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Nobuhisa Ueda

Publications and source records attributed to Nobuhisa Ueda.

At least 19 recordsLinked to original sources
PubMed2005

KEGG as a glycome informatics resource.

Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of biological and biochemical information on carbohydrates, this is insufficient for bioinformatics analysis. Thus, we have developed a glycome informatics resource (http://www.genome.jp/kegg/glycan/) in KEGG (Kyoto Encyclopedia of Genes and Genomes), an integrated knowledge base of protein networks, genomic information, and chemical information. This review describes three noteworthy features: (1) GLYCAN, a database of carbohydrate structures; (2) glycan-related pathways; and (3) Composite Structure Map (CSM), a map illustrating all possible variations of carbohydrate structures within organisms. GLYCAN includes two useful tools: an intuitive drawing tool called KegDraw, and an efficient glycan search and alignment tool called KEGG Carbohydrate Matcher (KCaM). KEGG's glycan biosynthesis and metabolism pathways, integrating carbohydrate structures, proteins, and reactions, are also a pivotal resource. CSM is constructed as a bridge between carbohydrate functions and structures. CSM is able to display, for example, expression data of glycosyltransferases in a compact manner. In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field.

Carbohydrates↗
PubMed2005

An open study of risperidone liquid in the acute phase of schizophrenia.

An open-label study was performed to investigate the clinical efficacy and mechanisms of risperidone liquid in ameliorating positive symptoms in the acute phase of schizophrenia. Eighty-eight patients (M/F: 50/38; age: 18-74 years;, mean +/- SD =32 +/- 16 years) meeting DSM-IV criteria for schizophrenia and treated with risperidone liquid (14 patients also used lorazepam) were evaluated with regard to their clinical improvement and extrapyramidal side effects using the positive and negative syndrome scale (PANSS) and the Simpson and Angus scale (SAS), while plasma concentrations of HVA and MHPG were analysed by HPLC-ECD before and 4 weeks after risperidone liquid administration. Patients showing a 50% or greater improvement in PANSS scores were defined as responders. An improvement in the PANSS scores related to excitement, hostility and poor impulse control was seen within 7 days after administration of risperidone liquid, and an improvement with regard to hallucinatory behaviour and uncooperativeness was seen within 14 days after its administration. Finally, 68% of patients were classified as responders 4 weeks after risperidone liquid administration. The scores of SAS were not changed after risperidone liquid administration. Pretreatment plasma homovanillic acid (HVA) levels in the responders (8.1 +/- 2.9 ng/ml) were higher than those in nonresponders (5.9 +/- 1.9 ng/ml). In addition, a negative correlation was seen between the changes in plasma HVA levels and the percentage of improvement in PANSS scores. On the other hand, there were no differences between pretreatment plasma 3-methoxy-4-hydroxyphenylglycol (MHPG) levels and those of nonresponders. These results suggest that risperidone liquid is effective and well tolerated for the treatment of acute phase schizophrenic patients, and that efficacy is related to its affects on dopaminergic activity, not noradrenergic activity.

Acute Disease↗
PubMed2005

Prediction of response to risperidone treatment with respect to plasma concencentrations of risperidone, catecholamine metabolites, and polymorphism of cytochrome P450 2D6.

In the present study, we examined the relationships between plasma concentrations of risperidone and clinical responses, extrapyramidal symptoms, plasma levels of cotinine and caffeine, or cytochrome (cyp)2D6 genotypes. In addition, we also investigated the relationships between plasma levels of 3-methoxy-4-hydroxyphenylglycol (MHPG) or homovanillic (HVA) acid and clinical responses to risperidone. One hundred and 36 patients (male/female: 58/78, age 37+/-13 years) who met DSM-IV criteria for schizophrenia, schizoaffective disorder, delusional disorder and brief psychotic disorder, and who were being treated with risperidone alone, were evaluated regarding their clinical improvement and extrapyramidal symptoms using the Positive and Negative Syndrome Scale (PANSS) and Simpson and Angus (SAS), respectively, and plasma levels of cotinine, caffeine, MHPG and HVA were analysed by high-performance liquid chromatography. The cyp2D6*5 and *10 alleles were identified using the polymerase chain reaction. There was a positive correlation between plasma levels of risperidone plus 9-hydroxyrisperidone (active moiety) and SAS scores, but not the PANSS. Pretreatment HVA levels in responders were higher than those in nonresponders. In addition, there was a negative correlation between changes in HVA levels and improvement in PANSS scores. There was no association between plasma levels of risperidone and plasma levels of cotinine or caffeine. Furthermore, there were no differences in the risperidone/9-hydroxyrisperidone ratio, clinical improvements and extrapyramidal symptoms among cyp2D6 genotypes. These results indicate that pretreatment HVA levels and plasma concentrations of active moiety might play a part in predicting the clinical response and occurrence of extrapyramidal symptoms, respectively, when treating patients with risperidone.

