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Takashi Gojobori

Publications and source records attributed to Takashi Gojobori.

3 recordsLinked to original sources

SenWave: Monitoring the Global Sentiments under the COVID-19 Pandemic

Since the first alert launched by the World Health Organization (5 January, 2020), COVID-19 has been spreading out to over 180 countries and territories. As of June 18, 2020, in total, there are now over 8,400,000 cases and over 450,000 related deaths. This causes massive losses in the economy and jobs globally and confining about 58% of the global population. In this paper, we introduce SenWave, a novel sentimental analysis work using 105+ million collected tweets and Weibo messages to evaluate the global rise and falls of sentiments during the COVID-19 pandemic. To make a fine-grained analysis on the feeling when we face this global health crisis, we annotate 10K tweets in English and 10K tweets in Arabic in 10 categories, including optimistic, thankful, empathetic, pessimistic, anxious, sad, annoyed, denial, official report, and joking. We then utilize an integrated transformer framework, called simpletransformer, to conduct multi-label sentimental classification by fine-tuning the pre-trained language model on the labeled data. Meanwhile, in order for a more complete analysis, we also translate the annotated English tweets into different languages (Spanish, Italian, and French) to generated training data for building sentiment analysis models for these languages. SenWave thus reveals the sentiment of global conversation in six different languages on COVID-19 (covering English, Spanish, French, Italian, Arabic and Chinese), followed the spread of the epidemic. The conversation showed a remarkably similar pattern of rapid rise and slow decline over time across all nations, as well as on special topics like the herd immunity strategies, to which the global conversation reacts strongly negatively. Overall, SenWave shows that optimistic and positive sentiments increased over time, foretelling a desire to seek, together, a reset for an improved COVID-19 world.

cs.SI↗

Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation

The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We here developed a method to identify candidates of horizontally transferred genes based on minimization of gene cluster insertions/deletions. To select a benchmark set of positively horizontally transferred genes against which the candidate set can be appraised, we devised another procedure using intergenetic alignments. Comparison with the benchmark set of horizontally transferred genes demonstrated the absence of a significant number of false positives in the candidates, showing that the method identifies horizontally transferred genes with a high degree of confidence. Horizontally transferred genes constitute at least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of which originate from other gamma-proteobacteria. Not only informational genes, but also operational genes (those involved in housekeeping) are horizontally transferred less frequently than expected. A gene-cluster analysis of Escherichia coli K-12 operons revealed that horizontal transfer produced four entire operons and expanded two operons, but deletion of intervening genes accounts for the formation of no operons. We propose that operons generally form by horizontal gene transfer. We further suggest that genes with related essential functions tend to reside in conserved operons, while genes in nonconserved operons generally confer slight advantage to the organisms and frequently undergo horizontal transfer and decay.

q-bio.PE↗