Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction

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Estimation of dynamic SNP-heritability with Bayesian Gaussian process models

Motivation: Improved DNA technology has made it practical to estimate single nucleotide polymorphism (SNP)-heritability among distantly related individuals with unknown relationships. For growth and development related traits, it is meaningful to base SNP-heritability estimation on longitudinal data due to the time-dependency of the process. However, only few statistical methods have been developed so far for estimating dynamic SNP-heritability and quantifying its full uncertainty. / Results: We introduce a completely tuning-free Bayesian Gaussian process (GP) based approach for estimating dynamic variance components and heritability as their function. For parameter estimation, we use a modern Markov Chain Monte Carlo (MCMC) method which allows full uncertainty quantification. Several data sets are analysed and our results clearly illustrate that the 95 % credible intervals of the proposed joint estimation method (which "borrows strength" from adjacent time points) are significantly narrower than of a two-stage baseline method that first estimates the variance components at each time point independently and then performs smoothing. We compare the method with a random regression model using MTG2 and BLUPF90 softwares and quantitative measures indicate superior performance of our method. Results are presented for simulated and real data with up to 1000 time points. Finally, we demonstrate scalability of the proposed method for simulated data with tens of thousands of individuals. / Availability: The C++ implementation dynBGP and simulated data are available in GitHub (https://github.com/aarjas/dynBGP). The programs can be run in R. Real datasets are available in QTL archive (https://phenome.jax.org/centers/QTLA). / Supplementary information: Supplementary data are available at Bioinformatics online

A Candidate Sub-Parsec Supermassive Binary Black Hole System

We identify SDSS J153636.22+044127.0, a QSO discovered in the Sloan Digital Sky Survey, as a promising candidate for a binary black hole system. This QSO has two broad-line emission systems separated by 3500 km/sec. The redder system at z=0.3889 also has a typical set of narrow forbidden lines. The bluer system (z=0.3727) shows only broad Balmer lines and UV Fe II emission, making it highly unusual in its lack of narrow lines. A third system, which includes only unresolved absorption lines, is seen at a redshift, z=0.3878, intermediate between the two emission-line systems. While the observational signatures of binary nuclear black holes remain unclear, J1536+0441 is unique among all QSOs known in having two broad-line regions, indicative of two separate black holes presently accreting gas. The interpretation of this as a bound binary system of two black holes having masses of 10^8.9 and 10^7.3 solar masses, yields a separation of ~ 0.1 parsec and an orbital period of ~100 years. The separation implies that the two black holes are orbiting within a single narrow-line region, consistent with the characteristics of the spectrum. This object was identified as an extreme outlier of a Karhunen-Loeve Transform of 17,500 z < 0.7 QSO spectra from the SDSS. The probability of the spectrum resulting from a chance superposition of two QSOs with similar redshifts is estimated at 2X10^-7, leading to the expectation of 0.003 such objects in the sample studied; however, even in this case, the spectrum of the lower redshift QSO remains highly unusual.Comment: 8 pages, 2 figures, Nature in pres

Microwave amplification with nanomechanical resonators

Sensitive measurement of electrical signals is at the heart of modern science and technology. According to quantum mechanics, any detector or amplifier is required to add a certain amount of noise to the signal, equaling at best the energy of quantum fluctuations. The quantum limit of added noise has nearly been reached with superconducting devices which take advantage of nonlinearities in Josephson junctions. Here, we introduce a new paradigm of amplification of microwave signals with the help of a mechanical oscillator. By relying on the radiation pressure force on a nanomechanical resonator, we provide an experimental demonstration and an analytical description of how the injection of microwaves induces coherent stimulated emission and signal amplification. This scheme, based on two linear oscillators, has the advantage of being conceptually and practically simpler than the Josephson junction devices, and, at the same time, has a high potential to reach quantum limited operation. With a measured signal amplification of 25 decibels and the addition of 20 quanta of noise, we anticipate near quantum-limited mechanical microwave amplification is feasible in various applications involving integrated electrical circuits.Comment: Main text + supplementary information. 14 pages, 3 figures (main text), 18 pages, 6 figures (supplementary information

Application of Photo-Fenton, Electro-Fenton, and Photo-Electro-Fenton processes for the treatment of DMSO and DMAC wastewaters

