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.
The Lusitano horse maternal lineage based on mitochondrial D-loop sequence variation. The analysis of mitochondrial D-loop sequences (408 bp) from 145 Lusitano founder mares yielded a total of 27 different haplotypes. The distribution of these mtDNA sequences was quite unequal, with the three most frequent ones representing 56.5% of all the Lusitano founder mares and 14 haplotypes (51.9%) being rare variants found only once in the sampling. Four main haplotype clusters were present in the Lusitano breed. The comparison of these sequences with other equine haplotypes shows that they fall in groups shared with other horse breeds. These data support the hypothesis of multiple dome...
Clustering of equine grass sickness cases in the United Kingdom: a study considering the effect of position-dependent reporting on the space-time K-function. Equine grass sickness (EGS) is a largely fatal, pasture-associated dysautonomia. Although the aetiology of this disease is unknown, there is increasing evidence that Clostridium botulinum type C plays an important role in this condition. The disease is widespread in the United Kingdom, with the highest incidence believed to occur in Scotland. EGS also shows strong seasonal variation (most cases are reported between April and July). Data from histologically confirmed cases of EGS from England and Wales in 1999 and 2000 were collected from UK veterinary diagnostic centres. The data did not repre...
Genetic clustering of Borna disease virus natural animal isolates, laboratory and vaccine strains strongly reflects their regional geographical origin. The aim of this study was to gain more detailed insights into the genetic evolution and variability of Borna disease virus (BDV). Phylogenetic analyses were performed on field viruses originating from naturally infected animals, the BDV vaccine strain 'Dessau', four widely used laboratory strains and the novel BDV subtype No/98. Four regions of the BDV genome were analysed: the complete p40, p10 and p24 genes and the 5'-untranslated region of the X/P transcript. BDV isolates from the same geographical area exhibited a clearly higher degree of identity to each other than to BDV isolates from ot...
Detection of spinal ataxia in horses using fuzzy clustering of body position uncertainty. Subjective neurological evaluation in horses is prone to bias. An objective method of spinal ataxia detection is not subject to these limitations and could be of use in equine practice and research. Objective: Kinematic data in the walking horse can differentiate normal and spinal ataxic horses. Methods: Twelve normal and 12 spinal ataxic horses were evaluated by kinematic analysis walking on a treadmill. Each body position signal was reduced to a scalar measure of uncertainty then fuzzy clustered into normal or ataxic groups. Correct classification percentage (CCP) was then calculated using m...
Mitochondrial D-loop sequence variation among Italian horse breeds. The genetic variability of the mitochondrial D-loop DNA sequence in seven horse breeds bred in Italy (Giara, Haflinger, Italian trotter, Lipizzan, Maremmano, Thoroughbred and Sarcidano) was analysed. Five unrelated horses were chosen in each breed and twenty-two haplotypes were identified. The sequences obtained were aligned and compared with a reference sequence and with 27 mtDNA D-loop sequences selected in the GenBank database, representing Spanish, Portuguese, North African, wild horses and an Equus asinus sequence as the outgroup. Kimura two-parameter distances were calculated and a clust...
Microsatellite diversity, population subdivision and gene flow in the Lipizzan horse. Blood samples of 561 Lipizzan horses from subpopulations (studs) of seven European countries representing a large fraction of the breed's population were used to examine the genetic diversity, population subdivision and gene flow in the breed. DNA analysis based on 18 microsatellite loci revealed that genetic diversity (observed heterozygosity = 0.663, gene diversity = 0.675 and the mean number of alleles = 7.056) in the Lipizzan horse is similar to other horse breeds as well as to other domestic animal species. The genetic differentiation between Lipizzan horses from different studs, although...
Characterization of the horse (Equus caballus) IGHA gene. Nucleotide sequences of the immunoglobulin constant heavy chain genes of the horse have been described for IGHM, IGHG and IGHE genes, but not for IGHA. Here, we provide the nucleotide sequence of the genomic IGHA gene of the horse ( Equus caballus), including its secretion region and the transmembrane exon. The equine IGHA gene shows the typical structure of a mammalian IGHA gene, with only three exons, separated by two introns of similar size. The hinge exon is located at the 5' end of the CH2 exon and encodes a hinge region of 11 amino acids, which contains five proline residues. The coding ...
