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Spinibarbus caldwelli is an important freshwater economic fish in China. Owing to uncontrolled fishing, wild resources of S. caldwelli have decreased rapidly and may be on the verge of extinction. In this study, utilizing single-molecule real-time (SMRT) sequencing technology and chromatin interaction mapping (Hi-C) technologies, we assembled the first chromosome-scale genome for S. caldwelli about 1.77 Gb in size, with a contig N50 length of 11.83 Mb and scaffold N50 length of 33.91 Mb. In total 1.72 Gb (97.01%) of the contig sequences were anchored onto fifty chromosomes with the longest scaffold being 56.20 Mb. Furthermore, proximately 49.41% of the genome was composed of repetitive elements. In total, 49,377 protein-coding genes were predicted, of which 47,724 (96.65%) genes have been functionally annotated. The high-quality chromosome-level reference genome and annotation are vital for supporting basic genetic studies and will be contribute to genetic structure, functional elucidation, evolutionary inquiry, and germplasm conservation for S. caldwelli. [ABSTRACT FROM AUTHOR]

The chloroplast genome of the synthetic octaploid Triticum timonovum Heslot et Ferrary k-43065 (France) was sequenced for the first time. Plastome sequencing was carried out on a Genolab M sequencer (GeneMind, China). The genome assembly was carried out using the NOVOwrap program. The size of the chloroplast genome of T. timonovum was 136 158 bp. The length of the inverted repeat region was 21 552 bp, that of the SSC region was 12 795 bp, and the LSC length was 80 257 bp. The chloroplast genomes of T. timonovum and different T. timopheevii accessions from the GenBank database were compared. As for the chloroplast genome, T. timonovum was closer to T. timopheevii (AB976560.1) but differed from it by the presence of one insert A at position 47891. [ABSTRACT FROM AUTHOR]

Holothuria scabra, a commercially valuable yet ecologically vulnerable tropical holothuroid, has experienced a severe decline in its wild populations, especially in China. Genomic resources are crucial for the development of effective genomic breeding projects and stock conservation strategies to restore these natural populations. Until now, a high-quality, chromosome-level reference genome for H. scabra has not been available. Here, we employed Oxford Nanopore and Hi-C sequencing technologies to assemble and annotate a high-quality, chromosome-level reference genome of H. scabra. The final genome comprised 31 scaffolds with a total length of 1.19 Gb and a scaffold N50 length of 53.52 Mb. Remarkably, 1,191.67 Mb (99.95%) of the sequences were anchored to 23 pseudo-chromosomes, with the longest one spanning 79.75 Mb. A total of 34,418 protein-coding genes were annotated in the final genome, with BUSCO analysis revealing 98.01% coverage of metazoa_odb10 genes, marking a significant improvement compared to the previous report. These chromosome-level sequences and annotations will provide an essential genomic basis for further investigation into molecular breeding and conservation management of H. scabra. [ABSTRACT FROM AUTHOR]

Meghimatium bilineatum is a notorious pest land slug used as a medicinal resource to treat ailments in China. Although this no-model species is unique in terms of their ecological security and medicinal value, the genome resource of this slug is lacking to date. Here, we used the Illumina, PacBio, and Hi-C sequencing techniques to construct a chromosomal-level genome of M. bilineatum. With the Hi-C correction, the sequencing data from PacBio system generated a 1.61 Gb assembly with a scaffold N50 of 68.08 Mb, and anchored to 25 chromosomes. The estimated assembly completeness at 91.70% was obtained using BUSCO methods. The repeat sequence content in the assembled genome was 72.51%, which mainly comprises 34.08% long interspersed elements. We further identified 18631 protein-coding genes in the assembled genome. A total of 15569 protein-coding genes were successfully annotated. This genome assembly becomes an important resource for studying the ecological adaptation and potential medicinal molecular basis of M. bilineatum. [ABSTRACT FROM AUTHOR]

