LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Dietary inclusion of dehydrated bocaiuva pulp increases the antioxidant potential of quail eggs

The aim of this study was to evaluate dietary supplementation of different levels of dehydrated bocaiuva pulp (DBP) on the productive performance of laying quails, and on lipid oxidation, and quality in their eggs. A total of 120 quails were distributed in a completely randomized design with six treatments (0%, 0.1%, 0.2%, 0.3%, 0.4% and 0.5% of DBP), five replicates and four birds per experimental unit. To evaluate lipid oxidation, the eggs were collected on five consecutive days at the end of the trial and distributed in a completely randomized experimental design in a 6 × 5 factorial scheme (eggs from quails fed different levels of DBP × evaluated fresh and after 7, 14, 21 and 28 days). The antioxidant potential of diets was improved (p < 0.05) when the DBP was added estimated as 2,2'‐azinobis‐3‐ethylbenzothiazolin‐6‐sulfonic acid (ABTS) free radical scavenging capacity. No effect (p > 0.05) was observed on feed intake, hen‐day egg production and feed conversion (kg/kg and kg/dz). There were no changes (p > 0.05) in the egg weight, Haugh unit, yolk index or eggshell percentage. Although no difference was observed (p > 0.05), when comparing each level with the control, a negative linear effect (p < 0.05) on specific gravity was observed. In addition, only the treatment with 0.5% pulp exhibited lower (p < 0.05) eggshell thickness compared with the control (0%). Thiobarbituric acid reactive substances (TBARS) analysis showed that as the dietary pulp level was increased, malondialdehyde content decreased linearly (p < 0.05) in the egg yolks, regardless of the storage period. Inclusion of DBP in the diets had no effect (p > 0.05) on the concentration of conjugated dienes in the eggs. The diets containing DBP showed a potential antioxidant effect, reducing the degree of lipid oxidation in egg yolk. However, no beneficial effects were observed on performance and egg quality.     

Cumulative racing-speed exercise distance cluster as a risk factor for fatal musculoskeletal injury in Thoroughbred racehorses in California

Thoroughbred racehorses which suffered a fatal musculoskeletal injury (FMI) while racing or race training at a California racetrack during 9 months of 1991 were studied to determine the importance of intensive, high-speed exercise schedules prior to injury. Seventy-seven horses which sustained an FMI while racing and 45 horses which sustained an FMI while race training were successfully matched by race or timed workout session with one control horse and included in the analyses. Race and timed workout (racing-speed exercise) histories were obtained for the case and control horses. Two-month cumulative, racing-speed cutoff distances were calculated from the control horse sample by two methods. Median racing-speed exercise frequencies and distances of the control horses were used to estimate age-specific (2, 3, 4 and ≥ 5 years), 2-month cumulative, racing-speed distances (Method 1). For the second method, the last race or timed workout for each control horse occurring just prior to, or on the date of injury for the matched case horse was identified. Cumulative racing-speed distances 2 months prior to these exercise events were determined for each control horse and used to estimate median age-specific (2, 3, 4 and ≥ 5 years), 2-month cumulative racing-speed distances (Method 2). The cumulative cutoff distances estimated from both methods were used to classify each matched pair according to the presence or absence of a 2-month cumulative, racing-speed distance which exceeded the age-appropriate cutoff distance (exercise distance cluster) within 6 months prior to injury. Manlel-Haenszel matched-pair odds ratios and 95% confidence limits were calculated separately for the racing and race-training fatal injuries. The relative risk for racing FMI was significantly greater for those horses which ran 2-month, cumulative racing and timed workout distances in excess of the cutoff values determined with Method 1 (relative risk (RR) = 3.0, 95% confidence interval (CI) = 1.2, 7.6) and Method 2 (RR = 7.2, 95% CI = 2.6, 20.6). The relative risk for race-training FMI was significantly greater for those horses which ran 2-month, cumulative racing and timed workout distances in excess of the cutoff values determined with Method 2 (RR = 3.4, 95% CI =1.0, 13.2).     

Plasma cholesterol and lipoprotein concentrations in the dog: The effects of age, breed, gender and endocrine disease

A combined ultracentrifugation and precipitation technique was used to quantify the plasma lipoprotein concentrations of control dogs (n=33) and dogs with diabetes mellitus (n=11), hyper-adrenocorticism (n=14), hypothyroidism (n=10) and obesity (n=20). In addition, the effect of breed type, age and gender on the lipoprotein phenotype was assessed. Breed type and age were found to have no effect upon cholesterol and lipoprotein concentrations but the high density lipoprotein cholesterol (HDL-C) concentration was greater in intact females than intact males. Cholesterol concentrations were significantly higher than those of the control group in dogs with diabetes mellitus (P<0·01), hyper-adrenocorticism (P<0·01) and hypothyroidism (P<0·001). In dogs with diabetes mellitus this was due to increased concentrations of very low density lipoprotein cholesterol (VLDL-C) (P<0·01) and HDL-C (P<0·05). The concentrations of low density lipoprotein cholesterol (LDL-C) (P<0·05) were significantly increased in dogs with hyperadrenocorticism, while in the hypothyroid dogs, VLDL-C (P<0·05), LDL-C (P<0·001) and HDL-C (P<0·05) were significantly higher than the control group. The cholesterol and lipoprotein concentrations in the obese population were not significantly different from control dogs.     

