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1.  Development of an ecological momentary assessment scale for appetite 
Background
An understanding of eating behaviors is an important element of health education and treatment in clinical populations. To understand the biopsychosocial profile of eating behaviors in an ecologically valid way, ecological momentary assessment (EMA) is appropriate because its use is able to overcome the recall bias in patient-reported outcomes (PROs). As appetite is a key PRO associated with eating behaviors, this study was done to develop an EMA scale to evaluate the within-individual variation of momentary appetite and uses this scale to discuss the relationships between appetite and various psychological factors.
Methods
Twenty healthy participants (age 23.6 ± 4.2 years old) wore a watch-type computer for a week. Several times a day, including just before and after meals, they recorded their momentary psychological stress, mood states, and ten items related to appetite. In addition, they recorded everything they ate and drank into a personal digital assistant (PDA)-based food diary. Multilevel factor analysis was used to investigate the factor structure of the scale, and the reliability and validity of the scale were also explored.
Results
Multilevel factor analyses found two factors at the within-individual level (hunger/fullness and cravings) and one factor at the between-individual level. Medians for the individually calculated Cronbach’s alphas were 0.89 for hunger/fullness, 0.71 for cravings, and 0.86 for total appetite (the sum of all items). Hunger/fullness, cravings, and total appetite all decreased significantly after meals compared with those before meals, and hunger/fullness, cravings, and total appetite before meals were positively associated with energy intake. There were significant negative associations between both hunger/fullness and total appetite and anxiety and depression as well as between cravings, and depression, anxiety and stress.
Conclusions
The within-individual reliability of the EMA scale to assess momentary appetite was confirmed in most subjects and it was also validated as a useful tool to understand eating behaviors in daily settings. Further refinement of the scale is necessary and further investigations need to be conducted, particularly on clinical populations.
doi:10.1186/s13030-014-0029-6
PMCID: PMC4302437  PMID: 25614760
Appetite; Ecological momentary assessment; Food diary; Multilevel factor analysis
2.  Next-Generation Sequencing of Genomic DNA Fragments Bound to a Transcription Factor in Vitro Reveals Its Regulatory Potential 
Genes  2014;5(4):1115-1131.
Several transcription factors (TFs) coordinate to regulate expression of specific genes at the transcriptional level. In Arabidopsis thaliana it is estimated that approximately 10% of all genes encode TFs or TF-like proteins. It is important to identify target genes that are directly regulated by TFs in order to understand the complete picture of a plant’s transcriptome profile. Here, we investigate the role of the LONG HYPOCOTYL5 (HY5) transcription factor that acts as a regulator of photomorphogenesis. We used an in vitro genomic DNA binding assay coupled with immunoprecipitation and next-generation sequencing (gDB-seq) instead of the in vivo chromatin immunoprecipitation (ChIP)-based methods. The results demonstrate that the HY5-binding motif predicted here was similar to the motif reported previously and that in vitro HY5-binding loci largely overlapped with the HY5-targeted candidate genes identified in previous ChIP-chip analysis. By combining these results with microarray analysis, we identified hundreds of HY5-binding genes that were differentially expressed in hy5. We also observed delayed induction of some transcripts of HY5-binding genes in hy5 mutants in response to blue-light exposure after dark treatment. Thus, an in vitro gDNA-binding assay coupled with sequencing is a convenient and powerful method to bridge the gap between identifying TF binding potential and establishing function.
doi:10.3390/genes5041115
PMCID: PMC4276929  PMID: 25534860
plant; transcription factor; HY5; in vitro binding; next-generation sequencing
3.  Quantitative Evaluation of the Use of Actigraphy for Neurological and Psychiatric Disorders 
Behavioural Neurology  2014;2014:897282.
Quantitative and objective evaluation of disease severity and/or drug effect is necessary in clinical practice. Wearable accelerometers such as an actigraph enable long-term recording of a patient's movement during activities and they can be used for quantitative assessment of symptoms due to various diseases. We reviewed some applications of actigraphy with analytical methods that are sufficiently sensitive and reliable to determine the severity of diseases and disorders such as motor and nonmotor disorders like Parkinson's disease, sleep disorders, depression, behavioral and psychological symptoms of dementia (BPSD) for vascular dementia (VD), seasonal affective disorder (SAD), and stroke, as well as the effects of drugs used to treat them. We believe it is possible to develop analytical methods to assess more neurological or psychopathic disorders using actigraphy records.