Chelidonichthys spinosus, a secondary economic fish, is increasingly being exploited and valued in China. However, overfishing has led to it being recognized as one of the most depleted marine species in China. In this study, we generated a chromosome-level genome of C. spinosus using PacBio, Illumina, and Hi-C sequencing data. Ultimately, we assembled a 624.7 Mb genome of C. spinosus, with a contig N50 of 13.77 Mb and scaffold N50 of 28.11 Mb. We further anchored and oriented the assembled sequences onto 24 pseudo-chromosomes using Hi-C techniques. In total, 25,358 protein-coding genes were predicted, of which 24,072 (94.93%) genes were functionally annotated. The dot plot reveals a prominent co-linearity between C. spinosus and Cyclopterus lumpus, indicating a remarkably close phylogenetic relationship between these two species. The assembled genome sequences provide valuable information for elucidating the genetic adaptation and potential molecular basis of C. spinosus. They also have the potential to provide insight into the evolutionary investigation of teleost fish and vertebrates. [ABSTRACT FROM AUTHOR]

This article explores the path of the National Bible Society of Scotland (NBSS) to publishing its annotated edition of Proverbs in the Mandarin Union Version in China during the Republican era. After providing an overview of how the NBSS became the first Bible society to publish annotated Chinese Gospels and Acts in the 1890s, this article examines why it took more than three decades thereafter for the NBSS to publish an annotated edition of another biblical book. It argues that one of the main reasons was that the NBSS had difficulty securing reputable scholarly Protestant missionaries' services to prepare the necessary annotations. Moreover, this article suggests that the familiarity of the Chinese people with short and pithy sayings was a condition favourable for the reception of Proverbs in China. This, together with the status of the Mandarin Union Version as the standard biblical text for Chinese Protestants, helps explain why the NBSS eventually published an annotated edition of Proverbs in the Mandarin Union Version. Annotations in that edition of Proverbs are analysed to understand how they could help bridge the gaps between Proverbs and its Chinese readers, so as to shed light on why such an edition of Proverbs was well-received as an evangelistic tool. [ABSTRACT FROM AUTHOR]

Purpose: Haemaphysalis longicornis (Neumann) is a hematophagous tick widely distributed in northern China. It not only causes enormous economic loss to animal husbandry, but also as a vector and reservoir of various zoonotic pathogens, it spreads natural focal diseases, such as severe fever with thrombocytopenia syndrome, seriously threatening human health. Lack of transcriptomic and genomic data from H. longicornis limits the study of this important medical vector. Methods: The engorged female H. longicornis from Gansu, China, was used for RNA extraction, de novo RNA-seq, functional annotation, and ORF prediction. Results: As a result, 53.09 million clean reads (98.88%) with a GC content of 54.29% were obtained. A total of 65,916 Unigenes were assembled, of which 34.59% (23,330) were successfully annotated. Of these Unigenes, 22,587 (34.27%) were annotated to species by NCBI non-redundant protein (nr). Ixodes scapularis, Limulus polyphemus, Parasteatoda tepidariorum, Stegodyphus mimosarum, and Metaseiulus occidentalis were the top BLAST hit species, accounting for 47.23%, 9.58%, 4.11%, 3.50%, and 2.69%, respectively. A total of 29,182 ORFs were predicted, and 35 complete ORFs for functional genes were identified, including ORFs involved in digestion (14), stress responses (8), anticoagulation (3), reproduction (3), antimicrobial (2), drug resistance (2), movement (2), autophagy (1), and immunity (1), respectively. The Unigene ORFs encoding cathepsin and heat shock proteins were further analyzed phylogenetically. Conclusion: De novo RNA-seq and functional annotation of H. longicornis were successfully completed for the first time, providing a molecular data resource for further research on blood-sucking, pathogen transmission mechanisms, and effective prevention and control strategies. [ABSTRACT FROM AUTHOR]

