DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio ...sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. We sequence a human genome HX1 and a Chlamydomonas reinhardtii genome using Nanopore sequencing, and then evaluate DeepMod on three types of genomes (Escherichia coli, Chlamydomonas reinhardtii and human genomes). For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species.
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot ...correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Abstract
Motivation
The Oxford Nanopore sequencing enables to directly detect methylation states of bases in DNA from reads without extra laboratory techniques. Novel computational methods are ...required to improve the accuracy and robustness of DNA methylation state prediction using Nanopore reads.
Results
In this study, we develop DeepSignal, a deep learning method to detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads of Homo sapiens (H. sapiens), Escherichia coli (E. coli) and pUC19 shows that DeepSignal can achieve higher performance at both read level and genome level on detecting 6 mA and 5mC methylation states comparing to previous hidden Markov model (HMM) based methods. DeepSignal achieves similar performance cross different DNA methylation bases, different DNA methylation motifs and both singleton and mixed DNA CpG. Moreover, DeepSignal requires much lower coverage than those required by HMM and statistics based methods. DeepSignal can achieve 90% above accuracy for detecting 5mC and 6 mA using only 2× coverage of reads. Furthermore, for DNA CpG methylation state prediction, DeepSignal achieves 90% correlation with bisulfite sequencing using just 20× coverage of reads, which is much better than HMM based methods. Especially, DeepSignal can predict methylation states of 5% more DNA CpGs that previously cannot be predicted by bisulfite sequencing. DeepSignal can be a robust and accurate method for detecting methylation states of DNA bases.
Availability and implementation
DeepSignal is publicly available at https://github.com/bioinfomaticsCSU/deepsignal.
Supplementary information
Supplementary data are available at bioinformatics online.
We present a tool that combines fast mapping, error correction, and de novo assembly (MECAT; accessible at https://github.com/xiaochuanle/MECAT) for processing single-molecule sequencing (SMS) reads. ...MECAT's computing efficiency is superior to that of current tools, while the results MECAT produces are comparable or improved. MECAT enables reference mapping or de novo assembly of large genomes using SMS reads on a single computer.
In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles in the regulation of biological processes. ...Although long Nanopore reads are advantageous in the detection of 5mCs comparing to short-read bisulfite sequencing, existing methods can only detect 5mCs in the CpG context, which limits their application in plants. Here, we develop DeepSignal-plant, a deep learning tool to detect genome-wide 5mCs of all three contexts in plants from Nanopore reads. We sequence Arabidopsis thaliana and Oryza sativa using both Nanopore and bisulfite sequencing. We develop a denoising process for training models, which enables DeepSignal-plant to achieve high correlations with bisulfite sequencing for 5mC detection in all three contexts. Furthermore, DeepSignal-plant can profile more 5mC sites, which will help to provide a more complete understanding of epigenetic mechanisms of different biological processes.
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•A new method was developed for TFN membrane preparation.•The incorporated zeolite nanoparticles had little agglomeration.•Water permeability was greatly improved with slight ...sacrifice of MgSO4 rejection.•The TFN membrane performed well in rejecting pharmaceuticals.