doi:10.1155/2014/897282
PMCID: PMC4156990  PMID: 25214709
4.  Shen-Zhi-Ling Oral Liquid Improves Behavioral and Psychological Symptoms of Dementia in Alzheimer's Disease 
We evaluated the effects of the traditional Chinese medicine (TCM) Shen-Zhi-Ling oral liquid (SZL) on the behavioral and psychological symptoms of dementia (BPSD) in patients with Alzheimer's disease (AD). Among 98 patients with AD and BPSD enrolled (mean age, 57.2 ± 8.9 years old), 91 (M = 55, F = 36; mean age, 57.2 ± 9.7 years old) completed the study. Patients took either SZL (n = 45) or placebo granules (n = 46) in a double-blind manner for 20 weeks while maintaining other anticognitive medications unchanged. Changes in BPSD between week 0, week 10, week 20, and week 25 were assessed using the behavioral pathology in Alzheimer's disease (BEHAVE-AD) rating scale and the neuropsychiatric inventory (NPI), detrended fluctuation analysis (DFA) represented by diurnal activity (DA), evening activity (EA), and nocturnal activity (NA) according to actigraphic recordings. SZL but not placebo oral liquid delayed the development of BPSD significantly according to the changes in some of the clinical scores and the EA and NA parameters of DFA at week 20 compared with week 0. No side effects were observed in laboratory tests. The results indicate that SZL might delay the development of BPSD in AD patients and thus is a potentially suitable drug for long-term use.
doi:10.1155/2014/913687
PMCID: PMC4052178  PMID: 24959193
5.  Exercise and Sleep Deprivation Do Not Change Cytokine Expression Levels in Patients with Chronic Fatigue Syndrome 
Clinical and Vaccine Immunology : CVI  2013;20(11):1736-1742.
A major hypothesis regarding the cause of chronic fatigue syndrome (CFS) is immune dysregulation, thought to be reflected in upregulated proinflammatory cytokines leading to the symptoms that are characteristic of this illness. Because the symptoms worsen with physical exertion or sleep loss, we hypothesized that we could use these stressors to magnify the underlying potential pathogenic abnormalities in the cytokine systems of people with CFS. We conducted repeat blood sampling for cytokine levels from healthy subjects and CFS patients during both postexercise and total sleep deprivation nights and assayed for protein levels in the blood samples, mRNA activity in peripheral blood lymphocytes (PBLs), and function in resting and stimulated PBLs. We found that these environmental manipulations did not produce clinically significant upregulation of proinflammatory cytokines. These data do not support an important role of immune dysregulation in the genesis of stress-induced worsening of CFS.
doi:10.1128/CVI.00527-13
PMCID: PMC3837776  PMID: 24027260
6.  ppdb: plant promoter database version 3.0 
Nucleic Acids Research  2013;42(Database issue):D1188-D1192.
ppdb (http://ppdb.agr.gifu-u.ac.jp) is a plant promoter database that provides information on transcription start sites (TSSs), core promoter structure (TATA boxes, Initiators, Y Patches, GA and CA elements) and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Since the last report in this journal, the database has been updated in three areas to version 3.0. First, new genomes have been included in the database, and now ppdb provides information on Arabidopsis thaliana, rice, Physcomitrella patens and poplar. Second, new TSS tag data (34 million) from A. thaliana, determined by a high throughput sequencer, has been added to give a ∼200-fold increase in TSS data compared with version 1.0. This results in a much higher coverage of ∼27 000 A. thaliana genes and finer positioning of promoters even for genes with low expression levels. Third, microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.
doi:10.1093/nar/gkt1027
PMCID: PMC3965062  PMID: 24194597
7.  The effects of exercise on dynamic sleep morphology in healthy controls and patients with chronic fatigue syndrome 
Physiological Reports  2013;1(6):e00152.
Effects of exercise on dynamic aspects of sleep have not been studied. We hypothesized exercise altered dynamic sleep morphology differently for healthy controls relative to chronic fatigue syndrome (CFS) patients. Sixteen controls (38 ± 9 years) and 17 CFS patients (41 ± 8 years) underwent polysomnography on baseline nights and nights after maximal exercise testing. We calculated transition probabilities and rates (as a measure of relative and temporal transition frequency, respectively) between sleep stages and cumulative duration distributions (as a measure of continuity) of each sleep stage and sleep as a whole. After exercise, controls showed a significantly greater probability of transition from N1 to N2 and a lower rate of transition from N1 to wake than at baseline; CFS showed a significantly greater probability of transition from N2 to N3 and a lower rate of transition from N2 to N1. These findings suggest improved quality of sleep after exercise. After exercise, controls had improved sleep continuity, whereas CFS had less continuous N1 and more continuous rapid eye movement (REM) sleep. However, CFS had a significantly greater probability and rate of transition from REM to wake than controls. Probability of transition from REM to wake correlated significantly with increases in subjective fatigue, pain, and sleepiness overnight in CFS – suggesting these transitions may relate to patient complaints of unrefreshing sleep. Thus, exercise promoted transitions to deeper sleep stages and inhibited transitions to lighter sleep stages for controls and CFS, but CFS also reported increased fatigue and continued to have REM sleep disruption. This dissociation suggests possible mechanistic pathways for the underlying pathology of CFS.
