Hiromichi Nagao

Local time features of geomagnetic jerks

The geomagnetic jerk amplitudes, which are defined as abruptness of changes in the trends of geomagnetic time series, are investigated with geomagnetic monthly means computed from hourly mean values at each local time. A statistical time series model in which the trend component is expressed by a second order spline function with variable knots is constructed for each time series. The optimum parameter values of the model including positions of knots are estimated by the maximum likelihood method, and the optimum number of parameters including the number of knots are determined based on the Akaike Information Criterion (AIC). The jerks are detected objectively and automatically by regarding the optimized positions of knots as the occurrence epochs. This analysis reveals that the spatial distributions of jerk amplitudes essentially do not depend on the local time, which indicates that the jerks cannot be explained by abrupt changes in intensities of latitudinally flowing external currents such as the field-aligned currents. Longitudinally flowing currents, on the other hand, such as the ring current could explain the distributions. The abrupt changes of the ring current intensity are estimated from the distributions of jerk amplitudes in the eastward component in 1969, 1978, and 1991 supposing that an abrupt change in the ring current intensity causes a jerk. However those estimated changes cannot consistently explain the distributions of the jerks in the northward and downward components. Therefore it is plausible that the jerks which occurred in 1969, 1978, and 1991 are not caused by external sources but internal ones. It is also confirmed that the occurrence epochs of jerks in the southern hemisphere are a few years after those of the 1969 and 1978 jerks in the northern hemisphere, and it is also found that the jerk in the southern hemisphere occurred a few years after the occurrence of the 1991 jerk in Europe. Taking these time lags in occurrence epochs into account, it can be said that the 1969, 1978, and 1991 jerks are global phenomena.

Scientific survey and monitoring of the off-shore seismogenic zone with Tokai SCANNER: submarine cabled network observatory for nowcast of earthquake recurrence in the Tokai region, Japan

Existence of fluid on seismogenic zones has a key role on great earthquakes. The electrical conductivity structures obtained by electromagnetic survey across the great earthquake zones show that the seismically locked zones correspond to the low conductive zones. The low conductivity is possibly interpreted as relatively low fluid content. For more discussion on the role of fluid to earthquake occurrence, we have just started an electromagnetic and seismological monitoring by using long submarine cables off Toyohashi, the southwest Japan Island. The cables are located on the Tokai seismogenic zone, where both slow-slipping and locked zones are obvious by GPS observation. Here, we introduce the recent and upcoming situations of the project.

Automatic Detection of Geomagnetic Jerks by Applying a Statistical Time Series Model to Geomagnetic Monthly Means

A geomagnetic jerk is defined as a sudden change in the trend of the time derivative of geomagnetic secular variation. A statistical time series model is applied to monthly means of geomagnetic eastward component obtained at 124 geomagnetic observatories to detect geomagnetic jerks objectively. The trend component in the model is expressed by a second order spline function with variable knots. The optimum parameter values of the model including positions of knots are estimated by the maximum likelihood method, and the optimum number of parameters is determined based on the Akaike Information Criterion. The geomagnetic jerks are detected objectively and automatically by regarding the determined positions of knots as the occurrence epochs. This analysis reveals that the geomagnetic jerk in 1991 is a local phenomenon while the 1969 and 1978 jerks are confirmed to be global phenomena.

Bayesian experts in exploring reaction kinetics of transcription circuits

Motivation Biochemical reactions in cells are made of several types of biological circuits. In current systems biology, making differential equation (DE) models simulatable in silico has been an appealing, general approach to uncover a complex world of biochemical reaction dynamics. Despite of a need for simulation-aided studies, our research field has yet provided no clear answers: how to specify kinetic values in models that are difficult to measure from experimental/theoretical analyses on biochemical kinetics. Results: We present a novel non-parametric Bayesian approach to this problem. The key idea lies in the development of a Dirichlet process (DP) prior distribution, called Bayesian experts, which reflects substantive knowledge on reaction mechanisms inherent in given models and experimentally observable kinetic evidences to the subsequent parameter search. The DP prior identifies significant local regions of unknown parameter space before proceeding to the posterior analyses. This article reports that a Bayesian expert-inducing stochastic search can effectively explore unknown parameters of in silico transcription circuits such that solutions of DEs reproduce transcriptomic time course profiles. Availability: A sample source code is available at the URL http://daweb.ism.ac.jp/∼yoshidar/lisdas/ Contact: yoshidar@ism.ac.jp

Estimating cellular parameters through optimization procedures: elementary principles and applications

Construction of quantitative models is a primary goal of quantitative biology, which aims to understand cellular and organismal phenomena in a quantitative manner. In this article, we introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. The aim of optimization is to minimize the sum of squared errors (SSE) in a prediction or to maximize likelihood. A (local) maximum of likelihood or (local) minimum of the SSE can efficiently be identified using gradient approaches. Addition of a stochastic process enables us to identify the global maximum/minimum without becoming trapped in local maxima/minima. Sampling approaches take advantage of increasing computational power to test numerous sets of parameters in order to determine the optimum set. By combining Bayesian inference with gradient or sampling approaches, we can estimate both the optimum parameters and the form of the likelihood function related to the parameters. Finally, we introduce four examples of research that utilize parameter optimization to obtain biological insights from quantified data: transcriptional regulation, bacterial chemotaxis, morphogenesis, and cell cycle regulation. With practical knowledge of parameter optimization, cell and developmental biologists can develop realistic models that reproduce their observations and thus, obtain mechanistic insights into phenomena of interest.

