PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-13 (13)
 

Clipboard (0)
None

Select a Filter Below

Journals
Year of Publication
Document Types
1.  Characterization of gut microbiota profiles by disease activity in patients with Crohn’s disease using data mining analysis of terminal restriction fragment length polymorphisms 
Biomedical Reports  2014;2(3):370-373.
The gut microbiota plays a significant role in the pathogenesis of Crohn’s disease (CD). In this study, we analyzed the disease activity and associated fecal microbiota profiles in 160 CD patients and 121 healthy individuals. Fecal samples from the CD patients were collected during three different clinical phases, the active (n=66), remission-achieved (n=51) and remission-maintained (n=43) phases. Terminal restriction fragment length polymorphism (T-RFLP) and data mining analysis using the Classification and Regression Tree (C&RT) approach were performed. Data mining provided a decision tree that clearly identified the various subject groups (nodes). The majority of the healthy individuals were divided into Node-5 and Node-8. Healthy subjects comprised 99% of Node-5 (91 of 92) and 84% of Node-8 (21 of 25 subjects). Node-3 was characterized by CD (136 of 160 CD subjects) and was divided into Node-6 and Node-7. Node-6 (n=103) was characterized by subjects in the active phase (n=48; 46%) and remission-achieved phase (n=39; 38%) and Node-7 was characterized by the remission-maintained phase (21 of 37 subjects; 57%). Finally, Node-6 was divided into Node-9 and Node-10. Node-9 (n=78) was characterized by subjects in the active phase (n=43; 55%) and Node-10 (n=25) was characterized by subjects in the remission-maintained phase (n=16; 64%). Differences in the gut microbiota associated with disease activity of CD patients were identified. Thus, data mining analysis appears to be an ideal tool for the characterization of the gut microbiota in inflammatory bowel disease.
doi:10.3892/br.2014.252
PMCID: PMC3990205  PMID: 24748976
data mining; microbiota; terminal restriction fragment length polymorphism; inflammatory bowel disease
2.  Applying Data Mining to Classify Age by Intestinal Microbiota in 92 Healthy Men Using a Combination of Several Restriction Enzymes for T-RFLP Experiments 
The composition of the intestinal microbiota was measured following consumption of identical meals for 3 days in 92 Japanese men, and terminal restriction fragment length polymorphism (T-RFLP) was used to analyze their feces. The obtained operational taxonomic units (OTUs) and the subjects’ ages were classified by using Data mining (DM) software that compared these data with continuous data and for 5 partitions for age divided at 5 years intervals between the ages of 30 and 50. The DM provided Decision trees in which the selected OTUs were closely related to the ages of the subjects. DM was also used to compare the OTUs from the T-RFLP data with seven restriction enzymes (two enzymes of 516f-BslI and 516f-HaeIII, two enzymes of 27f-MspI and 27f-AluI, three enzymes of 35f-HhaI, 35f-MspI and 35f-AluI) and their various combinations. The OTUs delivered from the five enzyme-digested partitions were analyzed to classify their age clusters. For use in future DM processing, we discussed the enzymes that were effective for accurate classification. We selected two OTUs (HA624 and HA995) that were useful for classifying the subject’s ages. Depending on the 16S rRNA sequences of the OTUs, Ruminicoccus obeum clones 1-4 were present in 18 of 36 bacterial candidates in the older age group-related OTU (HA624). On the other hand, Ruminicoccus obeum clones 1-33 were present in 65 of 269 candidates in the younger age group-related OUT (HA995).
doi:10.12938/bmfh.33.65
PMCID: PMC4081184  PMID: 25003020
Key wordshuman intestinal microbiota; operational taxonomic unit; classification of age; data mining analysis; decision tree; terminal restriction fragment length polymorphism; Ruminicoccus obeum
3.  Technical Aspects of Nominal Partitions on Accuracy of Data Mining Classification of Intestinal Microbiota — Comparison between 7 Restriction Enzymes 
The application of data mining analyses (DM) is effective for the quantitative classification of human intestinal microbiota (HIM). However, there remain various technical problems that must be overcome. This paper deals with the number of nominal partitions (NP) of the target dataset, which is a major technical problem. We used here terminal restriction fragment length polymorphism data, which was obtained from the feces of 92 Japanese men. Data comprised operational taxonomic units (OTUs) and subject smoking and drinking habits, which were effectively classified by two NP (2-NP; Yes or No). Using the same OTU data, 3-NP and 5-NP were examined here and results were obtained, focusing on the accuracies of prediction, and the reliability of the selected OTUs by DM were compared to the former 2-NP. Restriction enzymes for PCR were further affected by the accuracy and were compared with 7 enzymes. There were subjects who possess HIM at the border zones of partitions, and the greater the number of partitions, the lower the obtained DM accuracy. The application of balance nodes boosted and duplicated the data, and was able to improve accuracy. More accurate and reliable DM operations are applicable to the classification of unknown subjects for identifying various characteristics, including disease.
