Numerical analysis and optimization of key parts in the stirred tank based on solid-liquid flow field

In order to further improve the mixing performance of the mixing device, the structure of the agitator was optimized, and the effects of the diameter and pitch of the agitator on the solid-liquid suspension characteristics were analyzed by single factor method. Multiple reference frame (MRF), computational fluid dynamics, Euler multiphase flow model and standard K- ε turbulence model were used to investigate the effect of the height from the bottom of the agitator on the suspension characteristics of particles in the agitator was studied. The results show that reducing the height from the bottom of the agitator can promote the suspension of particles at the bottom of the tank, but too low height from the bottom will easily produce mixing dead zone at the bottom of the tank, and cause the accumulation of particles. Reducing the height of the agitator from the bottom will enlarge the clear liquid area of the flow field, cause uneven particle distribution and increase the stirring torque. With the increase of agitator diameter, the critical suspension speed of the flow field decrease, but the stirring power required by the flow field increase. Increasing the blade spacing in a certain range can promote the suspension of particles and make the distribution of particles in the flow field more uniform. Therefore, the mixing power and the uniformity of particle concentration distribution need to be considered together in order to make the mixing device more efficient and energy-saving.

ReGSP: a visualized application for homology-based gene searching and plotting using multiple reference sequences

The massively parallel nature of next-generation sequencing technologies has contributed to the generation of massive sequence data in the last two decades. Deciphering the meaning of each generated sequence requires multiple analysis tools, at all stages of analysis, from the reads stage all the way up to the whole-genome level. Homology-based approaches based on related reference sequences are usually the preferred option for gene and transcript prediction in newly sequenced genomes, resulting in the popularity of a variety of BLAST and BLAST-based tools. For organelle genomes, a single-reference–based gene finding tool that uses grouping parameters for BLAST results has been implemented in the Genome Search Plotter (GSP). However, this tool does not accept multiple and user-customized reference sequences required for a broad homology search. Here, we present multiple Reference–based Gene Search and Plot (ReGSP), a simple and convenient web tool that accepts multiple reference sequences for homology-based gene search. The tool incorporates cPlot, a novel dot plot tool, for illustrating nucleotide sequence similarity between the query and the reference sequences. ReGSP has an easy-to-use web interface and is freely accessible at https://ds.mju.ac.kr/regsp.

A New Multiprocess IRT Model With Ideal Points for Likert-Type Items

For surveys of complex issues that entail multiple steps, multiple reference points, and nongradient attributes (e.g., social inequality), this study proposes a new multiprocess model that integrates ideal-point and dominance approaches into a treelike structure (IDtree). In the IDtree, an ideal-point approach describes an individual’s attitude and then a dominance approach describes their tendency for using extreme response categories. Evaluation of IDtree performance via two empirical data sets showed that the IDtree fit these data better than other models. Furthermore, simulation studies showed a satisfactory parameter recovery of the IDtree. Thus, the IDtree model sheds light on the response processes of a multistage structure.

scMRA: A robust deep learning method to annotate scRNA-seq data with multiple reference datasets

Motivation Single-cell RNA-seq (scRNA-seq) has been widely used to resolve cellular heterogeneity. After collecting scRNA-seq data, the natural next step is to integrate the accumulated data to achieve a common ontology of cell types and states. Thus, an effective and efficient cell-type identification method is urgently needed. Meanwhile, high quality reference data remain a necessity for precise annotation. However, such tailored reference data are always lacking in practice. To address this, we aggregated multiple datasets into a meta-dataset on which annotation is conducted. Existing supervised or semi-supervised annotation methods suffer from batch effects caused by different sequencing platforms, the effect of which increases in severity with multiple reference datasets. Results Herein, a robust deep learning based single-cell Multiple Reference Annotator (scMRA) is introduced. In scMRA, a knowledge graph is constructed to represent the characteristics of cell types in different datasets, and a graphic convolutional network (GCN) serves as a discriminator based on this graph. scMRA keeps intra-cell-type closeness and the relative position of cell types across datasets. scMRA is remarkably powerful at transferring knowledge from multiple reference datasets, to the unlabeled target domain, thereby gaining an advantage over other state-of-the-art annotation methods in multi-reference data experiments. Furthermore, scMRA can remove batch effects. To the best of our knowledge, this is the first attempt to use multiple insufficient reference datasets to annotate target data, and it is, comparatively, the best annotation method for multiple scRNA-seq datasets. Availability An implementation of scMRA is available from https://github.com/ddb-qiwang/scMRA-torch Supplementary information Supplementary data are available at Bioinformatics online.

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.