Residues important for the function of a multihelical DNA binding domain in the new transcription factor family of Cam and Tet repressors

We report that some prokaryotic repressors including CamR andTetR belong to the same family. CamR and TetR bind to DNA usinga multihelical DNA binding domain (DBD) at the N-termini ofthe proteins, while the C-termini are important for regulatingthe DNA binding in a manner dependent on their co-factors (camphorfor CamR, tetracycline for TetR). In all, 11 important aminoacid positions have been identified in the CamR DBD by the systematicsubstitution of residues by Ala. Of the 11 positions, 10 areeither buried in the core, and thus important for creating thehydrophobic environment, or exposed on the surface, and thusimportant for binding to DNA. The eleventh residue, Gly, seemsto be important for a loop structure. The DNA binding mode ofthis type of DBD and a general mechanism of regulating theirDNA binding are discussed in reference to the crystal structureof TetR [Hinrichs et al., (1994) Science, 264, 418–420].     

Development of an epileptic seizure prediction algorithm using R–R intervals with self-attentive autoencoder

Epilepsy is a neurological disorder that may affect the autonomic nervous system (ANS) from 15 to 20 min before seizure onset, and disturbances of ANS affect R–R intervals (RRI) on an electrocardiogram (ECG). This study aims to develop a machine learning algorithm for predicting focal epileptic seizures by monitoring R–R interval (RRI) data in real time. The developed algorithm adopts a self-attentive autoencoder (SA-AE), which is a neural network for time-series data. The results of applying the developed seizure prediction algorithm to clinical data demonstrated that it functioned well in most patients; however, false positives (FPs) occurred in specific participants. In a future work, we will investigate the causes of FPs and optimize the developing seizure prediction algorithm to further improve performance using newly added clinical data.

     

FLASK-SG: A program to compute chemical equilibria in metamorphic petrology

Chemical equilibrium calculation program for metamorphic petrology, FLASK-SG, was written for Unix variants (Linux, IRIX, Tru64 UNIX). It is also ported to Windows 95/98. The user specifies a temperature, pressure, and substance amounts (in moles of any chemical formula in C–H–O–Si–Al–Ti–Fe–Mn–Mg–Ca–Na–K system) to this program, then it calculates the stable mineral assemblage, mineral amounts, and gas composition under the given conditions using Gibbs free energy minimization method with the Holland and Powell (1990) data set. Searching algorithm for the stable mineral assemblage is the Metropolis Monte Carlo method. The coding language is C++, and experimental object oriented programming style is adopted to make the main program part as a class library. Model-dependent functions such as fugacity coefficients and activities are implemented as virtual methods of the “systems” class, so they can be easily changed as methods of inherited class from the “systems” class. These characteristics are aimed for a future “simulation kit”.     

MC180295 Inhibited Epstein–Barr Virus-Associated Gastric Carcinoma Cell Growth by Suppressing DNA Repair and the Cell Cycle

DNA methylation of both viral and host DNA is one of the major mechanisms involved in the development of Epstein–Barr virus-associated gastric carcinoma (EBVaGC); thus, epigenetic treatment using demethylating agents would seem to be promising. We have verified the effect of {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295, which was discovered by screening for demethylating agents. {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295 inhibited cell growth of the EBVaGC cell lines YCCEL1 and SNU719 in a dose-dependent manner. In a cell cycle analysis, growth arrest and apoptosis were observed in both YCCEL1 and SNU719 cells treated with {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295. MKN28 cells infected with EBV were sensitive to {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295 and showed more significant inhibition of cell growth compared to controls without EBV infection. Serial analysis of gene expression analysis showed the expression of genes belonging to the role of BRCA1 in DNA damage response and cell cycle control chromosomal replication to be significantly reduced after {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295 treatment. We confirmed with quantitative PCR that the expression levels of BRCA2, FANCM, RAD51, TOP2A, and CDC45 were significantly decreased by {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295. LMP1 and BZLF1 are EBV genes with expression that is epigenetically regulated, and {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295 could up-regulate their expression. In conclusion, {"type":"entrez-nucleotide","attrs":{"text":"MC180295","term_id":"1885105835","term_text":"MC180295"}}MC180295 inhibited the growth of EBVaGC cells by suppressing DNA repair and the cell cycle.     