A novel approach to fabricating thin-film nanocomposite (TFN) nanofiltration membranes was reported in this study. It involved the preparation of a polysulfone support in situ embedded with zeolite nanoparticles followed by interfacial polymerization to form the polyamide layer. Compared with the TFN membranes prepared by the conventional method (TFN-C), the new TFN membrane (TFN-I) had higher loading and more uniform dispersion of nanoparticles in the polyamide layer. The nanoparticles incorporation resulted in an increase of surface roughness but no change of surface hydrophilicity. The TFN-I membrane doubled the water permeability compared with the control membrane (TFC). The TFN-I membrane had a similar rejection of MgSO4 (>93% at 150psi) and negatively charged pharmaceuticals (PhACs) with TFC, but a reduced rejection of NaCl and a slightly lower rejection of neutral and positively charged PhACs of small molecular weights. The TFN-I membrane performed much better than the TFN-C membrane. The demonstrated performance of TFN-I could be due to the internal pores of zeolite nanoparticles, the increased membrane surface roughness and, though undesirable, the microporous defects between the nanoparticles and the polyamide matrix. The newly developed approach is highly promising for the fabrication of TFN nanofiltration and reverse osmosis membranes of improved performance by incorporating various nanoparticles.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
The integral equation (IE) method is commonly utilized to model time-harmonic electromagnetic (EM) problems. One of the greatest challenges in its applications arises in the solution of the resulting ...ill-conditioned matrix equation. We introduce a new domain decomposition method (DDM) for the IE solution of EM wave scattering from non-penetrable objects. The proposed method is a non-overlapping/non-conformal DDM and it provides a computationally efficient and effective preconditioner for the IE matrix equations. Moreover, the proposed approach is very suitable for dealing with multi-scale electromagnetic problems since each sub-domain has its own characteristics length and will be meshed independently. Furthermore, for each sub-domain, we are free to choose the most effective IE sub-domain solver based on its local geometrical features and electromagnetic characteristics. Additionally, the multilevel fast multi-pole algorithm (MLFMA) is utilized to accelerate the computations of couplings between sub-domains. Numerical results demonstrate that the proposed method yields rapid convergence in the outer Krylov iterative solution process. Finally, simulations of several large-scale examples testify to the effectiveness and robustness of the proposed IE based DDM.
O3‐type Fe/Mn‐based layered oxide cathode materials with abundant reserves have a promising prospect in sodium‐ion batteries. However, the electrochemical reversibility of most O3‐type Fe/Mn‐based ...oxide cathode materials is still not high enough. Herein, the effect of different Cu contents on the electrochemical properties of O3‐NaFe0.50Mn0.50O2 materials is systematically investigated. The as‐prepared NaFe0.30Mn0.50Cu0.20O2 cathode achieves the synergistic optimization of the interface and bulk phase. It shows superior electrochemical performance, with an initial discharge specific capacity of 114 mAh g−1 at 0.1 C, a capacity retention rate of 94 % after 100 cycles at 0.5 C, and excellent chemical stability in air and water. In addition, the sodium ion full battery based on NaFe0.30Mn0.50Cu0.20O2 cathode and hard carbon anode has a capacity retention rate of 81 % after 100 cycles. This research provides a useful approach for the preparation of low‐cost and high‐performance O3‐type layered cathode materials.
The effect of different copper contents on the electrochemical performance of environmentally friendly CO/Ni‐free O3‐type Fe/Mn‐based cathode is systematically investigated. The introduction of a high proportion of copper can simultaneously regulate both the electrode‐electrolyte interface and the bulk phase. Therefore, the obtained cathode material with an optimized component of NaCu0.20Fe0.30Mn0.50O2 achieves a significant improvement in electrochemical performance.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This paper investigates variation in the failure behavior of shale in a ScCO2-immersion environment with different adsorption periods and layering orientations. Eight types of specimens are ...investigated, where the inclination of the layering to the applied force θ is 0°, 15°, 30°, 45°, 60°, 75°, 90°, and Divider type. The period of immersion ranges up to 60 days. The results indicate that after 60 days of ScCO2 adsorption, the Brazilian splitting strength (BSS), splitting modulus (E) and absorbed energy (U) of the shale were reduced by 46%, 22% and 50%, respectively, versus those of samples in which there was no adsorption. The root cause of this mechanical weakening is that damage done to the shale by ScCO2 results in the formation of a fragmented structure. Not only tensile failure but also shear failure occurs, making the failure mixed-mode. The mechanical properties of shale show clear changes with θ. Samples with no adsorption, 10-day adsorption, 30-day adsorption and 60-day adsorption show basically consistent change trends with inclination angle (θ).
•The influence of ScCO2 adsorption on the failure behavior of shale is investigated.•Properties considered: BSS, E, U, and fracture trace.•ScCO2 adsorption for 60 days was observed to reduce BSS by 46%, E by 22%, and U by 50%.•Fragmentation is the root cause of deterioration in the mechanical properties of shale.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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