Phylogenetic relationships of West Nile viruses isolated from birds and horses in Israel from 1997 to 2001. In November 1997, an outbreak of a neuroparalytic disease caused by West Nile (WN) virus was diagnosed in young goose flocks. Domestic geese were similarly affected in the late summer and fall of 1998, 1999, 2000 and 2001. WN viruses were also isolated from migratory and wild birds and horses in 1998-2001. A 1278 bp sequence of the envelope gene of 24 Israeli WN virus isolates was compared with those of seven isolates from Africa, Europe and New York. As a result, the Israeli isolates could then be grouped into two clusters. The 15 avian and three equine from 1997-2001 in the first cluster of ...
Characterization of enzootic foci of Venezuelan equine encephalitis virus in western Venezuela. The distribution of the sylvatic subtype ID Venezuelan equine encephalitis (VEE) viruses in the lowland tropical forests of western Venezuela was investigated using remote sensing and geographic information system technologies. Landsat 5 Thematic Mapper satellite imagery was used to study the reflectance patterns of VEE endemic foci and to identify other locations with similar reflectance patterns. Enzootic VEE virus variants isolated during this study are the closest genetic relatives of the epizootic viruses that emerged in western Venezuela during 1992-1993. VEE virus surveillance was condu...
Identification of sperm subpopulations with specific motility characteristics in stallion ejaculates. The aim of this study was to test the presence of separate sperm subpopulations, with specific motility characteristics, in stallion ejaculates by using a computer-assisted semen motility analysis (CASA) system. Motility data were analyzed with a hierarchical clustering of variables based on a correlation or covariance matrix to select like parameters of sperm motility descriptors that better explain the kinetics of spermatozoa. The statistical analyses clustered the whole motile sperm population in both fresh and 24 h stored ejaculates into four separate groups. There were significant differe...
Hierarchical analysis of genetic structure in Spanish donkey breeds using microsatellite markers. The hierarchical population structure of five, native-Spanish donkey breeds (Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa) has been studied using F-statistics. In addition, nine Moroccan asses and 24 Merens breed horses were included in the analysis. Data came from 15 DNA microsatellites. The analysis shows that Spanish donkeys are substructured at both hierarchical levels studied, among breeds and within breeds (between subpopulations). In the whole population, the deficit of heterozygotes was estimated to be about 21%. The fixation indices corresponding to differences ...
Effect heterogeneity by a matching covariate in matched case-control studies: a method for graphs-based representation. The authors describe a method for assessing and characterizing effect heterogeneity related to a matching covariate in case-control studies, using an example from veterinary medicine. Data are from a case-control study conducted in Texas during 1997-1998 of 498 pairs of horses with colic and their controls. Horses were matched by veterinarian and by month of examination. The number of matched pairs of cases and controls varied by veterinarian. The authors demonstrate that there is effect heterogeneity related to this characteristic (i.e., cluster size of veterinarians) for the association of c...
Mitochondrial DNA and the origins of the domestic horse. The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct p...
Genetic characterisation of the Uruguayan Creole horse and analysis of relationships among horse breeds. The genetic variability within the Uruguayan Creole horse and its relationship to a group of geographically or historically related breeds (Spanish Pure-bred, Barb, Quarter horse, Paso Fino, Peruvian Paso, Arabian and Thoroughbred horse), was evaluated using 25 loci (seven of blood groups, nine of protein polymorphisms and nine microsatellites) analyzed on a total of 145 Uruguayan Creole horses. In this study, blood group and protein polymorphism variants that are considered to be breed markers of Spanish Pure-bred and Barb horses were detected in the Creole breed. Conversely, some microsatell...
Demonstration of heterogeneous genotypes of Taylorella equigenitalis isolated from horses in six European countries by pulsed-field gel electrophoresis. Forty-six isolates of Taylorella equigenitalis were analysed by pulsed-field gel electrophoresis (PFGE) after separate digestion of the genomic DNA with ApaI and with NotI. The isolates had been obtained from horses in six European countries and were classified into 18 genotypes. In Belgium, 2 genotypes were detected in 2 isolates, in England 9 among 15, in Finland 2 in 2, in France 2 among 10, in Sweden 3 among 5, and in Switzerland 3 among 12. Two English isolates and 4 French isolates gave identical PFGE profiles to those of Kentucky 188 from the United States. A common genotype was found i...
Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers. Population demarcation of eight horse breeds was investigated using genotype information of 306 horses from 26 microsatellite loci. The breeds include the indigenous Norwegian breeds Fjord Horse, Nordland/Lyngen Horse, Døle Horse and Coldblooded Trotter together with Icelandic Horse, Shetland Pony, Standardbred and Thoroughbred. Both phylogenetic analysis and a maximum likelihood method were applied to examine the potential for breed allocation of individual animals. The phylogenetic analysis utilizing simple allele sharing statistics revealed clear demarcation among the breeds; 95% of the in...
The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from th...
Evaluation of temporal and spatial clustering of horses with Corynebacterium pseudotuberculosis infection. To determine whether horses with Corynebacterium pseudotuberculosis infections that were examined at a veterinary medical teaching hospital between July 1, 1992, and June 30, 1994 had patterns of temporal or spatial clustering. Methods: 134 case and 800 control horses randomly selected from all non-case horses admitted during the study period. Methods: Admission date and geographic location were determined. Scan, Cuzick & Edwards', and Knox tests were applied to determine whether case horses had patterns of temporal or spatial clustering. Results: For all windows > or = 3 days (134 case...
[Population genetic parameters of aboriginal Yakut horses as related to modern breeds of the domestic horse Equus caballus L]. This study was the first to analyze the polymorphic characteristics of a wide range of biochemical markers in aboriginal Yakut horses. A total of 124 alleles, including 48 alleles of seven blood-group loci and 76 alleles of ten loci for enzymes and other proteins, were studied. For these polymorphic systems, a computer analysis of the genetic distances between 85 horse breeds of different origin from all parts of the world was performed. The low level of hereditary variation in the Yakut horses confirmed that this breed is old and has long been an isolated population. Phylogenetic analysis dem...
Diversity among isolates of Actinobacillus equuli and related organisms as revealed by ribotyping. The objective of this work was to examine the diversity within Australian isolates of Actinobacillus equuli and related organisms by the genotypic method of ribotyping. Methods: Ribotyping, performed using the enzyme HaeIII, was used to examine the diversity in 12 field isolates of A equuli (five being capable of fermenting L-arabinose), one field isolate of Pasteurella caballi and two unclassifiable field isolates. Isolates were obtained from Australian horses, except for three isolates of A equuli (one L-arabinose positive and two L-arabinose negative) which were obtained from horses and a p...
Patterns of secretion of GnRH, LH and FSH during the postovulatory period in mares: mechanisms prolonging the LH surge. To study the mechanisms responsible for the unusually slow decline of the ovulatory LH surge in mares, secretion patterns of GnRH, LH and FSH were monitored in pituitary venous blood collected every 2 or 5 min for 10.5-18.0 h from five mares on the third (n = 4) or fifth day after ovulation (first sampling period). To determine the effectiveness of progesterone negative feedback, mares were then given a luteolytic dose of a prostaglandin analogue (PGF2 alpha) and pituitary venous sampling (every 2 or 5 min for 16 h) recommenced 20-22 h later (second sampling period). During the declining arm o...
Quantification of normal head morphometry of stallion spermatozoa. The heads of stallion spermatozoa were analysed by computer automated sperm head morphometry and the morphometric values of the major subpopulations of sperm heads were assessed. The criteria for normal dimensions of stallion sperm heads are proposed based on the analysis of these measurements. Semen samples were collected from 10 fertile and 10 subfertile stallions, processed by a standard method, smeared onto microscope slides and stained using haematoxylin. At least 200 properly digitized sperm heads were analysed from each stallion. The measurements for length, width, area, perimeter and w...
Analysis of spatial and temporal clustering of horses with Salmonella krefeld in an intensive care unit of a veterinary hospital. To determine whether clustering existed in the spatial or temporal distribution of horses that shed Salmonella krefeld in their feces during hospitalization. Methods: Retrospective analysis of medical records. Methods: 219 horses housed in the intensive care unit of a veterinary medical teaching hospital from October 1991 through May 1992. Methods: Bacteriologic culturing of fecal samples was used to identify horses shedding S krefeld. For affected horses, the scan statistic was used to analyze temporal clustering, and Knox's method was used to analyze temporal-spatial clustering. Results: 20 ...
