Asian horses deepen the MSY phylogeny.

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46 Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

To pace or not to pace: a pilot study of four- and five-gaited Icelandic horses homozygous for the DMRT3 'Gait Keeper' mutation.

The Icelandic horse is a breed known mainly for its ability to perform the ambling four-beat gait 'tölt' and the lateral two-beat gait pace. The natural ability of the breed to perform these alternative gaits is highly desired by breeders. Therefore, the discovery that a nonsense mutation (C>A) in the DMRT3 gene was the main genetic factor for horses' ability to perform gaits in addition to walk, trot and canter was of great interest. Although several studies have demonstrated that homozygosity for the DMRT3 mutation is important for the ability to pace, only about 70% of the homozygous mutant (AA) Icelandic horses are reported to pace. The aim of the study was to genetically compare four- and five-gaited (i.e. horses with and without the ability to pace) AA Icelandic horses by performing a genome-wide association (GWA) analysis. All horses (n = 55) were genotyped on the 670K Axiom Equine Genotyping Array, and a GWA analysis was performed using the genabel package in r. No SNP demonstrated genome-wide significance, implying that the ability to pace goes beyond the presence of a single gene variant. Despite its limitations, the current study provides additional information regarding the genetic complexity of pacing ability in horses. However, to fully understand the genetic differences between four- and five-gaited AA horses, additional studies with larger sample materials and consistent phenotyping are needed.

The evolutionary history of the DMRT3 'Gait keeper' haplotype.

A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3:Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.

Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene.

For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.

The effect of the 'Gait keeper' mutation in the DMRT3 gene on gaiting ability in Icelandic horses.

A nonsense mutation in DMRT3 ('Gait keeper' mutation) has a predominant effect on gaiting ability in horses, being permissive for the ability to perform lateral gaits and having a favourable effect on speed capacity in trot. The DMRT3 mutant allele (A) has been found in high frequency in gaited breeds and breeds bred for harness racing, while other horse breeds were homozygous for the wild-type allele (C). The aim of this study was to evaluate further the effect of the DMRT3 nonsense mutation on the gait quality and speed capacity in the multigaited Icelandic horse and demonstrate how the frequencies of the A- and C- alleles have changed in the Icelandic horse population in recent decades. It was confirmed that homozygosity for the DMRT3 nonsense mutation relates to the ability to pace. It further had a favourable effect on scores in breeding field tests for the lateral gait tölt, demonstrated by better beat quality, speed capacity and suppleness. Horses with the CA genotype had on the other hand significantly higher scores for walk, trot, canter and gallop, and they performed better beat and suspension in trot and gallop. These results indicate that the AA genotype reinforces the coordination of ipsilateral legs, with the subsequent negative effect on the synchronized movement of diagonal legs compared with the CA genotype. The frequency of the A-allele has increased in recent decades with a corresponding decrease in the frequency of the C-allele. The estimated frequency of the A-allele in the Icelandic horse population in 2012 was 0.94. Selective breeding for lateral gaits in the Icelandic horse population has apparently altered the frequency of DMRT3 genotypes with a predicted loss of the C-allele in relatively few years. The results have practical implications for breeding and training of Icelandic horses and other gaited horse breeds.

Mixed virtual reality simulation--taking endoscopic simulation one step further.

This pilot study aimed to assess medical students' appraisals of a "mixed" virtual reality simulation for endoscopic surgery (with a virtual patient case in addition to a virtual colonoscopy) as well as the impact of this simulation set-up on students' performance. Findings indicate that virtual patients can enhance contextualization of simulated endoscopy and thus facilitate an authentic learning environment, which is important in order to increase motivation.

Exploring the genetics underpinning dynamic laryngeal collapse associated with poll flexion in Norwegian-Swedish Coldblooded Trotter racehorses.

