RiceDB:A Web-Based Integrated Database for Annotating Rice Microarray

RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules. RiceMap module archives the process of Affymetrix probe sets mapping to different databases about rice, and aims to the genes represented by a microarray set by retrieving annotation information via the identifier or accession number of every database; RiceGO module indicates the association between a microarray set and gene ontology （GO） categories; RiceKO module is used to annotate a microarray set based on the KEGG biochemical pathways; RiceDO module indicates the information of domain associated with a microarray set; RiceUP module is used to obtain promoter sequences for all genes represented by a microarray set; RiceMR module lists potential microRNA which regulated the genes represented by a microarray set; RiceCD and RiceGF are used to annotate the genes represented by a microarray set in the context of chromosome distribution and rice paralogous family distribution. The results of automatic annotation are mostly consistent with manual annotation. Biological interpretation of the microarray data is quickened by the help of RiceDB.

SPORTS1.0: A Tool for Annotating and Profiling Non-coding RNAs Optimized for rRNA-and tRNA-derived Small RNAs

High-throughput RNAoseq has revolutionized the process of small RNA （sRNA） discovery, leading to a rapid expansion of sRNA categories. In addition to the previously wellcharacterized sRNAs such as microRNAs （miRNAs）, piwi-interacting RNAs （piRNAs）, and small nucleolar RNA （snoRNAs）, recent emerging studies have spotlighted on tRNA-derived sRNAs （tsRNAs） and rRNA-derived sRNAs （rsRNAs） as new categories of sRNAs that bear versatile functions. Since existing software and pipelines for sRNA annotation are mostly focused on analyzing miRNAs or piRNAs, here we developed the sRNA annotation pipeline _optimized for rRNA- and tRNA-derived s_RNAs （SPORTS 1 .0）. SPORTS1.0 is optimized for analyzing tsRNAs and rsRNAs from sRNA-seq data, in addition to its capacity to annotate canonical sRNAs such as miRNAs and piRNAs. Moreover, SPORTS1.0 can predict potential RNA modification sites based on nucleotide mismatches within sRNAs. SPORTS1.0 is precompiled to annotate sRNAs for a wide range of 68 species across bacteria, yeast, plant, and animal kingdoms, while additional species for analyses could be readily expanded upon end users＇ input. For demonstration, by analyzing sRNA datasets using SPORTS1.0, we reveal that distinct signatures are present in tsRNAs and rsRNAs from different mouse cell types. We also find that compared to other sRNA species, tsRNAs bear the highest mismatch rate, which is consistent with their highly modified nature. SPORTS1.0 is an opensource software and can be publically accessed at https：//github.com/junchaoshi/sports1.0.

BioTSA: Annotating Token Semantic Association to Support Biomedical Text Mining

Corpus is a kind of important resource for knowledge acquisition in the natural language processing （NLP）. However, up to now, in the biomedical domain comparatively fewer corpus focus on semantic association among all tokens in a sentence. We proposed an annotation scheme based on feature structure theory for enriching biomedical domain corpora with token semantic association （TSA）. There are 227 documents of the BioNLP GE ST training data annotated to form TSA corpus in which each annotated item shows a token semantic association that appears as a triple. The annotation of token semantic association has the potential to significantly advance biomedical text mining by providing rich token semantic information for NLP systems especially for the sophisticated IE systems, such as bio-event extraction.

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.

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.

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.

Mechanism of Guangdong Shenqu in regulating intestinal flora in mice with food stagnation and internal heat based on 16S rDNA sequencing

