The DNA methylation inhibitor 5-aza-2’-deoxycytidine retards cell growth and alters gene expression in canine mammary gland tumor cells

Disruption of gene expression by DNA methylation changes is widely involved in tumorigenesis. Here,to investigate DNA methylation changes in canine, we treated a canine mammary gland tumor cell line with a DNA methylation inhibitor, 5-aza-2’-deoxycytidine (5-aza). Cell growth was significantly retarded following 5-aza treatment and the epithelial marker genes CDH1 and KRT18 were significantly up-regulated, whereas the mesenchymal marker genes CDH2 and VIM were significantly downregulated. We also found a significant decrease in DNA methylation level in the CDH1 promoter region by 5-aza treatment. These results showed for the first time in canine mammary gland tumor cells that inhibition of DNA methylation caused cell growth retardation and affected epithelial mesenchymal transition-related gene expression via changes in DNA methylation level

A Consideration on Sub-Optimal Weighting in Parameter Estimation

This paper deals with a parameter estimation method which yields the more suitable estimate of the parameter using noisy data or measured values. The estimation method is one that uses a kind of a weighted mean, and weighting at taking a weighted mean is interested in particularly. That is to say, as the grade of 'more suitable' depends upon the weighting, we can obtain the more suitable estimate by choosing the weighting coefficients suitablly. When the function which yields the estimate using finite measured values, i.e., the estimator is a particular form, sub-optimal weighting in the practical sense is discussed. Here, the concept of 'optimal' implies that the variance of the final estimate is minimum. And the particular form is one that both the denominator and the numerator of the estimator are first order formulas or second order formulas of finite measured values. And two theorems in relation to this problem are proposed and proved. Moreover, for an exsample of application of these theorems, a parameter estimation method is dealt with, which estimates the parameters of the pulse transfer function of a control system using the sampled measured values of the impulse response of that system

System Identification Using Fast Fourier Transform

Algorithms for system identification applying throughout Fast Fourier Transform (FFT) to the major calculating operations are introduced. It is shown that by using data of about as twice length as system settling time and by truncating the incorrect correlation functions resulting from them, errors owing to finiteness of data can be avoided. It is shown that so as to suppress the effects owing to statistical fluctuation of input data or output noise, superposition of data in frequency domain is effective, and also the damping terms of poles or zeros can be efficiently evaluated by utilizing the phase change of the spectra of the impulse response sequence. The proposed method can be efficiently applied to relatively higher order systems or relatively rapidly time-variant systems because of high accuracy and high speed processing of FFT. Moreover, it needs not to assume the order of the system a priori, and yields a reasonable lower order approximating system in itself

A Unified Approach to System Data Handling in CAD System for Designing Control Systems

System data handling in CAD sY8tem for designing control systems is discussed. A man-oriented data description method for a wide sense block diagram and its automatical transformation into the state space description is proposed. This work is a part of CAD system: CADPACS-T which has been under development for designing control systems in our laboratory. The proposal data description for a wide sense block diagram has the following features: 1) to correspond nicety to the block diagram and to be suitable for a man-oriented expression, 2) to express even a large scale system compactly by partitioning into some subsystems defined externally, 3) to be easy to add /or alter the input-output terminals, parameters or elements, and 4) to need not to assign the connection relationship explicitly owing to adopting the input-output terminal/line names. Moreover, system data handling in designing the PI controller for an actual boiler system expressed in a block diagram is taken up as an example

A General Purpose Simulator for Multivariable Control Systems

A high speed and high accuracy simulator whose data-handling is light and whose weak stability is assured even for stiff systems is discussed. This work is a part of CAD package : CADPACS-T which has been under development for the purpose of designing control systems utilizing TSS of a large scale digital computer in our laboratory. This simulator realizes high accuracy, high computational speed and high reliability adopting A-stable extrapolation methods to transform into a difference system, a recursive formula of an output interval to solve the difference equation, automatic choice of an optimal step length such that minimizes an predicted error, and evaluating error bounds closely near the actual errors in the point of numerical calculation. Moreover, in the point of data management, this realizes separation of program modules from data, common utilization of data and separation of investigation from simulation

Search for the Infrared Emission Features from Deuterated Interstellar Polycyclic Aromatic Hydrocarbons

We report the results of a search for emission features from interstellar deuterated polycyclic aromatic hydrocarbons (PAHs) in the 4um region with the Infrared Camera (IRC) onboard AKARI. No significant excess emission is seen in 4.3-4.7um in the spectra toward the Orion Bar and M17 after the subtraction of line emission from the ionized gas. A small excess of emission remains at around 4.4 and 4.65um, but the ratio of their intensity to that of the band emission from PAHs at 3.3-3.5um is estimated as 2-3%. This is an order of magnitude smaller than the values previously reported and also those predicted by the model of deuterium depletion onto PAHs. Since the subtraction of the ionized gas emission introduces an uncertainty, the deuterated PAH features are also searched for in the reflection nebula GN 18.14.0, which does not show emission lines from ionized gas. We obtain a similar result that excess emission in the 4um region, if present, is about 2% of the PAH band emission in the 3um region. The present study does not find evidence for the presence of the large amount of deuterated PAHs that the depletion model predicts. The results are discussed in the context of deuterium depletion in the interstellar medium.Comment: 24 pages, 6 figures, to appear in Ap

