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A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)
Kakioka Ryo,Kokita Tomoyuki,Kumada Hiroki,Watanabe Katsutoshi
BMC Genomics , 2013, DOI: 10.1186/1471-2164-14-32
Abstract: Background The construction of linkage maps is a first step in exploring the genetic basis for adaptive phenotypic divergence in closely related species by quantitative trait locus (QTL) analysis. Linkage maps are also useful for comparative genomics in non-model organisms. Advances in genomics technologies make it more feasible than ever to study the genetics of adaptation in natural populations. Restriction-site associated DNA (RAD) sequencing in next-generation sequencers facilitates the development of many genetic markers and genotyping. We aimed to construct a linkage map of the gudgeons of the genus Gnathopogon (Cyprinidae) for comparative genomics with the zebrafish Danio rerio (a member of the same family as gudgeons) and for the future QTL analysis of the genetic architecture underlying adaptive phenotypic evolution of Gnathopogon. Results We constructed the first genetic linkage map of Gnathopogon using a 198 F2 interspecific cross between two closely related species in Japan: river-dwelling Gnathopogon elongatus and lake-dwelling Gnathopogon caerulescens. Based on 1,622 RAD-tag markers, a linkage map spanning 1,390.9 cM with 25 linkage groups and an average marker interval of 0.87 cM was constructed. We also identified a region involving female-specific transmission ratio distortion (TRD). Synteny and collinearity were extensively conserved between Gnathopogon and zebrafish. Conclusions The dense SNP-based linkage map presented here provides a basis for future QTL analysis. It will also be useful for transferring genomic information from a “traditional” model fish species, zebrafish, to screen candidate genes underlying ecologically important traits of the gudgeons.
On the Convergence of Observed Partial Likelihood under Incomplete Data with Two Class Possibilities  [PDF]
Tomoyuki Sugimoto
Open Journal of Statistics (OJS) , 2014, DOI: 10.4236/ojs.2014.42012
Abstract:

In this paper, we discuss the theoretical validity of the observed partial likelihood (OPL) constructed in a Coxtype model under incomplete data with two class possibilities, such as missing binary covariates, a cure-mixture model or doubly censored data. A main result is establishing the asymptotic convergence of the OPL. To reach this result, as it is difficult to apply some standard tools in the survival analysis, we develop tools for weak convergence based on partial-sum processes. The result of the asymptotic convergence shown here indicates that a suitable order of the number of Monte Carlo trials is less than the square of the sample size. In addition, using numerical examples, we investigate how the asymptotic properties discussed here behave in a finite sample.

Ko Tae Mun, Ko Chung Hee, and the Osaka Family Origins of North Korean Successor Kim Jong Un
Kokita Kiyohito,Tessa Morris-Suzuki,Mark Selden
Asia-Pacific Journal : Japan Focus , 2011,
Abstract: The following article by Kokita Kiyohito, on the family origins of Kim Jong Un, the leader designate of North Korea, is illuminating above all for the language, assumptions and treatment of issues related to North Korea in contemporary Japanese media, including the Asahi. Two brief commentaries locate some of the issues in broader perspective. The headline and article are taken from the Asahi’s weekly Aera; photos have been provided from other sources. The major story addressed in the commentary by Tessa Morris-Suzuki is the collaboration of the Japanese government and the International Red Cross in arranging the migration of more than 93,000 Korean residents of Japan, who had been deprived of Japanese citizenship following Japan’s wartime defeat, to North Korea. Mark Selden examines a range of issues related to the perspective of the Japanese journalist on Zainichi Koreans and North Korea.