BACKGROUND: Dynamic laryngeal collapse (DLC) associated with poll flexion is the most common disorder of the upper respiratory tract (URT) in the Norwegian-Swedish Coldblooded Trotter (NSCT). The disorder, which has also been diagnosed in other breeds of trotters and gaited horses, appears to be related to anatomic phenotypes and only occurs during poll flexion when the horse is exercised 'on the bit'. OBJECTIVES: Identify genomic regions associated with DLC in the NSCT by combining a rigorous phenotyping protocol with genomic data from a high-density equine genotyping array. STUDY DESIGN: Prospective case/control study. METHODS: High-speed treadmill endoscopy was used to phenotype horses (n = 61) for DLC, distinguishing between cases and controls. Genome-wide association (GWA) analysis of DLC status was then performed using a principal component approach (PCA) with haplotype analyses subsequently performed for regions containing single-nucleotide polymorphisms (SNPs) above the suggestive genome-wide significance (GWS) threshold (P<1.0 × 10-5 ). RESULTS: One region containing 10 SNPs (Equus caballus chromosome [ECA] 7: 89,601,935-94,647,192) was above the suggestive GWS threshold. Two inferred haplotypes in this region demonstrated significant differences (P<0.001) between cases and controls, with the most frequent haplotype resulting in a significantly increased risk of DLC. MAIN LIMITATIONS: Small sample size as a result of stringent phenotyping protocols. CONCLUSIONS: The current study highlights a candidate genomic region on ECA7 as potentially important with regard to the manifestation of DLC. Further exploration of this region and the genes included within it will bring veterinarians and researchers closer to fully understanding the biological mechanisms underlying DLC in horses.

Improving gait classification in horses by using inertial measurement unit (IMU) generated data and machine learning.

For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rate sensors combined with machine learning to fully automatically classify gait. Using data from 120 horses of four different domestic breeds, equipped with seven motion sensors, we included 7576 strides from eight different gaits. GC was trained using several machine-learning approaches, both from feature-extracted data and from raw sensor data. Our best GC model achieved 97% accuracy. Our technique facilitated accurate, GC that enables in-depth biomechanical studies and allows for highly accurate phenotyping of gait for genetic research and breeding. Our approach lends itself for potential use in other quadrupedal species without the need for developing gait/animal specific algorithms.

Competition lifespan survival analysis in the Norwegian-Swedish Coldblooded Trotter racehorse.

BACKGROUND: Studies of large racing populations have established clear differences in the career profile of stallions, mares and geldings. Multiple studies have also demonstrated positive effects on racing careers for horses that commence racing at a younger age. However, the applicability of these studies to small, native racing populations is unknown and warrants investigation. OBJECTIVES: To provide summary statistics for performance outcomes for the Norwegian-Swedish Coldblooded Trotter and to document and provide evidence on the current differences in racing careers across age at first start groups, sexes and country of birth. STUDY DESIGN: Cohort study. METHODS: Performance data on the population of Norwegian-Swedish Coldblooded Trotters born between 2000 and 2009 (n = 14,548) were acquired and used to describe and compare the racing careers of this native racing breed. Career length, career starts and career earnings were evaluated. Kaplan-Meier survival curves, stratified by sex, age group and country of birth were produced for career length. A Cox proportional hazards model was fitted to assess factors influencing the hazard rate of retirement from racing. RESULTS: Log-rank test for equality of career length survival functions showed significant differences (P<0.001) across sexes, countries of birth and age at first start groups. An increased age at first start increased the hazard rate of retirement from racing. MAIN LIMITATIONS: Racing career length is influenced by many factors. While this study accounts for some of the known influences on career length, the analysis would be strengthened by the inclusion of additional information, such as trainer and reasons for retirement. CONCLUSIONS: The results of this study suggest no adverse effects to the racing of young Norwegian-Swedish Coldblooded trotters. The study also establishes significant differences in career length based on sex and identifies that these differences are the opposite of what is seen in many other horse racing breeds. The Summary is available in Spanish - see Supporting Information.

Use of diagnostic reports to estimate prevalence and distribution of skeletal lesions in young Thoroughbreds.

Diagnostic reports written to assist stud managers in the sale of young Thoroughbreds have not previously been used as a data source for the study of skeletal lesions. However, analyses of these reports may provide efficient and cost-effective insights into the prevalence and distribution of skeletal lesions within a population. Diagnostic reports written by veterinarians were acquired from Thoroughbred stud managers in Australia and New Zealand. The reports were based on approximately 1300 sets of weanling and yearling radiographs taken between 2002 and 2007. The prevalence and anatomical distribution of skeletal lesions in weanlings (299 horses) and yearlings (1004 horses) were determined from these reports. Overall, 69.9% of weanlings and 64.5% of yearlings were reported as having one or more skeletal lesions. Diagnostic reports in weanlings were a strong indication of what was likely to be seen in subsequent yearling reports. These diagnostic reports are typically used by stud managers in the sales process and the potential drawback is that some categories of skeletal lesions may be under-reported. However, there was substantial agreement between the prevalence and distribution of several skeletal lesions reported in this study and those previously reported from direct evaluation of radiographs for Australian and New Zealand Thoroughbred yearlings. Strong agreement was found for osteophytes, enthesiophytes and other modelling in the hocks, and for lesions in the hind fetlocks and stifles. This indicates that written diagnostic reports are a useful and a reliable source of data for the study of some skeletal lesions in young Thoroughbred horses.

