Assessing genomic prediction accuracy for Holstein sires using bootstrap aggregation sampling and leave-one-out cross validation

Since the introduction of genome-enabled prediction for dairy cattle in 2009, genomic selection has markedly changed many aspects of the dairy genetics industry and enhanced the rate of response to selection for most economically important traits. Young dairy bulls are genotyped to obtain their genomic predicted transmitting ability (GPTA) and reliability (REL) values. These GPTA are a main factor in most purchasing, marketing, and culling decisions until bulls reach 5 yr of age and their milk-recorded offspring become available. At that time, daughter yield deviations (DYD) can be compared with the GPTA computed several years earlier. For most bulls, the DYD align well with the initial predictions. However, for some bulls, the difference between DYD and corresponding GPTA is quite large, and published REL are of limited value in identifying such bulls. A method of bootstrap aggregation sampling (bagging) using genomic BLUP (GBLUP) was applied to predict the GPTA of 2,963, 2,963, and 2,803 young Holstein bulls for protein yield, somatic cell score, and daughter pregnancy rate (DPR), respectively. For each trait, 50 bootstrap samples from a reference population comprising 2011 DYD of 8,610, 8,405, and 7,945 older Holstein bulls were used. Leave-one-out cross validation was also performed to assess prediction accuracy when removing specific bulls from the reference population. The main objectives of this study were (1) to assess the extent to which current REL values and alternative measures of variability, such as the bootstrap standard deviation (SD) of predictions, could detect bulls whose daughter performance deviates significantly from early genomic predictions, and (2) to identify factors associated with the reference population that inform about inaccurate genomic predictions. The SD of bootstrap predictions was a mildly useful metric for identifying bulls whose future daughter performance may deviate significantly from early GPTA for protein and DPR. Leave-one-out cross validation allowed us to identify groups of reference population bulls that were influential on other reference population bulls for protein yield and observe their effects on predictions of testing set bulls, as a whole and individually.     

Photoelectric properties of MISM phthalocyanine structure

Langmuir-Blodgett films have been prepared from copper tetra-4-t-butylphthalocyanine. A voltage dependence of capacitance can be attributed to the presence of a Schottky depletion layer. The barrier potential was determined as l·4eV, and the carrier concentration about 10²⁴m^?3     

Ipriflavone: an important bone-building isoflavone

Ipriflavone, an isoflavone synthesized from the soy isoflavone daidzein, holds great promise in the prevention and treatment of osteoporosis and other metabolic bone diseases. It has been widely studied in humans and found effective for inhibiting bone resorption and enhancing bone formation, the net result being an increase in bone density and a decrease in fracture rates in osteoporotic women. While ipriflavone appears to enhance estrogen's effect, it does not possess intrinsic estrogenic activity, making it an attractive adjunct or alternative to conventional hormone replacement therapy. Preliminary studies have also found ipriflavone effective in preventing bone loss associated with chronic steroid use, immobility, ovariectomy, renal osteodystrophy, and gonadotrophin hormone-releasing hormone agonists. In addition, it holds promise for the treatment of other metabolic diseases affecting the bones, including Paget's disease of the bone, hyperparathyroidism, and tinnitus caused by otosclerosis.     

Recovery of health related quality of life in the year after radical prostatectomy: early experience

