Bilateral Elimination Rule-Based Finite Class Bayesian Inference System for Circular and Linear Walking Prediction.

OBJECTIVE: The prediction of upcoming circular walking during linear walking is important for the usability and safety of the interaction between a lower limb assistive device and the wearer. This study aims to build a bilateral elimination rule-based finite class Bayesian inference system (BER-FC-BesIS) with the ability to predict the transition between circular walking and linear walking using inertial measurement units. METHODS: Bilateral motion data of the human body were used to improve the recognition and prediction accuracy of BER-FC-BesIS. RESULTS: The mean predicted time of BER-FC-BesIS in predicting the left and right lower limbs' upcoming steady walking activities is 119.32 ± 9.71 ms and 113.75 ± 11.83 ms, respectively. The mean time differences between the predicted time and the real time of BER-FC-BesIS in the left and right lower limbs' prediction are 14.22 ± 3.74 ms and 13.59 ± 4.92 ms, respectively. The prediction accuracy of BER-FC-BesIS is 93.98%. CONCLUSION: Upcoming steady walking activities (e.g., linear walking and circular walking) can be accurately predicted by BER-FC-BesIS innovatively. SIGNIFICANCE: This study could be helpful and instructional to improve the lower limb assistive devices' capabilities of walking activity prediction with emphasis on non-linear walking activities in daily living.

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.

The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.

The garden asparagus (Asparagus officinalis L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data.

Garden asparagus (Asparagus officinalis L.) is a horticultural crop with high nutritional and medical value, considered an ideal plant for sex determination research among many dioecious plants, whose genomic information can support genetic analysis and breeding programs. In this research, the entire mitochondrial genome of A. officinalis was sequenced, annotated and assembled using a mixed Illumina and PacBio data. The garden asparagus circular mitochondrial genome measures 492,062 bp with a GC value of 45.9%. Thirty-six protein-coding genes, 17 tRNA and 6 rRNA genes were annotated, among which 8 protein-coding genes contained 16 introns. In addition, 254 SSRs with 10 complete tandem repeats and 293 non-tandem repeats were identified. It was found that the codons of edited sites located in the amino acids showed a leucine-formation trend, and RNA editing sites mainly caused the mutual transformation of amino acids with the same properties. Furthermore, 72 sequence fragments accounting for 20,240 bp, presentating 4.11% of the whole mitochondrial genome, were observed to migrate from chloroplast to mitochondrial genome of A. officinalis. The phylogenetic analysis showed that the closest genetic relationship between A. officinalis with onion (Allium cepa) inside the Liliaceae family. Our results demonstrated that high percentage of protein-coding genes had evolutionary conservative properties, with Ka/Ks values less than 1. Therefore, this study provides a high-quality garden asparagus mitochondrial genome, useful to promote better understanding of gene exchange between organelle genomes.

Optimal design and development of a fast steering robot inspired by scallops.

The improvement of the steering performance of jet robots is challenging due to single inflexible jet aperture. Scallops provide a potential solution with hard shells and a double-hole jet propulsion, which are expected to achieve fast steering movement under water. Inspired by scallops, a bionic propulsion dynamic mesh is proposed in this article, and a three-dimensional computational model of scallops is established. We further calculated the scallop propulsion mechanism under the swing of shells with different shapes. The coupling of simultaneous swing of two shells and their coupling with velum are presented, revealing the unique movement mechanism of Bivalvia. Based on this, the advantages of the double-hole jet propulsion are applied to develop a scallop robot with excellent steering capabilities. Experiments are conducted to verify the steering performance of the scallop robot.

The entire chloroplast genome sequence of Asparagus setaceus (Kunth) Jessop: Genome structure, gene composition, and phylogenetic analysis in Asparagaceae.

Asparagus setaceus (Kunth) Jessop is a horticultural plant of the genus Asparagus. Herein, the whole chloroplast (cp) genome of A. setaceus was sequenced with PacBio and Illumina sequencing systems. The cp genome shows a characteristic quadripartite structure with 158,076 bp. In total, 135 genes were annotated, containing 89 protein-coding, 38 tRNA, and 8 rRNA genes. Contrast with the previous cp genome of A. setaceus registered in NCBI, we identified 7 single-nucleotide polymorphisms and 15 indels, mostly situated in noncoding areas. Meanwhile, 36 repeat structures and 260 simple sequence repeats were marked out. A bias for A/T-ending codons was shown in this cp genome. Furthermore, we predicted 78 RNA-editing sites in 29 genes, which were all for C-to-U transitions. And it was also proven that positive selection was exerted on the rpoC1 gene of A. setaceus with the K a/K s data. Meanwhile, a conservative gene order and highly similar sequences of protein-coding genes were revealed within Asparagus species. Phylogenetic tree analysis indicated that A. setaceus was a sister to Asparagus cochinchinensis. Taken together, our released genome provided valuable information for the gene composition, genetics comparison, and the phylogeny studies of A. setaceus.

