Genomic mosaicism arising from postzygotic mutations has long been associated with cancer and more recently with non-cancer diseases. It has also been detected in healthy individuals including healthy parents of children affected with genetic disorders, highlighting its critical role in the origin of genetic mutations. However, most existing software for the genome-wide identification of single-nucleotide mosaicisms (SNMs) requires a paired control tissue obtained from the same individual which is often unavailable for non-cancer individuals and sometimes missing in cancer studies. Here, we present MosaicHunter (http://mosaichunter.cbi.pku.edu.cn), a bioinformatics tool that can identify SNMs in whole-genome and whole-exome sequencing data of unpaired samples without matched controls using Bayesian genotypers. We evaluate the accuracy of MosaicHunter on both simulated and real data and demonstrate that it has improved performance compared with other somatic mutation callers. We further demonstrate that incorporating sequencing data of the parents can be an effective approach to significantly improve the accuracy of detecting SNMs in an individual when a matched control sample is unavailable. Finally, MosaicHunter also has a paired mode that can take advantage of matched control samples when available, making it a useful tool for detecting SNMs in both non-cancer and cancer studies.
A multi-objective chance-constrained programming integrated with Genetic Algorithm and robustness evaluation methods was proposed to weigh the conflict between system investment against risk for watershed load reduction, which was firstly applied to nutrient load reduction in the Lake Qilu watershed of the Yunnan Plateau, China. Eight sets of Pareto solutions were acceptable for both system investment and probability of constraint satisfaction, which were selected from 23 sets of Pareto solutions out of 120 solution sets. Decision-makers can select optimal decisions from the solutions above in accordance with the actual conditions of different sub-watersheds under various engineering measures. The relationship between system investment and risk demonstrated that system investment increased rapidly when the probability level of constraint satisfaction was higher than 0.9, but it reduced significantly if appropriate risk was permitted. Evaluation of robustness of the optimal scheme indicated that the Pareto solution obtained from the model provided the ideal option, since the solutions were always on the Pareto frontier under various distributions and mean values of the random parameters. The application of the multi-objective chance-constrained programming to optimize the reduction of watershed nutrient loads in Lake Qilu indicated that it is also applicable to other environmental problems or study areas that contain uncertainties.
Pore structures is a very critical parameter that affects the physical, mechanical and chemical properties of the reservoir rock. Pore shapes and pore size distributions can impact the transport and storage capacity of the reservoir rocks. This necessitates the adequate knowledge of the pore structures of the rocks. In this paper, we characterized and quantified the pore structures of rock samples from the Bakken Formation which is a typical unconventional shale oil reservoir. Samples of Upper and Middle Bakken were collected and studied based on the Scanning Electron Microscope (SEM) images. First, the threshold of each image was determined from overflow criteria and then the related pores were extracted from the corresponding image. In the next step, the pore microstructures such as pore size, pore shape distributions of different samples were calculated and compared. Finally, we used fractal theory to describe the pore structures of the shale formation and investigated the relationship between fractal dimension and pore structures. The results showed that pores with various sizes and shapes were widely distributed in the shale samples. Compared with samples from Middle Bakken, samples from Upper Bakken Formation with higher clay content showed higher fractal dimension and more complex pore structures. Finally, the fractal dimension was used to quantify the impact of the magnification on the pore structures.
Understanding the pore structures of unconventional reservoirs such as shale can assist in estimating their elastic transport and storage properties, thus enhancing the hydrocarbon recovery from such massive resources. Bakken Shale Formation is one of the largest shale oil reserves worldwide located in the Williston Basin, North America. In this paper, we collected a few samples from the Bakken and characterized their properties by using complementary methods including X-ray diffraction (XRD), N2 and CO2 adsorption, and Rock-Eval pyrolysis. The results showed that all range of pore sizes: micro (<2nm), meso (2–50nm) and macro-pores (>50nm) exist in the Bakken shale samples. Meso-pores and macro-pores are the main contributors to the porosity for these samples. Compared with the Middle Bakken, samples from Upper and Lower Bakken own more micro pore volumes. Fractal dimension analysis was performed on the pore size distribution data, and the results indicated more complex pore structures for samples taken from the Upper and Lower Bakken shales than the Middle Bakken. Furthermore, the deconvolution of the pore distribution function from the combination of N2 and CO2 adsorption results proved that five typical pore size families exist in the Bakken shale samples: one micro-pore, one macro-pore and three meso-pore size families. The studies on the correlations between the compositions and the pore structures showed that mostly feldspar and pyrite affect the total pore volume of samples from Middle Bakken Formation whereas clay dominates the total pore volume of samples from Upper/Lower Bakken Formation. TOC and clay content are the major contributors to the micro-pore size family in the Upper/Lower Bakken. Also, it was observed that the increase of hard minerals could increase the percentage of macro-pore family in the Middle Bakken Formation.
New particle formation (NPF) studies have been conducted in China since 2004. Formation of new atmospheric aerosol particles has been observed to take place in diverse environments, even under the circumstances of high pre-existing particle loading, challenging the traditional and present understanding of the physicochemical nucleation mechanisms, which have been proposed based on the investigations in clean environments and under laboratory experimental conditions. This paper summarizes the present status and gaps in understanding NPF in China and discusses the main directions opening for future research. (C) 2016 Elsevier B.V. All rights reserved.
