Comparison of prediction methodology for binary traits through Monte-Carlo simulation

SUMMARY: The purpose of this study was to evaluate simple alternatives to threshold models within the framework of a mixed-model procedure. Four models-linear model, threshold model, normit-transformation and pseudo-linear model-were compared by Monte-Carlo computer simulation. The normit-transformation model was based on simple normit transformation within a subclass while taking into account binomial error. The simulation experiments were carried out with combinations of five subclass sizes (5, 15, 25, 35, 45), five heritabilities (0.05, 0.15, 0.25, 0.35, 0.45) and 100 replications for each experiment. The loss of accuracy in the prediction models based on binary response was greater than that in the linear model based on continuous records. The accuracy of the threshold model was superior to that of the normit-transformation model and the pseudo-linear model in all the experiments. But the difference in accuracy between the threshold model and the pseudo-linear model was small when the heritability was low and the subclass size was small, while the difference in accuracy between the threshold and the normit transformation was small when the subclass size was large. ZUSAMMENFASSUNG: Vergleich von Michmodell-Voraussagen mittels Monte-Carlo Simulation Die Absicht dieser Untersuchung war die Bewertung einfacher Alternativen für Schwellenwert-Modelle im Rahmen von Mischmodell Methoden. Folgende vier Modelle wurden untersucht: Lineares, Schwellenwert, Normittransformation und pseudo-lineares Modell wurden mittels Monte-Carlo Computersimulation verglichen. Das Normittransformationsmodell beruhte auf einfachen Normittransformation innerhalb einer Unterklasse unter Berücksichtigung des binomialen Fehlers. Die Simulationsexperimente wurden mit fünf Unterklassen-Gr??en (5, 15, 25, 35, 45), fünf Heritabilit?ten (0,05, 0,15, 0,25, 0,35, 0,45) und 100 Wiederholungen für jeden Versuch durchgeführt. Der Genauigkeitsverlust in den Modellen für bin?re Ergebnisse war gr??er als in linearen Modellen mit kontinuierlichen Daten. Die Genauigkeit des Schwellenwert-Modells war der Normittransformation und dem pseudo-linearen Modell in alien Untersuchungen überlegen. Bei geringem h(2) und kleinen Unterklassen war die Genauigkeitsdifferenz zwischen Schwellenwert- und pseudolinearem Modell klein, ebenso wie die zwischen ersterem und Normittransformation bei gro?en Unterklassen.     

Molecular screening of canine GM1 gangliosidosis using blood smear specimens after prolonged storage: detection of carriers among shiba dogs in northern Japan

Molecular screening of GM1 gangliosidosis in Shiba dogs was carried out in northern Japan using blood smear specimens after prolonged storage. Of 125 specimens obtained from 3 veterinary teaching hospitals for this screening, 68 specimens (54%) were adequate for direct amplification in a polymerase chain reaction (PCR)-based DNA test, and the percentage of adequacy was different at each hospital (34%, 73%, and 100%), suggesting that the amount of blood on the smear and the storage condition of specimens may affect adequacy. Of the 68 dogs examined, 2 dogs (2.9%) were heterozygous carriers for this disease and the other dogs were all genotypically normal. The results suggest blood smear specimens can be useful for PCR testing after prolonged storage provided specimens contain a generous amount of blood and have been adequately stored. The study also suggests that GM1 gangliosidosis may be widely prevalent in the Shiba dog population in northern Japan.     

Evaluation of basal media for micropropagation of four highbush blueberry cultivars

Murashige and Skoog medium (MS), woody plant medium (WPM), and a mixture of equal parts of MS and WPM (MW) were compared for in vitro shoot proliferation and rooting of four highbush blueberry (Vaccinium spp.) cultivars. During the multiplication stage, the shoots on WPM showed worse growth than the other shoots. The MW produced the best shoot growth. The shoots on MS grew well but tended toward hyperhydricity in the multiplication stage, especially in the case of ‘Bluecrop’ shoots. Rooting was worst in the shoots multiplied on WPM, while the best rooting percentage of ‘Bluecrop’ shoots was obtained on MS, and that of ‘O’Neal’ on MW. The rooted shoots developed a good root system and were easily acclimatized after potting.     

Prognostic significance of hypermethylation of death‐associated protein kinase (DAPK) gene CpG island in dogs with high‐grade B‐cell lymphoma

