Predicting Protein Secondary Structure Using Stochastic Tree Grammars

We propose a new method for predicting protein secondary structure of a given amino acid sequence, based on a training algorithm for the probability parameters of a stochastic tree grammar. In particular, we concentrate on the problem of predicting -sheet regions, which has previously been considered difficult because of the unbounded dependencies exhibited by sequences corresponding to -sheets. To cope with this difficulty, we use a new family of stochastic tree grammars, which we call Stochastic Ranked Node Rewriting Grammars, which are powerful enough to capture the type of dependencies exhibited by the sequences of -sheet regions, such as the parallel and anti-parallel dependencies and their combinations. The training algorithm we use is an extension of the inside-outside algorithm for stochastic context-free grammars, but with a number of significant modifications. We applied our method on real data obtained from the HSSP database (Homology-derived Secondary Structure of Proteins Ver 1.0) and the results were encouraging: Our method was able to predict roughly 75 percent of the -strands correctly in a systematic evaluation experiment, in which the test sequences not only have less than 25 percent identity to the training sequences, but are totally unrelated to them. This figure compares favorably to the predictive accuracy of the state-of-the-art prediction methods in the field, even though our experiment was on a restricted type of -sheet structures and the test was done on a relatively small data size. We also stress that our method can predict the structure as well as the location of -sheet regions, which was not possible by conventional methods for secondary structure prediction. Extended abstracts of parts of the work presented in this paper have appeared in (Abe & Mamitsuka, 1994) and (Mamitsuka & Abe, 1994).     

Potential of the histoculture drug-response assay to contribute to cancer patient survival

The histoculture drug-response assay (HDRA) was recently evaluated in a retrospective clinical trial and was found to correlate to drug sensitivity, resistance, and patient survival. To further investigate the potential of HDRA to contribute to patient survival, 215 patients with gastric cancer from 45 medical centers were tested with the HDRA in a blinded study after resection of the primary lesion. One hundred sixty-eight patients received at least 20 mg/m2 of mitomycin C and a minimum of 30 g UFT, a mixture of tegafur and uracil at a molar ratio of 1:4, thereby making them eligible for the study. Of these cases 128 were evaluable by the HDRA. The evaluable patient tumors were tested by the HDRA with the [3H]thymidine incorporation end point measured by microautoradiography to be drug "sensitive" or "resistant." The in vitro conditions for distinguishing sensitivity and resistance that matched the response rates for historical controls for gastric carcinoma were 90% inhibition rate and 0.12 microgram/ml for mitomycin C and 70% inhibition rate and 1 microgram/ml for 5-fluorouracil, respectively. Most importantly in the blinded study, the overall and disease-free survival rates of the HDRA-sensitive group were found to be significantly higher than those of the HDRA-resistant group tested under the above conditions. The data further indicate the importance of three-dimensional tumor culture for obtaining accurate clinical information. The results demonstrate that the HDRA response correlates to patient survival, which suggests the potential of the HDRA to contribute to patient survival in gastric cancer when used prospectively.     

Japanese national project on intermetallics and composites

Since 1989 a group of national laboratories, universities and member companies have been challenging a series of tough research areas concerning advanced materials used by, for example, space planes, and hypersonic aircraft to withstand the severest of environments. As an eight-year national project, intermetallic compounds, Ti?Al and Nb?Al, petroleum pitch-based and coal tar pitch-based carbon/carbon composites, and fiber-reinforced intermetallic compound composites have been taken up. Extensive research activities have been covered as follows:

• fundamental characteristics,
• design of the material,
• casting, rolling, powdering, forming and near net shaping,
• surface treatment for oxidation resistance.

The authors briefly review major R&D activities and achievements obtained so far, focusing on these intermetallics, carbon/carbon composites, and fiber-reinforced intermetallic compounds.     

A concept of analog-digital merged circuit architecture for future VLSI's

This paper describes the new analog-digital merged circuit architecture which utilizes the pulse modulation signals. By reconsidering the information representing and processing principles, and the circuit operations governed by the physical law, the new circuit architecture is proposed to overcome the limitations of existent VLSI technologies. The proposed architecture utilizes the pulse width modulation (PWM) signal which has analog information in the time domain, and be constructed with the novel PWM circuits which carry out the multi-input arithmetic operations, the signal conversions and the data storage. It has a potential to exploit the high speed switching capability of deep sub-m devices, and to reduce the number of devices and the power dissipation to one-tenth of those of the binary digital circuits. Therefore it will effectively implement the intelligent processing systems utilizing 0.5–0.2 m scaled CMOS devices.     

