The Impacts of Read Length and Transcriptome Complexity for <i>De Novo</i> Assembly: A Simulation Study

<div><p>Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve transcriptome assembly, but it is unknown whether the read length really matters. In addition, though many assembly tools are available now, it is unclear whether the existing assemblers perform well enough for all data with different transcriptome complexities. In this paper, we studied these two open problems using two high-performing assemblers, Velvet/Oases and Trinity, on several simulated datasets of human, mouse and S.cerevisiae. The results suggest that (1) the read length of paired reads does not matter once it exceeds a certain threshold, and interestingly, the threshold is distinct in different organisms; (2) the quality of <i>de novo</i> assembly decreases sharply with the increase of transcriptome complexity, all existing <i>de novo</i> assemblers tend to corrupt whenever the genes contain a large number of alternative splicing events.</p></div

Statistics of five human datasets with different numbers of spliced isoforms.

<p>Statistics of five human datasets with different numbers of spliced isoforms.</p

Comparison of <i>de novo</i> assemblies on S.cerevisiae datasets with different sequencing error rates (the read length is 75 bp).

a<p>Full-length Percentage: the percentage of full-length reconstructed reference transcripts.</p

Comparison of <i>de novo</i> assemblies on five human datasets with different numbers of spliced isoforms.

<p>Comparison of <i>de novo</i> assemblies on five human datasets with different numbers of spliced isoforms.</p

Analyses of five human datasets with different numbers of spliced isoforms.

<p>(A) Boxplot of exon number of each gene. (B) Boxplot of spliced isoform length.</p

Four assessment metrics of assemblies on S.cerevisiae datasets with different lengths.

<p>Four assessment metrics of assemblies on S.cerevisiae datasets with different lengths.</p

Distribution of sequencing errors.

<p>(A) shows the sequencing errors occur randomly across one read and B) shows the error rate is almost the same among six human datasets with different read lengths.</p

Simulation and Validation of Discrete Element Parameter Calibration for Fine-Grained Iron Tailings

In order to improve the calculation efficiency of a discrete element EDEM (Discrete Element Method) numerical simulation software for micron particles, the particle model is linearly enlarged. At the same time, the parameters of the amplified particles were calibrated according to the Hertz-Mindlin with JKR (Johnson-Kendall-Roberts) contact model to make the amplified particles have the same particle flow characteristics as the actual particles. Actual tests were utilized to gather the angle of repose of the microfine iron tailings, which was then used as a reference value for response surface studies based on the JKR contact model from six factors connected to the fine iron tailings particles. The Plackett-Burman test was used to identify three parameters that had a significant effect on the rest angle: static friction factor; rolling friction factor; and JKR surface energy. The Box-Behnken experiment was used to establish a second-order regression model of the rest angle, and the significant parameters and the optimized parameters were: surface energy JKR coefficient 0.459; particle-particle static friction coefficient 0.393; and particle-particle dynamic friction coefficient 0.393, with a dynamic friction coefficient between particles of 0.106. By entering the parameters into the discrete element program, the angle of repose generated from the simulations was compared with the real test values, and the error was 1.56%. The contact parameters obtained can be used in the discrete element simulation of the amplified particles of fine-grained iron tailings, providing an EDEM model reference for the numerical simulation of fine-grained iron tailings particles. There is no discernible difference between the actual and simulated angles

Tailoring Heterogeneous Microstructure in a High-Strength Low-Alloy Steel for Enhanced Strength-Toughness Balance

The attainment of both strength and toughness is of vital importance to most structural materials, although unfortunately they are generally mutually exclusive. Here, we report that simultaneous increases in strength and toughness in a high-strength low-alloy (HSLA) steel were achieved by tailoring the heterogeneous microstructure consisting of soft intercritical ferrite and hard martensite via intercritical heat treatment. The heterogeneous microstructure features were studied from the perspective of morphology and crystallography to uncover the effect on mechanical properties. Specifically, the volume fraction of martensite increased with increasing annealing temperature, which resulted in increased back stress and effective stress, and thereby an improved strength-ductility combination. The enrichment of carbon and alloying elements in the martensite was lowered with the increase in annealing temperature. As a result, the hardness difference between the intercritical ferrite and martensite was reduced. In addition, the globular reversed austenite preferentially grew into the adjacent austenite grain that held no Kurdjumov-Sachs (K-S) orientation relationship with it, which effectively refined the coarse prior austenite grains and increased the density of high angle grain boundaries. The synergy of these two factors contributed to the improved low-temperature toughness. This work demonstrates a strategy for designing heterostructured HSLA steels with superior mechanical properties

Tailoring Heterogeneous Microstructure in a High-Strength Low-Alloy Steel for Enhanced Strength-Toughness Balance

The attainment of both strength and toughness is of vital importance to most structural materials, although unfortunately they are generally mutually exclusive. Here, we report that simultaneous increases in strength and toughness in a high-strength low-alloy (HSLA) steel were achieved by tailoring the heterogeneous microstructure consisting of soft intercritical ferrite and hard martensite via intercritical heat treatment. The heterogeneous microstructure features were studied from the perspective of morphology and crystallography to uncover the effect on mechanical properties. Specifically, the volume fraction of martensite increased with increasing annealing temperature, which resulted in increased back stress and effective stress, and thereby an improved strength-ductility combination. The enrichment of carbon and alloying elements in the martensite was lowered with the increase in annealing temperature. As a result, the hardness difference between the intercritical ferrite and martensite was reduced. In addition, the globular reversed austenite preferentially grew into the adjacent austenite grain that held no Kurdjumov-Sachs (K-S) orientation relationship with it, which effectively refined the coarse prior austenite grains and increased the density of high angle grain boundaries. The synergy of these two factors contributed to the improved low-temperature toughness. This work demonstrates a strategy for designing heterostructured HSLA steels with superior mechanical properties