Death‐associated protein kinase (DAPK) is a serine/threonine kinase and a tumour suppressor gene. Diffuse large B‐cell lymphomas with inactivated DAPK through hypermethylation of a CpG island is known to result in a biologically aggressive phenotype in humans. This retrospective study was carried out to analyse the prognostic significance of DAPK CpG island hypermethylation in canine lymphoma. We hypothesized that DAPK CpG island hypermethylation can be a negative prognostic indicator in dogs with nodal high‐grade B‐cell lymphoma. Forty‐seven dogs with high‐grade B‐cell lymphoma, according to the updated Kiel classification, were evaluated after being treated with a CHOP (vincristine, cyclophosphamide, doxorubicin and prednisolone)‐based chemotherapy protocol. The methylation status of the DAPK CpG island was examined by methylation‐specific PCR. Progression‐free survival (PFS) and overall survival (OS) were compared using the Kaplan‐Meier analysis and log‐rank test. The cox proportional hazard regression model was used to evaluate the effect of multiple variables. Hypermethylation of the DAPK CpG island was detected in 21 of the 47 dogs. The PFS and OS in dogs with the hypermethylation (median: 220 and 266 days, respectively) were significantly shorter than those of dogs without hypermethylation (median: 301 and 412 days, respectively) (PFS, P = .036; OS, P = .007). In the multivariate analysis, hypermethylation of the DAPK CpG island remained an independent prognostic factor in predicting shortened PFS (P = .047) and OS (P = .021) as well as clinical substage b. Overall, hypermethylation of the DAPK CpG island was a negative prognostic factor in canine high‐grade B‐cell lymphoma.     

Mineral and vegetable oils as effective dormancy release agents for sustainable viticulture in a sub-tropical region

Increasing restrictions on the use of agrochemicals in agriculture is a major limiting factor for grapevine (Vitis vinifera L.) growers, especially with respect to the use of hydrogen cyanamide as a bud dormancy-releasing compound, which is usually necessary in sub-tropical regions. In this context, a trial of the cultivar ‘Carmem’ was carried out in a commercial vineyard located in Paraná State, Southern Brazil, with the aim of developing an environmentally friendly and economically viable bud-break treatment. The following treatments were applied over two consecutive years: (i) control (water); (ii) 2% (v/v) vegetable oil (VO); (iii) 2% (v/v) mineral oil (MO); (iv) 2% (v/v) VO + 2% (v/v) MO; or (v) 3% (v/v) hydrogen cyanamide (HC). In both years, treatments (iv) and (v) increased bud-break percentages by a similar extent, from 24–25.0% to 60–95%. Both treatments also increased the number of berry clusters and yield, from 0.9–1.3 kg to 3.3–4.6 kg per vine, and decreased catalase activity in buds until 24 h after treatment. It appears that treatment (iv) could provide a substitute for the use of 3% (v/v) hydrogen cyanamide in viticulture in the sub-tropics, and could be a sustainable alternative based on lower cost and environmental impact.     

Comparison of the polymerase chain reaction-restriction fragment length polymorphism pattern of the fiber gene and pathogenicity of serotype-1 fowl adenovirus isolates from gizzard erosions and from feces of clinically healthy chickens in Japan.

The fiber gene sequence and pathogenicity of the serotype-1 fowl adenovirus (FAdV-1) isolated from gizzard erosions and from clinically normal chickens were compared among isolates. The FAdV-99ZH strain, which induced gizzard erosions, had a nucleotide sequence of the long fiber gene that was different from that of the Ote strain, which did not induce gizzard erosions. The differences could be distinguished by use of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The long fiber gene of 16 FAdV-1 isolates from gizzard erosions and 10 FAdV-1 isolates from the feces of clinically normal chickens was examined by use of PCR-RFLP analysis. All 16 FAdV-1 isolates from gizzard erosions had the same restriction patterns as those of strain 99ZH; however, 10 FAdV-1 isolates from normal chickens were classified into 3 groups. Specific-pathogen-free (SPF) chickens were inoculated orally with 2 FAdV-1 isolates from gizzard erosions or 3 FAdV-1 isolates from clinically normal chickens to determine the pathogenicity of each strain. Two of 2 FAdV-1 isolates from gizzard erosions induced gizzard erosions. Two of 3 FAdV-1 isolates from normal chickens had the same PCR-RFLP patterns as those of the Ote strain, but did not induce any gizzard erosions. However, 1 FAdV-1 isolate from clinically normal chickens had the same PCR-RFLP pattern as that of strain 99ZH and induced gizzard erosions. These results indicate that there are FAdV-1 strains that have different pathogenicity; one strain induces gizzard erosions, and the other does not. Use of PCR-RFLP analysis of long fiber genes may be able to distinguish between these two strains.     

Hypercholesterolemia in Shetland sheepdogs

Plasma lipoprotein cholesterol in 64 clinically healthy Shetland sheepdogs was evaluated to assess whether the breed is more susceptible to hypercholesterolemia. The incidence of hypercholesterolemia was clearly higher in Shetland sheepdogs and mean plasma cholesterol level was significantly higher in Shetland sheepdogs than in control dogs. Blood biochemical examinations did not evidence the abnormalities, which imply the causative disorders, and thyroid hormone levels were not significantly different from the controls. These results suggest that the cholesterolemia is a primary disorder. Cholesterol fractionation by agarose gel electrophoresis and ultracentrifugation revealed that accumulation of alpha2-migrating lipoproteins was the common characteristic of dogs showing cholesterol level over 250 mg/dl in the breed. Increase in prebeta-beta-lipoproteins was also found in Shetland sheepdogs with marked hypercholesterolemia over 500 mg/dl. Therefore. Shetland sheepdogs may include more dogs with primary disorders in lipoprotein metabolism, which cause hypercholesterolemia. at least in Japan.