Background Yellowhorn (Xanthoceras sorbifolium Bunge), a deciduous shrub or small tree native to north China, is of great economic value. Seeds of yellowhorn are rich in oil containing unsaturated long-chain fatty acids that have been used for producing edible oil and nervonic acid capsules. However, the lack of a high-quality genome sequence hampers the understanding of its evolution and gene functions. Findings In this study, a whole genome of yellowhorn was sequenced and assembled by integration of Illumina sequencing, Pacific Biosciences single-molecule real-time sequencing, 10X Genomics linked reads, Bionano optical maps, and Hi-C. The yellowhorn genome assembly was 439.97 Mb, which comprised 15 pseudo-chromosomes covering 95.42% (419.84 Mb) of the assembled genome. The repetitive fractions accounted for 56.39% of the yellowhorn genome. The genome contained 21,059 protein-coding genes. Of them, 18,503 (87.86%) genes were found to be functionally annotated with ≥1 "annotation" term by searching against other databases. Transcriptomic analysis showed that 341, 135, 125, 113, and 100 genes were specifically expressed in hermaphrodite flower, staminate flower, young fruit, leaf, and shoot, respectively. Phylogenetic analysis suggested that yellowhorn and Dimocarpus longan diverged from their most recent common ancestor ∼46 million years ago. Conclusions The availability and subsequent annotation of the yellowhorn genome, as well as the identification of tissue-specific functional genes, provides a valuable reference for plant comparative genomics, evolutionary studies, and molecular design breeding. [ABSTRACT FROM AUTHOR]

Background: Cardiovascular disease (CVD) has become the leading cause of death in China, and most of the cases can be prevented by controlling risk factors. The goal of this study was to build a corpus of CVD risk factor annotations based on Chinese electronic medical records (CEMRs). This corpus is intended to be used to develop a risk factor information extraction system that, in turn, can be applied as a foundation for the further study of the progress of risk factors and CVD.Results: We designed a light annotation task to capture CVD risk factors with indicators, temporal attributes and assertions that were explicitly or implicitly displayed in the records. The task included: 1) preparing data; 2) creating guidelines for capturing annotations (these were created with the help of clinicians); 3) proposing an annotation method including building the guidelines draft, training the annotators and updating the guidelines, and corpus construction. Meanwhile, we proposed some creative annotation guidelines: (1) the under-threshold medical examination values were annotated for our purpose of studying the progress of risk factors and CVD; (2) possible and negative risk factors were concerned for the same reason, and we created assertions for annotations; (3) we added four temporal attributes to CVD risk factors in CEMRs for constructing long term variations. Then, a risk factor annotated corpus based on de-identified discharge summaries and progress notes from 600 patients was developed. Built with the help of clinicians, this corpus has an inter-annotator agreement (IAA) F1-measure of 0.968, indicating a high reliability.Conclusion: To the best of our knowledge, this is the first annotated corpus concerning CVD risk factors in CEMRs and the guidelines for capturing CVD risk factor annotations from CEMRs were proposed. The obtained document-level annotations can be applied in future studies to monitor risk factors and CVD over the long term. [ABSTRACT FROM AUTHOR]

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The Chinese Proposition Bank (CPB) is a corpus annotated with semantic roles for the arguments of verbal and nominalized predicates. The semantic roles for the core arguments are defined in a predicate-specific manner. That is, a set of semantic roles, numerically identified, are defined for each sense of a predicate lemma and recorded in a valency lexicon called frame files. The predicate-specific manner in which the semantic roles are defined reduces the cognitive burden on the annotators since they only need to internalize a few roles at a time and this has contributed to the consistency in annotation. It was also a sensible approach given the contentious issue of how many semantic roles are needed if one were to adopt of set of global semantic roles that apply to all predicates. A downside of this approach, however, is that the predicate-specific roles may not be consistent across predicates, and this inconsistency has a negative impact on training automatic systems. Given the progress that has been made in defining semantic roles in the last decade or so, time is ripe for adopting a set of general semantic roles. In this article, we describe our effort to 're-annotate' the CPB with a set of 'global' semantic roles that are predicate-independent and investigate their impact on automatic semantic role labeling systems. When defining these global semantic roles, we strive to make them compatible with a recently published ISO standards on the annotation of semantic roles (ISO 24617-4:2014 SemAF-SR) while taking the linguistic characteristics of the Chinese language into account. We show that in spite of the much larger number of global semantic roles, the accuracy of an off-the-shelf semantic role labeling system retrained on the data re-annotated with global semantic roles is comparable to that trained on the data set with the original predicate-specific semantic roles. We also argue that the re-annotated data set, together with the original data, provides the user with more flexibility when using the corpus. [ABSTRACT FROM AUTHOR]

