A5087001999- Fluid Dynamics Simulations and Interactions
- Numerical methods in engineering
- Single-cell and spatial transcriptomics
- Lattice Boltzmann Simulation Studies
- Fluid Dynamics and Heat Transfer
- Advanced Numerical Methods in Computational Mathematics
- Topological and Geometric Data Analysis
- Dam Engineering and Safety
- Soybean genetics and cultivation
- Cell Image Analysis Techniques
- MicroRNA in disease regulation
- Fluid Dynamics and Vibration Analysis
- Immune Cell Function and Interaction
- Legume Nitrogen Fixing Symbiosis
- Gene Regulatory Network Analysis
- Geotechnical Engineering and Underground Structures
- Gene expression and cancer classification
- Elasticity and Material Modeling
- Plant tissue culture and regeneration
- Robotic Path Planning Algorithms
- Advanced Graph Neural Networks
- Computational Fluid Dynamics and Aerodynamics
- Plant Genetic and Mutation Studies
- Soil, Finite Element Methods
- Model Reduction and Neural Networks
Kyoto University
2019-2025
Obihiro University of Agriculture and Veterinary Medicine
2022
Tohoku University
2016-2019
Kyushu University
2014-2016
Hokkaido University
2008
Nihon University
2000
Germinal center (GC) reactions are tightly regulated to generate high-affinity antibodies. Although IL10+ Foxp3- follicular T cells have recently been described as contributing the suppression of GC reactions, their differentiation, localization, and heterogeneity remain incompletely understood. Additionally, it remains unclear whether represent a transient status or an independent subset. To address these gaps, we performed integrative single-cell analysis transcriptomes, epigenomes,...
Single-cell RNA sequencing (scRNA-seq) can determine gene expression in numerous individual cells simultaneously, promoting progress the biomedical sciences. However, scRNA-seq data are high-dimensional with substantial technical noise, including dropouts. During analysis of data, such noise engenders a statistical problem known as curse dimensionality (COD). Based on statistics, we herein formulate reduction method, RECODE (resolution dimensionality), for random sampling noise. We show that...
Highlights•IFN-γ and ERK/MAPK signaling activities alter upon aging in the small intestine•The balanced between IFN-γ maintain ISC pool•An equilibrium active quiescent states exists aged ISCs•Changes two pathways affect functions of differentiated cellsSummaryWhile intestinal epithelium has highest cellular turnover rates mammalian body, it is also considered one tissues most resilient to aging-related disorders. Here, we reveal an innate protective mechanism that safeguards stem cells...
Smoothed particle hydrodynamics (SPH) and moving semi-implicit (MPS) methods are representative meshfree used to compute Lagrangian mechanics. The approximations of differential operators in the SPH MPS have several similarities, but theoretical discussion difference between them is limited. This study mathematically describes via a comprehensive derivation first- second-order derivative for each method. indicates that consistent with pressure Poisson equation least-squares approximation,...
Differentiation into specific embryo cell types correlates with the processes that lead to accumulation of seed storage proteins in plants. The α subunit β-conglycinin, a major component soybean, accumulates at higher level cotyledons than embryonic axis developing embryos. To understand mechanisms underlying this phenomenon, we characterized upstream region gene terms transcriptional control using transgenic Arabidopsis thaliana plants carrying reporter constructs comprising 1357-bp...
A truncation error of the interpolant is considered for a class particle methods, which can describe Smoothed Particle Hydrodynamics (SPH). Owing to sufficient conditions weight function and regularity family discrete parameters, estimate established methods based on Voronoi decomposition. Moreover, some numerical results are shown, agree well with theoretical ones.
Truncation errors are considered for approximate differential operators with a class of particle methods. Introducing sufficient conditions the weight function and regularity family discrete parameters leads to truncation error estimates gradient Laplace method based on Voronoi decomposition. Moreover, some numerical results agree well theoretical ones.
