Ensemble learning for integrative prediction of genetic values with genomic variants.

BACKGROUND: Whole genome variants offer sufficient information for genetic prediction of human disease risk, and prediction of animal and plant breeding values. Many sophisticated statistical methods have been developed for enhancing the predictive ability. However, each method has its own advantages and disadvantages, so far, no one method can beat others. RESULTS: We herein propose an Ensemble Learning method for Prediction of Genetic Values (ELPGV), which assembles predictions from several basic methods such as GBLUP, BayesA, BayesB and BayesCπ, to produce more accurate predictions. We validated ELPGV with a variety of well-known datasets and a serious of simulated datasets. All revealed that ELPGV was able to significantly enhance the predictive ability than any basic methods, for instance, the comparison p-value of ELPGV over basic methods were varied from 4.853E-118 to 9.640E-20 for WTCCC dataset. CONCLUSIONS: ELPGV is able to integrate the merit of each method together to produce significantly higher predictive ability than any basic methods and it is simple to implement, fast to run, without using genotype data. is promising for wide application in genetic predictions.

Purgative components in rhubarbs: adrenergic receptor inhibitors linked with glucose carriers.

Rhubarbs and their extractives have been used as cathartic for many years. There have been numerous breakthroughs in the pharmacological research of the drug. However, as the key point of the mechanism, the targets of the effective components still remain unclear. In this paper, with an in vitro system of isolated intestine, we found that both the rhubarb extractives and the anthraquinone derivatives can antagonize the adrenaline effectively. Furthermore, computer based docking provided the binding model of the anthraquinone derivatives and adrenergic receptor. Then, based on the results of the small intestinal promotion and purgative effect experiments in vivo, we built an "inhibitor-carrier" hypothesis to elucidate the mechanism of rhubarb. This work provided key massages for the pharmacological research of rhubarb, such a common and active medicinal plant, and might be of help for the development of new purgative drugs.

[A meta-analysis on short and long term efficacy and safety of procedure for prolapse and hemorrhoids].

OBJECTIVE: To Systematic review and meta-analysis of short and long term efficacy and safety of procedure for prolapse and hemorrhoids. METHODS: Electronic databases including Cochrane Library, PubMed, OVID, SpringerLinker, ScinceDirect, EBSCO, CNKI, VIP, WanFang Data and CBM were searched. The date of search was between January 2000 and January 2013. Randomized controlled trials (RCTs) were indentified studying association of Compare PPH and Milligan-Mogan (MMH) treatment. Study selection and meta-analysis were conducted according to the Cochrane Handbook for RevMan 5.1 software. RESULTS: The trials involving 1343 patients were included. The results of meta-analysis indicated: compared with MMH, PPH operative time (OR = -11.05, 95%CI: -15.15--6.95, P < 0.01), duration of hospitalization (OR = -3.07, 95%CI: -4.46--1.69, P < 0.01) and return to normal activity time (OR = -7.17, 95%CI: - 9.13--5.20, P < 0.01) was short, postoperative pain light (OR = -3.13, 95%CI: -4.38--1.88, P < 0.01), but the high cost of treatment (OR = 2534.2, 95%CI: 509.0-4559.4, P = 0.01). Long-term efficacy, PPH was higher patient satisfaction (OR = 2.21, 95%CI: 1.03-4.75, P = 0.04), but the recurrence rate of prolapse (OR = 3.75, 95%CI: 1.75-8.06, P < 0.01) and reoperation rate (OR = 7.90, 95%CI: 1.78-35.03, P < 0.01) higher. The incidence of anal stenosis and anal incontinence postoperative were higher than MMH (P > 0.05). The difference of post operative anal stenosis and anal incontinence and residual skin tag rate were not statistically significant (all P > 0.05). CONCLUSIONS: PPH surgery can be used as replacement therapy of MMH for III°-IV° prolapsed hemorrhoids. But we should inform patients of prolapse recurrence and reoperation risk of PPH in the long term.

Multitrait analysis of quantitative trait loci using Bayesian composite space approach.

