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.
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.
Abstract
In order to realize the voltage stable output of the LLC resonant converter under different loads, a voltage gain fluctuation suppression technology of the LLC resonant converter based on a ...chaotic spread spectrum is proposed. The gain fluctuation electromagnetic interference signal is eliminated by the Chua’s circuit; The rated voltage value is discretized, and the target network and the evaluation network are used to form a deep Q network, with the multi-threshold judgment method and the variable step method respectively completed the gain fluctuation suppression target under different working conditions. The experimental results show that the proposed technology can achieve stable voltage output in both dynamic and steady-state conditions, with good gain fluctuation suppression effect and strong timeliness. It provides data reference for the rational application of the LLC resonant converter.
According to the bipolar resistive switching characteristics of CdZnTe films, fabricated devices with sandwiched structure of Cu/CdZnTe/ITO and Cu/CdZnTe/Cu were made in this study. The different ...resistance switching behaviors were then observed for the Cu/CdZnTe/ITO and Cu/CdZnTe/Cu structures. The fitting of the I–V curve was used to analyze the conduction mechanism. For a high resistance state, space charge-limited current conduction and Schottky emission were used to analyze the conduction mechanism of the Cu/CdZnTe/Cu structure, and Ohmic-like behavior was held in the Cu/CdZnTe/ITO structure. In a low resistance state, the conductions of the ITO/CdZnTe/Cu and Cu/CdZnTe/Cu structure was ascribed to the polarization of the CdZnTe film in the low resistance state. The above results were interpreted according to the different quality of films deposited on the Cu and ITO bottom electrodes.
Bile acid (BA) is de novo synthesized exclusively in the liver and has direct or indirect antimicrobial effects. On the other hand, the composition and size of the BA pool can be altered by ...intestinal microbiota via the biotransformation of primary BAs to secondary BAs, and subsequently regulate the nuclear farnesoid X receptor (FXR; NR1H4). The BA-activated FXR plays important roles in BA synthesis and metabolism, glucose and lipid metabolism, and even hepatic autophagy. BAs can also play a role in the interplays among intestinal microbes. In this review, we mainly discuss the interactions between BAs and intestinal microbiota and their roles in regulating host metabolism, and probably the autophagic signaling pathway.
•Contrasting six deterministic spatial interpolation methods responses to different spatial scales.•In the prediction process of using RK and GWRK methods, the “mutation phenomenon” affects the ...interpolation accuracy of the two methods.•As a local regression model, GWRK introduces many auxiliary variables under the condition of a small spatial scale, which will cause over-fitting.•During the establishment of RK and GWRK models, soil parameters have a more significant effect than environmental parameters.
Accurate estimation of SOM content of Mollisols influences fundamental sub-micron to global-scale biogeochemical processes and carbon-climate feedbacks. Comparative analysis of the responses of Multiple deterministic Interpolation models to spatial scale variations is the basis for multiscale soil organic carbon (SOC) pools simulation and evaluation. This study mainly manifested as spatial variation at different analytical levels of spatial correlation and the change of characteristic data attributes that characterize this change. Three spatial scales were selected (HQ, endemic area; XF, local area; JX, most area). A set of 164 topsoils (0–20 cm, sampling density of 0.1 points / km2) samples were taken, and 14 environmental variables and 14 soil characters variables were employed to contrast prediction accuracy of ordinary kriging (OK), inverse distance weighting (IDW), radial basis function (RBF), global polynomial (GPI), local polynomial (LPI), regression kriging interpolation methods such as (RK) and geographically weighted regression kriging (GWRK) responses to different spatial scale. Using a cross-validation procedure to evaluate the performance of the models. Overall, RK and GWRK, due to the introduction of the auxiliary variables, effectively predict SOM content and the improvement of prediction accuracy depends on the spatial scale, compared with IDW, RBF, GPI, and LPI.
Furthermore, soil characters variables (TN, pH) as covariates have a more significant impact on the final prediction than environmental variables (Elevation, Slope, etc.). Therefore, the mutations and trends associated with the spatial resolution are analyzed in different spaces. The root means square error (RMSE) of RK and GWRK are reduced by 46.66 % and 64.26 % compared with OK. RK with fixed the regression coefficient obtained by OLS reveals that the uniformity of the object distribution in HQ and XF have Adjusted R2 0.955 and 0.915. Otherwise, the RI of GWRK with 0.792 adjusted R2 in JX is relatively 17.6 % higher than RK. The results from our case study highlight a key role in selecting the optimal spatial interpolation method for a given dataset associated with spatial scales and analyzing their regularity and applicability on different spatial scales.
The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy ...reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.
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•The volatile evolution during thermal treatment of an oily sludge was discussed.•Internal diffusion had a great influence on the reaction rate during 120–360 °C.•The proportion of ...light and unsaturated hydrocarbons increased during 360–550 °C.•The evolution profiles of typical compounds in volatile were characterized.
The volatile evolution during thermal treatment of an oily sludge derived from petroleum refinery wastewater treatment plant was investigated by in-situ pyrolytic and kinetic analysis. According to kinetic mechanism model, it was found that the internal diffusion had a great influence on volatile release during 120–360 °C, while the devolatilization rate during 360–550 °C would more depend on the concentration of remaining hydrocarbons. By Py-GC/MS, oils were trapped and analyzed respectively during 60–360 °C and 360–550 °C, and above 300 compounds were identified and semi-quantified of the volatiles. During 60–360 °C, the detected volatile was mainly composed of saturated aliphatics, accounting for 68.69%. More proportion of light chain aliphatic hydrocarbons and monoaromtics were observed during 360–550 °C, and the relative content of unsaturated aliphatics increased to 33.81%. From the evolution profiles of typical oil products, the volatile release during 120–360 °C would follow the order of molecular weight. But during 360–550 °C, as a result of increasing thermal-cracking degree, the release peaks of the different volatile species were corresponded to similar temperature. The gaseous and sulfur-containing compounds were also traced. Among them, CO2 was the main product above 550 °C for the decomposition of minerals, and sulfur-containing compounds were mainly generated during < 450 °C.
Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), ...especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.
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