The entire chloroplast genome sequence of Asparagus cochinchinensis and genetic comparison to Asparagus species.

Asparagus cochinchinensis is a traditional Chinese medicinal plant. The chloroplast (cp) genome study on A. cochinchinensis is poorly understood. In this research, we collected the data from the cp genome assembly and gene annotation of A. cochinchinensis, followed by further comparative analysis with six species in the genus Asparagus. The cp genome of A. cochinchinensis showed a circular quadripartite structure in the size of 157,095 bp, comprising a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions. A total of 137 genes were annotated, consisting of 86 protein-coding genes, 8 ribosomal RNAs, 38 transfer RNAs, and 5 pseudo-genes. Forty scattered repetitive sequences and 247 simple sequence repeats loci were marked out. In addition, A/T-ending codons were shown to have a basis in the codon analysis. A cp genome comparative analysis revealed that a similar gene composition was detected in the IR and LSC/SSC regions with Asparagus species. Based on the complete cp genome sequence in Asparagaceae, the result showed that A. cochinchinensis was closely related to A. racemosus by phylogenetic analysis. Therefore, our study providing A. cochinchinensis genomic resources could effectively contribute to the phylogenetic analysis and molecular identification of the genus Asparagus.

The complete chloroplast genome of two traditional medical plants: Asparagus cochinchinensis (Lour.) Merr. and Asparagus dauricus Fisch. ex Link.

Asparagus cochinchinensis (Lour.) Merr. and Asparagus dauricus Fisch. ex Link are two traditional medical plants with therapeutic effects, distributed in mountainous regions of China. In the current study, the complete chloroplast (cp) genomes of A. cochinchinensis and A. dauricus were sequenced on the Illumina Hiseq 2500, and obtained with a length of 157,095 bp and 156,918 bp, respectively, both containing a large single-copy region and a small single-copy region separated by a pair of inverted repeat regions. The cp genome of A. cochinchinensis has 132 annotated genes including 86 protein-coding genes, 38 tRNA, and eight rRNA genes. A. dauricus has 112 annotated genes containing 78 protein genes, 30 tRNA, and four rRNA genes. The maximum-likelihood tree was reconstructed with 17 species, indicating that A. cochinchinensis is a sister group to the clade including A. officinalis to A. racemosa. This clade includes five species of Asparagus.

The complete chloroplast genome of Asparagus densiflorus (Kunth) Jessop L.

Asparagus densiflorus (Kunth) Jessop L. is a horticultural plant widely cultivated in China. Herein, we reported the complete chloroplast (cp) genome of A. densiflorus from the genus Asparagus. The entire cp genome of A. densiflorus was 157,141 bp in length with one large single-copy region of 91,255 bp and one small single-copy region of 20,355 bp, separated by a pair of inverted-repeat regions of 45,531 bp. The GC content is 36.46% in this cp genome. A total of 134 genes were annotated including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The maximum-likelihood phylogenetic analysis showed that A. densiflorus was the most closely related to Asparagus cochinchinensis.

Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail.

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear. Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail. Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

Finite Class Bayesian Inference System for Circle and Linear Walking Gait Event Recognition Using Inertial Measurement Units.

Accurate and fast human motion pattern recognition is the key to ensuring lower limb assistive devices' appropriate assistance. The research on human motion pattern recognition of lower limb assistive devices mainly focuses on sagittal gait. The motion pattern such as circular walking (CW) is asymmetric about the sagittal plane of the body. CW is common in daily living. However, the recognition algorithm of CW is rarely reported. Since lower limb assistive devices interact with humans, lacking the capability of recognizing CW is dangerous. Thus, to realize the accurate and fast recognition of CW, this article proposed a finite class Bayesian interference system (FC-BesIS). FC-BesIS is designed to recognize walking activities (linear walking and CW) and gait events (heel contact, load response, mid stance, terminal stance, pre-swing, initial swing, mid swing, and terminal swing). A finite class method which reduces the number of potential classes according to elimination rules before decision-making is introduced. Elimination rules are designed based on likelihood estimation and sensor information. The experiments show that walking activities and gait events can be accurately and fastly recognized by FC-BesIS. The experiments also show that the performance of FC-BesIS in mean recognition accuracy (MRA) and mean decision time (MDT) is improved compared with BesIS. The MRA of walking activities and gait events are 100% and 97.38%, respectively. The MDT of walking activities and gait events are 28.19 ms and 33.94 ms, respectively. Overall, FC-BesIS has been proved to be an accurate and fast recognition algorithm for human motion patterns using wearable sensors.

