BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

Prediction of Mind-Wandering with Electroencephalogram and Non-linear Regression Modeling

Mind-wandering (MW), task-unrelated thought, has been examined by researchers in an increasing number of articles using models to predict whether subjects are in MW, using numerous physiological variables. However, these models are not applicable in general situations. Moreover, they output only binary classification. The current study suggests that the combination of electroencephalogram (EEG) variables and non-linear regression modeling can be a good indicator of MW intensity. We recorded EEGs of 50 subjects during the performance of a Sustained Attention to Response Task, including a thought sampling probe that inquired the focus of attention. We calculated the power and coherence value and prepared 35 patterns of variable combinations and applied Support Vector machine Regression (SVR) to them. Finally, we chose four SVR models: two of them non-linear models and the others linear models; two of the four models are composed of a limited number of electrodes to satisfy model usefulness. Examination using the held-out data indicated that all models had robust predictive precision and provided significantly better estimations than a linear regression model using single electrode EEG variables. Furthermore, in limited electrode condition, non-linear SVR model showed significantly better precision than linear SVR model. The method proposed in this study helps investigations into MW in various little-examined situations. Further, by measuring MW with a high temporal resolution EEG, unclear aspects of MW, such as time series variation, are expected to be revealed. Furthermore, our suggestion that a few electrodes can also predict MW contributes to the development of neuro-feedback studies

博士論文要旨 : マインドワンダリングへの柔軟性がマインドフルネスの抑うつに対する効果を媒介する

departmental bulletin pape

A method of measuring the ability of disengagement from mind-wandering using electroencephalogram and its relationship to mindfulness and depressive symptoms

Objective: Mindfulness meditation might improve the ability of disengagement from mind-wandering, that is, the ability to shift attention from mind-wandering. Disengagement from mind-wandering could mediate the relationship between mindfulness and reduced depression. However, no studies have confirmed this relationship because of limitations in measurement methodology. Therefore, we propose a novel method to evaluate the ability of disengagement from mind-wandering, based on mind-wandering intensity estimation by machine-learning using electroencephalography. Methods: Mind-wandering intensity was estimated using one-second electroencephalogram samples and a machine-learning model developed in previous research. Thus, fluctuations in mind-wandering were observed during a meditation and the time required to shift attention from mind-wandering was defined as an index of mind-wandering disengagement. Two experiments were performed: The first targeted experienced meditators and the second assessed non-meditators before and after participating in a mindfulness-based intervention. Results: The experiments revealed that disengagement from mind-wandering correlated with the extent of meditation experience. A correlation was also found between the magnitude of change in disengagement and severity of depression following the intervention. Conclusions: Though further verification of validity is required, this study suggested the possibility that disengagement from mind-wandering has a mediating function on reducing depression by mindfulness-based intervention, and that improved disengagement from mind-wandering is more essential for mindfulness than trait mind-wandering

Ecological momentary assessment of mind-wandering: meta-analysis and systematic review

Mind-wandering (MW) is a universal human phenomenon and revealing its nature contributes to understanding consciousness. The ecological momentary assessment (EMA), in which subjects report a momentary mental state, is a suitable method to investigate MW in a natural environment. Previous studies employed EMA to study MW and attempted to answer the most fundamental question: How often do we let our minds wander? However, reported MW occupancies vary widely among studies. Further, while some experimental settings may induce bias in MW reports, these designs have not been explored. Therefore, we searched PubMed and Web of Science for articles published until the end of 2020 and systematically reviewed 25 articles, and performed meta-analyses on 17 of them. Our meta-analysis found that people spend 34.504% of daily life in mind-wandering, and meta-regression revealed that using subject smartphones for EMA, frequent sampling, and long experimental duration significantly affect MW reports. This result indicates that EMA using subject smartphones may tend to collect sampling under habitual smartphone use. Furthermore, these results indicate the existence of reactivity, even in MW research. We provide fundamental knowledge of MW and discuss rough standards for EMA settings in future MW studies

Changes in depression and anxiety through mindfulness group therapy in Japan: the role of mindfulness and self-compassion as possible mediators