doi:10.1002/phy2.152
PMCID: PMC3871467  PMID: 24400154
Chronic fatigue syndrome; cumulative duration distributions; exercise; sleep stage dynamics; transition probability
8.  Co-Variation of Depressive Mood and Locomotor Dynamics Evaluated by Ecological Momentary Assessment in Healthy Humans 
PLoS ONE  2013;8(9):e74979.
Computerized ecological momentary assessment (EMA) is widely accepted as a “gold standard” method for capturing momentary symptoms repeatedly experienced in daily life. Although many studies have addressed the within-individual temporal variations in momentary symptoms compared with simultaneously measured external criteria, their concurrent associations, specifically with continuous physiological measures, have not been rigorously examined. Therefore, in the present study, we first examined the variations in momentary symptoms by validating the associations among self-reported symptoms measured simultaneously (depressive mood, anxious mood, and fatigue) and then investigated covariant properties between the symptoms (especially, depressive mood) and local statistics of locomotor activity as the external objective criteria obtained continuously. Healthy subjects (N = 85) from three different populations (adolescents, undergraduates, and office workers) wore a watch-type computer device equipped with EMA software for recording the momentary symptoms experienced by the subjects. Locomotor activity data were also continuously obtained by using an actigraph built into the device. Multilevel modeling analysis confirmed convergent associations by showing positive correlations among momentary symptoms. The increased intermittency of locomotor activity, characterized by a combination of reduced activity with occasional bursts, appeared concurrently with the worsening of depressive mood. Further, this association remained statistically unchanged across groups regardless of group differences in age, lifestyle, and occupation. These results indicate that the temporal variations in the momentary symptoms are not random but reflect the underlying changes in psychophysiological variables in daily life. In addition, our findings on the concurrent changes in depressive mood and locomotor activity may contribute to the continuous estimation of changes in depressive mood and early detection of depressive disorders.
doi:10.1371/journal.pone.0074979
PMCID: PMC3773004  PMID: 24058642
9.  Characterization and Modeling of Intermittent Locomotor Dynamics in Clock Gene-Deficient Mice 
PLoS ONE  2013;8(3):e58884.
The scale-invariant and intermittent dynamics of animal behavior are attracting scientific interest. Recent findings concerning the statistical laws of behavioral organization shared between healthy humans and wild-type mice (WT) and their alterations in human depression patients and circadian clock gene (Period 2; Per2) mutant mice indicate that clock genes play functional roles in intermittent, ultradian locomotor dynamics. They also claim the clinical and biological importance of the laws as objective biobehavioral measures or endophenotypes for psychiatric disorders. In this study, to elucidate the roles of breakdown of the broader circadian regulatory circuit in intermittent behavioral dynamics, we studied the statistical properties and rhythmicity of locomotor activity in Per2 mutants and mice deficient in other clock genes (Bmal1, Clock). We performed wavelet analysis to examine circadian and ultradian rhythms and estimated the cumulative distributions of resting period durations during which locomotor activity levels are continuously lower than a predefined threshold value. The wavelet analysis revealed significant amplification of ultradian rhythms in the BMAL1-deficient mice, and instability in the Per2 mutants. The resting period distributions followed a power-law form in all mice. While the distributions for the BMAL1-deficient and Clock mutant mice were almost identical to those for the WT mice, with no significant differences in their parameter (power-law scaling exponent), only the Per2 mutant mice showed consistently and significantly lower values of the scaling exponent, indicating the increased intermittency in ultradian locomotor dynamics. Furthermore, based on a stochastic priority queuing model, we explained the power-law nature of resting period distributions, as well as its alterations shared with human depressive patients and Per2 mutant mice. Our findings lead to the development of a novel mathematical model for abnormal behaviors in psychiatric disorders.
doi:10.1371/journal.pone.0058884
PMCID: PMC3596351  PMID: 23516567
10.  Diurnal variation of tension-type headache intensity and exacerbation: An investigation using computerized ecological momentary assessment 
Backgrounds
Tension-type headache is a common psychosomatic disease. However, diurnal variation of headache is yet to be clarified, perhaps due to the lack of an appropriate method to investigate it. Like other painful diseases, it would be helpful to know if there is diurnal variation in tension-type headaches, both for managing headaches and understanding their pathophysiology. The aim of this study was to determine if there is diurnal variation in the intensity and exacerbation of tension-type headache.
