宿主体内生存戦略のための大腸菌ゲノム制御ネットワークの研究

博士(理工学)法政大学 (Hosei University

How We Know the Practical Impact of Clone Analysis

In order to develop and improve clone analysis techniques for industrial application, it is necessary to know about how those techniques provide impacts on clone management in industry. In this position paper, we discuss approaches to observing the practical impact of clone analysis on the basis of our experience in applying clone analysis into an industrial development process

Smoothness Analysis of Adversarial Training

Deep neural networks are vulnerable to adversarial attacks. Recent studies about adversarial robustness focus on the loss landscape in the parameter space since it is related to optimization and generalization performance. These studies conclude that the difficulty of adversarial training is caused by the non-smoothness of the loss function: i.e., its gradient is not Lipschitz continuous. However, this analysis ignores the dependence of adversarial attacks on model parameters. Since adversarial attacks are optimized for models, they should depend on the parameters. Considering this dependence, we analyze the smoothness of the loss function of adversarial training using the optimal attacks for the model parameter in more detail. We reveal that the constraint of adversarial attacks is one cause of the non-smoothness and that the smoothness depends on the types of the constraints. Specifically, the $L_\infty$ constraint can cause non-smoothness more than the $L_2$ constraint. Moreover, our analysis implies that if we flatten the loss function with respect to input data, the Lipschitz constant of the gradient of adversarial loss tends to increase. To address the non-smoothness, we show that EntropySGD smoothens the non-smooth loss and improves the performance of adversarial training.Comment: 22 pages, 7 figures. In V3, we add the results of EntropySGD for adversarial trainin

Bayesian Approach to Find a Long-Term Trend in Erratic Polarization Variations Observed in Blazars

We developed a method to separate a long-term trend from observed temporal variations of polarization in blazars using a Bayesian approach. The temporal variation of the polarization vector is apparently erratic in most blazars, while several objects occasionally exhibited systematic variations, for example, an increase of the polarization degree associated with a flare of the total flux. We assume that the observed polarization vector is a superposition of distinct two components, a long-term trend and a short-term variation component responsible for short flares. Our Bayesian model estimates the long-term trend which satisfies the condition that the total flux correlates with the polarized flux of the short-term component. We demonstrate that assumed long-term polarization components are successfully separated by the Bayesian model for artificial data. We applied this method to photopolarimetric data of OJ 287, S5 0716+714, and S2 0109+224. Simple and systematic long-term trends were obtained in OJ 287 and S2 0109+224, while no such a trend was identified in S5 0716+714. We propose that the apparently erratic variations of polarization in OJ 287 and S2 0109+224 are due to the presence of the long-term polarization component. The behavior of polarization in S5 0716+714 during our observation period implies the presence of a number of polarization components having a quite short time-scale of variations.Comment: 12 pages, 7 figures, accepted for publication in PAS

Towards an Analysis of Who Creates Clone and Who Reuses it

Code clone analysis is valuable because it can reveal reuse behaviours efficientlyfrom software repositories. Recently, some code reuse analyses using clonegenealogies and code clones over multiple projects were conducted. However, mostof the conventional analyses do not consider the developers’ individual difference toreuse behaviors. In this paper, we propose a method for code reuse analysis whichtakes particular note of the differences among individuals. Our analysis methodclarifies who reused whose source code across multiple repositories. We believethe result might provide us with constructive perceptions such as characteristics ofreused code itself by multiple developers, and developers who implement reusablecode

Increase of GADD34 expression in skeletal muscle by ATRA

All-trans retinoic acid (ATRA) increases the sensitivity to unfolded protein response in differentiating leukemic blasts. The downstream transcriptional factor of PERK, a major arm of unfolded protein response, regulates muscle differentiation. However, the role of growth arrest and DNA damage-inducible protein 34 (GADD34), one of the downstream factors of PERK, and the effects of ATRA on GADD34 expression in muscle remain unclear. In this study, we identified ATRA increased the GADD34 expression independent of the PERK signal in the gastrocnemius muscle of mice. ATRA up-regulated GADD34 expression through the transcriptional activation of GADD34 gene via inhibiting the interaction of homeobox Six1 and transcription co-repressor TLE3 with the MEF3-binding site on the GADD34 gene promoter in skeletal muscle. ATRA also inhibited the interaction of TTP, which induces mRNA degradation, with AU-rich element on GADD34 mRNA via p-38 MAPK, resulting in the instability of GADD34 mRNA. Overexpressed GADD34 in C2C12 cells changes the type of myosin heavy chain in myotubes. These results suggest ATRA increases GADD34 expression via transcriptional and post-transcriptional regulation, which changes muscle fiber type

Nanocomposite of silk fibroin nanofiber and montmorillonite: Fabrication and morphology

The purpose of our research is creating a new nanocomposite material. Generally silk fibroin (SF) is regarded as a promising base material for biomedical uses. The incorporation of montmorillonite (MMT) into SF fibers would improve physical properties of the SF fibers. We investigated a new method of combining electospun SF with MMT. Specifically, electrospun silk nanofibers were treated with methanol and dipped in a MMT suspension. We could obtain a nanosheet composite of silk nanofibers and MMT. Their ultrastructures were successfully visualized by high resolution transmission electron microscopy. This compound was comprised of individual silk nanofibers surrounded by thin layers of MMT, each with a thickness of about 1.2 nm. This structure was confirmed by elemental analysis. We also performed IR, NMR and X-ray diffraction analyses in conjunction with morphological data. Conclusively we obtained a new composite of silk nanofiber and MMT, which has never been reported. Using this unique nanocomposite biological tests of its application for a scaffold for tissue engineering are under way.ArticleINTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES. 57:124-128 (2013)journal articl

Regional Assessment of Recharge Elevation of Tap Water Sources Using the Isoscape Approach

The importance of mountains as “natural water towers” has been quantified by comparing water budgets in upstream (mountain) and downstream (lowland) areas, but their importance for tap water supplies has not been assessed. Here, we propose an isoscape approach to estimate the mean recharge elevation of tap water sources (rivers, reservoirs, springs, and wells) and apply it to a region in central Japan as a case study. Errors in the estimation of mean recharge elevation were estimated at 90–140 m. Results show that mean recharge elevations for about 90% of sources in the region are at 1000 m above sea level or higher. A little over half of the land area is above that elevation, while 98% of the population lives below it. These findings indicate that tap water disproportionally depends on recharge in mountains and is disproportionately supplied to lowland residents. Higher locations of spring water sources and longer (vertical) distances of groundwater flow for well water sources make the recharge-to-population disproportionality more remarkable. Furthermore, our results suggest that larger cities require higher natural water towers to meet greater water demand, complemented by intermunicipal water suppliers. Some low-elevation municipalities depend heavily on water recharged in mountains well outside their territories. The method proposed here helps clarify how people depend on water supplies from mountains, providing essential knowledge for integrated management of mountains and water resources