“Sidewalk” as a Realm of Users’ Interactions: simulating pedestrians’ densities at a commercial street in Cairo City

During the last four decades, researchers have developed many tools in order to investigate pedestrians’ behavior at sidewalks. Those tools tried to study sidewalks by investigating two main components: built environment and pedestrians’ movement. This paper presents a simulation for the pedestrians’ movement at a commercial street in Cairo, using an agent-based model. The model was designed in a way by which we could examine: pedestrians’ densities, the influence of types of uses on densities, the influence of flow-generators and destinations. In addition, we categorized the uses along the selected case of study by type of service and time spent by customer. The method which we utilized for this work could be divided into two main phases: The first phase, included site video-based survey at different times and days, by which we could calculate flow rates at each generator point, and test the influence of uses on the density along the sidewalk. The second phase was to develop the model. In parallel, we focused on the uses’ types and how it affects controls pedestrians’ densities. Our results referred to a strong relation between use’s type and densities’ distribution along the street

Comparison of DNA methylation levels of repetitive loci during bovine development

<p> Abstract</p> <p>Background</p> <p>DNA methylation of cytosine residues in CpG dinucleotide controls gene expression and dramatically changes during development. Its pattern is disrupted in cloned animals suggesting incomplete reprogramming during somatic cell nuclear transfer (the first reprogramming). However, the second reprogramming occurs in the germ cells and epigenetic errors in somatic cells of cloned animals should be erased. To analyze the DNA methylation changes on the spermatogenesis of bulls, we measured DNA methylation levels of three repetitive elements in blastocysts, blood and sperm.</p> <p>Methods</p> <p>DNA from PBLs (peripheral blood leukocytes), sperm and individual IVF (<it>in vitro</it> fertilized) and parthenogenetic blastocysts was isolated and bisulfite converted. Three repetitive elements; Satellite I, Satellite II and <it>art2</it> sequences were amplified by PCR with specific pairs of primers. The PCR product was then cut by restriction enzymes and analyzed by agarose gel electrophoresis for determining the DNA methylation levels.</p> <p>Results</p> <p>Both Satellite I and Satellite II sequences were highly methylated in PBLs, whereas hypo-methylated in sperm and blastocysts. The <it>art2</it> sequence was half methylated both in PBLs and sperm but less methylated in blastocysts. There was no difference in DNA methylation levels between IVF and parthenogenetic blastocysts.</p> <p>Conclusions</p> <p>These results suggest that there is a dynamic change of DNA methylation during embryonic development and spermatogenesis in cattle. Satellite I and Satellite II regions are methylated during embryogenesis and then de-methylated during spermatogenesis. However, <it>art2</it> sequences are not de-methylated during spermatogenesis, suggesting that this region is not reprogrammed during germ cell development. These results show dynamic changes of DNA methylation levels during bovine embryogenesis, especially genome-wide reprogramming in germ cells.</p

Modelling and Simulation of Urban Mobile Agents for Analyzing Mixed Flows in Urban Pedestrian Space

Since the 1990s, complex systems research has been developing agent simulations to explain the phenomena observed in urban spaces. In recent years, agent-based modelling has often been employed to successfully simulate pedestrian behaviour. In such studies, explanations using pedestrian counter flow phases have appeared sporadically. Most state-of-the-art models, however, do not generally consider mobile agents other than pedestrians or counter flows in at least two directions. In this paper, we consider agents such as pedestrians, vehicles, wheelchairs, bicycles and so on in urban pedestrian space (UPS), which we call urban mobile agents (UMAs). The aim of this research is to develop a simulation platform to support urban simulation research. The models of rule-based UMAs that we have been developing are used to analyze the micro-meso behaviours of the mixed flows in UPS. The content of this class of agent includes the pedestrian agent as per the simplified agent simulation of pedestrian flow (sASPF) rules as well as the vehicle agent and bicycle agent in the UPS, including a wheelchair agent in the coming research. Using these models, we explore the following approaches: (a) theoretical analyses of phase transitions such as laminar flow formation or blockade of pedestrian counter flows, with clarification of the relationship between the degree of pedestrian global density and the bias of the diagonal stepping probability, which is the right or left selection probability of avoidance behaviour; (b) the implementation of obstacle avoidance rules in the sASPF pedestrian agent model, and their comparison with published evacuation experiment results, so as to evaluate the performance of the obstacle avoidance function; (c) the development of a vehicle agent model to simulate pedestrian-vehicle mixed flow at a crossroads assuming a disaster scenario; (d) the development of a bicycle agent model by extending sASPF rules; and (e) consideration of a conceptual framework for interaction fields representing heterogeneous agent mixed flows, including vehicle, bicycle, pedestrian and wheelchair agents