Adolescent↗
PubMed2004

Clustering under the line graph transformation: application to reaction network.

BACKGROUND: Many real networks can be understood as two complementary networks with two kind of nodes. This is the case of metabolic networks where the first network has chemical compounds as nodes and the second one has nodes as reactions. In general, the second network may be related to the first one by a technique called line graph transformation (i.e., edges in an initial network are transformed into nodes). Recently, the main topological properties of the metabolic networks have been properly described by means of a hierarchical model. While the chemical compound network has been classified as hierarchical network, a detailed study of the chemical reaction network had not been carried out. RESULTS: We have applied the line graph transformation to a hierarchical network and the degree-dependent clustering coefficient C(k) is calculated for the transformed network. C(k) indicates the probability that two nearest neighbours of a vertex of degree k are connected to each other. While C(k) follows the scaling law C(k) approximately k(-1.1) for the initial hierarchical network, C(k) scales weakly as k0.08 for the transformed network. This theoretical prediction was compared with the experimental data of chemical reactions from the KEGG database finding a good agreement. CONCLUSIONS: The weak scaling found for the transformed network indicates that the reaction network can be identified as a degree-independent clustering network. By using this result, the hierarchical classification of the reaction network is discussed.

Algorithms↗
PubMed2004

Application of a new probabilistic model for recognizing complex patterns in glycans.

MOTIVATION: The study of carbohydrate sugar chains, or glycans, has been one of slow progress mainly due to the difficulty in establishing standard methods for analyzing their structures and biosynthesis. Glycans are generally tree structures that are more complex than linear DNA or protein sequences, and evidence shows that patterns in glycans may be present that spread across siblings and into further regions that are not limited by the edges in the actual tree structure itself. Current models were not able to capture such patterns. RESULTS: We have applied a new probabilistic model, called probabilistic sibling-dependent tree Markov model (PSTMM), which is able to inherently capture such complex patterns of glycans. Not only is the ability to capture such patterns important in itself, but this also implies that PSTMM is capable of performing multiple tree structure alignments efficiently. We prove through experimentation on actual glycan data that this new model is extremely useful for gaining insight into the hidden, complex patterns of glycans, which are so crucial for the development and functioning of higher level organisms. Furthermore, we also show that this model can be additionally utilized as an innovative approach to multiple tree alignment, which has not been applied to glycan chains before. This extension on the usage of PSTMM may be a major step forward for not only the structural analysis of glycans, but it may consequently prove useful for discovering clues into their function.

Algorithms↗
PubMed2004

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

KCaM (KEGG Carbohydrate Matcher) is a tool for the analysis of carbohydrate sugar chains, or glycans. It consists of a web-based graphical user interface that allows users to enter glycans easily with the mouse. The glycan structure is then transformed into our KCF (KEGG Chemical Function) file format and sent to our program which implements an efficient tree-structure alignment algorithm, similar to sequence alignment algorithms but for branched tree structures. Users can also retrieve glycan tree structures in KCF format from their local computers for visualization over the web. The tree-matching algorithm provides several options for performing different types of tree-matching procedures on glycans. These options consist of whether to incorporate gaps in a match, whether to take the linkage information into consideration and local versus global alignment. The results of this program are returned as a list of glycan structures in order of similarity based on these options. The actual alignment can be viewed graphically, and the annotation information can also be viewed easily since all this information is linked with KEGG's comprehensive suite of genomic data. Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp.

Algorithms↗
PubMed2004

Protein homology detection using string alignment kernels.

MOTIVATION: Remote homology detection between protein sequences is a central problem in computational biology. Discriminative methods involving support vector machines (SVMs) are currently the most effective methods for the problem of superfamily recognition in the Structural Classification Of Proteins (SCOP) database. The performance of SVMs depends critically on the kernel function used to quantify the similarity between sequences. RESULTS: We propose new kernels for strings adapted to biological sequences, which we call local alignment kernels. These kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences. When tested in combination with SVM on their ability to recognize SCOP superfamilies on a benchmark dataset, the new kernels outperform state-of-the-art methods for remote homology detection. AVAILABILITY: Software and data available upon request.

Algorithms↗
PubMed2004

Clinical response to antidepressant treatment and 3-methoxy-4-hydroxyphenylglycol levels: mini review.

Plasma 3-methoxy-4-hydroxyphenylglycol (MHPG) may provide valuable information regarding central noradrenergic activity. In this article, we mainly reviewed about the associations between plasma MHPG levels and responses to antidepressant treatment. There exists heterogeneity of depression with regards to plasma levels of MHPG; in other words, depressed patients might be dichotomized into one group characterized by anxiety and/or perceptions of powerlessness with high plasma MHPG levels and another group characterized by psychomotor retardation with low plasma MHPG levels. In addition, it is possible that patients with lower pretreatment MHPG levels might respond to drugs that affect both noradrenergic neurons and serotonergic neurons or predominantly noradrenergic neurons. On the other hand, patients with higher pretreatment MHPG levels might respond to drugs that affect predominantly serotonergic neurons or GABAergic neurons. It is possible to predict the responses to antidepressant drugs by means of plasma MHPG levels in depressed patients.

Antidepressive Agents↗
PubMed2004

Associations between baseline plasma MHPG (3-methoxy-4-hydroxyphenylglycol) levels and clinical responses with respect to milnacipran versus paroxetine treatment.

The purpose of this study was to investigate the effects of milnacipran and paroxetine on plasma levels of catecholamine metabolites, and we attempted to elucidate the differences between the mechanisms of these drugs in catecholaminergic neurons. In depressed patients, we investigated the relationships among pretreatment levels of catecholamine metabolites, the changes in plasma catecholamine metabolite levels before and after administration of milnacipran or paroxetine, and clinical response to these drugs. Responders to milnacipran showed lower pretreatment levels of plasma 3-methoxy-4-hydroxyphenylglycol (pMHPG) than did nonresponders to milnacipran; there was also a positive correlation between changes in pMHPG levels and percent improvement of the score on the 17-item Hamilton Rating Scale for Depression (HRSD). On the other hand, responders to paroxetine showed higher pretreatment levels of pMHPG than did nonresponders to paroxetine, and a negative correlation was observed between changes in pMHPG levels and percent improvement of the HRSD score. However, a significant difference was not observed in the pretreatment plasma level of homovanillic acid between responders and nonresponders to treatment with milnacipran or paroxetine. These results suggest that there is an association between baseline pMHPG levels and clinical responses with respect to milnacipran versus paroxetine treatment.

Adult↗
PubMed2004

A simple method for inferring strengths of protein-protein interactions.

Various computational methods have been proposed for inference of protein-protein interactions since protein-protein interaction plays an essential role in many cellular processes. One of well-studied approaches is to infer protein-protein interactions based on domain-domain interactions. To extend this approach, we proposed a method called LPNM to infer ratios of interactions, which outperformed other existing methods in terms of error of predicted ratios. However, since the LPNM method is based on the linear programming approach, it may require a large amount of time to infer interactions for a large data set. In this paper, we propose a simple method to infer the ratios of protein-protein interactions based on the association method by Sprinzak et al. In an experiment with a data set of protein-protein interactions in yeast, it runs more than 150 times as fast as the LPNM method, and achieves almost the same accuracy. On implementing algorithms for the inference problem, it is essential to understand how difficult the problem is. Even though various methods for the problem have been already proposed, it has not been analyzed rigorously from a computational point of view. We hence define a problem to maximize correctly classified examples, and prove the problem is MAX SNP-hard, which also means the problem is NP-hard.

Algorithms↗
PubMed2003

Schneiderian first-rank symptoms associated with fluvoxamine treatment: a case report.

This communication describes a patient who developed Schneiderian first-rank symptoms in the course of treatment with fluvoxamine. The patient, a 28-year-old man suffering from panic disorder, developed several first-rank symptoms during fluvoxamine administration. These symptoms abated 1 week after fluvoxamine treatment was discontinued and haloperidol was started. Although haloperidol was discontinued, no further hallucinations or delusions occurred. This finding suggests that fluvoxamine can precipitate Schneiderian first-rank symptoms in some susceptible patients.

Adult↗
PubMed2003

Inferring strengths of protein-protein interactions from experimental data using linear programming.

MOTIVATION: Several computational methods have been proposed for inference of protein-protein interactions. Most of the existing methods assume that protein-protein interaction data are given as binary data (i.e. whether or not each protein pair interacts). However, multiple biological experiments are performed for the same protein pairs and thus the ratio (strength) of the number of observed interactions to the number of experiments is available for each protein pair. RESULTS: We propose a new method for inference of protein-protein interactions from such experimental data. This method tries to minimize the errors between the ratios of observed interactions and the predicted probabilities in training data, where this problem is formalized as a linear program based on a probabilistic model. We compared the proposed method with the association method, the EM method and the SVM-based method using real interaction data. It is shown that a variant of the method is comparable to existing methods for binary data. It is also shown that the method outperforms existing methods for numerical data. AVAILABILITY: Programs transforming input data into LP format files are available upon request.

Algorithms↗
PubMed2003

Plasma levels of homovanillic acid and the response to risperidone in first episode untreated acute schizophrenia.