doi:10.12938/bmfh.33.129
PMCID: PMC4098652  PMID: 25032086
human intestinal microbiota; operational taxonomic unit; data mining analysis; decision tree; nominal partitions of data; accuracy of classification; balance node
4.  Data mining analysis of terminal restriction fragment length polymorphism shows geographical differences in the human gut microbiota 
Biomedical Reports  2013;1(4):559-562.
Environmental factors are important for shaping the gut microbiota. In this study, terminal-restriction fragment length polymorphism (T-RFLP) analysis was performed, and data mining analysis was applied to investigate the geographical differences in the gut microbiota in Japan. A total of 121 healthy individuals living in four different districts (Shiga, Hyogo, Fukuoka and Chiba prefectures) in Japan were enrolled. Their gut microbiota profiles were evaluated by T-RFLP analysis, and data mining analysis using the Classification and Regression Tree (C&RT) approach was performed. Data mining analysis provided a decision tree that clearly identified the various groups of subjects (nodes). Some nodes characterized the subjects from the four geographically distinct regions. Overall, 21 of the 35 subjects from the Hyogo Prefecture were mainly included in Node 21, 11 of the 16 subjects from the Shiga Prefecture were mainly included in Node 19, 37 of 40 subjects from the Chiba Prefecture were mainly included in Node 6 and 28 of 30 subjects from the Fukuoka Prefecture were included in Node 3. Only eight operational taxonomic units (OTUs) of the total 100 OTUs contributed to the characterization of the gut microbiota of the four geographically distinct districts in Japan. Geographical differences in the human gut microbiota were identified in Japan. Data mining analysis appears to be one of the optimal tools for characterization of the human gut microbiota.
doi:10.3892/br.2013.127
PMCID: PMC3916989  PMID: 24648986
data mining; microbiota; terminal-restriction fragment length polymorphism
5.  Identification of Heavy Smokers through Their Intestinal Microbiota by Data Mining Analysis 
The intestinal microbiota compositions of 92 Japanese men were identified following consumption of identical meals for 3 days, and collected feces were analyzed through terminal restriction fragment length polymorphism. The obtained operational taxonomic units and smoking habits of subjects were analyzed by a data mining software. The constructed decision tree was able to identify explicitly the groups of smokers and nonsmokers. In particular, 4 smokers, who smoked 20 cigarettes/day, i.e., heavy smokers, were gathered in the same group of the decision tree and were clearly identified. Related operational taxonomic unit were traced to understand the species of bacteria, but all were found to be uncultured bacteria.
doi:10.12938/bmfh.32.77
PMCID: PMC4034320  PMID: 24936365
human intestinal microbiota; restriction enzyme; operational taxonomic unit; smoking habit; heavy smoker; data mining analysis; decision tree
6.  Comparison of the Accuracy and Mechanism of Data Mining Identification of the Intestinal Microbiota with 7 Restriction Enzymes 
The intestinal microbiota compositions of 92 Japanese men were identified following consumption of identical meals for 3 days, and collected feces were analyzed through terminal restriction fragment length polymorphism. The obtained operational taxonomic units (OTUs) and subjects’ smoking and drinking habits, which had 2 nominal partitions, yes or no, were analyzed by Data mining software. Identification of subjects for each habit was successfully performed and reported previously, but the identification accuracy was closely dependent on the species of the applied restriction enzymes for PCR. For the sake of better selection of enzymes and understanding the mechanisms of Data mining analysis, 516f-BslI and 516f-HaeIII, 27f-MspI and 27f-AluI and 35f-HhaI, 35f-MspI and 35f-AluI, altogether 7 enzymes, were examined comparatively. Data mining analysis provides a Decision tree for identification of subjects and their dividing pathways that is produced using a limited number of OTUs, which affects the accuracy of the results. The present report discusses not only a global comparison of accuracies for characteristics, but also the detailed mechanisms that result in better or worse results and the practical roles and functions of OTUs. The OTU at the 1st step of the constructed Decision tree was the most important for any identification, and for all cases, the combination of subsequent OTUs, which formed later in the Decision tree, was also unignorable. Detailed dividing pathways were traced and compared for the 7 enzymes and the future supporting ideas were provided for better Data mining analysis of the human intestinal microbiota.
