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Pairs of sense and antisense transcriptions that are adjacent at their 5′ and 3′ regions are called divergent and convergent transcription, respectively. However, the structural properties of divergent/convergent transcription in different species or RNA biotypes are poorly characterized. Here, we developed CCIVR2, a program that facilitates identification of both overlapping and non-overlapping antisense transcripts produced from divergent/convergent transcription whose transcription start sites (TSS) or transcript end sites (TES) are located within a specified region. We used CCIVR2 to analyze antisense transcripts starting around the sense TSS (from divergent transcription) or ending around the sense TES (from convergent transcription) in 11 different species and found species- and RNA biotype-specific features of divergent/convergent transcription. Furthermore, we confirmed that CCIVR2 enables the identification of multiple sense/antisense transcript pairs from divergent transcription, including those with known functions in processes such as embryonic stem cell differentiation and TGFβ stimulation. CCIVR2 is therefore a valuable bioinformatics tool that facilitates the characterization of divergent/convergent transcription in different species and aids the identification of functional sense/antisense transcript pairs from divergent transcription in specified biological processes. [ABSTRACT FROM AUTHOR]

Cis-natural antisense transcripts (cis-NATs) are transcribed from the same genomic locus as their partner gene but from the opposite DNA strand and overlap with the partner gene transcript. Here, we developed a simple and convenient program termed CCIVR (comprehensive cis-NATs identifier via RNA-seq data) that comprehensively identifies all kinds of cis-NATs based on genome annotation with expression data obtained from RNA-seq. Using CCIVR with genome databases, we demonstrated total cis-NAT pairs from 11 model organisms. CCIVR analysis with RNA-seq data from parthenogenetic and androgenetic embryonic stem cells identified well-known imprinted cis-NAT pair, KCNQ1/KCNQ1OT1, ensuring the availability of CCIVR. Finally, CCIVR identified cis-NAT pairs that demonstrate inversely correlated expression upon TGFβ stimulation including cis-NATs that functionally repress their partner genes by introducing epigenetic alteration in the promoters of partner genes. Thus, CCIVR facilitates the investigation of structural characteristics and functions of cis-NATs in numerous processes in various species. [ABSTRACT FROM AUTHOR]

We attempted to predict activity/dominance for soccer games, where activity is defined as the degree of activity of the game as perceived by the viewer, whereas dominance is the degree at which the viewer perceives a particular team to dominate over the other team. Such activity/dominance information would help a layman viewer understand the game. It would also enable construction of an automatic digest creation system that extracts scenes having high activity/dominance. There are two facets of this study: 1. The main part of the underlying prediction model consists of a Stick-Breaking Hidden Markov Model, where the data automatically estimates the number of states of the Markov process behind the data. 2. The data used in this paper is vector time-series data consisting of player, referee, and ball positions, together with team information, acquired by a set of fixed cameras. The problem was approached with a Bayesian framework where learning and prediction were implemented by three different methods: Markov Chain Monte Carlo, Expectation Maximization, and Variational Bayes. The proposed method was tested using a dataset consisting of 10 professional soccer games and was compared against standard regression methods. [ABSTRACT FROM AUTHOR]

Purpose: Achieving cost-effectiveness while maintaining strict quality regulations is an emerging topic in pharmaceutical manufacturing. With a focus on the use process of excipients, e.g., reception, storage, testing, and actual usage, this paper presents a multiobjective design method for determining the optimal process setup. Method: The method consists of setup of the problem, creation of models for quality and economic evaluation, and finally multiobjective optimization. A case study was performed using benzyl alcohol, an oxidation-sensitive material; we designated the amount of oxidized impurities and the costs associated with testing as the quality and economic objectives, respectively. The process was simulated, considering container volume and purchase frequency as the design variables, and also the use of Raman spectroscopy as an alternative to conventional identification testing. Results: The multiobjective evaluation indicated options on the Pareto frontier, i.e., the set of non-dominant options. Here, the process with larger containers and less frequent purchases resulted in reduced testing costs but more impurities and vice versa for the opposite combination. The use of Raman spectroscopy was more effective in reducing the cost of identification testing than in preventing the degree of oxidation by not opening the container. Conclusions: Through the case study, we showed that the method was capable of identifying the promising process settings, especially with the aid of graphical analysis on the Pareto frontier. The method, which is currently focused on excipients, could be extended to similar design cases using raw materials for pharmaceutical manufacturing. [ABSTRACT FROM AUTHOR]

A questionnaire survey was conducted to investigate the sleeping habits of young children in relation to their lifestyles and psychological state. The study revealed that, while they were not associated with the occupation of their parents, their sleeping habits correlated with their habits of watching TV, playing games, soporific actions or the habit of napping, among others. The results suggested that young children who have regular sleeping habits have been properly guided to get up and go to bed in their daily life. It was further suggested that young children with regular sleeping habits are emotionally more stable than those with irregular sleeping habits. [ABSTRACT FROM AUTHOR]