Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so on.The genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of B.oleracea,has been widely used as a common reference in biological research.Although its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 transcripts.Additionally,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress.Meanwhile,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS analysis.Overall,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

Label Recovery and Trajectory Designable Network for Transfer Fault Diagnosis of Machines With Incorrect Annotation

The success of deep transfer learning in fault diagnosis is attributed to the collection of high-quality labeled data from the source domain.However,in engineering scenarios,achieving such high-quality label annotation is difficult and expensive.The incorrect label annotation produces two negative effects:1)the complex decision boundary of diagnosis models lowers the generalization performance on the target domain,and2)the distribution of target domain samples becomes misaligned with the false-labeled samples.To overcome these negative effects,this article proposes a solution called the label recovery and trajectory designable network(LRTDN).LRTDN consists of three parts.First,a residual network with dual classifiers is to learn features from cross-domain samples.Second,an annotation check module is constructed to generate a label anomaly indicator that could modify the abnormal labels of false-labeled samples in the source domain.With the training of relabeled samples,the complexity of diagnosis model is reduced via semi-supervised learning.Third,the adaptation trajectories are designed for sample distributions across domains.This ensures that the target domain samples are only adapted with the pure-labeled samples.The LRTDN is verified by two case studies,in which the diagnosis knowledge of bearings is transferred across different working conditions as well as different yet related machines.The results show that LRTDN offers a high diagnosis accuracy even in the presence of incorrect annotation.

Meibomian glands segmentation in infrared images with limited annotation

●AIM:To investigate a pioneering framework for the segmentation of meibomian glands(MGs),using limited annotations to reduce the workload on ophthalmologists and enhance the efficiency of clinical diagnosis.●METHODS:Totally 203 infrared meibomian images from 138 patients with dry eye disease,accompanied by corresponding annotations,were gathered for the study.A rectified scribble-supervised gland segmentation(RSSGS)model,incorporating temporal ensemble prediction,uncertainty estimation,and a transformation equivariance constraint,was introduced to address constraints imposed by limited supervision information inherent in scribble annotations.The viability and efficacy of the proposed model were assessed based on accuracy,intersection over union(IoU),and dice coefficient.●RESULTS:Using manual labels as the gold standard,RSSGS demonstrated outcomes with an accuracy of 93.54%,a dice coefficient of 78.02%,and an IoU of 64.18%.Notably,these performance metrics exceed the current weakly supervised state-of-the-art methods by 0.76%,2.06%,and 2.69%,respectively.Furthermore,despite achieving a substantial 80%reduction in annotation costs,it only lags behind fully annotated methods by 0.72%,1.51%,and 2.04%.●CONCLUSION:An innovative automatic segmentation model is developed for MGs in infrared eyelid images,using scribble annotation for training.This model maintains an exceptionally high level of segmentation accuracy while substantially reducing training costs.It holds substantial utility for calculating clinical parameters,thereby greatly enhancing the diagnostic efficiency of ophthalmologists in evaluating meibomian gland dysfunction.

基于Transformer的司法文书命名实体识别方法

命名实体识别是自然语言处理领域的关键任务之一,是实现下游任务的基础。目前针对司法领域的相关研究相对较少,司法系统的信息化和智能化转型仍有许多问题亟需解决。相比其他领域的文本,司法文书存在专业性强、语料资源少等局限,导致现有的司法文书识别结果较低。因此,从以下3方面开展研究:首先,提出了一种多标签层级迭代的文本标注方式,可以对原始司法文书文本进行自动化标注,同时有效地提升司法文书命名实体识别任务的实体识别效果;其次,提出了一种交融式的Transformer神经网络模型,对汉字固有属性的深层特征进行了充分利用,用于对司法文书进行命名实体识别;最后,对所提出的标注方法和模型与其他神经网络模型进行了对比实验。所提出的文本标注方式可以较为准确地实现司法文书的标注任务;同时,所提出的模型在通用数据集中相对于对照模型有较大的提高,并在司法领域数据集中取得了良好的效果。

A Novel Auto-Annotation Technique for Aspect Level Sentiment Analysis

In machine learning,sentiment analysis is a technique to find and analyze the sentiments hidden in the text.For sentiment analysis,annotated data is a basic requirement.Generally,this data is manually annotated.Manual annotation is time consuming,costly and laborious process.To overcome these resource constraints this research has proposed a fully automated annotation technique for aspect level sentiment analysis.Dataset is created from the reviews of ten most popular songs on YouTube.Reviews of five aspects—voice,video,music,lyrics and song,are extracted.An N-Gram based technique is proposed.Complete dataset consists of 369436 reviews that took 173.53 s to annotate using the proposed technique while this dataset might have taken approximately 2.07 million seconds(575 h)if it was annotated manually.For the validation of the proposed technique,a sub-dataset—Voice,is annotated manually as well as with the proposed technique.Cohen’s Kappa statistics is used to evaluate the degree of agreement between the two annotations.The high Kappa value(i.e.,0.9571%)shows the high level of agreement between the two.This validates that the quality of annotation of the proposed technique is as good as manual annotation even with far less computational cost.This research also contributes in consolidating the guidelines for the manual annotation process.