Transmaxillary anchored silicon embedded gauze plug in the post-operative treatment of a large oromaxillary fistula caused by a supernumerary cheek tooth

A 9-year-old Hungarian sport horse gelding was presented to the clinic in poor condition displaying malodorous bilateral purulent nasal discharge. Oral examination revealed the presence of supernumerary 111 and 211. Bilateral diastema formation between the third maxillary molars and the supernumerary teeth with deep periodontal pockets and massive food impactions were diagnosed endoscopically. Radiography revealed inhomogenous sinus opacities in the left and right paranasal sinuses. Following bilateral oral extractions of the supernumerary cheek teeth and third maxillary molars, bilateral oromaxillary fistula formations were diagnosed (about 17 mm diameter on the right side). Bilateral frontal and right-sided maxillary trephinations and resection of the right bulla of the maxillary septum were performed. Massive food impactions of the left and right paranasal sinuses were removed under endoscopic control. Repeated trans-endoscopic sinus lavage was performed post-operatively. After 2.5 months, the large right-sided oromaxillary communication was temporarily closed with a transmaxillary anchored, gauze-cored silicon plug on an outpatient basis. Follow-up examination after 187 days revealed complete closure of the oromaxillary fistula and absence of sinusitis. In a 1.5-year follow-up control, no pathological conditions were found.     

Incidence of and breed-related risk factors for gastric dilatation-volvulus in dogs

OBJECTIVE: To compare incidence of and breed-related risk factors for gastric dilatation-volvulus (GDV) among 11 dog breeds (Akita, Bloodhound, Collie, Great Dane, Irish Setter, Irish Wolfhound, Newfoundland, Rottweiler, Saint Bernard, Standard Poodle, and Weimaraner). DESIGN: Prospective cohort study. ANIMALS: 1,914 dogs. PROCEDURE: Owners of dogs that did not have a history of GDV were recruited at dog shows, and the dog's length and height and depth and width of the thorax and abdomen were measured. Information concerning the dogs' medical history, genetic background, personality, and diet was obtained from owners, and owners were contacted by mail and telephone at approximately 1-year intervals to determine whether dogs had developed GDV or died. Incidence of GDV based on the number of dog-years at risk was calculated for each breed, and breed-related risk factors were identified. RESULTS AND CLINICAL RELEVANCE: Incidence of GDV for the 7 large (23 to 45 kg [50 to 99 lb]) and 4 giant (> 45 kg [> 99 lb]) breeds was 23 and 26 cases/1,000 dog-years at risk, respectively. Of the 105 dogs that developed GDV, 30 (28.6%) died. Incidence of GDV increased with increasing age. Cumulative incidence of GDV was 5.7% for all breeds. The only breed-specific characteristic significantly associated with a decreased incidence of GDV was an owner-perceived personality trait of happiness.     

Ultrasonographic tissue characterization of equine superficial digital flexor tendons by means of gray level statistics

OBJECTIVE: To correlate quantitative analysis of ultrasonographic images of normal (injury-free) equine superficial digital flexor (SDF) tendons and equine SFD tendons that have pathologic changes with corresponding histologic sections. SAMPLE POPULATION: 4 SDF tendons, 2 of which had various stages of tissue integrity. The 2 ipsilateral tendons were used as points of reference. PROCEDURE: Tendons were mounted in a custom-made device that permitted sequential scanning, transversely and perpendicular to the tendon long axis. At precise steps of 0.5 mm, transverse ultrasonographic images were collected. Subsequently, tendons were fixed and prepared for histologic examination. The following 8 tissue types were discerned: normal young, normal old, necrotic, early granulation, late granulation, early fibrotic, late fibrotic, and scar tissues. In areas of interest, the corresponding ultrasonographic images were selected for gray level statistical analysis. RESULTS: Compared with other tissue types, early-stage granulation tissue was characterized by substantially lower mean gray level and a clearly different histogram. Necrotic tissue had a higher mean gray level, with a virtually normal histogram. In late granulation and early fibrotic tissues, the mean gray level and the histogram could not be discerned from those of normal tendon tissue. The same applied to late fibrotic and scar tissues; mean gray levels were fractionally lower than those of normal tendon tissue with a completely normal histogram. CONCLUSIONS: Although quantification of the transverse ultrasonographic image by use of first-order gray level statistics may be helpful, the method is not sufficiently sensitive to accurately and unequivocally determine the type of tendon tissue. Quantitative analysis should incorporate transverse and longitudinal information.