We have previously reported that risperidone might improve negative symptoms in schizophrenia by influencing noradrenergic neurons. In the present study, we focused on the clinical efficacy and mechanisms of risperidone towards positive symptoms in the acute phase of schizophrenia. Thirty-four patients meeting DSM-IV criteria for schizophrenia and treated with risperidone alone were evaluated regarding their clinical improvement using the Positive and Negative Syndrome Scale (PANSS) before and 2 weeks after risperidone administration, and blood samples were also drawn at the same times. Plasma concentrations of homovanillic acid (HVA) and 3-methoxy-4-hydroxyphenylglycol were analysed by high-performance liquid chromatography with electrochemical detection. Plasma HVA levels in the responders to the risperidone treatment (more than 50% improvement in scores of positive symptoms in PANSS) were higher than those of non-responders before risperidone administration. Furthermore, there was a negative trend between changes in plasma HVA levels and improvement of total scores for positive symptoms in PANSS. These results suggest that higher levels of plasma HVA before risperidone administration might be a predictor of a good response to risperidone treatment, and the influence of risperidone on dopaminergic activity might be associated with its efficacy in treating symptoms of schizophrenia in the acute phase.

Acute Disease↗
PubMed2003

Higher plasma 5-hydroxyindoleacetic acid levels are associated with SSRI-induced nausea.

We investigated the association between selective serotonin reuptake inhibitors (SSRIs; paroxetine or fluvoxamine) and nausea with regard to plasma 5-hydroxyindoleacetic acid (p5-HIAA) levels. Forty-eight patients meeting the DSM-IV criteria for major depressive disorder and treated with paroxetine or fluvoxamine participated in this study. p5-HIAA levels after SSRI administration were significantly higher in the nausea group than those in the nonnausea group (nausea group: 8.0 +/- 4.6 ng/ml; nonnausea group: 3.6 +/- 2.2 ng/ml; p < 0.01). On the other hand, no significant difference was found between the nausea and nonnausea group in terms of p5-HIAA levels before each drug administration. These results suggest that SSRI-induced nausea is associated with serotonergic hyperactivity in the gastrointestinal tract.

Acetophenones↗
PubMed2003

Efficient tree-matching methods for accurate carbohydrate database queries.

One aspect of glycome informatics is the analysis of carbohydrate sugar chains, or glycans, whose basic structure is not a sequence, but a tree structure. Although there has been much work in the development of sequence databases and matching algorithms for sequences (for performing queries and analyzing similarity), the more complicated tree structure of glycans does not allow a direct implementation of such a database for glycans, and further, does not allow for the direct application of sequence alignment algorithms for performing searches or analyzing similarity. Therefore, we have utilized a polynomial-time dynamic programming algorithm for solving the maximum common subtree of two trees to implement an accurate and efficient tool for finding and aligning maximally matching glycan trees. The KEGG Glycan database for glycan structures released recently incorporates our tree-structure alignment algorithm with various parameters to adapt to the needs of a variety of users. Because we use similarity scores as opposed to a distance metric, our methods are more readily used to display trees of higher similarity. We present the two methods developed for this purpose and illustrate its validity.

Algorithms↗
PubMed2002

Interaction between fluvoxamine and cotinine or caffeine.

We examined the relationships between plasma fluvoxamine concentrations and plasma levels of cotinine and caffeine, respectively, under steady-state conditions in 30 patients who met DSM-IV criteria for a major depressive disorder and who were being treated with fluvoxamine. The daily dosages of fluvoxamine ranged from 50 to 200 mg (mean +/- SD 108 +/- 42 mg). Eleven patients were smokers and the remaining 19 were nonsmokers. The plasma fluvoxamine concentrations were significantly higher in nonsmokers (0.92 +/- 0.40 ng/ml/mg) than in smokers (0.56 +/- 0.28 ng/ml/mg); in addition, a trend towards negative correlations was observed between the plasma fluvoxamine concentrations and the plasma cotinine levels, although it was not significant. Significant positive correlations were found between the plasma fluvoxamine concentrations and the plasma caffeine levels. These findings are compatible with those in earlier reports that cytochrome P450 1A2 plays a major role in fluvoxamine metabolism.

Adult↗
PubMed2000

Possible relationships between plasma carbamazepine-10,11-epoxide levels and antimanic efficacy and side effects in patients with schizoaffective disorde.

We examined the relationships of plasma levels of carbamazepine (CBZ) and its two major metabolites, carbamazepine-10,11-epoxide (CBZ-E) and carbamazepine-10,11-diol (CBZ-D), with antimanic efficacy and side effects in patients with schizoaffective disorder. Positive relationships were found among plasma concentrations of CBZ-E and the degree of clinical improvement and side effects, whereas neither plasma CBZ nor CBZ-D levels were correlated with the degree of clinical improvement or side effects. Copyright 2000 John Wiley & Sons, Ltd.

Journal Article↗