This study examines how subtitlers in underground subtitle groups in China perform skills and display competence in applying the rules around which annotations are built. I argue that by annotating, the act of creating notes, representing information not linguistically coded in the original US TV programs, subtitlers engage in a performative act in concert. Annotations reveal not only subtitlers' stances toward the contents being translated, but also their meta-thinking on these contents. The analysis shows that two contradictory forces provide the impetus for annotations. On the one hand, the desire for objectivity refers to subtitlers' attempts to represent a professional and organized account of how Chinese subtitles are produced in the process of explicating knowledge. On the other hand, the desire for authenticity is implicit in the subtitlers' narrative of what they actually experience when translating US TV programs. [ABSTRACT FROM AUTHOR]

Anyu, found in ancient Chinese bibliographies, is an author's note that adds extra information to the prefaces of different classificatory sections, and may record annotations concerning individual books. Siku quanshu zongmu, which contains 127 occurrences of anyu, may be regarded as typical. While anyu are valuable and beneficial to the bibliographical study of ancient Chinese books and to Chinese literary history, study of them has long been neglected and only a few articles have been written. This paper tries to redress this neglect by providing a more comprehensive investigation of the distribution, content and contribution to the bibliographical study of ancient Chinese books and Chinese scholarly history by the anyu contained in the Siku quanshu zongmu. [ABSTRACT FROM AUTHOR]

As school networks get more available, reading instruction in a computer classroom has become more and more popular in China. Although information and communication technology (ICT) has brought about some improvements in classroom teaching, it must be admitted that the phenomenon of fast reading with low-level cognitions is threatening school children's reading literacy. In order to address this problem, a collaborative annotation tool called Sharing Unique Reading Feeling (SURF) was developed for creating and sharing annotations. This study explored SURF-based collaborative reading instruction, and investigated the effect of collaborative annotation supported by SURF on primary school students' Chinese reading levels with methods of equal group experiment, interview and comparative analysis. Finally, some suggestions were proposed for the development of instructional annotation tools and the implementation of current reading instruction especially in computer classrooms. Results showed that the collaborative annotation supported by SURF could promote students' reading performance, enhance their Chinese reading levels in primary schools, and it was also helpful to develop the higher-level cognitive abilities such as analyzing, summarizing and evaluating. Practitioner Notes What is already known about this topic Annotation could improve students' reading and writing., Annotation could enhance reading comprehension., Full annotation sharing could improve learning outcome., Reading passages with hypermedia annotations significantly benefited passage comprehension and vocabulary., What this paper adds Collaborative annotation could enhance Chinese reading levels in primary schools of China, and is very helpful in addressing the issue of surface reading in Chinese class., Collaborative annotation is also helpful to develop higher-level cognitive abilities such as analyzing, summarizing and evaluating., Implications for practice and/or policy Collaborative reading assisted by annotation tool should be given profound attention and be applied more generally., Collaboration is rather significant in developing students' reading literacy, but abuse of collaboration will be a waste of time and will not get good effect., Do not lose the dominant role of teachers, because excessive freedom for students will result in failure in achieving teaching objectives., Some competition activities (eg, setting up Reading Stars, giving little and red flowers) should be provided to inspire students to do annotating passionately and seriously., The Ministry of Education in China should actively encourage Chinese teachers in primary and secondary schools to implement annotation reading instruction in computer classrooms., Some wonderful annotation tools just like SURF should be developed and generalized in a larger scope supported by the government. [ABSTRACT FROM AUTHOR]

Based on literature review, this paper further concludes the time and place of three Ci presented to Shi Shu by Wu Mengchuang. They were all composed in Suzhou CangMu period, the Mu Lan Flower • Shi Shu Goes to East of Zhejiang with XiuJie in 1236 when he didn't go there as Ti--Xing--Si; the Shao Hua You • Present Shi Shu in 1237 when he in Hangzhou as Xing--Yi; and the Ba Sheng Gan Zhou • Gu Shou Platform in 1243, which is to express his ambition from the historical sites. [ABSTRACT FROM AUTHOR]

This article presents a detailed account of the various revisions and annotations of the Annals of Taizu (Taizu benji) in the Draft History of the Qing dynasty (Qing shigao). Since different parts of the Draft History were housed in Beijing and Taipei, scholars have not been able to compare the versions until 1978, when Taiwanese scholars published the first annotated Draft History of the Qing Dynasty. Between 2007 and 2008, further refinements of unpublished sections of ji (annals of emperors), zhi (record of events), biao (lists of officials), zhuan (biographies of notable figures) were published for the first time by the National Palace Museum in Taipei. Based on these and other historical materials, the author discusses the reasons for the errors in the Annals of Taizu.