Evaluation of travel and use as a risk factor for seropositivity to Ehrlichia risticii in horses of New York state. To determine whether mean annual frequency and destination of equine travel was associated with exposure to Ehrlichia risticii and whether these associations were modified by horses' place of residence. Methods: Cross-sectional study. Methods: 511 equine operations containing 2,587 horses were visited in New York state from a target population of 39,000 operations. Methods: Each horse was tested for serum antibodies against E risticii, using indirect fluorescent antibody. Information on the horse's travel history, farm's management practices, and surrounding ecology was obtained by personal in...
Epidemiologic evidence for clustering of equine motor neuron disease in the United States. To examine the regional variations in the distribution of equine motor neuron disease (EMND) in the United States and the factors that might explain those variations. Methods: Cluster investigation and case-control study. Methods: The study population consisted of 97 horses with histopathologically confirmed EMND and 698 controls with diagnosis of other spinal cord disorders at 21 US veterinary teaching hospitals participating in the Veterinary Medical Data Base. Methods: The total horse population of the United States was divided into 21 regions, and the regional incidence rates of EMND from ...
Comparative ribotyping of Staphylococcus intermedius from dogs, pigeons, horses and mink. Strains of Staphylococcus (S.) intermedius from dogs, pigeons, horses and mink were typed by comparison of rRNA gene restriction fragment length polymorphisms (ribotyping) and the resulting ribotypes examined by cluster-analysis. Digestion of whole-cell DNA with HindIII resulted in 9 ribotypes with 3 to 4 bands. Separation of isolates from different host animal species was not possible. EcoRI yielded 11 different patterns with 4 to 9 fragments. The EcoRI-ribotypes of all canine strains grouped in one cluster encompassing four closely related ribotypes. Isolates were indistinguishable with resp...
Morphological analysis of cervical vertebrae in ataxic foals. Morphological differences between cervical vertebrae were statistically analyzed in ataxic foals to clarify abnormal structural factors in the pathogenesis of this problem. At first, multiple regression analysis and cluster analysis were performed with 28 variables in C3-C7 of 39 control foals without lameness. As a result, there were no sex differences in the growth of all cervical vertebral sites, and the most suitable categorization of the age of the foals was 3 clusters of 8 months old or younger, 9-12 months old and 13 months old or older in any sites in the cervical vertebrae. Twenty-eig...
Short-term secretion patterns of corticotropin-releasing hormone, arginine vasopressin and ACTH as shown by intensive sampling of pituitary venous blood from horses. To characterize the short-term ACTH secretion pattern and to investigate factors regulating it, pituitary venous (PV) blood was collected using our nonsurgical method from 8 unperturbed horses every 20 or 30 s for approximately 1 h. In all but 1 horse, sampling occurred during the broad circadian maximum in plasma cortisol concentrations. Concentrations of corticotropin-releasing hormone (CRH; n = 7 horses), arginine vasopressin (AVP), ACTH and cortisol were measured by radioimmunoassay. In all horses, CRH, AVP and ACTH secretion patterns appeared irregular in time and amplitude. The mean (+/-...
Geographical variation of seropositivity to Ehrlichia risticii (equine monocytic ehrlichiosis) of horses in New York state. A total of 2,579 serum samples from horses in New York state during 1985-1986 were examined for seropositivity to Ehrlichia risticii using the indirect fluorescent antibody technique. Cluster analysis statistical technique was used to group counties according to their estimated EME-disease rate (seropositive proportion of sampled horses). Counties were clustered into 4 groups of different EME-disease rates, representing high (86% seropositive), medium (66% seropositive), medium-low (47% seropositive) and low (6% seropositive) risk regions. The logistic regression statistical technique was used...
The dynamics of gonadotrophin-releasing hormone, LH and FSH secretion during the spontaneous ovulatory surge of the mare as revealed by intensive sampling of pituitary venous blood. Conflicting views exist on the mode of gonadotrophin-releasing hormone (GnRH) secretion during the ovulatory LH surge and the relative importance of changes in pituitary responsiveness to GnRH in generating the LH surge. This disagreement may stem from species differences and/or methodological problems. To provide data on the exact relationship between GnRH and gonadotrophin secretion during the spontaneous LH surge, we collected pituitary venous (PV) blood every 30 s for 3-4 h from eight mares and then assayed GnRH (in six of the mares), FSH and LH. Jugular blood was also collected from twelv...