Biomedical subjects
Toshio Shimizu
Publications and source records attributed to Toshio Shimizu.
Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction.
Reported performance of existing transmembrane (TM) topology prediction methods were often based on evaluations which neglected the risk of signal peptides (SP) being predicted as putative TM as well. Here, we evaluated 12 selected TM topology prediction methods (TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0, HMMTOP 2.0, SPLIT 3.5, TM Finder, and MPEx) for the effect of SP in prediction performance considering three SP treatments, namely: "remain" (untreated), "removed first", and "removed later". The results showed that the presence of SP significantly affected the prediction performance of the 12 selected TM topology prediction methods for all three predicted attributes (the number of transmembrane segments (TMSs), the number of TMSs plus position, and the N-tail location) and for the predicted topology (combined predictions of three attributes) by causing a reduction in prediction accuracy. In particular, lower prediction accuracies were obtained if SP is left untreated (remain) while significant increases were observed if SP is removed either first or later. However, between "removed first" and "removed later" SP treatments, the difference was statistically insignificant. In addition, we found that machine learning-based prediction methods were less affected by the presence of SP than hydropathy-based methods, but still the potential risk of degrading the prediction performance is there however to a lesser degree. Thus, when performing genome-wide analysis, the SP issue should be addressed during TM topology prediction.
[A case of myelopathy of unknown etiology with transient spinal automatism--electrophysiological study].
We reported a case of myelopathy of unknown etiology with transient spinal automatism. A 50-years old woman suffered from gait disturbance with weakness and abnormal involuntary movement of both lower limbs. The involuntary movement showed like as triple flexion reflex and appeared in the interval between some seconds and some ten seconds. It was consisted of non-reciprocal phasic-tonic discharges. In electrophysiological examination, long latency muscular responses were observed following F wave and MEP (motor evoked potential) in the abductor hallucis muscle. Excitability of motoneurons of lower limb muscles following stimulation of sural nerve was evaluated by means of H reflex and averaged surface EMGs. Short latency facilitation was induced in the soleus and tibialis anterior muscles contrary to inhibition in the control subjects. In this case, reduced activity of inhibitory and/or enhanced activity of excitatory interneurons to motoneurons attributed to the pathophysiology of spinal automatism.
Optically Active Seleninic Acids: Optical Resolution and Stability.
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Optical Resolution and Configurational Stability of Selenoxides Stabilized by Intramolecular Coordination.
2-((Dimethylamino)methyl)phenyl alkyl (or aryl) selenoxides, configurationally stabilized by intramolecular coordination of an amino group to the selenium atom, were optically resolved into their enantiomeric isomers by means of high-performance liquid chromatography using an optically active column packed with amylosecarbamate derivative/silica gel. This is the first example of the isolation of optically pure selenoxides without bulky substituents and also the first isolation of optically pure alkyl aryl selenoxides. The absolute configuration of the (-)-isomers could be assigned to be the S-form by comparison of their specific rotations, circular dichroism spectra, and behavior on the optically active column with those of the sulfur analogue, prepared by Andersen's method. Racemization of the optically active selenoxides was accelerated not only in acidic solution but also in basic media. This result indicates there are two different mechanisms for their racemization in acidic and basic media. The stabilization energy of the selenoxides by the intramolecular coordination of an amino group to the selenium atom was estimated to be ca. 3 kcal mol(-)(1) on the basis of variable-temperature (1)H NMR measurements.
Syntheses and Peculiar Behavior in Solutions of Optically Active Telluronium Salts.
A diastereomeric (epimeric) mixture of ethylmethylphenyltelluronium (1S)-(+)-camphor-10-sulfonate (dia.-1) was optically resolved by fractional recrystallization into the diastereomerically pure isomers (R)(Te)-1 and (S)(Te)-1. The absolute configurations of the isomers were determined by the X-ray crystallographic analysis of (R)(Te)-1. Enantiomerically pure (R)-ethylmethylphenyltelluronium perchlorate, tetrafluoroborate, p-chlorobenzenesulfonate, bornane-10-sulfonate, tetraphenylborate, and picrylsulfonate (R)-2-7 were isolated, respectively, by anion-exchange reactions of diastereomerically pure (R)(Te)-1. The optically active telluronium salts were found to show peculiar optical properties on their specific rotations and circular dichroism spectra in solutions compared with those of the corresponding sulfonium and selenonium salts. On the basis of NMR studies, the behavior on the optical properties of the optically active telluronium salts was found to be caused by a strong solvation in polar solvents.
Automatic brain tissue extraction method using erosion-dilation treatment (BREED) from three-dimensional magnetic resonance imaging T1-weighted data.
To improve the efficiency of brain image analysis, we propose a full-automatic method for extracting brain tissue from three-dimensional magnetic resonance imaging of T1-weighted data on the human head (brain tissue extraction method using erosion-dilation treatment [BREED]). The extraction processing is realized by combining signal intensity thresholding by means of the discriminant analysis method and an erosion-dilation treatment of the image. The accuracy of BREED is evaluated using both simulated and subject data. BREED can extract brain tissues with high accuracy (approximately 97%) for either simulated or subject data.
Clinical application of immunoreactivity of dihydropyrimidine dehydrogenase (DPD) in gastric scirrhous carcinoma treated with S-1, a new DPD inhibitory fluoropyrimidine.
BACKGROUND: A highly specific antibody against recombinant human dihydropyrimidine dehydrogenase (DPD) has been developed to immunohistochemically assess DPD expression in tumors. A new oral DPD inhibitory fluoropyrimidine (DIF), S-1, is reportedly effective against gastric scirrhous carcinoma. PATIENTS AND METHODS: In this study, the relationship between immunoreactivity to DPD in biopsy specimens and the effects of chemotherapy were investigated in 61 patients treated with first-line fluoropyrimidine-based chemotherapy (S-1:DIF, 5-FU:non-DIF) for gastric scirrhous carcinoma. RESULTS: The response rate was significantly higher in patients with DPD-positive tumors than in those with DPD-negative tumors in the S-1 group (45.5%, 10.0%: p < 0.05), as compared to the 5-FU group (0%, 5.6%: p = 0.398). According to the median survival time, there was no significant difference between patients with DPD-positive tumors (364 days) and those with DPD-negative tumors (406 days; p = 0.626) in either the S-1 group or the 5-FU group (181 days and 256 days, respectively; p = 0.543). CONCLUSION: This study indicates that S-1 may be effective even in gastric scirrhous carcinoma with a high level of DPD activity.