Effect of single nucleotide polymorphism on the total number of piglets born per parity of three different pig breeds

Objective To determine the effects of genomic breeding values (GBV) and single nucleotide polymorphisms (SNP) on the total number of piglets born (TNB) in 3 pig breeds (Berkshire, Landrace, and Yorkshire). Methods After collecting genomic information (Porcine SNP BeadChip) and phenotypic TNB records for each breed, the effects of GBV and SNP were estimated by using single step best linear unbiased prediction (ssBLUP) method. Results The heritability estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were 0.078, 0.107, and 0.121, respectively. The breeding value estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were in the range of −1.34 to 1.47 heads, −1.79 to 1.87 heads, and −2.60 to 2.94 heads, respectively. Of sows having records for TNB, the reliability of breeding value for individuals with SNP information was higher than that for individuals without SNP information. Distributions of the SNP effects on TNB did not follow gamma distribution. Most SNP effects were near zero. Only a few SNPs had large effects. The numbers of SNPs with absolute value of more than 4 standard deviations in Berkshire, Landrace, and Yorkshire breeds were 11, 8, and 19, respectively. There was no SNP with absolute value of more than 5 standard deviations in Berkshire or Landrace. However, in Yorkshire, four SNPs (ASGA 0089457, ASGA0103374, ALGA0111816, and ALGA0098882) had absolute values of more than 5 standard deviations. Conclusion There was no common SNP with large effect among breeds. This might be due to the large genetic composition differences and the small size of reference population. For the precise evaluation of genetic performance of individuals using a genomic selection method, it may be necessary to establish the appropriate size of reference population

Analysis of genetic characteristics of pig breeds using information on single nucleotide polymorphisms

Objective This study was undertaken to investigate the genetic characteristics of Berkshire (BS), Landrace (LR), and Yorkshire (YS) pig breeds raised in the Great Grandparents pig farms using the single nucleotide polymorphisms (SNP) information. Methods A total of 25,921 common SNP genotype markers in three pig breeds were used to estimate the expected heterozygosity (HE), polymorphism information content, F-statistics (FST), linkage disequilibrium (LD) and effective population size (Ne). Results The chromosome-wise distribution of FST in BS, LR, and YS populations were within the range of 0–0.36, and the average FST value was estimated to be 0.07±0.06. This result indicated some level of genetic segregation. An average LD (r2) for the BS, LR, and YS breeds was estimated to be approximately 0.41. This study also found an average Ne of 19.9 (BS), 31.4 (LR), and 34.1 (YS) over the last 5th generations. The effective population size for the BS, LR, and YS breeds decreased at a consistent rate from 50th to 10th generations ago. With a relatively faster Ne decline rate in the past 10th generations, there exists possible evidence for intensive selection practices in pigs in the recent past. Conclusion To develop customized chips for the genomic selection of various breeds, it is important to select and utilize SNP based on the genetic characteristics of each breed. Since the improvement efficiency of breed pigs increases sharply by the population size, it is important to increase test units for the improvement and it is desirable to establish the pig improvement network system to expand the unit of breed pig improvement through the genetic connection among breed pig farms

Neighborhood size and local geographic variation of health and social determinants

BACKGROUND: Spatial filtering using a geographic information system (GIS) is often used to smooth health and ecological data. Smoothing disease data can help us understand local (neighborhood) geographic variation and ecological risk of diseases. Analyses that use small neighborhood sizes yield individualistic patterns and large sizes reveal the global structure of data where local variation is obscured. Therefore, choosing an optimal neighborhood size is important for understanding ecological associations with diseases. This paper uses Hartley's test of homogeneity of variance (F(max)) as a methodological solution for selecting optimal neighborhood sizes. The data from a study area in Vietnam are used to test the suitability of this method. RESULTS: The Hartley's F(max )test was applied to spatial variables for two enteric diseases and two socioeconomic determinants. Various neighbourhood sizes were tested by using a two step process to implement the F(max)test. First the variance of each neighborhood was compared to the highest neighborhood variance (upper, F(max1)) and then they were compared with the lowest neighborhood variance (lower, F(max2)). A significant value of F(max1 )indicates that the neighborhood does not reveal the global structure of data, and in contrast, a significant value in F(max2 )implies that the neighborhood data are not individualistic. The neighborhoods that are between the lower and the upper limits are the optimal neighbourhood sizes. CONCLUSION: The results of tests provide different neighbourhood sizes for different variables suggesting that optimal neighbourhood size is data dependent. In ecology, it is well known that observation scales may influence ecological inference. Therefore, selecting optimal neigborhood size is essential for understanding disease ecologies. The optimal neighbourhood selection method that is tested in this paper can be useful in health and ecological studies

Longitudinal Patterns in Antithrombotic Therapy in Patients with Atrial Fibrillation after Percutaneous Coronary Intervention in the Non-Vitamin K Oral Anticoagulant Era:A Nationwide Population-Based Study