Methods
Patients (N = 31) with tension-type headache recorded for one week their momentary headache intensity several times a day and their acute headache exacerbations using a watch-type computer as an electronic diary (computerized ecological momentary assessment). Multilevel modeling was used to test the effects of time of day on momentary headache intensity and on the occurrence of acute exacerbations.
Results
A significant diurnal variation in momentary headache intensity was shown (P = 0.0005), with the weakest headaches in the morning and a peak in the late afternoon. A between-individual difference in the diurnal pattern was suggested. On-demand medication use was associated with a different diurnal pattern (P = 0.025), suggesting that headache intensity decreases earlier in the evening in subjects who used on-demand medication, while headache subtype, prophylactic medication use, and sex were not associated with the difference. The occurrence of acute headache exacerbation also showed a significant diurnal variation, with a peak after noon (P = 0.0015).
Conclusions
Tension-type headache was shown to have a significant diurnal variation. The relation to pathophysiology and psychosocial aspects needs to be further explored.
doi:10.1186/1751-0759-6-18
PMCID: PMC3479012  PMID: 22943264
Tension-type headache; Ecological momentary assessment; Electronic diary; Diurnal variation
11.  Enhanced Persistency of Resting and Active Periods of Locomotor Activity in Schizophrenia 
PLoS ONE  2012;7(8):e43539.
Patients with schizophrenia frequently exhibit behavioral abnormalities associated with its pathological symptoms. Therefore, a quantitative evaluation of behavioral dynamics could contribute to objective diagnoses of schizophrenia. However, such an approach has not been fully established because of the absence of quantitative biobehavioral measures. Recently, we studied the dynamical properties of locomotor activity, specifically how resting and active periods are interwoven in daily life. We discovered universal statistical laws (“behavioral organization”) and their alterations in patients with major depressive disorder. In this study, we evaluated behavioral organization of schizophrenic patients (n = 19) and healthy subjects (n = 11) using locomotor activity data, acquired by actigraphy, to investigate whether the laws could provide objective and quantitative measures for a possible diagnosis and assessment of symptoms. Specifically, we evaluated the cumulative distributions of resting and active periods, defined as the periods with physical activity counts successively below and above a predefined threshold, respectively. Here we report alterations in the laws governing resting and active periods; resting periods obeyed a power-law cumulative distribution with significantly lower parameter values (power-law scaling exponents), whereas active periods followed a stretched exponential distribution with significantly lower parameter values (stretching exponents), in patients. Our findings indicate enhanced persistency of both lower and higher locomotor activity periods in patients with schizophrenia, probably reflecting schizophrenic pathophysiology.
doi:10.1371/journal.pone.0043539
PMCID: PMC3429496  PMID: 22952701
12.  Non-Gaussianity of Low Frequency Heart Rate Variability and Sympathetic Activation: Lack of Increases in Multiple System Atrophy and Parkinson Disease 
The correlates of indices of long-term ambulatory heart rate variability (HRV) of the autonomic nervous system have not been completely understood. In this study, we evaluated conventional HRV indices, obtained from the daytime (12:00–18:00) Holter recording, and a recently proposed non-Gaussianity index (λ; Kiyono et al., 2008) in 12 patients with multiple system atrophy (MSA) and 10 patients with Parkinson disease (PD), known to have varying degrees of cardiac vagal and sympathetic dysfunction. Compared with the age-matched healthy control group, the MSA patients showed significantly decreased HRV, most probably reflecting impaired vagal heart rate control, but the PD patients did not show such reduced variability. In both MSA and PD patients, the low-to-high frequency (LF/HF) ratio and the short-term fractal exponent α1, suggested to reflect the sympathovagal balance, were significantly decreased, as observed in congestive heart failure (CHF) patients with sympathetic overdrive. In contrast, the analysis of the non-Gaussianity index λ showed that a marked increase in intermittent and non-Gaussian HRV observed in the CHF patients was not observed in the MSA and PD patients with sympathetic dysfunction. These findings provide additional evidence for the relation between the non-Gaussian intermittency of HRV and increased sympathetic activity.
doi:10.3389/fphys.2012.00034
PMCID: PMC3284201  PMID: 22371705
heart rate variability; ambulatory ECG; multiple system atrophy; Parkinson disease; autonomic failure
13.  Identification of Cis-Acting Promoter Elements in Cold- and Dehydration-Induced Transcriptional Pathways in Arabidopsis, Rice, and Soybean 
The genomes of three plants, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and soybean (Glycine max), have been sequenced, and their many genes and promoters have been predicted. In Arabidopsis, cis-acting promoter elements involved in cold- and dehydration-responsive gene expression have been extensively analysed; however, the characteristics of such cis-acting promoter sequences in cold- and dehydration-inducible genes of rice and soybean remain to be clarified. In this study, we performed microarray analyses using the three species, and compared characteristics of identified cold- and dehydration-inducible genes. Transcription profiles of the cold- and dehydration-responsive genes were similar among these three species, showing representative upregulated (dehydrin/LEA) and downregulated (photosynthesis-related) genes. All (46 = 4096) hexamer sequences in the promoters of the three species were investigated, revealing the frequency of conserved sequences in cold- and dehydration-inducible promoters. A core sequence of the abscisic acid-responsive element (ABRE) was the most conserved in dehydration-inducible promoters of all three species, suggesting that transcriptional regulation for dehydration-inducible genes is similar among these three species, with the ABRE-dependent transcriptional pathway. In contrast, for cold-inducible promoters, the conserved hexamer sequences were diversified among these three species, suggesting the existence of diverse transcriptional regulatory pathways for cold-inducible genes among the species.
doi:10.1093/dnares/dsr040
PMCID: PMC3276264  PMID: 22184637
plant genome; cis-acting promoter elements; cold; dehydration; microarray
14.  Increased Non-Gaussianity of Heart Rate Variability Predicts Cardiac Mortality after an Acute Myocardial Infarction 
Non-Gaussianity index (λ) is a new index of heart rate variability (HRV) that characterizes increased probability of the large heart rate deviations from its trend. A previous study has reported that increased λ is an independent mortality predictor among patients with chronic heart failure. The present study examined predictive value of λ in patients after acute myocardial infarction (AMI). Among 670 post-AMI patients, we performed 24-h Holter monitoring to assess λ and other HRV predictors, including SD of normal-to-normal interval, very-low frequency power, scaling exponent α1 of detrended fluctuation analysis, deceleration capacity, and heart rate turbulence (HRT). At baseline, λ was not correlated substantially with other HRV indices (|r| < 0.4 with either indices) and was decreased in patients taking β-blockers (P = 0.04). During a median follow-up period of 25 months, 45 (6.7%) patients died (32 cardiac and 13 non-cardiac) and 39 recurrent non-fatal AMI occurred among survivors. While all of these HRV indices but λ were significant predictors of both cardiac and non-cardiac deaths, increased λ predicted exclusively cardiac death (RR [95% CI], 1.6 [1.3–2.0] per 1 SD increment, P < 0.0001). The predictive power of increased λ was significant even after adjustments for clinical risk factors, such as age, diabetes, left ventricular function, renal function, prior AMI, heart failure, and stroke, Killip class, and treatment ([95% CI], 1.4 [1.1–2.0] per 1 SD increment, P = 0.01). The prognostic power of increased λfor cardiac death was also independent of all other HRV indices and the combination of increased λ and abnormal HRT provided the best predictive model for cardiac death. Neither λ nor other HRV indices was an independent predictor of AMI recurrence. Among post-AMI patients, increased λ is associated exclusively with increased cardiac mortality risk and its predictive power is independent of clinical risk factors and of other HRV predictors.
doi:10.3389/fphys.2011.00065
PMCID: PMC3183481  PMID: 21994495
heart rate variability; myocardial infarction; ambulatory ECG; sudden cardiac death; mortality; non-Gaussianity; prospective study; ENRICHD study
15.  Does sleep aggravate tension-type headache?: An investigation using computerized ecological momentary assessment and actigraphy 
Background
Both insufficient sleep and oversleeping have been reported as precipitating and aggravating factors of tension-type headache (TTH). However, previous studies relied on recalled self-reports, and the relationship has not been confirmed prospectively and objectively in a daily life situation. Recently, ecological momentary assessment (EMA) using electronic diaries, i.e., computerized EMA, is used to record subjective symptoms with the advantages of avoiding recall bias and faked compliance in daily settings. In addition, actigraphy has become an established method to assess sleep outside laboratories. Therefore, the aim of this study was to investigate the within-individual effect of sleep on the following momentary headache intensity in TTH patients during their daily lives utilizing EMA and actigraphy.
Methods
Twenty-seven patients with TTH wore watch-type computers as electronic diaries for seven consecutive days and recorded their momentary headache intensity using a visual analog scale of 0-100 approximately every six hours, on waking up, when going to bed, and at the time of headache exacerbations. They also recorded their self-report of sleep quality, hours of sleep and number of awakenings with the computers when they woke up. Physical activity was continuously recorded by an actigraph inside the watch-type computers. Activity data were analyzed by Cole's algorithm to obtain total sleep time, sleep efficiency, sleep latency, wake time after sleep onset and number of awakenings for each night. Multilevel modeling was used to test the effect of each subjective and objective sleep-related variable on momentary headache intensity on the following day.
Results
Objectively measured total sleep time was significantly positively associated with momentary headache intensity on the following day, while self-reported sleep quality was significantly negatively associated with momentary headache intensity on the following day.
Conclusions
Using computerized EMA and actigraphy, longer sleep and worse sleep quality were shown to be related to more intense headache intensity on within-individual basis and they may be precipitating or aggravating factors of TTH.
doi:10.1186/1751-0759-5-10
PMCID: PMC3163177  PMID: 21835045
16.  Characteristics of Core Promoter Types with respect to Gene Structure and Expression in Arabidopsis thaliana 
It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent transcription. Several transcriptional characteristics are known to be associated with core types, including distribution patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive expression profiles. However, their relationship to gene structure is poorly understood. In this report, we carried a comparative analysis of three Arabidopsis core types, TATA, GA, and Coreless, with regard to gene structure. Our genome-wide investigation was based on the peak TSS positions in promoters that had been identified in a large-scale experimental analysis. This analysis revealed that the types of core promoter are related with the room for promoters that is measured as the distance from the TSS to the end of the upstream gene, the distance from the TSS to the start position of the coding sequence (CDS), and the number and species of the cis-regulatory elements. Of these, it was found that the distance from the TSS to the CDS has a tight, inverse correlation to the expression level, and thus the observed relationship to the core type appears to be indirect. However, promoter length and preference of cis-elements are thought to be a direct reflection of core type-specific transcriptional initiation mechanisms.
doi:10.1093/dnares/dsr020
PMCID: PMC3190954  PMID: 21745829
plant genome; core promoter; environmental response; 5′ UTR
17.  Traditional Chinese Medicine Improves Activities of Daily Living in Parkinson's Disease 
Parkinson's Disease  2011;2011:789506.
We evaluated the effects of a traditional Chinese medicine (TCM), named Zeng-xiao An-shen Zhi-chan 2 (ZAZ2), on patients with Parkinson's disease (PD). Among 115 patients with idiopathic PD enrolled (mean age, 64.7 ± 10.2 years old), 110 patients (M = 65, F = 45; mean age, 64.9 ± 10.7 years old) completed the study. Patients took either ZAZ2 (n = 59) or placebo granule (n = 56) in a blind manner for 13 weeks while maintaining other anti-Parkinson medications unchanged. All participants wore a motion logger, and we analyzed the power-law temporal autocorrelation of the motion logger records taken on 3 occasions (before, one week, and 13 weeks after the drug administration). Drug efficacy was evaluated with the conventional Unified Parkinson Disease Rating Scale (UPDRS), as well as the power-law exponent α, which corresponds to the level of physical activity of the patients. ZAZ2 but not placebo granule improved the awake-sleep rhythm, the UPDRS Part II, Part II + III, and Part IV scores, and the α values. The results indicate that ZAZ2 improved activities of daily living (ADL) of parkinsonism and, thus, is a potentially suitable drug for long-term use.
doi:10.4061/2011/789506
PMCID: PMC3109418  PMID: 21687764
18.  Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data 
BMC Plant Biology  2011;11:39.
Background
Phytohormones organize plant development and environmental adaptation through cell-to-cell signal transduction, and their action involves transcriptional activation. Recent international efforts to establish and maintain public databases of Arabidopsis microarray data have enabled the utilization of this data in the analysis of various phytohormone responses, providing genome-wide identification of promoters targeted by phytohormones.
Results
We utilized such microarray data for prediction of cis-regulatory elements with an octamer-based approach. Our test prediction of a drought-responsive RD29A promoter with the aid of microarray data for response to drought, ABA and overexpression of DREB1A, a key regulator of cold and drought response, provided reasonable results that fit with the experimentally identified regulatory elements. With this succession, we expanded the prediction to various phytohormone responses, including those for abscisic acid, auxin, cytokinin, ethylene, brassinosteroid, jasmonic acid, and salicylic acid, as well as for hydrogen peroxide, drought and DREB1A overexpression. Totally 622 promoters that are activated by phytohormones were subjected to the prediction. In addition, we have assigned putative functions to 53 octamers of the Regulatory Element Group (REG) that have been extracted as position-dependent cis-regulatory elements with the aid of their feature of preferential appearance in the promoter region.
Conclusions
Our prediction of Arabidopsis cis-regulatory elements for phytohormone responses provides guidance for experimental analysis of promoters to reveal the basis of the transcriptional network of phytohormone responses.
doi:10.1186/1471-2229-11-39
PMCID: PMC3058078  PMID: 21349196
19.  Cytokines across the Night in Chronic Fatigue Syndrome with and without Fibromyalgia▿  
The symptoms of chronic fatigue syndrome (CFS) are consistent with cytokine dysregulation. This has led to the hypothesis of immune dysregulation as the cause of this illness. To further test this hypothesis, we did repeated blood sampling for cytokines while patients and matched healthy controls slept in the sleep lab. Because no one method for assaying cytokines is acknowledged to be better than another, we assayed for protein in serum, message in peripheral blood lymphocytes (PBLs), and function in resting and stimulated PBLs. We found no evidence of proinflammatory cytokine upregulation. Instead, in line with some of our earlier studies, we did find some evidence to support a role for an increase in interleukin-10, an anti-inflammatory cytokine. Although the changes were small, they may contribute to the common complaint in CFS patients of disrupted sleep.
doi:10.1128/CVI.00379-09
PMCID: PMC2849324  PMID: 20181767
20.  Synchronization of spontaneous eyeblinks while viewing video stories 
Blinks are generally suppressed during a task that requires visual attention and tend to occur immediately before or after the task when the timing of its onset and offset are explicitly given. During the viewing of video stories, blinks are expected to occur at explicit breaks such as scene changes. However, given that the scene length is unpredictable, there should also be appropriate timing for blinking within a scene to prevent temporal loss of critical visual information. Here, we show that spontaneous blinks were highly synchronized between and within subjects when they viewed the same short video stories, but were not explicitly tied to the scene breaks. Synchronized blinks occurred during scenes that required less attention such as at the conclusion of an action, during the absence of the main character, during a long shot and during repeated presentations of a similar scene. In contrast, blink synchronization was not observed when subjects viewed a background video or when they listened to a story read aloud. The results suggest that humans share a mechanism for controlling the timing of blinks that searches for an implicit timing that is appropriate to minimize the chance of losing critical information while viewing a stream of visual events.
doi:10.1098/rspb.2009.0828
PMCID: PMC2817301  PMID: 19640888
spontaneous eyeblink; synchronization; attention
21.  A real-time assessment of the effect of exercise in chronic fatigue syndrome 
Physiology & behavior  2007;92(5):963-968.
Patients with chronic fatigue syndrome (CFS) report substantial symptom worsening after exercise. However, the time course over which this develops has not been explored. Therefore, the objective of this study was to investigate the influence of exercise on subjective symptoms and on cognitive function in CFS patients in natural settings using a computerized ecological momentary assessment method, which allowed us to track the effects of exercise within and across days. Subjects were 9 female patients with CFS and 9 healthy women. A watch-type computer was used to collect real time data on physical and psychological symptoms and cognitive function for one week before and two weeks after a maximal exercise test. For each variable, we investigated temporal changes after exercise using multilevel modeling. Following exercise, physical symptoms did get worse but not until a five-day delay in CFS patients. Despite this, there was no difference in the temporal pattern of changes in psychological symptoms or in cognitive function after exercise between CFS patients and controls. In conclusion, physical symptoms worsened after a several day delay in patients with CFS following exercise while psychological symptoms or cognitive function did not change after exercise.
doi:10.1016/j.physbeh.2007.07.001
PMCID: PMC2170105  PMID: 17655887
chronic fatigue syndrome; ecological momentary assessment; multilevel modeling
22.  Panic disorder and locomotor activity 
Background
Panic disorder is one of the anxiety disorders, and anxiety is associated with some locomotor activity changes such as "restlessness". However, there have been few studies on locomotor activity in panic disorder using actigraphy, although many studies on other psychiatric disorders have been reported using actigraphy. Therefore, the aim of the present study was to investigate the relationship between panic disorder and locomotor activity pattern using a wrist-worn activity monitor. In addition, an ecological momentary assessment technique was used to record panic attacks in natural settings.
