Perspectives of people with schizophrenia on clinical outcome scales and patient-reported outcome measures: a qualitative study.

Background: Over the past half-century, numerous scales have been designed to quantify outcomes in people with severe mental health disorders. However, little is known about the views of people diagnosed with schizophrenia on individual outcome scales, particularly outside of European countries.

Aim: We conducted a qualitative study to examine the perspectives of people with schizophrenia on multiple scales in Japan.

Riboswitch Design Using MODENA.

In silico design of artificial riboswitches is a challenging and intriguing task. Since experimental approaches such as in vitro selection are time-consuming processes, computational tools that guide riboswitch design are desirable to accelerate the design process. In this chapter, we describe the usage of the MODENA web server to design ON riboswitches on the basis of a multi-objective genetic algorithm and RNA secondary structure prediction.

Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon depends on chromosomal location.

Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon .

A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs.

The programmability of RNA-RNA interactions through intermolecular base-pairing has been successfully exploited to design a variety of RNA devices that artificially regulate gene expression. An in silico design for interacting structured RNA sequences that satisfies multiple design criteria becomes a complex multi-objective problem. Although multi-objective optimization is a powerful technique that explores a vast solution space without empirical weights between design objectives, to date, no web service for multi-objective design of RNA switches that utilizes RNA-RNA interaction has been proposed.

Assessing stable validity and reliability of the Japanese version of the individualized supported employment fidelity scale: A replication.

Background: The Japanese version of the individualized Supported Employment Fidelity scale (JiSEF) was developed by modifying the 25-item Individual Placement and Support Fidelity Scale (IPS-25). While a preliminary study partly confirmed the concurrent validity with vocational outcomes, this replication study aimed to examine the stability of the concurrent validity and the inter-rater reliability of the JiSEF and to test its convergent validity with IPS-25.

Methods: Fidelity assessments were conducted in 2016 (n = 17), 2017 (n = 13), and 2018 (n = 18) to examine the employment rate and the fidelity scores at the agency level.

Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis.

Accidental transmission of hop stunt viroid (HSVd) from grapevine to hop has led to several epidemics of hop stunt disease with convergent evolution of HSVd-g(rape) into HSVd-h(op) containing five mutations. However, the biological function of these five mutations remains unknown. In this study, we compare the biological property of HSVd-g and HSVd-h by bioassay and analyze HSVd-specific small RNA (HSVd-sRNA) using high-throughput sequencing.

COSMO: A dynamic programming algorithm for multicriteria codon optimization.

Codon optimization in protein-coding sequences (CDSs) is a widely used technique to promote the heterologous expression of target genes. In codon optimization, a combinatorial space of nucleotide sequences that code a given amino acid sequence and take into account user-prescribed forbidden sequence motifs is explored to optimize multiple criteria. Although evolutionary algorithms have been used to tackle such complex codon optimization problems, evolutionary codon optimization tools do not provide guarantees to find the optimal solutions for these multicriteria codon optimization problems.

Development and psychometric properties of a new brief scale for subjective personal agency (SPA-5) in people with schizophrenia.

Aims: Personal agency is a variable which potentially facilitates personal recovery in people with serious mental illness. This study aimed to develop a new brief measure for subjective personal agency that can be completed by people with serious mental illness.

Methods: Two focus group interviews were first conducted with 11 people with schizophrenia to understand the fundamental components of subjective personal agency for people with serious mental illness living in the community.

Effect of Escherichia coli on phospholipid monolayers: surface tensiometry and Brewster angle microscopy measurements.

The effect of Escherichia coli (E. coli) cells on two phospholipids [dipalmitoyl phosphatidylcholine (DPPC) and dimyristoyl phosphatidylcholine (DMPC)] monolayers at the surface of a 1.5 wt% NaCl salt solution has been investigated using surface tension measurement and Brewster angle microscopy.

Ant colony optimization for predicting RNA folding pathways.

RNA folding dynamics plays important roles in various functions of RNAs. To date, coarse-grained modeling has been successfully employed to simulate RNA folding dynamics on the energy landscape composed of secondary structures. In such a modeling, the energy barrier height between metastable structures is a key parameter that crucially affects the simulation results.

Development and Validation of a Japanese Fidelity Scale for Supported Employment.

The Individual Placement and Support (IPS) model of supported employment is an evidence based practice. Although several agencies have been trying to implement the IPS-model since 2005 in Japan, there was no tool to assess the quality. This study developed a Japanese version of the 25-item Individualized Supported Employment Fidelity Scale (J-ISEF), a new Japanese fidelity tool for supported employment based on the IPS model.

RNA inverse folding using Monte Carlo tree search.

Background: Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. However, their performance is not satisfactory in complicated cases.

Efficacy of a Peer-Led, Recovery-Oriented Shared Decision-Making System: A Pilot Randomized Controlled Trial.

Objective: The effects of a comprehensive shared decision-making system based on the CommonGround approach and incorporating peer support and a computerized decision aid were investigated.

Methods: A pilot randomized controlled trial with six-month follow-up was conducted in Japan. Fifty-six outpatients with mental illness were randomly allocated to a shared decision-making system (intervention) group or treatment as usual (control) group.

Evolutionary design of multiple genes encoding the same protein.

Motivation: Enhancing expression levels of a target protein is an important goal in synthetic biology. A widely used strategy is to integrate multiple copies of genes encoding a target protein into a host organism genome. Integrating highly similar sequences, however, can induce homologous recombination between them, resulting in the ultimate reduction of the number of integrated genes.

Characterization of host-dependent mutations of apple fruit crinkle viroid replicating in newly identified experimental hosts suggests maintenance of stem-loop structures in the left-hand half of the molecule is important for replication.

Apple fruit crinkle viroid (AFCVd) is a tentative member of the genus Apscaviroid, family Pospiviroidae. AFCVd has a narrow host range and is known to infect apple, hop and persimmon as natural hosts. In this study, tomato, cucumber and wild hop have been identified as new experimental herbaceous hosts.

Does improvement of cognitive functioning by cognitive remediation therapy effect work outcomes in severe mental illness? A secondary analysis of a randomized controlled trial.

Aim: The aim of this study was to clarify whether improvement of cognitive functioning by cognitive remediation therapy can improve work outcome in schizophrenia and other severe mental illnesses when combined with supported employment.

Methods: The subjects of this study were persons with severe mental illness diagnosed with schizophrenia, major depression, or bipolar disorder (ICD-10) and cognitive dysfunction who participated in both cognitive remediation using the Thinking Skills for Work program and a supported employment program in a multisite, randomized controlled study. Logistic and multiple linear regression analyses were performed to clarify the influence of cognitive functioning on vocational outcomes, adjusting for demographic and clinical variables.

Development of Japanese version of King's Stigma Scale and its short version: Psychometric properties of a self-stigma measure.

Aim: The study aimed to develop two Japanese versions of King's Stigma Scale, a full version (KSS-J-1) and a short version (KSS-J-2), through psychometric property testing.

Methods: The sample included 112 people with mental illness. We tested the constructs of the scales using both confirmatory and exploratory factor analyses.

Cost-effectiveness of cognitive remediation and supported employment for people with mental illness: a randomized controlled trial.

Background: Little is known about the economic benefits of cognitive remediation and supported employment (CR + SE). The present study aimed to investigate the cost-effectiveness of CR + SE compared with traditional vocational services (TVS).

Method: Individuals with mental illness and low cognitive function were recruited at six sites in Japan.

Multi-objective optimization for RNA design with multiple target secondary structures.

Background: RNAs are attractive molecules as the biological parts for synthetic biology. In particular, the ability of conformational changes, which can be encoded in designer RNAs, enables us to create multistable molecular switches that function in biological circuits. Although various algorithms for designing such RNA switches have been proposed, the previous algorithms optimize the RNA sequences against the weighted sum of objective functions, where empirical weights among objective functions are used.

Association between stigmatisation and experiences of evidence-based practice by psychiatric rehabilitation staff in Japan: a cross-sectional survey.

Background: Mental health professionals are one of the groups holding harmful stigmatisation towards people with mental illness.

Aims: To investigate the association between the performance of evidence-based practice (EBP) and the staff's level of stigmatisation in Japan.

Methods: The study enrolled 179 staff members in psychiatric day-care, psychiatric community outreach teams, and psychiatric rehabilitation teams at 14 psychiatric hospitals.

Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia.

Background: Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties.

Multi-objective genetic algorithm for pseudoknotted RNA sequence design.

RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding.

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome.

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype.

MODENA: a multi-objective RNA inverse folding.

Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure.