Comparative mitogenomic analyses of three scallops (Bivalvia: Pectinidae) reveal high level variation of genomic organization and a diversity of transfer RNA gene sets

<p>Abstract</p> <p>Background</p> <p>It can be seen from the available mollusk mitogenomes that the family Pectinidae exhibits the most variation in genome organization. In this study, comparative mitogenomic analyses were performed for three scallops from the subfamily Chlamydinae (Pectinidae), with the goal of characterizing the degree of variability of mitogenome organization and other characteristics among species from the same subfamily and exploring their possible evolution route.</p> <p>Findings</p> <p>The complete or nearly complete mtDNA sequences of scallop <it>Mimachlamys nobilis </it>(17 935 bp), <it>Mizuhopecten yessoensis </it>(20 964 bp) and <it>Chlamys farreri </it>(17 035 bp) were determined using long PCR amplification and primer walking sequencing strategy. Highly variable size difference of the three genomes resulted primarily from length and number variations of non-coding regions, and the major difference in gene content of the three scallop species are due to varying tRNA gene sets. Only 21, 16, and 17 tRNA genes were detected in the mitogenomes of <it>M. nobilis</it>, <it>M. yessoensis </it>and <it>C. farreri</it>, respectively. Remarkably, no <it>trnS </it>gene could be identified in any of the three scallops. A newly-detected <it>trnA</it>-like sequence within the mitogenome of <it>M. yessoensis </it>seems to exemplify the functional loss of a tRNA gene, and the duplication of <it>trnD </it>in <it>M. yessoensis </it>raises a fundamental question of whether the retention of the tRNA gene copy of 2-tRNAs is easier than that of 4-tRNAs. Analysis of putative evolutionary pathways of gene rearrangement indicates that transposition of neighboring gene blocks may play an important role in the evolution of mitogenomes in scallops. Parsimonious analysis of the genomic variations implies that the mitogenomes of <it>M. yessoensis </it>and <it>C. farreri </it>are likely to derive independently from a common ancestor that was closely related to <it>M. nobilis</it>.</p> <p>Conclusion</p> <p>Comparative mitogenomic analyses among three species from the subfamily Chlamydinae show that the three genomes exhibit a high level of genomic variation and a diversity of tRNA gene sets, characterized by extensive translocation of genes. These features provide useful clues and information for evolutionary analysis of scallop mitogenomes.</p

ANALYSIS AND STUDY ON 47 CASES OF ADVERSE REACTIONS OF CHINESE MEDICINE INJECTION

Background: Along with efficacy, Chinese medicine is increasingly being known to people, Chinese medicine and its preparations are increasingly widespread in clinical use. People generally believe that Chinese medicine has few side effects and is safe, especially Chinese medicine injections. Due to the direct injection in blood, rapid onset and good efficacy, they are welcomed by people. However, with increased use, adverse reactions are increasing, even causing serious consequences. The objective is to learn about the characteristics and laws of the adverse effects of Chinese medicine injections, provide references for the clinical safe drug use, and reduce the incidence of adverse reactions. Materials and Methods: The method was established to analyze the data of 47 cases of adverse reactions caused by Chinese medicine injections in our hospital from the year, 2009 to 2010. Results: The organs / systems involved in the 47 cases of adverse reactions are primarily skin and its accessories and secondly systemic damage, involving a total of eight varieties of drugs. Conclusion: The adverse reactions of Chinese medicine injections are mostly in Chinese patent drugs, which should be paid attention to, to find out the problems and laws, use the drugs rationally, and reduce the incidence of the adverse reactions

Genome-Wide Identification, Evolutionary Expansion, and Expression Profile of Homeodomain-Leucine Zipper Gene Family in Poplar (Populus trichocarpa)