The viscoelastic properties of soybean curd (tofu) as affected by soymilk concentration and type of coagulant

The viscoelastic properties of different types of tofu were investigated. Soymilk concentrations were 5, 6, 7, 8 and 9%. Coagulants used were 30 mm CaSO₄ or 30 mm glucono‐delta‐lactone (GDL). As the concentration of soymilk was increased viscosity and handling difficulties increased. A high concentration of soymilk in tofu gave a high break stress and produced hard tofu. The four‐element Burgers model fitted the creep behaviour and both viscous and elastic parameters could be acquired from model analysis, reflecting changes in elasticity and viscosity of tofu. The constant viscous parameter in the model increased with increasing soymilk concentration. The viscous parameters of viscoelastic materials like tofu gel, obtained from small deformation tests, seemed to correlate, to some extent, with the break stress obtained from large deformation tests. For hard tofu production increasing the soymilk concentration within a certain range and the partial replacement of calcium sulphate coagulant by GDL could be effective options.     

Improvement in D-E Hysteresis Curve Squareness of PZT Thin Films—Effect of Oxygen Partial Pressure in High-Pressure Post-Annealing

A high-pressure annealing was applied to a post-annealing process for sol-gel derived PZT thin films. The squareness of D-E hysteresis curves changes depending on both total pressure and oxygen concentration. Moreover, the change follows the product of the total pressure and the oxygen concentration, which correspond to oxygen partial pressure P_O2. Where the P_O2 is higher than 0.03 MPa, few of the squareness of the hysteresis curve are excellent. The squareness of the hysteresis curves dramatically improve as the P_O2 decreases. Where the P_O2 is lower than 0.01 MPa, the squareness deteriorates slightly. These changes in the D-E hysteresis curves are thought to be explained by the generation of lead and oxygen vacancies as a function of the P_O2.     

Augmented reality-based block piling game with superimposed collapse prediction

Understanding what cannot be seen is difficult. Physical behavior can be explained on the basis of physical theories even if the behavior cannot be observed. Explanation of what is physically happening in the real world would become easy, however, if annotations were superimposed on the real objects. Herein, the authors demonstrate how an understanding of a physical event can be facilitated by overlapping a real-world situation with a simulation that predicts a future state. This idea is demonstrated in a game application in which a player stacks blocks into a pile until it collapses. In general, it is easy to estimate whether a block on the edge of a table will fall or not. However, it is more difficult to predict whether a stack of many blocks will collapse, and in what manner the stack will collapse. Even though previous research has demonstrated that the problem of how two-dimensionally stacked blocks collapse can be reduced to solving a sequence of convex quadratic programs, algorithms for convex quadratic programs require massive computational resources. Hence, the authors developed a fast and new algorithm based on a linear program. The proposed algorithm realizes real-time simulation based on physics that superimposes predicted collapse. The block that is predicted to fall is superimposed on the real block with a lit background projection. The system was evaluated in an experiment, and superimposed augmented reality annotation was observed to be efficient. The system was also demonstrated in game contests and received positive feedback and comments.     

Voltage Control of Static Var Compensator for a Remote System Interconnected by Long‐Distance AC Cables

The voltage variation in a remote system is large when the system is connected by long‐distance AC cables due to the cable capacitance. In Japan, the longest 54‐km 66‐kV AC submarine cable interconnection between the Kyushu mainland and Goto Islands was commissioned in 2005. It was requested to mitigate the voltage variation caused by switching off and on one circuit of the two circuits in the AC cables when a fault occurs. Since the conventional voltage control methods such as transformer tap changer or shunt capacitor and reactor banks are not sufficient because of their slow response time, a static var compensator (SVC) was installed on the Goto Islands. In such an application, an SVC control method should be developed so as not to override the existing voltage control systems. This paper describes the SVC control method developed for the Goto Islands AC interconnection project, which can be applied to similar situations. The effectiveness of the control method was verified by the results of effective value simulation and of field testing, which was implemented before the SVC was commissioned in 2007. © 2013 Wiley Periodicals, Inc. Electr Eng Jpn, 186(3): 19–30, 2014; Published online in Wiley Online Library ( wileyonlinelibrary.com ). DOI 10.1002/eej.22337     

Processing of nanolitre liquid plugs for microfluidic cell-based assays

Plugs, i.e. droplets formed in a microchannel, may revolutionize microfluidic cell-based assays. This study describes a microdevice that handles nanolitre-scale liquid plugs for the preparation of various culture setups and subsequent cellular assays. An important feature of this mode of liquid operation is that the recirculation flow generated inside the plug promotes the rapid mixing of different solutions after plugs are merged, and it keeps cell suspensions homogeneous. Thus, serial dilutions of reagents and cell suspensions with different cell densities and cell types were rapidly performed using nanolitres of solution. Cells seeded through the plug processing grew well in the microdevice, and subsequent plug processing was used to detect the glucose consumption of cells and cellular responses to anticancer agents. The plug-based microdevice may provide a useful platform for cell-based assay systems in various fields, including fundamental cell biology and drug screening applications.