This is the final version. Available from Elsevier via the DOI in this record. Biological treatment, due to the formation of hazardous chemicals to remove organic compounds such as dimethyl sulfoxide (DMSO) and N, N-dimethylacetamide (DMAC), has limited potential. Advanced oxidation processes (AOPs) are regarded as a viable alternative for treating molecules containing carbon-hydrogen bonds that cannot be broken down by traditional physico-chemical methods. In this investigation, various AOPs such as Photo-Fenton, Electro-Fenton, and Photo-Electro-Fenton processes were studied to treat wastewaters containing DMSO and DMAC. The effects of the operating parameters, including various initial concentrations of DMSO and DMAC, initial pH, reaction time, different concentrations of Fenton's reagent, power of UV lamp, different concentrations of electrolytes, the distance between electrodes and current intensity, were investigated. The findings of the experiments revealed that a pH of 3 and a reaction time of 120 min were optimal. At 2000 mg L−1 of DMSO, maximum degradation and the final concentration of TOC were 98.64 % and 256.8 mg L−1, respectively, by the Electro-Fenton process under the optimal conditions. The Electro-Fenton process was successful in determining the maximum degradation of DMAC (96.31 %) and the final TOC concentration (10.03 mg L−1) at 250 mg L−1 of DMAC under optimal conditions. Finally, it can be concluded that the Electro-Fenton process was the best process for the efficient removal of DMSO and DMAC. The second step of the kinetic model follows a pseudo-first-order reaction for 250 and 500 mg L−1 of pollutants and obeyed a pseudo-second-order kinetic model for concentrations of 1000, 2000 mg L−1.Bushehr province water company, Ira

Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits

Background: In the analysis of complex traits, genetic effects can be confounded with non-genetic effects, especially when using full-sib families. Dominance and epistatic effects are typically confounded with additive genetic and non-genetic effects. This confounding may cause the estimated genetic variance components to be inaccurate and biased

Predicting Unobserved Phenotypes for Complex Traits from Whole-Genome SNP Data

Genome-wide association studies (GWAS) for quantitative traits and disease in humans and other species have shown that there are many loci that contribute to the observed resemblance between relatives. GWAS to date have mostly focussed on discovery of genes or regulatory regions habouring causative polymorphisms, using single SNP analyses and setting stringent type-I error rates. Genome-wide marker data can also be used to predict genetic values and therefore predict phenotypes. Here, we propose a Bayesian method that utilises all marker data simultaneously to predict phenotypes. We apply the method to three traits: coat colour, %CD8 cells, and mean cell haemoglobin, measured in a heterogeneous stock mouse population. We find that a model that contains both additive and dominance effects, estimated from genome-wide marker data, is successful in predicting unobserved phenotypes and is significantly better than a prediction based upon the phenotypes of close relatives. Correlations between predicted and actual phenotypes were in the range of 0.4 to 0.9 when half of the number of families was used to estimate effects and the other half for prediction. Posterior probabilities of SNPs being associated with coat colour were high for regions that are known to contain loci for this trait. The prediction of phenotypes using large samples, high-density SNP data, and appropriate statistical methodology is feasible and can be applied in human medicine, forensics, or artificial selection programs

Associations between neck musculoskeletal complaints and work related factors among public service computer workers in Kaunas

Objectives:Information technologies have been developing very rapidly, also in the case of occupational activities. Epidemiological studies have shown that employees, who work with computers, are more likely to complain of musculoskeletal disorders (MSD). The aim of this study was to evaluate associations between neck MSD and individual and work related factors. Materials and Methods: The investigation which consisted of two parts - a questionnaire study (using Nordic Musculoskeletal questionnaire and Copenhagen Psychosocial Questionnaire) and a direct observation (to evaluate ergonomic work environment using RULA method) was carried out in three randomly selected public sector companies of Kaunas. The study population consisted of 513 public service office workers. Results: The survey showed that neck MSDs were very common in the investigated population. The prevalence rate amounted to 65.7%. According to our survey neck MSDs were significantly associated with older age, bigger work experience, high quantitative and cognitive job demands, working for longer than 2 h without taking a break as well as with higher ergonomic risk score. The fully adjusted model working for longer than 2 h without taking a break had the strongest associations with neck complaints. Conclusion: It was confirmed, that neck MSDs were significantly associated with individual factors as well as conditions of work, therefore, preventive acions against neck complaints should be oriented at psychosocial and ergonomic work environment as well as at individual factors

Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC2DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m²,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials