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Biomedical subjects

I Uchiyama

Publications and source records attributed to I Uchiyama.

At least 19 recordsLinked to original sources
PubMed1998

DBGET/LinkDB: an integrated database retrieval system.

The integrated database retrieval system DBGET/LinkDB is the backbone of the Japanese GenomeNet service. DBGET is used to search and extract entries from a wide range of molecular biology databases, while LinkDB is used to search and compute links between entries in different databases. DBGET/LinkDB is designed to be a network distributed database system with an open architecture, which is suitable for incorporating local databases or establishing a specialized server environment. It also has an advantage of simple architecture allowing rapid daily updates of all the major databases. The WWW version of DBGET/LinkDB at GenomeNet is integrated with other search tools, such as BLAST, FASTA and MOTIF, and with local helper applications, such as RasMol. In addition to factual links between database entries, LinkDB is being extended to included similarity links and biological links toward computerization of logical reasoning processes.

Databases, Factual↗
PubMed1998

[E coli genomes].

Explore the source record for details and available documents.

Base Sequence↗
PubMed1997

Age-related changes in ventilatory and heart rate responses to acute ozone exposure in the conscious rat.

To evaluate the effect of age on toxicant-induced pulmonary and extrapulmonary changes, we examined the effect of inhalation exposure to oxone (O3) on the ventilatory and heart rate (HR) responses in 4-6 and 20-22-month-old male rats. The rats, chronically implanted with an electrocardiographic (ECG) electrodes, were placed in a head-out plethysmograph for continuous ventilatory measurements of tidal volume and breathing frequency. Simultaneous measurements of HR were also obtained. A 6-hr exposure of each rat to filtered air was followed 2 days later by a 5-hr exposure to 0.1 ppm O3, 5 days later by a 5-hr exposure to 0.3 ppm O3 and 10 days later by a 5-hr exposure to 0.5 ppm O3. Each of the O3 exposures was preceded by a 1-hr exposure to filtered air. Transient rapid shallow breathing with slightly increased HR appeared 1-2 min after the start of O3 exposure. It was suggested on the basis of the electroencephalographic (EEG) activity of the olfactory bulb that this transient response was mediated through olfactory sensation. Persistent rapid shallow breathing with a progressive decrease in HR occurred with a latent period of 1-2 hr. The last 90-min averaged values for relative minute ventilation tended to decrease with the increase in the level of exposure to O3 and these values for young rats were significantly lower than those for old rats. An exposure of young rats to 0.1 ppm O3 for shorter than 5 hr significantly decreased the tidal volume and HR and increased breathing frequency, but no significant changes were observed in old rats. There were no differences between young and old rats in non-observable-adverse-effect-levels (NOAELs) for the O3-induced persistent ventilatory and HR responses, when the NOAELs were determined by exposure to 0.3 and 0.5 ppm O3. The present results, as well as the reported decrease in body temperature and blood pressure, suggested that the age-related changes in patterns and magnitude of the persistent rapid shallow breathing with a progressive decrease in HR are mediated through some age-related defense mechanism acting against O3 inhalation. The validity of the occupational exposure limit for O3 in workplaces was discussed in the light of the present findings.

Aging↗
PubMed1997

Automatic construction of knowledge base from biological papers.

We designed a system that acquires domain specific knowledge from human written biological papers, and we call this system IFBP (Information Finding from Biological Papers). IFBP is divided into three phases, Information Retrieval (IR), Information Extraction (IE) and Dictionary Construction (DC). We propose a query modification method using automatically constructed thesaurus for IR and a statistical keyword prediction method for IE. A dictionary of domain specific terms, which is one of the central knowledge sources for the task of knowledge acquisition, is also constructed automatically in the DC phase. IFBP is currently used for constructing the Transcription Factor DataBase (TFDB) and shows good performance. Since the model of knowledge base construction that is adopted into IFBP is carried out entirely automatically, this system can be easily ported across domains.

Algorithms↗
PubMed1996

Construction of a normalized directionally cloned cDNA library from adult heart and analysis of 3040 clones by partial sequencing.

Large-scale sequencing of clones from cDNA libraries derived from specific tissues is a rapid and efficient way of discovering novel genes expressed in those tissues. However, because the heart is continually contracting and relaxing, it strongly expresses muscle-contractile genes and/or mitochondrial genes, a bias that reduces the efficiency of this method. To improve the efficiency of identifying novel genes expressed in the heart, we constructed a normalized directionally cloned cDNA library from adult heart and partially sequenced 3040 clones. Comparisons of these sequence data with known DNA sequences in the database revealed that 57.1% of the clones matched human genes already known, 23.4% were identical or almost identical to human expressed sequence tags (ESTs), 14.2% bore no significant homology to any sequences in the database, and 1.2% represented repetitive sequences. The remaining 4.1% showed some homology with known genes, and Northern blot analysis of several clones in this category revealed that most of them were expressed mainly in the heart and skeletal muscle. After redundancy was excluded, the 3040 clones accounted for 1395 distinctive ESTs, 446 of which exhibited no match to any known sequence. Our results suggest that our normalized library is less redundant than standard libraries and is a useful resource for cataloging genes expressed in the heart.

Adult↗
PubMed1996

Construction and analysis of a profile library characterizing groups of structurally known proteins.

A new sequence motif library StrProf was constructed characterizing the groups of related proteins in the PDB three-dimensional structure database. For a representative member of each protein family, which was identified by cross-referencing the PDB with the PIR superfamily classification, a group of related sequences was collected by the BLAST search against the nonredundant protein sequence database. For every group, the motifs were identified automatically according to the criteria of conservation and uniqueness of pentapeptide patterns and with a dual dynamic programming algorithm. In the StrProf library, motifs are represented by profile matrices rather than consensus patterns to allow more flexible search capabilities. Another dynamic programming algorithm was then developed to search this motif library. When the computationally derived StrProf was compared with PROSITE, which is a manually derived motif library in the best consensus pattern representation, the numbers of identified patterns were comparable. StrProf missed about one third of the PROSITE motifs, but there were also new motifs lacking in PROSITE. The new library was incorporated in SMART (Sequence Motif Analysis and Retrieval Tool), a computer tool designed to help search and annotate biologically important sites in an unknown protein sequence. The client program is available free of charge through the Internet.

Algorithms↗
PubMed1995

Physiological reaction and manual performance during work in cold storages.

Subjects were 10 workers (Group R) working in two cold storages (air temperature was between -20 degrees C and -23.2 degrees C), and eight workers (Group C) working in a general storehouse (air temperature was between 12 degrees C and 15.2 degrees C). They were all male workers operating forklift-trucks. Average (SE) age for Group R was 41.4(1.3) years and for Group C was 47.3(1.6) years. Hand tremor, handgrip strength, pinch strength, counting task, flicker value, peak flow rate and blood pressure were measured five times (before work, at 10 a.m., before lunch, at 3 p.m. and after work) per day. Blood samples were collected before lunch. Free fatty acid (FFA) of Group R was significantly higher than that of Group C. There were no significant differences in handgrip strength, pinch strength, counting task, flicker value and peak flow rate between Group R and Group C. However, changes in hand tremor and diastolic blood pressure for Group R were significantly greater than those for Group C. Only for Group R, there was a significant relationship between FFA and the hand tremor values measured the second time. Work loads of Group R would be increased by not only the extreme coldness but also large temperature difference between the inside and the outside of the cold storages. The actual forklift work in these cold storages did not cause a distinct reduction in manual performance, but caused an increase in stress which would be expressed as an increase in catecholamine excretion.

Adaptation, Physiological↗
PubMed1995

[Relationship between daily high temperature and mortality in Kyushu, Japan].

We analyzed the relationship between daily high temperature and mortality in Kyushu, Japan, 1972-1990. Mortality rate was obtained by dividing the number of deaths in a certain daily high temperature category by person-days in the same category. The results were as follows: (1) With daily high temperature on the x-axis and mortality rate on the y-axis, the relationship between the two variables appeared to be V-shaped. The minimum mortality rate was observed at the 28 degrees C-33 degrees C level. (2) Among all deaths at 33+ degrees C level, the proportion of deaths from "excessive heat" never exceeded 0.4%. This suggested that heat stroke is not a major contributor to the V-shape formation. (3) The V-shape was observed even in 1990, suggesting that the rapid spread of air conditioners did not alter the relationship between daily high temperature and mortality rate. (4) For the 0-4 years age group, mortality was not temperature dependent. However, the 5-14 years age group showed high mortality rates at 33+ degrees C. This may be attributed to outdoor activities during summer. After 30 years of age, the overall mortality rates rose with age, with greater increases at lower ambient temperature levels. As a result, the 65+ years age group had the greatest temperature dependence. (5) Deaths from respiratory diseases, circulatory diseases, and senility were highly temperature dependent, whereas death from cancer was not temperature dependent. Deaths from digestive diseases, infectious diseases, and accidents showed moderate temperature dependence.

Adolescent↗
PubMed1994

Gnome--an Internet-based sequence analysis tool.

Gnome (GenomeNet Open Mail-service Environment) is a sequence analysis tool that enables an end-user to make use of several Internet- (mainly e-mail) based services with an easy-to-use graphical user interface. Users can conduct homology and motif searches, and database-entry retrieval against the latest databases by emitting search requests to and receiving their results form a search-server by e-mail. The search results are viewed and managed efficiently with this system. The Macintosh and X (Motif) versions of the Gnome client and the UNIX version of the Gnome server are available to academic users free of charge.

Computer Communication Networks↗
PubMed1993

[Perception of foreign residents toward Japanese smoking habits].

A questionnaire written in English was developed for a survey of attitude of foreign residents toward smoking in Japan. The questionnaire was mailed to 69 foreign companies and 101 foreign language schools and also distributed to foreign residents on a US military base and at Christian churches. Responses from 342 persons (116 female, 221 male, and 5 sex undefined) contributed to this research. More than half (64%) of the respondents were from North America. When classified according to smoking habits, 72 persons were smokers (21%) and 78 were ex-smokers (23%). The subjects felt the biggest difference in smoking habits to be at "restaurants", and expressed that they would most like to see smoking prohibited at "restaurants". Almost all subjects (89%) thought that, compared to smoking habits in their own countries, Japanese were "markedly worse" or "worse". The main reasons why Japanese smoking habits were different from their countries were perceived to be "lack of education or knowledge" (31%) and "lack of legal restrictions" (28%). Half of the female subjects thought that the number of smokers in the next decade in Japan will be "markedly increased" or "increased". The subjects answered that education was the most effective means to prevent young people from smoking and also the best way to reduce smoking in society.

Adult↗
PubMed1992

Construction of a dictionary of sequence motifs that characterize groups of related proteins.

An automatic procedure is proposed to identify, from the protein sequence database, conserved amino acid patterns (or sequence motifs) that are exclusive to a group of functionally related proteins. This procedure is applied to the PIR database and a dictionary of sequence motifs that relate to specific superfamilies constructed. The motifs have a practical relevance in identifying the membership of specific superfamilies without the need to perform sequence database searches in 20% of newly determined sequences. The sequence motifs identified represent functionally important sites on protein molecules. When multiple blocks exist in a single motif they are often close together in the 3-D structure. Furthermore, occasionally these motif blocks were found to be split by introns when the correlation with exon structures was examined.

Amino Acid Sequence↗
PubMed1992

Differentiation of fear, anger, and joy.

The purpose of the present study was to identify the physiological characteristics corresponding to three affects (fear, anger, and joy), which were elicited through real situations in a laboratory. The subjects were asked to rate their psychological responses using the Affect Rating Scales for each affective situation. Physiological indices (diastolic and systolic blood pressures, heart rate, respiration rate and frequency of galvanic skin response) were measured. The subjects' affects can be characterized by two functions obtained through discriminant analysis. One discriminant function separated positive from negative affects; the other set apart anger from the remaining affects.

Adolescent↗
PubMed1992

Acute effects of ozone on EEG activity, sleep-wakefulness and heart rate in rats.

Effects of exposure to O3 on EEG activity, sleep-wakefulness and heart rate were examined using conscious rats which had been chronically implanted with electrodes for EEG, EMG and ECG recordings. Exposure to 0.5 ppm O3 for 6 hrs and 1.0 ppm O3 for 3 hrs suppressed amounts of wakefulness (W) and paradoxical sleep (PS) at the expense of an increase in slow-wave sleep (SWS), and lowered the amplitude of fast EEG waves and heart rate (HR). The lowered EEG amplitude and the suppressed PS recovered more rapidly during the post-exposure period than did the lowered HR. The ip administration of atropine sulfate blocked the suppressed W, the increased SWS and the lowered HR, while the lowered EEG amplitude and the suppressed PS were not blocked. These observations suggest that the O3-induced bradycardia results from enhanced activity of cardiac parasympathetic nerves and that the O3-induced changes in W and SWS result secondarily from some circulatory factor including the bradycardia.

Animals↗
PubMed1990

Ozone-induced bradycardia and arrhythmia and their relation to sleep-wakefulness in rats.

Rats were chronically implanted with electrodes for EEG, EMG and ECG recordings and exposed to 0.1 ppm, 0.2 ppm ozone (O3) or clean air as control for 5 consecutive days. Amounts of wakefulness (W), slow-wave sleep (SWS) and paradoxical sleep (PS) of the O3-exposed rats were not statistically different from respective control values. Compared with control rats, heart rates of the O3-exposed rats decreased and the number of bradyarrhythmic episodes increased with an increase in O3 levels. The O3-induced bradyarrhythmias occurred more prevalently in the order of W, SWS and PS state. Parasympathetic mechanisms were suggested on those cardiac abnormalities.

Animals↗
PubMed1989

Effects of short- and long-term exposure to ozone on heart rate and blood pressure of emphysematous rats.

Electrocardiogram and arterial blood pressure of elastase-treated emphysematous rats (E rats) and saline-treated control rats (S rats) were recorded continuously during exposure to either 1 ppm ozone (O3) for 3 hr or 0.5 ppm O3 for 6 hr. The heart rates (HRs) of both groups decreased to about 50 and 65% of the initial levels at the end of 1 ppm and 0.5 ppm O3 exposure, respectively. Mean arterial blood pressures (MAPs) also decreased to about 76 and 82%, respectively. There was no significant difference in these responses between E and S rats, although the levels of HRs and MAPs of the E rats were always a little lower than those of the S rats. Another group of E and S rats was continuously exposed to 0.2 ppm O3 for 4 weeks. The HRs of both E and S groups decreased to about 81 and 88% of the initial levels on the first day, respectively, although they recovered completely by the third day. No significant difference in the variation of HRs during exposure was noted between E and S rats. However, the HR responses of these rats to a challenge exposure of 0.8 ppm O3 for 1.5 hr appeared to be different. That is, S rats were more tolerant of the challenge exposure to O3 for 1.5 hr than the E rats.

Animals↗
PubMed1988

4-Hydroxyretinal, a new visual pigment chromophore found in the bioluminescent squid, Watasenia scintillans.

The bioluminescent squid, Watasenia scintillans has three visual pigments. The major pigment, based on retinal (lambda max 484 nm), is distributed over the whole retina. Another pigment based on 3-dehydroretinal (lambda max approximately 500 nm) and the third pigment (lambda max approximately 470 nm) are localized in the specific area of the ventral retina just receiving the downwelling light. Visual pigment was extracted and purified from the dissected retina. The chromophores were then extracted and analyzed with HPLC, NMR, infrared and mass spectroscopy, being compared with the synthetic 4-hydroxyretinal. A new retinal derivative, 11-cis-4-hydroxyretinal, is identified as the chromophore of the third visual pigment of the squid.

Animals↗
PubMed1988

Adaptation of a deep-sea cephalopod to the photic environment. Evidence for three visual pigments.

Watasenia scintillans, a bioluminescent deep-sea squid, has a specially developed eye with a large open pupil and three visual pigments. Photoreceptor cells (outer segment: 476 micron; inner segment: 99 micron) were long in the small area of the ventral retina receiving downwelling light, whereas they were short (outer segment: 207 micron; inner segment: 44 micron) in the other regions of the retina. The short photoreceptor cells contained the visual pigment with retinal (lambda max approximately 484 nm), probably for the purpose of adapting to their environmental light. The outer segment of the long photoreceptor cells consisted of two strata, a pinkish proximal area and a yellow distal area. The visual pigment with 3-dehydroretinal (lambda max approximately 500 nm) was located in the pinkish proximal area, giving high sensitivity at longer wavelengths. A newly found pigment (lambda max approximately 471 nm) was in the yellow distal area. The small area of the ventral retina containing two visual pigments is thought to have a high and broad spectral sensitivity, which is useful for distinguishing the bioluminescence of squids of the same species in their environmental downwelling light. These findings were obtained by partial bleaching of the extracted pigment from various areas of the retina and by high-performance liquid chromatographic analysis of the chromophore, complemented by microscopic observations.

Adaptation, Physiological↗