The latest report has estimated the number of rice genes to be approximately 32,000. To elucidate the functions of a large population of rice genes and to search efficiently for agriculturally useful genes, we have been taking advantage of the Full-length cDNA Over-eXpresser (FOX) gene-hunting system. This system is very useful for analyzing various gain-of-function phenotypes from large populations of transgenic plants overexpressing cDNAs of interest and others with unknown or important functions. We collected the plasmid DNAs of 13,980 independent full-length cDNA (FL-cDNA) clones to produce a FOX library by placing individual cDNAs under the control of the maize Ubiquitin-1 promoter. The FOX library was transformed into rice by Agrobacterium-mediated high-speed transformation. So far, we have generated approximately 12,000 FOX-rice lines. Genomic PCR analysis indicated that the average number of FL-cDNAs introduced into individual lines was 1.04. Sequencing analysis of the PCR fragments carrying FL-cDNAs from 8615 FOX-rice lines identified FL-cDNAs in 8225 lines, and a database search classified the cDNAs into 5462 independent ones. Approximately 16.6% of FOX-rice lines examined showed altered growth or morphological characteristics. Three super-dwarf mutants overexpressed a novel gibberellin 2-oxidase gene,confirming the importance of this system. We also show here the other morphological alterations caused by individual FL-cDNA expression. These dominant phenotypes should be valuable indicators for gene discovery and functional analysis.

We applied the full-length cDNA overexpressor (FOX) gene-hunting system for systematic and genome-wide functional analysis of rice genes. In this study, we constructed a novel binary vector carrying the Gateway site-specific recombination cassette and then constructed rice FOX libraries containing a maximum of 13,823 independent, full-length cDNAs (fl-cDNAs) that correspond to approximately half the total number of rice fl-cDNA clones. By introducing the FOX libraries via Agrobacterium, we generated 2,586 FOX-rice lines exhibiting various visible alterations (e.g., plant height, tillers, leaves, and heading dates). The introduced flcDNAs, integrated into individual transgenic rice genomes, were amplified by genomic PCR and identified using sequencing analysis. The fl-cDNAs were PCR-amplified in 2,251 (94.2%) of the 2,389 FOX-rice lines that were examined, identifying 1,920 independent fl-cDNAs in the FOX lines. In addition to the previously generated FOX-rice plants, our new collection of FOX-rice lines produced through the Gateway system should be a useful tool for the efficient identification of gene functions in rice. Moreover, this Gateway-based technology should be applicable to other species in which a collection of fl-cDNA clones is available.

This paper proposes a methodology which discriminates the articles by the target authors ("true" articles) from those by other homonymous authors ("false" articles). Author name searches for 2,595 "source" authors in six subject fields retrieved about 629,000 articles. In order to extract true articles from the large amount of the retrieved articles, including many false ones, two filtering stages were applied. At the first stage any retrieved article was eliminated as false if either its affiliation addresses had little similarity to those of its source article or there was no citation relationship between the journal of the retrieved article and that of its source article. At the second stage, a sample of retrieved articles was subjected to manual judgment, and utilizing the judgment results, discrimination functions based on logistic regression were defined. These discrimination functions demonstrated both the recall ratio and the precision of about 95% and the accuracy (correct answer ratio) of 90-95%. Existence of common coauthor(s), address similarity, title words similarity, and interjournal citation relationships between the retrieved and source articles were found to be the effective discrimination predictors. Whether or not the source author was from a specific country was also one of the important predictors. Furthermore, it was shown that a retrieved article is almost certainly true if it was cited by, or cocited with, its source article. The method proposed in this study would be effective when dealing with a large number of articles whose subject fields and affiliation addresses vary widely.

This study investigated papers posted on bioRXiv. In 2013–19, 17,818 papers were published in academic journals, accounting for 40.67% of the total publication. Among them, the Web of Science (WoS) Core Collection recorded journals of 16,525 published papers, accounting for 92.74% of the total. The following conclusions can be drawn. (1) Results indicate scientists' attention to the preprint system. (2) A large number of papers still use traditional publishing as the ultimate goal. (3) Because the posted papers scrutinized in this study were published in journals with a high impact factor, they have attracted the attention of many scientists. Nevertheless, we believe that the preprint platform will play a greater role from the academic exchange perspective.