Individuals with an increased risk of colorectal cancer: perceived benefits and psychological aspects of surveillance by means of regular colonoscopies.

PURPOSE: To evaluate the psychological consequences of genetic counseling followed by a surveillance program using colonoscopy among individuals with increased risk of colorectal cancer. PATIENTS AND METHODS: Two hundred sixty-five individuals, participating in a surveillance program with colonoscopy, were mailed a survey questionnaire that assessed their experience of the surveillance program and their perception of the risk of colorectal cancer. The Hospital Anxiety and Depression scale and the Swedish Short Form-36 Health Survey was also included. RESULTS: Two hundred forty individuals completed the questionnaire and were divided into the following risk groups: risk group 1, an individual with a mutation in hMLH1 or hMSH2 and a lifetime colorectal cancer risk of 80% (n = 28); risk group 2, a lifetime colorectal cancer risk of 40% (n = 129); and risk group 3, a lifetime colorectal cancer risk of 20% (n = 83). Among all individuals, the mean for perceived benefit was 8.0, and the perception of discomfort was 3.3 on the visual analog scale (1-10). In risk group 1, 61% underestimated personal risks as being 40% or less. Approximately 50% of the subjects in risk groups 2 and 3 either under- or overestimated their lifetime risk. According to the Swedish Short Form-36 Health Survey and the Hospital Anxiety and Depression scale, the study sample resembled the reference population. CONCLUSION: A majority of the study sample understood why they were under surveillance, and regular colonoscopies were well-tolerated. The wide range of risk perception as well as low-risk perception in mutation positive subjects is acceptable, as long as these individuals adhere to surveillance programs and do not demonstrate increased levels of anxiety or depression.

International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources.

A comprehensive male linkage map was generated by adding 359 new, informative microsatellites to the International Equine Gene Map half-sibling reference families and by combining genotype data from three independent mapping resources: a full sibling family created at the Animal Health Trust in Newmarket, United Kingdom, eight half-sibling families from Sweden and two half-sibling families from the University of California, Davis. Because the combined data were derived primarily from half-sibling families, only autosomal markers were analyzed. The map was constructed from a total of 766 markers distributed on the 31 equine chromosomes. It has a higher marker density than that of previously reported maps, with 626 markers linearly ordered and 140 other markers assigned to a chromosomal region. Fifty-nine markers (7%) failed to meet the criteria for statistical evidence of linkage and remain unassigned. The map spans 3,740 cM with an average distance of 6.3 cM between markers. Fifty-five percent of the intervals are < or = 5 cM and only 3% > or = 20 cM. The present map demonstrates the cohesiveness of the different data sets and provides a single resource for genome scan analyses and integration with the radiation hybrid map.

Normal variability of static perimetric threshold values across the central visual field.

We assessed the variability of results in normal subjects of computerized static threshold perimetry of the central 30 degrees field. Variability of measured threshold values was highly dependent on eccentricity. This included variability among individuals, test-to-test variability within individuals, and intratest variability. All values were significantly larger in the midperiphery than centrally. We found that the mean sensitivity decrement with age was eccentricity dependent, so that the age-corrected normal visual field became not only depressed but also steeper with age. Distributions of individual pointwise deviations from the age-corrected normal mean thresholds were significantly nongaussian. The dependency of variability on test point location, the nongaussian distributions of deviations from age-corrected means, and the variability of age-induced sensitivity reduction should all be considered in the interpretation of computerized visual fields, and particularly in the design of statistical programs for field analysis. Programs not considering these factors are likely to result in misleading analyses.

The effect of perimetric experience in normal subjects.