Time-Series Modeling of Tide Gauge Records for Monitoring of the Crustal Activities Related to Oceanic Trench Earthquakes Around Japan

Tide gauge observations along the coastline of Japan have recorded the land sinking due to the continuous subduction of the oceanic plates, indicating that stress and strain energies have been accumulating at the plate boundary, which would eventually cause large oceanic trench earthquakes like the 2011 Great East Japan Earthquake. The proposed method extracts such long-term activities of the Earths crust together with rapid displacements related to earthquakes, even before the establishment of the global positioning system, from monthly mean data of the sea levels. A state space model decomposes the tide gauge time series into trend, seasonal, autoregressive and observation noise components, each of which are estimated using the particle filter algorithm. The spatial and temporal distributions of the extracted trend component clearly indicate high-risk regions, near which giant earthquakes have occurred or are predicted to occur. A multivariate analysis of the observatories located at the northeast coast of Japan successfully determines the past crustal displacement in the case of the 1978 Off-Miyagi Earthquake. The proposed method has the potential application for monitoring crustal activities related to the accumulation of earthquake energy.

Development of a New Cabled Observatory "Tokai SCANNER"

A new cabled observatory Tokai SCANNER (Tokai Submarine Cabled Network Observatory for Nowcast of Earthquake Recurrences) was completed in April 2007. The system is located off the coast of Toyohashi-city where huge earthquakes are anticipated and continuous long-term monitoring is needed to promote seismic study. A new junction box which is equipped with underwater mateable connectors was installed at the end of the cable. The cable itself will be also applied to electromagnetically study for the inner structure of crust. This paper describes the outline of the Tokai SCANNER and initial evaluation results of the component units.

Bayesian Inference of Forces Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes

Cellular structures are hydrodynamically interconnected, such that force generation in one location can move distal structures. One example of this phenomenon is cytoplasmic streaming, whereby active forces at the cell cortex induce streaming of the entire cytoplasm. However, it is not known how the spatial distribution and magnitude of these forces move distant objects within the cell. To address this issue, we developed a computational method that used cytoplasm hydrodynamics to infer the spatial distribution of shear stress at the cell cortex induced by active force generators from experimentally obtained flow field of cytoplasmic streaming. By applying this method, we determined the shear-stress distribution that quantitatively reproduces in vivo flow fields in Caenorhabditis elegans embryos and mouse oocytes during meiosis II. Shear stress in mouse oocytes were predicted to localize to a narrower cortical region than that with a high cortical flow velocity and corresponded with the localization of the cortical actin cap. The predicted patterns of pressure gradient in both species were consistent with species-specific cytoplasmic streaming functions. The shear-stress distribution inferred by our method can contribute to the characterization of active force generation driving biological streaming.

Chapter 12 - Stacking Strategy for Acquisition of an ACROSS Transfer Function

Abstract Development of a powerful stacking technique is important in active monitoring in order to effectively enhance the signal-to-noise ratio (SNR) by utilizing not only quiet nighttime data but also noisy daytime data. Here we propose a stacking technique for data obtained by the Accurately Controlled Routinely Operated Signal System (ACROSS) with a reasonable method for noise level evaluation. An essential point is that the SNR would enhance by data stacking in reciprocal proportion to the square root of the observation time period. We show an application of this stacking method to real seismic and electromagnetic data obtained at our observation test site of ACROSS.

Seismic Wavefield Imaging of Long-Period Ground Motion in the Tokyo Metropolitan Area, Japan

Long-period ground motions due to large earthquakes can cause devastating disasters, especially in urbanized areas located on sedimentary basins. To assess and mitigate such damage, it is essential to rapidly evaluate seismic hazards for infrastructures, which can be simulated by seismic response analyses that use waveforms at the base of each infrastructure as an input ground motion. The present study reconstructs the seismic wavefield in the Tokyo metropolitan area located on the Kanto sedimentary basin, Japan, from seismograms of the Metropolitan Seismic Observation network (MeSO-net). The obtained wavefield fully explains the observed waveforms in the frequency band of 0.10–0.20 Hz. This is attributed to the seismic wavefield imaging technique proposed by Kano et al. [2017], which implements the replica exchange Monte Carlo method to simultaneously estimate model parameters related to the subsurface structure and source information. Further investigation shows that the reconstructed seismic wavefield lower than 0.30 Hz is of high quality in terms of variance reduction, which quantifies a misfit in waveforms, but that the variance reduction rapidly worsens in higher frequencies. Meanwhile, the velocity response spectra show good agreement with observations up to 0.90 Hz in terms of the combined goodness-of-fit, which is a measure of misfit in the velocity response spectra. Inputting the reconstructed wavefield into seismic response analyses, we can rapidly assess the overall damage to infrastructures immediately after a large earthquake.