PURPOSE: We determined the temporal course of patient return to baseline quality of life after treatment with radical prostatectomy for early stage prostate cancer. MATERIALS AND METHODS: After establishing a longitudinal observational database of men undergoing radical retropubic prostatectomy we used established, validated quality of life questionnaires (RAND 36-Item Health Survey and University of California, Los Angeles Prostate Cancer Index) to document changes in general and disease specific health related quality of life (HRQOL). We assessed 90 patients at baseline before surgery and then at 3-month intervals for 1 year postoperatively. Logistic regression was used to explore predictors of the return to baseline. RESULTS: After prostatectomy patients had a significant decrease in all domains of HRQOL. Return to baseline was rapid in the general and bowel domains with at least two-thirds to three-fourths of patients reaching pretreatment levels within 6 months of surgery. Return to baseline was slower in the urinary and sexual function domains with 61 and 31% of the men, respectively, reaching pretreatment levels by 1 year after surgery. Of those who reached baseline the average intervals for the bowel, sexual and urinary domains were 5, 6 and 7 months, respectively. Married and white patients were more likely to achieve a return to baseline HRQOL during year 1 postoperatively. However, education level was inversely associated with the likelihood of returning to baseline. CONCLUSIONS: During the year after radical prostatectomy for early stage prostate cancer patient quality of life steadily improved. By 3 months postoperatively 30 to 40% of the patients had already recovered baseline levels of physical, mental and social functioning, and by 6 months more than 70% had reached baseline in the general HRQOL domains. By 12 months after surgery 86 to 97% of the patients had returned to baseline levels in each domain. Each domain continued to improve throughout the year. For the patients who reached baseline general HRQOL during followup average recovery time was 5 to 6 months.     

A conserved LIM protein that affects muscular adherens junction integrity and mechanosensory function in Caenorhabditis elegans

The glycosylation of the equine interhaemal barrier and areola was studied throughout the period of gestation. Placentae of 35, 37, 50, 119, 152, 200, 280 and 300 days gestation were investigated, using semithin plastic embedded sections and a panel of 15 biotinylated lectins with an avidin-peroxidase revealing system. Glycosylation of the trophoblast and maternal epithelium showed the most change during the first 50 days of gestation, being associated with the initial stages of adhesion and attachment. In the trophoblast, non-bisected tri/tetraantennary complex N-glycan was only evident after day 37 and terminal N-acetyl galactosamine, alpha2,3- and alpha2,6-linked sialic acids disappeared at the same time. The areolar trophoblast exhibited some differences from microcotyledonary areas, especially with respect to 2-deoxy, 2-acetamido alpha-galactose and tri/tetraantennary, non-bisected complex N-glycan, suggesting that the differences in function between microcotyledonary and areolar trophoblast are reflected at both the morphological and the biochemical level. Granules of the maternal uterine epithelium bound many lectins, particularly those with specificity for bisected and non-bisected bi/triantennary N-linked glycan, 2-deoxy, 2-acetamido alpha-galactosyl, beta-galactosyl and some fucosylated termini. Binding to sialic acids in alpha2,3- and alpha2,6-linkage was sparse. Maternal and fetal capillaries showed little change in glycan expression over the period studied, being rich in bisected and non-bisected bi/triantennary N-linked glycan and sialic acids, with some terminal N-acetyl galactosamine and no detectable terminal fucosyl residues.     

Management practices associated with conception rate and service rate of lactating Holstein cows in large, commercial dairy herds

Data from lactating Holstein cows in herds that participate in a commercial progeny testing program were analyzed to explain management factors associated with herd-average conception and service rates on large commercial dairies. On-farm herd management software was used as the source of data related to production, reproduction, culling, and milk quality for 108 herds. Also, a survey regarding management, facilities, nutrition, and labor was completed on 86 farms. A total of 41 explanatory variables related to management factors and conditions that could affect conception and service rate were considered in this study. Models explaining conception and service rates were developed using a machine learning algorithm for constructing model trees. The most important explanatory variables associated with conception rate were the percentage of repeated inseminations between 4 and 17 d post-artificial insemination, stocking density in the breeding pen, length of the voluntary waiting period, days at pregnancy examination, and somatic cell score. The most important explanatory variables associated with service rate were the number of lactating cows per breeding technician, use of a resynchronization program, utilization of soakers in the holding area during the summer, and bunk space per cow in the breeding pen. The aforementioned models explained 35% and 40% of the observed variation in conception rate and service rate, respectively, and underline the association of herd-level management factors not strictly related to reproduction with herd reproductive performance.