doi:10.12938/bmfh.32.139
PMCID: PMC4034332  PMID: 24936373
human intestinal microbiota; restriction enzyme; operational taxonomic unit; smoking and drinking habit; data mining analysis; decision tree; accuracy and mechanism of identification
7.  Identification of Human Intestinal Microbiota of 92 Men by Data Mining for 5 Characteristics, i.e., Age, BMI, Smoking Habit, Cessation Period of Previous Smokers and Drinking Habit 
The intestinal microbiota compositions of 92 men living in Japan were identified following consumption of identical meals for 3 days. Fecal samples were analyzed by terminal restriction fragment length polymorphism with 4 primer-restriction enzyme systems, and the 120 obtained operational taxonomic units (OTUs) were analyzed by Data mining software focusing on the following 5 characteristics, namely, age, body mass index, present smoking habit, cessation period of previous smokers and drinking habit, according to the answers of the subjects. After performing Data mining analyses with each characteristic, the details of the constructed Decision trees precisely identified the subjects or discriminated them into various suitable groups. Through the pathways to reach the groups, practical roles of the related OTUs and their quantities were clearly recognized. Compared with the other identification methods for OTUs such as bicluster analyses, correlation coefficients and principal component analyses, the clear difference of this Data mining technique was that it set aside most OTUs and emphasized only some closely related ones. For example for a selected characteristic, such as smoking habit, only 7 OTUs out of 120 were able to identify all smokers, and the remaining 113 OTUs were thought of as data noise for smoking. Data mining analyses were affirmed as an effective method of subject discrimination for various physiological constitutions. The species of bacteria that were closely related to heavy smokers, i.e., HaeIII-291, were also discussed.
doi:10.12938/bmfh.32.129
PMCID: PMC4034333  PMID: 24936372
terminal restriction fragment length polymorphism; operational taxonomic units; decision tree; node; identical meals; discrimination of subjects; human intestinal microbiota
8.  In the Nepalese context, can a husband’s attendance during childbirth help his wife feel more in control of labour? 
Background
A husband’s support during childbirth is vital to a parturient woman’s emotional well-being. Evidence suggests that this type of support enables a woman to feel more in control during labour by reducing maternal anxiety during childbirth. However, in Nepal, where childbearing is considered an essential element of a marital relationship, the husband’s role in this process has not been explored. Therefore, we examined whether a woman in Nepal feels more in control during labour when her husband is present, compared to when another woman accompanies her or when she has no support person.
Methods
The study participants were low risk primigravida women in the following categories: women who gave birth with their husband present (n = 97), with a female friend present (n = 96), with mixed support (n = 11), and finally, a control group (n = 105). The study was conducted in the public maternity hospital in Kathmandu in 2011. The Labour Agentry Scale (LAS) was used to measure the extent to which women felt in control during labour. The study outcome was compared using an F-test from a one-way analysis of variance, and multiple regression analyses.
Results
The women who gave birth with their husband’s support reported higher mean LAS scores (47.92 ± 6.95) than the women who gave birth with a female friend’s support (39.91 ± 8.27) and the women in the control group (36.68 ± 8.31). The extent to which the women felt in control during labour was found to be positively associated with having their husband’s company during childbirth (β = 0.54; p < 0.001) even after adjusting for background variables. In addition, having a female friend’s company during childbirth was related to the women’s feeling of being in control during labour (β = 0.19; p < 0.001) but the effect size was smaller than for a husband’s company.
Conclusion
The results show that when a woman’s husband is present at the birth, she feels more in control during labour. This finding has strong implications for maternity practices in Nepal, where maternity wards rarely encourage a woman to bring her husband to a pregnancy appointment and to be present during childbirth.
doi:10.1186/1471-2393-12-49
PMCID: PMC3464724  PMID: 22698006
9.  Possible effects of diets on serum lipids, fatty acids and blood pressure levels in male and female Japanese university students 
Objectives
To prepare a dietary recommendation for young Japanese for the prevention of coronary heart disease, we surveyed the dietary habits, serum lipids, serum fatty acids and blood pressure levels among male and female students.
Methods
In this study, 175 male and 246 female university students were interviewed for the frequency of consumption of selected food items and the habit of skipping breakfast. Serum fatty acids were analyzed by gas chromatography.
Results
The frequencies of consumption of dishes cooked with oil and intake of vegetables were higher in female students than in male students. Serum n-6 polyunsaturated fatty acids were slightly higher in females students than in male students while that of serum n-3 polyunsaturated fatty acids was 6.4% in both sexes. For both males and females, those who skipped breakfast at least once a week were less likely to consume vegetables and fruits than those who did not. Female students who skipped breakfast were also less likely to consume fish and had lower composition of n-3 polyunsaturated fatty acid and higher systolic and diastolic blood pressure levels than males. For female, the intake of milk and dairy products correlated inversely with systolic blood pressure levels and the intake of n-3 polyunsaturated fatty acids correlated inversely with diastolic blood pressure levels. For males, the intake of fruits and consumption of dishes cooked with oil correlated inversely with systolic and diastolic blood pressure levels.
Conclusion
Our findings suggest that increased intake of fish, milk and dairy products, fruits and vegetables from early adulthood and a regular dietary pattern are important to reduce the risk factors for coronary heart disease.
doi:10.1265/ehpm.10.42
PMCID: PMC2723630  PMID: 21432162
diets; lipids; fatty acids; coronary risk factors; students
10.  Dementia-specific risks of scabies: Retrospective epidemiologic analysis of an unveiled nosocomial outbreak in Japan from 1989–90 
Background
Although senile dementia patients in long-term care facilities are at leading risk of scabies, the epidemiologic characteristics of this disease have yet to be fully clarified. This study documents the findings of a ward-scale nosocomial outbreak in western Japan from 1989–90, for which permission to publish was only recently obtained.
Methods
A retrospective epidemiologic study was performed to identify specific risk factors of scabies among patients with dementia. Analyses were based on a review of medical and nursing records. All inpatients in the affected ward at the time of the outbreak were included in the study. Observational and analytical approaches were employed to assess the findings.
Results
Twenty of 65 inpatients in the ward met the case definition of scabies. The outbreak lasted for almost 10 months and as a result, the spatial distribution of infections showed no localized patterns in the latter phase of the outbreak. The duration of illness significantly decreased after initiation of control measures (P = 0.0067). Movement without assistance (Odds Ratio [OR] = 11.3; 95% Confidence Interval [CI]: 2.9, 44.8) and moving beyond the room (but within the ward) (OR = 4.1; 95% CI: 1.4, 12.5) were significantly associated with infection, while types of room (Western or Japanese) and sleeping arrangement (on beds or futons laid directly on the floor) appeared not to be risk factors.
Conclusion
Univariate analysis demonstrated the importance of patients' behaviours during daily activities in controlling scabies among senile dementia patients. The findings also support previous evidence that catching scabies from fomites is far less common. Moreover, since cognitive disorders make it difficult for individuals to communicate and understand the implications of risky contacts as well as treatment method, and given the non-specific nature of individual contacts that are often unpredictable, real-time observations might help improve control practices.
doi:10.1186/1471-2334-5-85
PMCID: PMC1276794  PMID: 16225694
11.  Differences in dietary habits, serum fatty acid compositions and other coronary risk characteristics between freshmen and fourth-year male university students 
Westernization of lifestyles among Japanese, in particular among young generations, is a matter of concern for future increase in coronary heart disease. We surveyed a total of 349 male university students to examine changes in lifestyles and coronary risk factors in campus life. We compared dietary habits and serum fatty acid compositions as well as other coronary risk characteristics between freshmen (n=171) and fourth-year (senior) students (n=178). Serum fatty acid compositions and dietary intakes of selected foods as well as serum lipids, blood pressures and physical characteristics were examined at the 1996 and 1997 annual health examinations.
Compared to freshmen, senior students had a lower frequency of fish, vegetable, milk and egg intake, and a higher frequency of oil and fat intake. The proportions of serum saturated and monounsaturated fatty acids were significantly higher among senior students than among freshmen, whereas the proportion of serum polyunsaturated fatty acids was significantly lower among senior students than among freshmen. Senior students also had higher systolic and diastolic blood pressures, percent body fat, smoking rate and alcohol usage than freshmen. Mean body weight and mean body mass index were not different between the two groups.
Senior students generally showed Westernized dietary habits and higher coronary risk profiles than freshmen as indicated by the change of serum fatty acid compositions. Modification of these dietary habits and lifestyles may be important for the prevention of future CHD among Japanese young adults.
doi:10.1007/BF02897961
PMCID: PMC2723300  PMID: 21432252
dietary habit; cardiovascular risk factor; serum lipid; serum fatty acid; male university student
12.  Pharmacokinetic Evaluation of Amphotericin B in Lung Tissue: Lung Lymph Distribution after Intravenous Injection and Airspace Distribution after Aerosolization and Inhalation of Amphotericin B 
We have studied the pharmacokinetics of amphotericin B (AmB) in lung lymph circulation and bronchial-wash fluid after intravenous infusion and inhalation, respectively. For two experiments with awake sheep, we used lung lymph fistulas and tracheotomy. In experiment 1, AmB concentrations in plasma and lung lymph after intravenous infusion of AmB (1 mg/kg of body weight) over 1.5 h were measured. The mean peak in plasma level was 756.0 ± 188.8 ng/ml at 3 h after the start of infusion, and the level then decreased gradually to 194.8 ± 28.9 ng/ml at 24 h. The stable and maximal levels in lung lymph last 5 to 9 h after the start of AmB infusion. The concentrations in lung lymph after 9 h were slightly higher than those in plasma. Thus, the lung lymph-to-plasma ratio of AmB concentrations increased gradually during infusion, and the ratio was more than 1.0 after the end of infusion, suggesting that AmB could be easily moved from plasma to pulmonary interstitium and/or lung lymph circulation. In another experiment, 5 or 30 mg of aerosol AmB was inhaled, and the concentration of AmB in the bronchial-wash fluid was determined by bronchoalveolar lavage. The peak AmB concentration in the fluid was observed at 0.5 h. After that, AmB was slowly eliminated over 24 h. The area under the concentration-time curve for 30 mg of inhaled AmB was higher than that for 5 mg, but maximum concentrations of AmB in serum for 5 and 30 mg were almost similar. These observations identify the pharmacokinetic characteristics of AmB in the lung and may provide a new insight into the strategy for clinical treatment of fungal pneumonia.
PMCID: PMC105652  PMID: 9660990
13.  Year-round high physical activity levels in agropastoralists of Bolivian Andes: Results from repeated measurements of DLW method in peak and slack seasons of agricultural activities 
American Journal of Human Biology  2009;21(3):337-345.
By the repeated use of the doubly labeled water method (DLW), this study aimed to investigate (1) the extent of changes in energy expenditure and physical activity level (PAL) in response to increased agricultural work demands, and (2) whether the seasonal work demands induce the changes in the fairly equitable division of work and similarity of energy needs between men and women observed in our previous study (Phase 1 study; Kashiwazaki et al., 1995: Am J Clin Nutr 62: 901–910). In a rural small agropastoral community of the Bolivian Andes, we made the follow-up study (Phase 2, 14 adults; a time of high agricultural activity) of the Phase 1 study (12 adults; a time of low agricultural activity). In the Phase 2 study, both men and women showed very high PAL (mean±SD), but there was no significant difference by sex (men; 2.18 ± 0.23 (age; 64 ± 11 years, n = 7), women; 2.26 ± 0.25 (63 ± 10 years, n = 7)). The increase of PAL by 11% (P = 0.023) in the Phase 2 was equally occurred in both men and women. The factorial approach underestimated PAL significantly by ≈15% (P < 0.05). High PAL throughout the year ranging on average 2.0 and 2.2 was attributable to everyday tasks for subsistence and domestic works undertaking over 9–11 h (men spent 2.7 h on agricultural work and 4.7 h on animal herding, whereas women spent 7.3 h almost exclusively on animal herding). The seasonal increase in PAL was statistically significant, but it was smaller than those anticipated from published reports. A flexible division of labor played an important role in the equitable energetic increase in both men and women. Am. J. Hum. Biol., 2009. © 2009 Wiley-Liss, Inc.
doi:10.1002/ajhb.20864
PMCID: PMC2842569  PMID: 19127525

Results 1-13 (13)