features associated with risk of West Nile virus transmission as defined by the presence of confirmed horse cases. SPOT-4 images of Camargue area were used to generate a map of landscape categories of epidemic foci and the geographic information system was employed to determine the proportion of landscape components surrounding 10 horse case sites and 17 control sites. The spatio-temporal analysis of the cases outbreak gave the best results for a spatial window of 9 km and a temporal window of 18 days...
Genetic structure and phylogenetic relationships of the Polish Heavy horse. In this study a wide range of genetic markers (12 microsatellites, 7 blood-group loci, 10 blood-protein loci) and mitochondrial DNA (mtDNA) were used to assess genetic diversity in Polish Heavy horses. Three random samples were sequenced for 421 bp of the mitochondrial D-loop region, but no clear phylogenetic patterns were seen in mtDNA variation. Both heterozygosity and diversity levels are fairly high in Polish Heavy horses. In phylogenetic analysis the draught horses form a distinct cluster that pairs with the true pony breeds. Within this 'cold-blooded' group, the Polish Heavy Horse cluste...
Analysis of genetic diversity and the determination of relationships among western Mediterranean horse breeds using microsatellite markers. The distribution of genetic diversity and the genetic relationships among western Mediterranean horse breeds were investigated using microsatellite markers. The examined sample included seven Spanish and three Italian local horse breeds and populations, plus a Spanish Thoroughbred outgroup. The total number of animals examined was 682 (on average 62 animals per breed; range 20-122). The microsatellite marker set analysed provided 128 alleles (10.7 alleles per locus). Within-breed genetic diversity was always high (>0.70), with breeds contributing about 8% of the total genetic variability. T...
Distribution and characterization of Borrelia burgdorferi isolates from Ixodes scapularis and presence in mammalian hosts in Ontario, Canada. The blacklegged tick, Ixodes scapularis Say (Acari: Ixodidae), has a wide geographical distribution in Ontario, Canada, with a detected range extending at least as far north as the 50th parallel. Our data of 591 adult I. scapularis submissions collected from domestic animals (canines, felines, and equines) and humans during a 10-yr period (1993-2002) discloses a monthly questing activity in Ontario that peaks in May and October. The Lyme disease spirochete Borrelia burgdorferi Johnson, Schmidt, Hyde, Steigerwalt & Brenner was detected in 12.9% of I. scapularis adults collected from domesti...
Development of the Lipizzan horse breed. The development and a brief history of the Lipizzan horse breed are reviewed. The contribution of several breeds, some of them already extinct, to the development of the Lipizzan horse, gives it a special status representing an important gene pool. This well-documented breed is a part of the common European natural and cultural heritage. Breeding practices establishing stallion and mare family lines as well as availability of pedigrees are described. Molecular analysis of mitochondrial DNA (mtDNA) and microsatellite data allowed us to analyse the structure of the Lipizzan population, to estima...