Data_Sheet_1_Assessing Lexical Psychological Properties in Second Language Production: A Dynamic Semantic Similarity Approach.doc

Previous studies of the lexical psycholinguistic properties (LPPs) in second language (L2) production have assessed the degree of an LPP dimension of an L2 corpus by computing the mean ratings of unique content words in the corpus for that dimension, without considering the possibility that learners at different proficiency levels may perceive the degree of that dimension of the same words differently. This study extended a dynamic semantic similarity algorithm to estimate the degree of five different LPP dimensions of several sub-corpora of the Education First-Cambridge Open Language Database representing L2 English learners at different proficiency levels. Our findings provide initial evidence for the validity of the algorithm for assessing the LPPs in L2 production and contribute useful insights into between-proficiency relationships and cross-proficiency differences in the LPPs in L2 production as well as the relationships among different LPP dimensions.</p

sj-docx-1-sgo-10.1177_21582440211069386 – Supplemental material for The Evolutionary Pattern of Language in English Fiction Over the Last Two Centuries: Insights From Linguistic Concreteness and Imageability

Supplemental material, sj-docx-1-sgo-10.1177_21582440211069386 for The Evolutionary Pattern of Language in English Fiction Over the Last Two Centuries: Insights From Linguistic Concreteness and Imageability by Kun Sun and Rong Wang in SAGE Open</p

Description of the parameters of sebnif and their default values.

<p>Description of the parameters of sebnif and their default values.</p

Data_Sheet_1_The impact factors of social media users' forwarding behavior of COVID-19 vaccine topic: Based on empirical analysis of Chinese Weibo users.PDF

IntroductionSocial media, an essential source of public access to information regarding the COVID-19 vaccines, has a significant effect on the transmission of information regarding the COVID-19 vaccines and helps the public gain correct insights into the effectiveness and safety of the COVID-19 vaccines. The forwarding behavior of social media users on posts concerned with COVID-19 vaccine topics can rapidly disseminate vaccine information in a short period, which has a significant effect on transmission and helps the public access relevant information. However, the factors of social media users' forwarding posts are still uncertain thus far. In this paper, we investigated the factors of the forwarding COVID-19 vaccines Weibo posts on Chinese social media and verified the correlation between social network characteristics, Weibo textual sentiment characteristics, and post forwarding.MethodsThis paper used data mining, machine learning, sentiment analysis, social network analysis, and regression analysis. Using “新冠疫苗 (COVID-19 vaccine)” as the keyword, we used data mining to crawl 121,834 Weibo posts on Sina Weibo from 1 January 2021 to 31 May 2021. Weibo posts not closely correlated with the topic of the COVID-19 vaccines were filtered out using machine learning. In the end, 3,158 posts were used for data analysis. The proportions of positive sentiment and negative sentiment in the textual of Weibo posts were calculated through sentiment analysis. On that basis, the sentiment characteristics of Weibo posts were determined. The social network characteristics of information transmission on the COVID-19 vaccine topic were determined through social network analysis. The correlation between social network characteristics, sentiment characteristics of the text, and the forwarding volume of posts was verified through regression analysis.ResultsThe results suggest that there was a significant positive correlation between the degree of posting users in the social network structure and the amount of forwarding. The relationship between the closeness centrality and the forwarding volume was significantly positive. The betweenness centrality was significantly positively correlated with the forwarding volume. There was no significant relationship between the number of posts containing more positive sentiments and the forwarding volume of posts. There was a significant positive correlation between the number of Weibo posts containing more negative sentiments and the forwarding volume.ConclusionAccording to the characteristics of users, COVID-19 vaccine posts from opinion leaders, “gatekeepers,” and users with high-closeness centrality are more likely to be reposted. Users with these characteristics should be valued for their important role in disseminating information about COVID-19 vaccines. In addition, the sentiment contained in the Weibo post is an important factor influencing the public to forward vaccine posts. Special attention should be paid to the negative sentimental tendency contained in this post on Weibo to mitigate the negative impact of the information epidemic and improve the transmission effect of COVID-19 vaccine information.</p

Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells

<div><p><i>Ab initio</i> assembly of transcriptome sequencing data has been widely used to identify large intergenic non-coding RNAs (lincRNAs), a novel class of gene regulators involved in many biological processes. To differentiate real lincRNA transcripts from thousands of assembly artifacts, a series of filtering steps such as filters of transcript length, expression level and coding potential, need to be applied. However, an easy-to-use and publicly available bioinformatics pipeline that integrates these filters is not yet available. Hence, we implemented sebnif, an integrative bioinformatics pipeline to facilitate the discovery of <i>bona fide</i> novel lincRNAs that are suitable for further functional characterization. Specifically, sebnif is the only pipeline that implements an algorithm for identifying high-quality single-exonic lincRNAs that were often omitted in many studies. To demonstrate the usage of sebnif, we applied it on a real biological RNA-seq dataset from Human Skeletal Muscle Cells (HSkMC) and built a novel lincRNA catalog containing 917 highly reliable lincRNAs. Sebnif is available at <a href="http://sunlab.lihs.cuhk.edu.hk/sebnif/" target="_blank">http://sunlab.lihs.cuhk.edu.hk/sebnif/</a>.</p></div

Data_Sheet_3_Comparative Analyses of Phyllosphere Bacterial Communities and Metabolomes in Newly Developed Needles of Cunninghamia lanceolata (Lamb.) Hook. at Four Stages of Stand Growth.xlsx

Host-plant-associated bacteria affect the growth, vigor, and nutrient availability of the host plant. However, phyllosphere bacteria have received less research attention and their functions remain elusive, especially in forest ecosystems. In this study, we collected newly developed needles from sapling (age 5 years), juvenile (15 years), mature (25 years), and overmature (35 years) stands of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook]. We analyzed changes in phyllosphere bacterial communities, their functional genes, and metabolic activity among different stand ages. The results showed that phyllosphere bacterial communities changed, both in relative abundance and in composition, with an increase in stand age. Community abundance predominantly changed in the orders Campylobacterales, Pseudonocardiales, Deinococcales, Gemmatimonadales, Betaproteobacteriales, Chthoniobacterales, and Propionibacteriales. Functional predictions indicated the genes of microbial communities for carbon metabolism, nitrogen metabolism, antibiotic biosynthesis, flavonoids biosynthesis, and steroid hormone biosynthesis varied; some bacteria were strongly correlated with some metabolites. A total of 112 differential metabolites, including lipids, benzenoids, and flavonoids, were identified. Trigonelline, proline, leucine, and phenylalanine concentrations increased with stand age. Flavonoids concentrations were higher in sapling stands than in other stands, but the transcript levels of genes associated with flavonoids biosynthesis in the newly developed needles of saplings were lower than those of other stands. The nutritional requirements and competition between individual trees at different growth stages shaped the phyllosphere bacterial community and host–bacteria interaction. Gene expression related to the secondary metabolism of shikimate, mevalonate, terpenoids, tocopherol, phenylpropanoids, phenols, alkaloids, carotenoids, betains, wax, and flavonoids pathways were clearly different in Chinese fir at different ages. This study provides an overview of phyllosphere bacteria, metabolism, and transcriptome in Chinese fir of different stand ages and highlights the value of an integrated approach to understand the molecular mechanisms associated with biosynthesis.</p

Snapshots of sebnif web server.

<p>(A) The data upload page. All the parameters of sebnif could be specified by the users through this page. (B) The result page showing the report of novel lincRNAs identified in Human Skeletal Muscle Cells. The final list of novel lincRNAs in standard GFF format and the iSeeRNA noncoding score for each transcript can be downloaded directly; statistic numbers during the filtering steps and the FRFE Profile and STGE Profile generated by FRFE and STGE algorithms were also provided for users to evaluate the quality of the data.</p

Data_Sheet_4_Comparative Analyses of Phyllosphere Bacterial Communities and Metabolomes in Newly Developed Needles of Cunninghamia lanceolata (Lamb.) Hook. at Four Stages of Stand Growth.xlsx