We investigated whether longitudinal patterns in antithrombotic therapy have changed after the introduction of non-vitamin K oral anticoagulants (NOACs) in patients with atrial fibrillation (AF) who underwent percutaneous coronary intervention (PCI). Using a claims database of the Korean AF population who underwent PCI between 2012 and 2016 (n = 18,691), we analyzed prescription records of oral anticoagulants (OACs) and antiplatelets at 3-month intervals over 2 years after PCI. The study population was stratified (pre-NOAC, transition, and NOAC era) using time-periods of NOAC introduction in Korea and an expansion of reimbursement for NOAC in AF as indicators. The overall rates of OAC were low at baseline (24.9%, 26.9%, and 35.2% in pre-NOAC, transition, and NOAC era, respectively), contrary to high rates of dual antiplatelet therapy (DAPT) (73.3%, 71.4%, and 63.6%). However, OAC prescription rates were increased at 1-year (18.5%, 22.5%, and 31.6%), and 2-year follow-up (17.8%, 24.2%, and 31.8%) from pre-NOAC to NOAC era. In NOAC era, 63.5% of baseline OAC prescriptions comprised NOAC, of which 96.4% included triple therapy with DAPT. Over 2 years, we observed increasing rates of double therapy with a single antiplatelet (18.3% and 20.0% at 1- and 2-year follow-up) and OAC monotherapy (2.7% and 8.9% at 1- and 2-year follow-up)

Net clinical benefit of antithrombotic therapy for atrial fibrillation patients with stable coronary artery disease

OBJECTIVES: To compare the net clinical benefit of oral anticoagulant (OAC) monotherapy to OAC plus single antiplatelet therapy (SAPT) in patients with atrial fibrillation (AF) and stable coronary artery disease (CAD) at 1- and 3-year after percutaneous coronary intervention (PCI). BACKGROUND: It has not been studied whether the net clinical benefit of the antithrombotic treatment options differs depending on the elapsed time from the index PCI. METHODS: Using the Korean nationwide claims database, we included AF patients who underwent PCI from 2009 to 2019 and constructed two cohorts: 1- and 3-year after PCI. In each cohort, the baseline characteristics of two groups were balanced using propensity score weighting. Ischemic stroke, myocardial infarction, major bleeding, and composite clinical outcomes were analyzed. RESULTS: Among patients with 1-year after PCI, OAC monotherapy (n = 678), and OAC plus SAPT (n = 3,159) showed comparable results for all clinical outcomes. In patients with 3-year after PCI, OAC monotherapy (n = 1,038) and OAC plus SAPT (n = 2,128) showed comparable results for ischemic stroke and myocardial infarction, but OAC monotherapy was associated with a lower risk of composite clinical outcomes (HR 0.762, 95% CI 0.607–0.950), mainly driven by the reduction of major bleeding risk (HR 0.498, 95% CI 0.345–0.701). CONCLUSION: Oral anticoagulant monotherapy may be a comparable choice for patients with AF and stable CAD compared to OAC plus SAPT. In patients with stable CAD more than 3-year after index PCI, OAC monotherapy would be a better choice, being associated with less major bleeding and a positive net clinical benefit

Torsional Vibration Transduction in a Solid Shaft by MPTs

In this study, we aim to investigate the feasibility to use MPTs (Magnetostrictive Patch Transducers) for torsional vibration measurement in solid ferromagnetic cylinders. MPTs consisting of thin magnetostrictive patches, permanent magnets and a solenoid coil have been widely used for elastic wave transduction in the ultrasound frequency range [1] but they have been seldom used for sonic-frequency range vibration measurement, in spite of their unique wireless transduction characteristics. While a MPT was used in Ref. [2] to perform torsional modal testing in a hollow cylinder or a pipe having relatively small torsional rigidity, no investigation has been reported yet on the use of MPTs in “solid” “ferromagnetic” shafts, common torsional power carrying elements in machines.While we will be mainly focused here on the torsional wave measurement in stationary shafts, the MPT-based torsional measurement can be also applied to rotating shafts. Because the torsional rigidities of solid shafts are much larger than those of hollow cylinders of the same radii, it is important to find optimal MPT configurations, such as the optimal number of rectangular patches to be installed around the surface of a solid shaft. Thereby, we performed numerical investigations and accordingly designed a series of experiments for torsional vibration testing in steel shafts. The actual modal testing experiments with the designed MPTs were found to predict the torsional Eigen-frequencies and Eigen-modes that agree well with the theoretical predictions. Also the relation between the measured vibration signals from MPTs and those from strain gages was checked experimentally and in fact, the experimental result favorably agreed with the theoretical prediction. Potential applications of the MPT-based torsional vibration measurement technique in rotating solid shafts for structural health monitoring are also briefly discussed

Arabidopsis ABCG14 is essential for the root-to-shoot translocation of cytokinin.

Cytokinins are phytohormones that induce cytokinesis and are essential for diverse developmental and physiological processes in plants. Cytokinins of the trans-zeatin type are mainly synthesized in root vasculature and transported to the shoot, where they regulate shoot growth. However, the mechanism of long-distance transport of cytokinin was hitherto unknown. Here, we report that the Arabidopsis ATP-binding cassette (ABC) transporter subfamily G14 (AtABCG14) is mainly expressed in roots and plays a major role in delivering cytokinins to the shoot. Loss of AtABCG14 expression resulted in severe shoot growth retardation, which was rescued by exogenous trans-zeatin application. Cytokinin content was decreased in the shoots of atabcg14 plants and increased in the roots, with consistent changes in the expression of cytokinin-responsive genes. Grafting of atabcg14 scions onto wild-type rootstocks restored shoot growth, whereas wild-type scions grafted onto atabcg14 rootstocks exhibited shoot growth retardation similar to that of atabcg14. Cytokinin concentrations in the xylem are reduced by similar to 90% in the atabcg14 mutant. These results indicate that AtABCG14 is crucial for the translocation of cytokinin to the shoot. Our results provide molecular evidence for the long-distance transport of cytokinin and show that this transport is necessary for normal shoot development.open118380Ysciescopu