Specimen identification keys are still the most commonly created tools used by systematic biologists to access biodiversity information. Creating identification keys requires analyzing and synthesizing large amounts of information from specimens and their descriptions and is a very labor-intensive and time-consuming activity. Automating the generation of identification keys from text descriptions becomes a highly attractive text mining application in the biodiversity domain. Fine-grained semantic annotation of morphological descriptions of organisms is a necessary first step in generating keys from text. Machine-readable ontologies are needed in this process because most biological characters are only implied (i.e., not stated) in descriptions. The immediate question to ask is “How well do existing ontologies support semantic annotation and automated key generation?” With the intention to either select an existing ontology or develop a unified ontology based on existing ones, this paper evaluates the coverage, semantic consistency, and inter-ontology agreement of a biodiversity character ontology and three plant glossaries that may be turned into ontologies. The coverage and semantic consistency of the ontology/glossaries are checked against the authoritative domain literature, namely, Flora of North America and Flora of China. The evaluation results suggest that more work is needed to improve the coverage and interoperability of the ontology/glossaries. More concepts need to be added to the ontology/glossaries and careful work is needed to improve the semantic consistency. The method used in this paper to evaluate the ontology/glossaries can be used to propose new candidate concepts from the domain literature and suggest appropriate definitions. [ABSTRACT FROM AUTHOR]

The article discusses the reception of the poetry of John Milton in China, and examines reasons why Milton's work is less popular in that country than the works of the dramatist and poet William Shakespeare including the difficulties of translating Milton and the less relatable nature of his work. The author's project of annotating Milton's work specifically for Chinese readers is also commented on.

The topic of this issue of Contemporary Chinese Thought is the authorship, annotations, and philosophical interpretation of the Wuxing and evidence of the thought of Zisi and Mencius in the Wuxing. Four of the essays translated here are by Chen Lai, formerly professor of Chinese philosophy at Peking University and now dean of the School of Traditional Chinese Learning at Tsinghua University. An essay by Xing Wen, of Dartmouth College, provides context for a proper understanding of the Wuxing and Chen Lai's scholarship on the Wuxing. [ABSTRACT FROM AUTHOR]

• A full-length transcriptome of Ascosphaera apis was constructed and annotated. • 1205 long non-coding RNAs were identified in Ascosphaera apis mycelium. • 253 members from 17 transcription factor families in Ascosphaera apis. Ascosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mycelia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis. [ABSTRACT FROM AUTHOR]

Background: Health professionals and consumers use different terms to express medical events or concerns, which makes the communication barriers between the professionals and consumers. This may lead to bias in the diagnosis or treatment due to the misunderstanding or incomplete understanding. To solve the issue, a consumer health vocabulary was developed to map the consumer-used health terms to professional-used medical terms.Methods: In this study, we extracted Chinese consumer health terms from both online health forum and patient education monographs, and manually mapped them to medical terms used by professionals (terms in medical thesauri or in medical books). To ensure the above annotation quality, we developed annotation guidelines.Results: We applied our method to extract consumer-used disease terms in endocrinology, cardiology, gastroenterology and dermatology. In this study, we identified 1349 medical mentions from 8436 questions posted in an online health forum and 1428 articles for patient education monographs. After manual annotation and review, we released 1036 Chinese consumer health terms with mapping to 480 medical terms. Four annotators worked on the manual annotation work following the Chinese consumer health term annotation guidelines. Their average inter-annotator agreement (IAA) score was 93.91% ensuring high consistency of the released terms.Conclusions: We extracted Chinese consumer health terms from online forum and patient education monographs, and mapped them to medical terms used by professionals. Manual annotation efforts have been made for term annotating and mapping. Our study may contribute to the Chinese consumer health vocabulary construction. In addition, our annotated corpus, both the contexts of consumer health terms and consumer-professional term mapping, would be a useful resource for automatic methodology development. The dataset of the Chinese consumer health terms (CHT) is publicly available at http://www.phoc.org.cn/cht/ . [ABSTRACT FROM AUTHOR]