Objective:To investigate the effect of Guangdong Shenqu(GSQ)on intestinal flora structure in mice with food stagnation through 16S rDNA sequencing.Methods: Mice were randomly assigned to control,model,GSQ low-dose(GSQL),GSQ medium-dose(GSQM),GSQ high-dose(GSQH),and lacidophilin tablets(LAB)groups,with each group containing 10 mice.A food stagnation and internal heat mouse model was established through intragastric administration of a mixture of beeswax and olive oil(1:15).The control group was administered normal saline,and the model group was administered beeswax and olive oil to maintain a state.The GSQL(2 g/kg),GSQM(4 g/kg),GSQH(8 g/kg),and LAB groups(0.625 g/kg)were administered corresponding drugs for 5 d.After administration,16S rDNA sequencing was performed to assess gut microbiota in mouse fecal samples.Results: The model group exhibited significant intestinal flora changes.Following GSQ administration,the abundance and diversity index of the intestinal flora increased significantly,the number of bacterial species was regulated,andαandβdiversity were improved.GSQ administration increased the abundance of probiotics,including Clostridia,Lachnospirales,and Lactobacillus,whereas the abundance of conditional pathogenic bacteria,such as Allobaculum,Erysipelotrichaceae,and Bacteroides decreased.Functional prediction analysis indicated that the pathogenesis of food stagnation and GSQ intervention were primarily associated with carbohydrate,lipid,and amino acid metabolism,among other metabolic pathways.Conclusion: The digestive mechanism of GSQ may be attributed to its role in restoring diversity and abundance within the intestinal flora,thereby improving the composition and structure of the intestinal flora in mice and subsequently influencing the regulation of metabolic pathways.

Unlocking the Potential:A Comprehensive Systematic Review of ChatGPT in Natural Language Processing Tasks

As Natural Language Processing(NLP)continues to advance,driven by the emergence of sophisticated large language models such as ChatGPT,there has been a notable growth in research activity.This rapid uptake reflects increasing interest in the field and induces critical inquiries into ChatGPT’s applicability in the NLP domain.This review paper systematically investigates the role of ChatGPT in diverse NLP tasks,including information extraction,Name Entity Recognition(NER),event extraction,relation extraction,Part of Speech(PoS)tagging,text classification,sentiment analysis,emotion recognition and text annotation.The novelty of this work lies in its comprehensive analysis of the existing literature,addressing a critical gap in understanding ChatGPT’s adaptability,limitations,and optimal application.In this paper,we employed a systematic stepwise approach following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA)framework to direct our search process and seek relevant studies.Our review reveals ChatGPT’s significant potential in enhancing various NLP tasks.Its adaptability in information extraction tasks,sentiment analysis,and text classification showcases its ability to comprehend diverse contexts and extract meaningful details.Additionally,ChatGPT’s flexibility in annotation tasks reducesmanual efforts and accelerates the annotation process,making it a valuable asset in NLP development and research.Furthermore,GPT-4 and prompt engineering emerge as a complementary mechanism,empowering users to guide the model and enhance overall accuracy.Despite its promising potential,challenges persist.The performance of ChatGP Tneeds tobe testedusingmore extensivedatasets anddiversedata structures.Subsequently,its limitations in handling domain-specific language and the need for fine-tuning in specific applications highlight the importance of further investigations to address these issues.

基于Annotation的Spring AOP系统设计

简要介绍AOP(Aspect Oriented Programming)技术和Annotation技术,讨论了Spring中的AOP的两种实现。通过同一个案例阐述了在Spring中通过XML配置来实现AOP和使用了Annotation在Spring中实现AOP,比较了两种实现方式的优缺点。对在Spring使用Annotation实现AOP作了总结,从而体现了Annotation在设计系统时其简洁性和良好的扩展性。

SSH架构中方法级缓存依赖的解决方案

缓存是提高系统性能的重要手段之一。实现缓存依赖就是要在被依赖对象与缓存对象之间建立一个有效关联,使数据得到合理的刷新。通过对EhCache、Map、An-notation以及AOP等相关技术的研究,提出了SSH架构中方法级依赖缓存的解决方案:使用EhCache结合Concur-rentHashMap实现缓存的细粒度化,使用Annotation存储依赖信息,通过AOP实现缓存服务代码与业务方法的分离。这种方案解决了实际应用中不能合理刷新数据、细粒度化较难等问题。实践表明,这种方案具有容易实现、便于维护和扩展、使用方便等特点。

基于XML和Annotation的异构系统数据集成方式的研究

论文运用XML的强大数据表达能力以及J2EE的反射以及Annotation编程来实现异构系统数据集成方式。该方式通过对原始结构代码进行简单的标记,将不同的数据结构串联起来。同时在转换的过程中将细节屏蔽起来并封装成标准接口,用户只需要将提供输入以及所需要的数据结构类型就可以方便地进行转换。最后论文给出集成系统详细的设计方法。

Product image sentence annotation based on kernel descriptors and tag-rank

Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words＇ weights. A new word integration algorithm named word sequence blocks building （WSBB） is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines.