Pressure effect on anomalous suppression ofT c around x=1/8 in La2−xBaxCuO4 and La1.8−xx Nd0.2BaxCuO4

In La_2–xBa_xCuO₄ (LBCO) and La_1.8–xNd_0.2Ba_xCuO₄ (LNBCO), the low-temperature structural change at T₁ (=60–110K), resulting from tilt of the CuO₆ octahedra, is easily suppressed at high pressures. However, the structural change of LNBCO (x=0.125) remains up to 2GPa though it jumps from T₁(110K) to T* (60K), where the electric resistivity begins to upturn, at 0-1.5GPa. The upturn of is also suppressed at high pressures, and the superconducting critical temperature T_c is fully restored except in a very narrow x-range around x=0.125. The T_c for x 0.125 is appreciably lower at 2GPa than those for other Ba-contents.     

Paracrine stimulation of cell growth by cholecystokinin/gastrin through cholecystokinin-B receptor on GH3 cells in vitro

Self-reported reproductive histories of male employees of a lead-zinc smelter were related to pre-conception measures of lead exposure to examine associations between paternal occupational lead exposure and adverse pregnancy outcome. The participants reported 2,021 pregnancies which resulted in 1,684 normal live births, 12 stillbirths, 30 birth defects, 203 spontaneous abortions, and 92 "other" outcomes. Birth defects and stillbirths were combined for the analysis. The risk of a stillbirth or birth defect was elevated for pre-conception employment in a high-lead-exposure compared with a low-lead-exposure job (odds ratio = 2.7, 95% confidence interval = 0.7, 9.6). A similar risk was found for pre-conception blood lead levels of 25-39 μg/dL and >/= 40 μg/dL when compared with blood lead levels of < 25 μg/dL (OR = 2.9, 95% CI = 0.6, 13.3, and OR = 2.5, 95% CI = 0.5, 11.6, respectively). No association was found between pre-conception lead exposure and spontaneous abortion. A relatively low response rate to the questionnaire and potentially erroneous reporting of reproductive outcomes by male workers are limitations of the study.     

Size estimation method for patch used in reconstruction of LV cavity

The reconstruction of LV cavity is accomplished by suturing a patch to the viable myocardium to exclude the infarcted area from the high LV pressures. However, there is no clear guideline to estimate the size of patch used for LV reconstruction. We have designed a new method to determine the correct patch size, and applied it in 5 cases. The suture line of the patch is at the junction of contractile (functional) and infarcted portions of LV. The patch size is determined by the length of AB, termed "a", as the base, where "point A" represents the junction on the LV anterior wall side, and "point B" the junction of the LV posterior wall side, from RAO 30 degrees projection of the left ventriculogram obtained by cardiac catheterization. In LV aneurysm, we designed the patch in the range of a/2 < l < or = pi a/2, where patch length on RAO 30 degrees is considered "l". An effort was made to reconstruct to normalize LV volume and contour by designing the patch size to be a/2 < l < a, particularly when the contractile portion was enlarged by aneurysm. On the other hand, in post AMI VSD, LV contractile portion is not enlarged in early stage. Therefore, the patch was designed in the range of a < l < or = pi a/2 to maintain LV volume. Postoperative LV volume can be calculated prior to surgery, by using the lengths of the designed patch. Postoperative analysis indicated that the actual LV volume and contour were almost identical to our estimation. This method is very useful in planning the patch size for LV reconstruction.     

Effect of strong gravitational field on oriented crystalline perovskite-type manganese oxide La<Subscript>1−<Emphasis Type="Italic">x</Emphasis></Subscript>Sr<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>MnO<Subscript>3</Subscript>

We report the effect of a strong gravitational field on oriented crystalline perovskite-type manganese oxide La_1?x Sr _x MnO₃ (LSMO). The perovskite-type manganese oxides La_1?x Sr _x MnO₃ (LSMO) have been investigated for giant magnetoresistance (GMR) by controlling the hole-doping level (x). A strong gravitational field can change in crystalline state and the enhancement of usual diffusion. We subjected oriented crystalline La_1?x Sr _x MnO₃ with different grain and grain-boundary (GBs) Sr concentrations to a strong gravitational field and investigated the resulting changes in the A-site cation diffusion and physical properties of the material. Electron probe micro-analysis (EPMA) results showed appearance of the GBs where the Sr concentration was quite high compared with in other GBs. The quantitative analysis at the grain and GBs indicated that cation diffusion was more enhanced than the annealed one. The temperature dependence of the magnetic susceptibility of the gravity samples changed with the Sr concentration in the grains. The temperature dependence of the resistivity curves of the gravity sample showed several abrupt changes, which corresponded to phase transitions at the grains and GBs, which may be caused by composition changes.     

Experiment and modelling of cantilever-based electromagnetic energy harvester driven by direct impact of spherical ball

Microsystem Technologies - We carried out a numerical analysis and an experimental investigation of the nonlinear resonance characteristics of an electromagnetic vibration energy harvester driven...