BACKGROUND: Homeodomain-leucine zipper (HD-ZIP) proteins are plant-specific transcriptional factors known to play crucial roles in plant development. Although sequence phylogeny analysis of Populus HD-ZIPs was carried out in a previous study, no systematic analysis incorporating genome organization, gene structure, and expression compendium has been conducted in model tree species Populus thus far. PRINCIPAL FINDINGS: In this study, a comprehensive analysis of Populus HD-ZIP gene family was performed. Sixty-three full-length HD-ZIP genes were found in Populus genome. These Populus HD-ZIP genes were phylogenetically clustered into four distinct subfamilies (HD-ZIP I-IV) and predominately distributed across 17 linkage groups (LG). Fifty genes from 25 Populus paralogous pairs were located in the duplicated blocks of Populus genome and then preferentially retained during the sequential evolutionary courses. Genomic organization analyses indicated that purifying selection has played a pivotal role in the retention and maintenance of Populus HD-ZIP gene family. Microarray analysis has shown that 21 Populus paralogous pairs have been differentially expressed across different tissues and under various stresses, with five paralogous pairs showing nearly identical expression patterns, 13 paralogous pairs being partially redundant and three paralogous pairs diversifying significantly. Quantitative real-time RT-PCR (qRT-PCR) analysis performed on 16 selected Populus HD-ZIP genes in different tissues and under both drought and salinity stresses confirms their tissue-specific and stress-inducible expression patterns. CONCLUSIONS: Genomic organizations indicated that segmental duplications contributed significantly to the expansion of Populus HD-ZIP gene family. Exon/intron organization and conserved motif composition of Populus HD-ZIPs are highly conservative in the same subfamily, suggesting the members in the same subfamilies may also have conservative functionalities. Microarray and qRT-PCR analyses showed that 89% (56 out of 63) of Populus HD-ZIPs were duplicate genes that might have been retained by substantial subfunctionalization. Taken together, these observations may lay the foundation for future functional analysis of Populus HD-ZIP genes to unravel their biological roles

Functional conservation and divergence of Miscanthus lutarioriparius GT43 gene family in xylan biosynthesis

Background: Xylan is the most abundant un-cellulosic polysaccharides of plant cell walls. Much progress in xylan biosynthesis has been gained in the model plant species Arabidopsis. Two homologous pairs Irregular Xylem 9 (IRX9)/9L and IRX14/14L from glycosyltransferase (GT) family 43 have been proved to play crucial roles in xylan backbone biosynthesis. However, xylan biosynthesis in grass such as Miscanthus remains poorly understood

Proving Computational Geometry Algorithms in TLA+2

International audienceGeometric algorithms are widely used in many scientific fields like computer vision, computer graphics. To guarantee the correctness of these algorithms, it's important to apply formal method to them.We propose an approach to proving the correctness of geometric algorithms. The main contribution of the paper is that a set of proof decomposition rules is proposed which can help improve the automation of the proof of geometric algorithms. We choose TLA+2, a structural specification and proof language, as our experiment environment. The case study on a classical convex hull algorithm shows the usability of the method

Predicting Multi-Codebook Vector Quantization Indexes for Knowledge Distillation

Knowledge distillation(KD) is a common approach to improve model performance in automatic speech recognition (ASR), where a student model is trained to imitate the output behaviour of a teacher model. However, traditional KD methods suffer from teacher label storage issue, especially when the training corpora are large. Although on-the-fly teacher label generation tackles this issue, the training speed is significantly slower as the teacher model has to be evaluated every batch. In this paper, we reformulate the generation of teacher label as a codec problem. We propose a novel Multi-codebook Vector Quantization (MVQ) approach that compresses teacher embeddings to codebook indexes (CI). Based on this, a KD training framework (MVQ-KD) is proposed where a student model predicts the CI generated from the embeddings of a self-supervised pre-trained teacher model. Experiments on the LibriSpeech clean-100 hour show that MVQ-KD framework achieves comparable performance as traditional KD methods (l1, l2), while requiring 256 times less storage. When the full LibriSpeech dataset is used, MVQ-KD framework results in 13.8% and 8.2% relative word error rate reductions (WERRs) for non -streaming transducer on test-clean and test-other and 4.0% and 4.9% for streaming transducer. The implementation of this work is already released as a part of the open-source project icefall.Comment: Submitted to ICASSP 202

A First Look at Security Risks of Android TV Apps

In this paper, we present to the community the first preliminary study on the security risks of Android TV apps. To the best of our knowledge, despite the fact that various efforts have been put into analyzing Android apps, our community has not explored TV versions of Android apps. There is hence no publicly available dataset containing Android TV apps. To this end, We start by collecting a large set of Android TV apps from the official Google Play store. We then experimentally look at those apps from four security aspects: VirusTotal scans, requested permissions, security flaws, and privacy leaks. Our experimental results reveal that, similar to that of Android smartphone apps, Android TV apps can also come with different security issues. We hence argue that our community should pay more attention to analyze Android TV apps