BACKGROUND: Multitrait analysis of quantitative trait loci can capture the maximum information of experiment. The maximum-likelihood approach and the least-square approach have been developed to jointly analyze multiple traits, but it is difficult for them to include multiple QTL simultaneously into one model. RESULTS: In this article, we have successfully extended Bayesian composite space approach, which is an efficient model selection method that can easily handle multiple QTL, to multitrait mapping of QTL. There are many statistical innovations of the proposed method compared with Bayesian single trait analysis. The first is that the parameters for all traits are updated jointly by vector or matrix; secondly, for QTL in the same interval that control different traits, the correlation between QTL genotypes is taken into account; thirdly, the information about the relationship of residual error between the traits is also made good use of. The superiority of the new method over separate analysis was demonstrated by both simulated and real data. The computing program was written in FORTRAN and it can be available for request. CONCLUSION: The results suggest that the developed new method is more powerful than separate analysis.

Correlations between growth parameters of spoilage micro-organisms and shelf-life of pork stored under air and modified atmosphere at -2, 4 and 10 degrees C.

The correlations of the growth parameters (the initial cell number (N(0)), maximum cell number (N(max)), maximum specific growth rate (mu(max)), lag-phase (lambda)) of typical spoilage micro-organisms (lactic acid bacteria (LAB), coliforms, pseudomonads, Brochothrix thermosphacta) growing on sliced pork to the sensory shelf-life and microbial shelf-life were investigated. The changes in sensory quality and proliferation of micro-organisms on pork shoulder were studied at different atmosphere conditions (air and 40%CO(2)/59%N(2)/1%O(2)) and temperatures (-2, 4 and 10 degrees C). Microbial counts were fitted to the modified-Gompertz equation to obtain the growth parameters of different micro-organisms. B. thermosphacta and coliforms were predominant bacteria associated with spoilage of pork under all temperatures and air conditions. However, pseudomonads could only dominate under regular atmosphere condition. Using multiple linear regression, high correlations were found between the lag-time (lambda) of LAB (0.9814, 0.9830), B. thermosphacta (0.9895, 0.9849), or the maximum specific growth rate (mu(max)) of coliforms (-0.9583, -0.9695) and the microbial shelf-life and sensory shelf-life, respectively. The mu(max) and lambda of micro-organisms correlated well with microbial and sensory shelf-life. The shelf-life of pork is mainly correlated with the growth parameters of mu(max) and lambda than by N(max).

[Maximum likelihood analysis for mapping dynamic trait QTL in outbred population. I . Methodology].

The quantitative traits whose phenotypic values change with time in life or other quantitative factors, were defined as dynamic traits. Based on the idea about random regression test-day model for estimating breeding values in animal evaluation, a mathematic model was constructed for mapping dynamic trait loci by using Legendre polynomials to model dynamic changes of each genetic effect. The Maximum likelihood analysis implemented via EM algorithm was used to estimate the parameters, including QTL position, fixed genetic regression effects for dynamic trait QTL mapping in outbred population. Compared with the existing method for dynamic trait mapping QTL, the new method presented here not only allowed to sample dynamic trait in disequillibrium way, but also can achieve to map dynamic traits QTL in any resource population by just one step. The further study on dynamic trait mapping QTL was theoretically discussed by incorporating genetic analysis of dynamic trait into general mapping QTL.

[Maximum likelihood analysis for mapping dynamic trait QTL in outbred population II. Simulation].

Based on the maximum likelihood analysis principle for dynamic trait QTL mapping, selecting three orders Legendre polynomial as sub-model,the effects of the individual number, the frequency of test day,the marker density and heritability on detecting power are investigated by Monte-Carlo simulation. Each factor is divided into three levels such as the high,middle and low,the combinations of which are arranged by using orthologal design. The simulating result shows that the high heritability needs less number of individuals and frequency of test day than the low one, but the number of individuals of more than 300 and the frequency of test day of 5% above can guarantee sufficient detecting power no matter what the heritability is like. The number of individuals has almost the same effect as the frequency of test day in dynamic traits QTL mapping and the number of individuals and the frequency of test day compensate each other under the same size of samples. As to the QTL detection for a dynamic point,simulation indicates that the presented dynamic trait QTL mapping method that focuses on the whole dynamic process is significantly superior to the classical mapping methods on each individual dynamic point.