Asymptotic Optimality of Estimating Function Estimator for CHARN Model
Tomoyuki Amano
Advances in Decision Sciences , 2012, DOI: 10.1155/2012/515494
Abstract: CHARN model is a famous and important model in the finance, which includes many financial time series models and can be assumed as the return processes of assets. One of the most fundamental estimators for financial time series models is the conditional least squares (CL) estimator. However, recently, it was shown that the optimal estimating function estimator (G estimator) is better than CL estimator for some time series models in the sense of efficiency. In this paper, we examine efficiencies of CL and G estimators for CHARN model and derive the condition that G estimator is asymptotically optimal. 1. Introduction The conditional least squares (CL) estimator is one of the most fundamental estimators for financial time series models. It has the two advantages which can be calculated with ease and does not need the knowledge about the innovation process (i.e., error term). Hence this convenient estimator has been widely used for many financial time series models. However, Amano and Taniguchi [1] proved it is not good in the sense of the efficiency for ARCH model, which is the most famous financial time series model. The estimating function estimator was introduced by Godambe ([2, 3]) and Hansen [4]. Recently, Chandra and Taniguchi [5] constructed the optimal estimating function estimator (G estimator) for the parameters of the random coefficient autoregressive (RCA) model, which was introduced to describe occasional sharp spikes exhibited in many fields and ARCH model based on Godambe's asymptotically optimal estimating function. In Chandra and Taniguchi [5], it was shown that G estimator is better than CL estimator by simulation. Furthermore, Amano [6] applied CL and G estimators to some important time series models (RCA, GARCH, and nonlinear AR models) and proved that G estimator is better than CL estimator in the sense of the efficiency theoretically. Amano [6] also derived the conditions that G estimator becomes asymptotically optimal, which are not strict and natural. However, in Amano [6], G estimator was not applied to a conditional heteroscedastic autoregressive nonlinear model (denoted by CHARN model). CHARN model was proposed by H？rdle and Tsybakov [7] and H？rdle et al. [8], which includes many financial time series models and is used widely in the finance. Kanai et al. [9] applied G estimator to CHARN model and proved its asymptotic normality. However, Kanai et al. [9] did not compare efficiencies of CL and G estimators and discuss the asymptotic optimality of G estimator theoretically. Since CHARN model is the important and rich model, which
1,1′,2,2′,3,3′,4,4′-Octamethylferrocenium 2,5-dibromo-4-hydroxy-3,6-dioxocyclohexa-1,4-dien-1-olate
Tomoyuki Mochida
Acta Crystallographica Section E , 2011, DOI: 10.1107/s1600536811025499
Abstract: In the title salt, octamethylferrocenium bromanilate, [Fe(C9H13)2](C6HBr2O4), the Fe atom and the bromanilate anion lie on a mirror plane. The octamethylferrocenium cation adopts an eclipsed conformation. An intramolecular O—H...O hydrogen bond is present in the bromanilate anion. In the crystal, the cations and anions are stacked alternately, forming a one-dimensional columnar structure along [010].
Politically Correct Racism and the Geisha Novel: The Psychology of Sophisticated Racism Mirrors that of Ethnic Jokes
TANAKA, Tomoyuki
Electronic Journal of Contemporary Japanese Studies , 2006,
Abstract: In Section 1, politically correct racism (PC racism) is defined as an act with racist intent, justified by righteous appearance, with popularity or near-total acceptance because of its righteous appearance. In Section 2, after presenting a theory of jokes based on analyses by Sigmund Freud and Marvin Minsky, I show that the pleasure one derives from PC racism is similar to that derived from ethnic jokes. In Section 3, I point out the inaccuracies and prejudice contained in the novel Memoirs of a Geisha by comparing it with the Japanese version. Based on the study by Anne Allison of the American reception of the novel, I explain its surprising popularity using PC racism. Pleasures of romanticized subjugation and pleasures of hating the Japanese are made acceptable by the politically-correct appearance. Finally in Section 4, I characterize the geisha film as a watered-down version with the novel's most racist elements removed.
Multifragmentation through Exotic Shape Nuclei in alpha(5GeV/u) + Au Reactions
Tomoyuki Maruyama
Physics , 1995, DOI: 10.1143/PTP.97.579
Abstract: We simulate the fragmentation processes in the {$\alpha$~$+$~Au~} collisions at a bombarding energy of 5 GeV/u using the simplified RQMD approach plus the statistical decay model. We find from the simulation that the angular-distribution of the intermediate mass fragments has a sideward peak, more strongly in the transverse direction than in the beam-direction, when the intermediate nucleus formed by the dynamical process has an annular eclipse shape, which explains the experimental results.
Multifragmentation in alpha(5GeV/u) + Au Reactions
Tomoyuki Maruyama
Physics , 1995,
Abstract: We simulate the fragmentation processes in the \alAu collisions at the bombarding energy 5 GeV/u using the simplified RQMD approach. The statistical decay calculation is connected to obtain the final state. >From the simulation we find that the residual nucleus created by this collision has a annular eclipse shape, and then expands more strongly to the transverse direction than to the beam-direction. Then the angular-distribution of the intermediate mass fragments has a sideward peak; this result explains the experimental result.
Dirac-Fock Current and Magnetic-Moment in the Relativistic Approach
Tomoyuki Maruyama
Physics , 1996,
Abstract: We define the Dirac-Fock current to hold the current conservation in the momentum-dependent Dirac fields, and discuss its effect on the magnetic-moment in the nuclear matter. It is shown that the Dirac-Fock current can largely reduce the magnetic-moment even in the isovector case, whose value has been too big due to the small effective mass in the usual relativistic Hartree approximation.
Vacuum entanglement governs the bosonic character of magnons
Tomoyuki Morimae
Physics , 2010, DOI: 10.1103/PhysRevA.81.060304
Abstract: It is well known that magnons, elementary excitations in a magnetic material, behave as bosons when their density is low. We study how the bosonic character of magnons is governed by the amount of a multipartite entanglement in the vacuum state on which magnons are excited. We show that if the multipartite entanglement is strong, magnons cease to be bosons. We also consider some examples, such as ground states of the Heisenberg ferromagnet and the transverse Ising model, the condensation of magnons, the one-way quantum computer, and Kitaev's toric code. Our result provides insights into the quantum statistics of elementary excitations in these models, and into the reason why a non-local transformation, such as the Jordan-Wigner transformation, is necessary for some many-body systems.
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