Host-plant-associated bacteria affect the growth, vigor, and nutrient availability of the host plant. However, phyllosphere bacteria have received less research attention and their functions remain elusive, especially in forest ecosystems. In this study, we collected newly developed needles from sapling (age 5 years), juvenile (15 years), mature (25 years), and overmature (35 years) stands of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook]. We analyzed changes in phyllosphere bacterial communities, their functional genes, and metabolic activity among different stand ages. The results showed that phyllosphere bacterial communities changed, both in relative abundance and in composition, with an increase in stand age. Community abundance predominantly changed in the orders Campylobacterales, Pseudonocardiales, Deinococcales, Gemmatimonadales, Betaproteobacteriales, Chthoniobacterales, and Propionibacteriales. Functional predictions indicated the genes of microbial communities for carbon metabolism, nitrogen metabolism, antibiotic biosynthesis, flavonoids biosynthesis, and steroid hormone biosynthesis varied; some bacteria were strongly correlated with some metabolites. A total of 112 differential metabolites, including lipids, benzenoids, and flavonoids, were identified. Trigonelline, proline, leucine, and phenylalanine concentrations increased with stand age. Flavonoids concentrations were higher in sapling stands than in other stands, but the transcript levels of genes associated with flavonoids biosynthesis in the newly developed needles of saplings were lower than those of other stands. The nutritional requirements and competition between individual trees at different growth stages shaped the phyllosphere bacterial community and host–bacteria interaction. Gene expression related to the secondary metabolism of shikimate, mevalonate, terpenoids, tocopherol, phenylpropanoids, phenols, alkaloids, carotenoids, betains, wax, and flavonoids pathways were clearly different in Chinese fir at different ages. This study provides an overview of phyllosphere bacteria, metabolism, and transcriptome in Chinese fir of different stand ages and highlights the value of an integrated approach to understand the molecular mechanisms associated with biosynthesis.</p

Data_Sheet_2_Comparative Analyses of Phyllosphere Bacterial Communities and Metabolomes in Newly Developed Needles of Cunninghamia lanceolata (Lamb.) Hook. at Four Stages of Stand Growth.xls

Host-plant-associated bacteria affect the growth, vigor, and nutrient availability of the host plant. However, phyllosphere bacteria have received less research attention and their functions remain elusive, especially in forest ecosystems. In this study, we collected newly developed needles from sapling (age 5 years), juvenile (15 years), mature (25 years), and overmature (35 years) stands of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook]. We analyzed changes in phyllosphere bacterial communities, their functional genes, and metabolic activity among different stand ages. The results showed that phyllosphere bacterial communities changed, both in relative abundance and in composition, with an increase in stand age. Community abundance predominantly changed in the orders Campylobacterales, Pseudonocardiales, Deinococcales, Gemmatimonadales, Betaproteobacteriales, Chthoniobacterales, and Propionibacteriales. Functional predictions indicated the genes of microbial communities for carbon metabolism, nitrogen metabolism, antibiotic biosynthesis, flavonoids biosynthesis, and steroid hormone biosynthesis varied; some bacteria were strongly correlated with some metabolites. A total of 112 differential metabolites, including lipids, benzenoids, and flavonoids, were identified. Trigonelline, proline, leucine, and phenylalanine concentrations increased with stand age. Flavonoids concentrations were higher in sapling stands than in other stands, but the transcript levels of genes associated with flavonoids biosynthesis in the newly developed needles of saplings were lower than those of other stands. The nutritional requirements and competition between individual trees at different growth stages shaped the phyllosphere bacterial community and host–bacteria interaction. Gene expression related to the secondary metabolism of shikimate, mevalonate, terpenoids, tocopherol, phenylpropanoids, phenols, alkaloids, carotenoids, betains, wax, and flavonoids pathways were clearly different in Chinese fir at different ages. This study provides an overview of phyllosphere bacteria, metabolism, and transcriptome in Chinese fir of different stand ages and highlights the value of an integrated approach to understand the molecular mechanisms associated with biosynthesis.</p

Schematic overview of sebnif.

<p>Key steps and filters are illustrated. FRFE: Fully Reconstruction Fraction Estimation; STGE: Single-exonic Transcript Gaussian/Gamma Estimation.</p