The complete mitochondrial genome of Asparagus officinalis L.

Asparagus officinalis L. is a horticultural plant in nature and belongs to the genus Asparagus of Asparagaceae family. The complete mitochondrial (mt) genome of A. officinalis was 492,062 bp in length with a 45.9% GC content. A total of 60 genes were annotated including 37 protein-coding genes, 17 tRNA genes, and 6 rRNA genes. Phylogenetic tree analysis using the neighbor-joining method demonstrated that A. officinalis was most closely related to Allium cepa and separated from Beta vulgaris subsp. Vulgaris based on the complete mt genome sequence.

Base composition is the primary factor responsible for the variation of amino acid usage in zebra finch (Taeniopygia guttata).

In the present study, we carried out an examination of the amino acid usage in the zebra finch (Taeniopygia guttata) proteome. We found that tRNA abundance, base composition, hydrophobicity and aromaticity, protein second structure, cysteine residue (Cys) content and protein molecular weight had significant impact on the amino acid usage of the zebra finch. The above factors explained the total variability of 22.85%, 25.37%, 10.91%, 5.06%, 4.21%, and 3.14%, respectively. Altogether, approximately 70% of the total variability in zebra finch could be explained by such factors. Comparison of the amino acid usage between zebra finch, chicken (Gallus gallus) and human (Homo sapiens) suggested that the average frequency of various amino acid usage is generally consistent among them. Correspondence analysis indicated that base composition was the primary factor affecting the amino acid usage in zebra finch. This trend was different from chicken, but similar to human. Other factors affecting the amino acid usage in zebra finch, such as isochore structure, protein second structure, Cys frequency and protein molecular weight also showed the similar trends with human. We do not know whether the similar amino acid usage trend between human and zebra finch is related to the distinctive neural and behavioral traits, but it is worth studying in depth.

Overexpression of SKP2 Inhibits the Radiation-Induced Bystander Effects of Esophageal Carcinoma.

BACKGROUND: To investigate the effects of S-phase kinase protein 2 (SKP2) expression on the radiation induced bystander effect (RIBE) in esophageal cancer (EC) cells. MATERIALS AND METHODS: Western blot was used to detect the levels of SKP2, Rad51, and Ku70 in EC cells. Positive transfection, RNAi, micronucleus (MN), and γ-H2AX focus formation assay were used to investigate the effects of SKP2 on RIBE induced by irradiated cells. RESULTS: We found a significant negative correlation between SKP2 expression and MN frequency (p < 0.05) induced by RIBE. The results were further confirmed by positive transfection, RNAi, and rescue experiments.γ-H2AX focus formation assay results indicated that overexpression of SKP2 in the irradiated cells inhibited the DNA damage of RIBE cells. However, when SKP2 expression decreased in irradiated cells, the DNA damage of RIBE cells increased. Increased or decreased expression levels of SKP2 had effects on Rad51 expression under the conditions of RIBE. CONCLUSIONS: These results showed, for the first time, that SKP2 expression can inhibit RIBE of EC cells. The mechanism may function, at least partly, through the regulation of Rad51 in the ability to repair DNA damage.

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress.

Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei'ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress.

Uptake of trifluralin and lindane from water by ryegrass.

Understanding of the plant uptake of organic chemicals is essential to assessing contaminant mobility in the ecosystem, exposure to humans, and phytoremediation technologies. In this study, we measured the uptake of trifluralin and lindane from water by ryegrass as a function of uptake time for periods of 96 and 120 h, respectively. Trifluralin concentration in ryegrass increased sharply at the early stage of uptake and reached the maximum at 10 h, and then decreased with uptake time. 14C-labelled trifluralin uptake displayed a similar trend but a higher 14C-concentration than that of extracted parent compound, indicating metabolism and formation of bound residues following trifluralin uptake. Lindane concentration in ryegrass slowly increased with uptake time and approached a plateau, indicating minimal metabolism and formation of bound residues. The difference in the uptake characteristics of these two chemicals may be related to the differences in their lipophilicity, and chemical and biological reactivities. A two-compartment model accounting for the contributions of transpiration, metabolism and formation of bound residues to overall uptake was developed to assess the uptake kinetics. The model adequately described the uptake of trifluralin and lindane into ryegrass by providing the first-order rate constants of uptake, release, transpiration, and metabolism and formation of bound residues. These rate constants are used in calculating plant concentration factor (PCF). The ratios of trifluralin concentrations in ryegrass to its aqueous concentrations are between the PCF at thermodynamic equilibrium and the PCF at steady state, suggesting the utility of both PCF values.