Two groups of normal subjects were submitted to repeated automated static threshold perimetry. Perimetric results were strongly affected by the level of experience in some subjects; in the majority, however, the effect of experience was small. Initial field tests often showed high numbers of depressed points. Sensitivity increased with perimetric training, particularly between the first sessions. Those subjects who improved most started low, gradually approaching normal levels with experience. Learning effects were more pronounced peripherally than paracentrally and "untrained" fields characteristically showed concentric contraction with numerous points with low sensitivity peripherally. An important practical conclusion is to allow repeated testing of all inexperienced patients in whom initial fields do not agree with clinical findings. A chart showing a concentrically narrowed field should be viewed with particular suspicion. Furthermore, a single initial field may constitute an inadequate baseline for clinical follow-up.

Visual field interpretation with empiric probability maps.

Automated visual field charts may be difficult to interpret partly because of the magnitude and complex nature of normal threshold variability. We devised two types of empiric probability maps in which this variability is taken into account and the significances of measured threshold values are displayed. These maps are highly sensitive to nonobvious but significant paracentral field loss but will at the same time deemphasize false-positive patterns commonly found more peripherally. They also frequently show field defects before these are obvious in conventional threshold printouts. In addition, they differentiate between generalized loss of sensitivity and localized field defects.

A prospective study of dense spontaneous vitreous hemorrhage.

PURPOSE: We studied the incidence of vitreous hemorrhage in a well-defined population to determine the underlying causes of such hemorrhages. METHODS: We prospectively studied all eyes with dense spontaneous first-time vitreous hemorrhage during a 2 1/2-year period in the greater Göteborg area (542,000 inhabitants). Follow-up time was one year. RESULTS: Ninety-four patients (95 eyes) were included, corresponding to a yearly incidence of seven cases per 100,000 inhabitants. Because of demographic factors and the organization of Swedish ophthalmologic care, we believe that this is close to the true incidence. The cause of vitreous hemorrhage could be verified in all but four eyes but frequently not until late in the follow-up period. The most common underlying cause was vitreous detachment and traction to a retinal vessel (39 eyes). In 28 of these eyes a retinal tear was also present. Five of these eyes developed a retinal detachment. In 19 eyes, bleeding was caused by proliferative diabetic retinopathy. This figure was relatively smaller than in previous studies. Retinal vein occlusion was the cause of hemorrhage in 15 eyes. Retinal macroaneurysm (seven eyes) was an easily overlooked cause, often diagnosed late in the follow-up period. CONCLUSIONS: Because of the common diagnostic difficulties and the frequent need for laser treatment, vitrectomy, or both, it is recommended that eyes with vitreous hemorrhage be followed up in centers with ultrasonographic and surgical expertise.

Test-retest variability in glaucomatous visual fields.

We measured test-retest variations in computerized visual fields from glaucomatous eyes. Fifty-one patients were tested four times within a four-week period; the severity of disease varied from incipient to advanced. We determined the dependence of threshold variability on defect depth and test point location. In areas of the visual field initially found to have moderate loss of sensitivity, variation in follow-up measurements ranged from normal sensitivity to absolute defect, with little dependence on distance from fixation. Conversely, large changes were considerably more unusual in locations initially showing normal or near-normal sensitivities, and variability was lowest in the most central portion of the field. Our findings suggest that differentiation between true progression and random variation will be facilitated if these factors are taken into account, as well as if comparisons are based on more than two tests. The complex nature of interest variation in glaucoma makes it natural to approach this problem with the help of computer-assisted analyses.

Basal cell carcinoma of the eyelids and solar ultraviolet radiation exposure.

AIMS: To compare the distribution of eyelid basal cell carcinoma (BCC) with the relative ultraviolet radiation (UVR) exposure to different sites on the eyelids. METHODS: The location of BCC on the eyelids was allocated to one of seven regions. The UVR exposure was recorded with a polymer film attached to the eyelids at seven sites in a manikin and in human subjects. RESULTS: Localisation of the 329 tumours was mainly on the lower eyelids (225 tumours), and the medial canthal regions (87 tumours). There was no association between UVR doses at the seven sites of the eyelids and the location of BCCs. The UVR exposure was similar on the upper and lower eyelids, while the number of tumours on the lower eyelids outnumbered the upper lids by a factor of 13 (17 upper, 225 lower) CONCLUSION: UVR exposure only partially explains the aetiology of periorbital BCC.