Automatic Image Annotation Using Adaptive Convolutional Deep Learning Model

Every day,websites and personal archives create more and more photos.The size of these archives is immeasurable.The comfort of use of these huge digital image gatherings donates to their admiration.However,not all of these folders deliver relevant indexing information.From the outcomes,it is dif-ficult to discover data that the user can be absorbed in.Therefore,in order to determine the significance of the data,it is important to identify the contents in an informative manner.Image annotation can be one of the greatest problematic domains in multimedia research and computer vision.Hence,in this paper,Adap-tive Convolutional Deep Learning Model(ACDLM)is developed for automatic image annotation.Initially,the databases are collected from the open-source system which consists of some labelled images(for training phase)and some unlabeled images{Corel 5 K,MSRC v2}.After that,the images are sent to the pre-processing step such as colour space quantization and texture color class map.The pre-processed images are sent to the segmentation approach for efficient labelling technique using J-image segmentation(JSEG).Thefinal step is an auto-matic annotation using ACDLM which is a combination of Convolutional Neural Network(CNN)and Honey Badger Algorithm(HBA).Based on the proposed classifier,the unlabeled images are labelled.The proposed methodology is imple-mented in MATLAB and performance is evaluated by performance metrics such as accuracy,precision,recall and F1_Measure.With the assistance of the pro-posed methodology,the unlabeled images are labelled.

Automatic Placement of GIS Vector Map Annotation in Area Feature by Long Diagonal

This paper discusses the placement of Chinese annotation from point of view of graphics. Area Feature is classified as simple polygon, complex polygon and special polygon. For simple ones, annotations are placed along the longest edge. For complex ones, firstly the polygon are simplified according to close points, then the longest diagonal is gotten by comparing length, lastly, annotations are placed along long diagonal. For special ones, the polygon are partitioned into several parts by a certain rule for getting their sub\|diagonals, then their annotation are placed by means of the second.

Amycolatopsis sp.的全基因组测序及香兰素合成途径分析

拟无枝酸菌(Amycolatopsis sp.)CCTCC NO:M2011265是一株可以转化阿魏酸生成香兰素菌株,该研究利用Illumina Hiseq测序平台对拟无枝酸菌进行全基因组测序、拼接、基因预测及功能注释,并从拟无枝酸菌的全基因组中筛选和鉴定参与香兰素合成的功能基因。结果表明,总共组装得到64个scaffolds,整个基因组组装大小约为8425551 bp,总GC含量为71.89%。通过生物信息学分析发现了香兰素合成关键基因ech、fcs和ech2基因,及香兰素分解代谢基因vdh基因,其中ech和fcs为一个基因簇,并进一步构建过表达ech-fcs-ech2菌株,其摇瓶发酵表明转化阿魏酸生成香兰素速率加快,发酵时间显著缩短。该研究获得的拟无枝酸菌的全基因组信息为解析其转化阿魏酸生成香兰素发酵过程中的代谢机理提供遗传信息基础,也为通过代谢工程获得高产香兰素菌株的研究提供理论支持。

The History of the Former Han Dynasty:A Critical Translation with Annotations Translated by Homer Hasenpflug Dubs

Translation is an important medium of cultural communication.It is not a mere transfer of two languages,but the interaction of two cultures.Cultural misreading,which results from cultural discrepancy and translator’s subjectivity,truly reflects where the blockade and conflict in the cultural communication is.Cultural misreading is an objective phenomenon that exists in the entire process of translation.This paper intends to make a comprehensive analysis and discussion on The History of the Former Han Dynasty:a Critical Translation with Annotations translated by Homer Hasenpflug Dubs.As for the reasons of cultural misreading,this paper divides them into three types—language,thinking habit,traditional culture.It is to be hoped that this paper will draw more attention from the translation circle to the phenomena,and make contribution to the development of literary translation.

A Method of Gene-Function Annotation Based on Variable Precision Rough Sets

It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods.

Bridge Ontology: A Multi-Ontologies-Based Approach for Semantic Annotation

Representing the relationships between ontologies is the key problem of semantic annotations based on multi-ontologies. Traditional approaches only had the ability of denoting the simple concept subsumption relations between ontologies. Through analyzing and classifying the relationships between ontologies, the idea of bridge ontology was proposed, which had the powerful capability of expressing the complex relationships between concepts and relationships between relations in multi-ontologies. Meanwhile, a new approach employing bridge ontology was proposed to deal with the multi-ontologies-based semantic annotation problem. The bridge ontology is a peculiar ontology, which can be created and maintained conveniently, and is effective in the multi-ontologies-based semantic annotation. The approach using bridge ontology has the advantages of low-cost, scalable, robust in the web circumstance, and avoiding the unnecessary ontology extending and integration. Key words semantic web - bridge ontology - multi-ontologies - semantic annotation CLC number TP 391 Foundation item: Supported by the National Natural Science Foundation of China (60373066, 60303024). National Grand Fundamental Research 973 Program of China (2002CB312000), National Re-search Foundation for the Doctoral Program of Higher Education of China (20020286004)Biography: WANG Peng (1977-), male, Ph.D candidate, research direction: semantic web, ontology, and knowledge representation on the Web.

Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing

The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.

Author Correction:Updated annotation of the wild strawberry Fragaria vesca V4 genome

Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize for this error.

Ontology-Based Semantic Annotation for Problem Set Archives in the Web

Aimming at the difficulty in getting semantic informarton from each problem in problem set archives, We propose a new method of ontology based semantic annotation for problem set archives, which utilizes programming knowledge domain ontology to add semantic annotations to problems in the Web. The system we developed adds semantic annotation for each problem in the form of Extensible Makeup Language. Our method overcomes the difficulty of extracting semantics from problem set archives and the efficiency of this method is demonstrated through a case study. Having semantic annotations of problems, a student can efficiently locate the problems that logically corre spond to his knowledge.

Identification of metastasis-associated genes in colorectal cancer through an integrated genomic and transcriptomic analysis

Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroarray data was presented, by combined with evidence acquired from comparative genornic hybridization （CGH） data. Methods： Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus （GEO） website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray （SAM） was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery （DAVID）. Finally, SVM-T-RFE gene selection algorithm was applied to identify ted genes in CRC. Results： A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy （100%） in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions- Our results demonstrated that integration analysis is an effective strategy for mining cancer- associated genes.

Semi-supervised learning based probabilistic latent semantic analysis for automatic image annotation

In recent years,multimedia annotation problem has been attracting significant research attention in multimedia and computer vision areas,especially for automatic image annotation,whose purpose is to provide an efficient and effective searching environment for users to query their images more easily. In this paper,a semi-supervised learning based probabilistic latent semantic analysis( PLSA) model for automatic image annotation is presenred. Since it's often hard to obtain or create labeled images in large quantities while unlabeled ones are easier to collect,a transductive support vector machine( TSVM) is exploited to enhance the quality of the training image data. Then,different image features with different magnitudes will result in different performance for automatic image annotation. To this end,a Gaussian normalization method is utilized to normalize different features extracted from effective image regions segmented by the normalized cuts algorithm so as to reserve the intrinsic content of images as complete as possible. Finally,a PLSA model with asymmetric modalities is constructed based on the expectation maximization( EM) algorithm to predict a candidate set of annotations with confidence scores. Extensive experiments on the general-purpose Corel5k dataset demonstrate that the proposed model can significantly improve performance of traditional PLSA for the task of automatic image annotation.

Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

A Novel Visualization Tool for Manual Annotation when Building Large Speech Corpora

A novel visualized sound description, called sound dendrogram is proposed to make manual annotation easier when building large speech corpora. It is a lattice structure built from a group of ＂seed regions＂ and through an iterative procedure of mergence. A simple but reliable extraction method of ＂seed regkms＂ and advanced distance metric are adopted to construct the sound dendrogram, so that it can present speech＇s structure character ranging from coarse to fine in a visualized way. Tests show that all phonemic boundaries are contained in the lattice structure of sound dendrogram and very easy to identify. Sound dendrogram can be a powerful assistant tool during the process of speech corporals manual annotation.

Genome-wide characterization of miRNA and siRNA pathways in the parasitoid wasp Pteromalus puparum

microRNAs(miRNAs) and small interfering RNAs(siRNAs) are small non-coding RNAs(ncRNAs) that trigger RNA interference(RNAi) in eukaryotic organisms. The biogenesis pathways for these ncRNAs are well established in Drosophila melanogaster, Aedes aegypti, Bombyx mori and other insects, but lacking in hymenopteran species, particularly in parasitoid wasps. Pteromalus puparum is a parasitoid of pupal butterflies. This study identified and analyzed two pathways by interrogating the P. puparum genome. All core genes of the two pathways are present in the genome as a single copy, except for two genes in the siRNA pathway, R2D2(two copies) and Argonaute-2(three). Conserved domain analyses showed the protein structures in P. puparum were similar to cognate proteins in other insect species. Phylogenetic analyses of hymenopteran Dicer and Argonaute genes suggested that the siRNA pathway-related genes evolved faster than those in the miRNA pathway. The study found a decelerated evolution rate of P. puparum Dicer-2 with respect to Dicer-1, which was contrary to other hymenopterans. Expression analyses revealed high mRNA levels for all miRNA pathway genes in P. puparum adults and the siRNA related genes were expressed in different patterns. The findings add valuable new knowledge of the miRNA and siRNA pathways and their regulatory actions in parasitoid wasps.