Methods
Sixteen patients with panic disorder were asked to wear a watch-type computer as an electronic diary for recording panic attacks for two weeks. In addition, locomotor activity was measured and recorded continuously in an accelerometer equipped in the watch-type computer. Locomotor activity data were analyzed using double cosinor analysis to calculate mesor and the amplitude and acrophase of each of the circadian rhythm and 12-hour harmonic component. Correlations between panic disorder symptoms and locomotor activity were investigated.
Results
There were significant positive correlations between the frequency of panic attacks and mesor calculated from double cosinor analysis of locomotor activity (r = 0.55) and between HAM-A scores and mesor calculated from double cosinor analysis of locomotor activity (r = 0.62).
Conclusion
Panic disorder patients with more panic attacks and more anxiety have greater objectively assessed locomotor activity, which may reflect the "restlessness" of anxiety disorders.
doi:10.1186/1751-0759-2-23
PMCID: PMC2596169  PMID: 19017383
23.  Application of ecological momentary assessment in stress-related diseases 
Many physical diseases have been reported to be associated with psychosocial factors. In these diseases, assessment relies mainly on subjective symptoms in natural settings. Therefore, it is important to assess symptoms and/or relationships between psychosocial factors and symptoms in natural settings. Symptoms are usually assessed by self-report when patients visit their doctors. However, self-report by recall has an intrinsic problem; "recall bias". Recently, ecological momentary assessment (EMA) has been proposed as a reliable method to assess and record events and subjective symptoms as well as physiological and behavioral variables in natural settings. Although EMA is a useful method to assess stress-related diseases, it has not been fully acknowledged, especially by clinicians. Therefore, the present brief review introduces the application and future direction of EMA for the assessment and intervention for stress-related diseases.
doi:10.1186/1751-0759-2-13
PMCID: PMC2475521  PMID: 18616833
24.  Of Mice and Men — Universality and Breakdown of Behavioral Organization 
PLoS ONE  2008;3(4):e2050.
Mental or cognitive brain functions, and the effect on them of abnormal psychiatric diseases, are difficult to approach through molecular biological techniques due to the lack of appropriate assay systems with objective measures. We therefore study laws of behavioral organization, specifically how resting and active periods are interwoven throughout daily life, using objective criteria, and first discover that identical laws hold both for healthy humans subject to the full complexity of daily life, and wild-type mice subject to maximum environmental constraints. We find that active period durations with physical activity counts successively above a predefined threshold, when rescaled with individual means, follow a universal stretched exponential (gamma-type) cumulative distribution, while resting period durations below the threshold obey a universal power-law cumulative distribution with identical parameter values for both of the mammalian species. Further, by analyzing the behavioral organization of mice with a circadian clock gene (Period2) eliminated, and humans suffering from major depressive disorders, we find significantly lower parameter values (power-law scaling exponents) for the resting period durations in both these cases. Such a universality and breakdown of the behavioral organization of mice and humans, revealed through objective measures, is expected to facilitate the understanding of the molecular basis of the pathophysiology of neurobehavioral diseases, including depression, and lay the foundations for formulating a range of neuropsychiatric behavioral disorder models.
doi:10.1371/journal.pone.0002050
PMCID: PMC2323110  PMID: 18446212
25.  ppdb: a plant promoter database 
Nucleic Acids Research  2007;36(Database issue):D977-D981.
ppdb (http://www.ppdb.gene.nagoya-u.ac.jp) is a plant promoter database that provides promoter annotation of Arabidopsis and rice. The database contains information on promoter structures, transcription start sites (TSSs) that have been identified from full-length cDNA clones and also a vast amount of TSS tag data. In ppdb, the promoter structures are determined by sets of promoter elements identified by a position-sensitive extraction method called local distribution of short sequences (LDSS). By using this database, the core promoter structure, the presence of regulatory elements and the distribution of TSS clusters can be identified. Although no differentiation of promoter architecture among plant species has been reported, there is some divergence of utilized sequences for promoter elements. Therefore, ppdb is based on species-specific sets of promoter elements, rather than on general motifs for multiple species. Each regulatory sequence is hyperlinked to literary information, a PLACE entry served by a plant cis-element database, and a list of promoters containing the regulatory sequence.
doi:10.1093/nar/gkm785
PMCID: PMC2238996  PMID: 17947329

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