Abstract Background Mindfulness-based interventions are increasingly being implemented worldwide for problems with depression and anxiety, and they have shown evidence of efficacy. However, few studies have examined the effects of a mindfulness-based group therapy based on standard programs for depression and anxiety until follow-up in Japan. This study addresses that gap. Furthermore, this study explored the mechanisms of action, focusing on mindfulness, mind wandering, self-compassion, and the behavioral inhibition and behavioral activation systems (BIS/BAS) as possible mediators. Methods We examined 16 people who suffered from depression and/or anxiety in an 8-week mindfulness group therapy. Measurements were conducted using questionnaires on depression and trait-anxiety (outcome variables), mindfulness, mind wandering, self-compassion, and the BIS/BAS (process variables) at pre- and post-intervention and 2-month follow-up. Changes in the outcome and process variables were tested, and the correlations among the changes in those variables were explored. Results Depression and anxiety decreased significantly, with moderate to large effect sizes, from pre- to post-intervention and follow-up. In process variables, the observing and nonreactivity facets of mindfulness significantly increased from pre- to post-intervention and follow-up. The nonjudging facet of mindfulness and self-compassion significantly increased from pre-intervention to follow-up. Other facets of mindfulness, mind wandering, and the BIS/BAS did not significantly change. Improvements in some facets of mindfulness and self-compassion and reductions in BIS were significantly correlated with decreases in depression and anxiety. Conclusions An 8-week mindfulness group therapy program may be effective for people suffering from depression and anxiety in Japan. Mindfulness and self-compassion may be important mediators of the effects of the mindfulness group therapy. Future studies should confirm these findings by using a control group. Trial registration University Hospital Medical Information Network (UMIN CTR) UMIN000022966. Registered July 1, 2016, https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R00002642

Pavlovian-based neurofeedback enhances meta-awareness of mind-wandering

Absorption in mind-wandering (MW) may worsen our mood and can cause psychological disorders. Researchers indicate the possibility that meta-awareness of MW prevents these mal-effects and enhances favorable consequences of MW, such as boosting creativity; thus, meta-awareness has attracted psychological and clinical attention. However, few studies have investigated the nature of meta-awareness of MW, because there has been no method to isolate and operate this ability. Therefore, we propose a new approach to manipulate the ability of meta-awareness. We used Pavlovian conditioning, tying to it an occurrence of MW and a neutral tone sound inducing the meta-awareness of MW. To perform paired presentations of the unconditioned stimulus (neutral tone) and the conditioned stimulus (perception accompanying MW), we detected participants’ natural occurrence of MW via electroencephalogram and a machine-learning estimation method. The double-blinded randomized controlled trial with 37 participants found that a single 20-min conditioning session significantly increased the meta-awareness of MW as assessed by behavioral and neuroscientific measures. The core protocol of the proposed method is real-time feedback on participants’ neural information, and in that sense, we can refer to it as neurofeedback. However, there are some differences from typical neurofeedback protocols, and we discuss them in this paper. Our novel classical conditioning is expected to contribute to future research on the modulation effect of meta-awareness on MW

Validity, reliability, and correlates of the Smartphone Addiction Scale–Short Version among Japanese adults

Background The short version of the smartphone addiction scale (SAS-SV) is widely used to measure problematic smartphone use (PSU). This study examined the validity and reliability of the SAS-SV among Japanese adults, as well as cross-sectional and longitudinal associations with relevant mental health traits and problems. Methods Datasets from a larger project on smartphone use and mental health were used to conduct two studies. Participants were adults aged over 20 years who carried a smartphone. Results Study 1 (n = 99,156) showed the acceptable internal consistency and structural validity of the SAS-SV with a bifactor model with three factors. For the test-retest reliability of the SAS-SV, the intraclass correlation coefficient (ICC) was .70, 95% CI [.69, 70], when the SAS-SV was measured seven and twelve months apart (n = 20,389). Study 2 (n = 3419) revealed that when measured concurrently, the SAS-SV was strongly positively correlated with another measure of PSU and moderately correlated with smartphone use time, problematic internet use (PIU), depression, the attentional factor of impulsiveness, and symptoms related to attention-deficit hyperactivity disorder and obsessive-compulsive disorder. When measured 12 months apart, the SAS-SV was positively strongly associated with another measure of PSU and PIU and moderately associated with depression. Discussion The structural validity of the SAS-SV appeared acceptable among Japanese adults with the bifactor model. The reliability of the SAS-SV was demonstrated in the subsequent seven- and twelve-month associations. Conclusion The cross-sectional and longitudinal associations of the SAS-SV provided further evidence regarding PSU characteristics