论杜预《春秋经传集解》(下)

Du Yu’s Annotation of Classics and Elucidations in "Spring and Autumn Annals" is considered as a milestone for the studies of Spring and Autumn Annals, In Du’s book, the Preface to the Spring and Autumn Annals is a theoretical summary and revision for the previous studies on the Spring and Autumn Annals and the Tso Chuan. Its combination of classics and elucidations makes Tso Chuan a real elucidating study on Spring and Autumn Annals. Du expounds his philosophy and political ideas in this book.

Detecting abnormalities for empty nest elder in smart monitoring system

In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical hidden Markov model is adopted to Abstract these discrete action sequences captured by multi-modal joint sensors into an occupant’s high-level behavior—event,then structure representation models of occupant normality are modeled from large amounts of spatio-temporal data. These models are used as classifiers of normality to detect an occupant’s abnormal behavior.In order to express context information needed by reasoning and detection,multi-media ontology （MMO） is designed to annotate and reason about the media information in the smart monitoring system.A pessimistic emotion model （PEM） is improved to analyze multi-interleaving events of multi-active devices in the home.Experiments demonstrate that the PEM can enhance the accuracy and reliability for detecting active devices when these devices are in blind regions or are occlusive. The above approach has good performance in detecting abnormalities involving occupants and devices in a real-time way.

基于Annotation的Spring AOP日志处理的设计与实现

系统维护和错误排查需要程序能自动的输出日志信息,将用户的操作记录下来。而日志本身不太可能是你开发的主程序的主要任务。如果能将"不可见的"、通用的日志代码注入主程序中,而保证自身业务逻辑的纯洁性,降低代码之间的耦合度,增加程序的灵活性和可重用性。本文使用Spring AOP的Annotation方式,写一个切面,并且指定切入的范围(切入点),当系统运行后,日志信息将可以自动输出或记录在指定的文件及数据库中。

翻译中实现社会语用等效(英文)

As a medium between two different languages, between peoples of two countries, translation is not only a matter of language, but also of cross-cultural transference. According to Professor He Ziran, socio-pragmatic translation is the kind of translation which examines the conditions on language use that stem from the social and cultural situations to serve cross-cultural communication. This paper focuses on the ways used to achieve socio-pragmatic equivalence in translation practice.

两千年来古人语法分析说略(下)

It is believed that in ancient China,there were only works on graphology,phonology and critical interpretation,but no works on grammar.In works of grammar history published in modern times,they just dwell briefly on ancient grammar,and they consider that there were only some explanations of form words,a few books of form words,but no syntactic analyses.However,in fact,in ancient classical works there were abundant materials of grammatical analyses.Ancient scholars worked out quite a few grammar rules,some of which were profound and coincidental with modern grammar theories.In the present research of ancient Chinese grammar,grammatical analyses made by ancient scholars should be summed up and inherited.

基于Annotation的Spring事务应用设计

本文简要介绍Spring的事务实现技术,讨论了Spring中的事务的两种实现方式。通过同一个案例阐述了在Spring中通过xml配置来实现事务和使用了Annotation实现事务,比较了两种实现方式的优缺点。

基于Annotation数据结构自动生成的研究与实现

为了使整个数据库设计更加工程化、规范化和便捷化,使用Annotation注解技术实现数据库物理结构的自动生成,使之从数据库设计文档自动生成关系型数据库结构代码的方法,从而大大缩减了相关数据库开发的周期,提高了数据库开发的效率.

用Annotation简化Java程序的开发

简要介绍了Annotation技术本身的实现原理,并通过具体实例阐述了如何在软件开发中使用Annotation技术来简化Java程序开发的复杂性,提高程序的可读性和易用性。同时归纳了Annotation技术与XML技术各自的优缺点及适用范围。