Hyper-dual numbers (HDN) are defined by using nilpotent elements that differ from each other. The introduction of an operator to extend the domain functions HDN space based on Taylor expansion allows higher-order derivatives be obtained coefficients. This study inductively defines matrix representations and proposes a numerical method for derivatives, called HDN-M differentiation, HDN. proposed is characterized so can computed with operation rules without implementations
Adzuki bean is an important legume crop originating in temperate regions, with photoperiod sensitivity being a key factor its latitudinal adaptation. The Flowering Date1 (FD1) gene has large effect on the photoperiodic response of flowering time, but molecular basis for this locus undetermined. present study delimited FD1 to 17.1 kb sequence, containing single gene, E1 ortholog (VaE1). A comparison between Vigna angularis 'Shumari' (photoperiod insensitive) and 'Acc2265' sensitive)...
When numerically computing high Reynolds number cavity flow, it is known that by formulating the Navier-Stokes equations using stream function and vorticity as unknown functions, possible to reproduce finer flow structures. Although numerical computations applying methods such finite difference method are well known, best of our knowledge, there no examples particle-based like SPH this problem. Therefore, we applied equations, formulated with conducted flow. The results confirmed...
Mapper, a topological data analysis method for high-dimensional data, represents structure as simplicial complex or graph based on the nerve of clusters. We propose V-Mapper (velocity Mapper), an extension with velocity. simultaneously describes and flow weighted directed (V-Mapper graph) by embedding velocity in edges Mapper graph. apply to single-cell gene expression using inferring expression. Moreover, application Hodge decomposition enhances interpretation within
Abstract Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues interpretability computational cost. We present scEGOT, comprehensive framework for single-cell trajectory inference, as generative model with high low Applied human primordial germ cell-like (PGCLC) induction system, scEGOT identified PGCLC progenitor population bifurcation time...
Node2vec is a graph embedding method that learns vector representation for each node of weighted while seeking to preserve relative proximity and global structure. Numerical experiments suggest struggles recreate the topology input graph. To resolve this we introduce topological loss term be added training which tries align persistence diagram (PD) resulting as closely possible Following results in computational optimal transport, carefully adapt entropic regularization PD metrics, allowing...
A bstract Single-cell sequencing generates vast amounts of genomic and epigenomic data from thousands individual cells can reveal insights into biological principles at the single-cell resolution. However, challenges such as technical noise (dropout) batch effects hinder obtaining high-resolution structures that are essential for tasks identification rare cell types dataset comparison across different cultures. Here, I introduce integrative RECODE (iRECODE) , a comprehensive method reduction...
The stability of persistent homology has led to wide applications the persistence diagram as a trusted topological descriptor in presence noise. However, with increasing demand for high-dimension and low-sample-size data processing modern science, it is questionable whether diagrams retain their reliability high-dimensional This work aims study setting. By analyzing asymptotic behavior random data, we show that are no longer reliable descriptors under noise perturbations. We refer this loss...
Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues interpretability computational cost. We present scEGOT, comprehensive framework for single-cell trajectory inference, as generative model with high low Applied human primordial germ cell-like (PGCLC) induction system, scEGOT identified PGCLC progenitor population bifurcation time of...
非圧縮性 Navier–Stokes 方程式に対する粒子法の一つである安定化 ISPH 法は,通常の非圧縮性 SPH 法 (ISPH 法) に粒子密度に関する安定化項を圧力 Poisson 方程式に付加した手法である.この安定化項により,粒子の偏在化を防ぐことができ,計算安定,体積保存,精度向上などが数値計算によって確かめられている.この安定化 法に対して,我々は先行研究で安定化項が非圧縮性条件と局所密度一定の条件の誤差を重み付きで近似的に最小化するという解釈ができることを理論的に示した.しかしながら,その誤差の重みを表す安定化係数については,いくらかの数値実験によって最適な範囲や傾向が見積もられているものの,それらを理解するための理論は存在しなかった.そこで,本論文では,経験的に知られている安定化係数の範囲や他のパラメータとの関係性を,誤差評価に基づいて安定化係数を最適化する.さらに,その最適化された安定化係数の性質を示すことで経験則で知られていたことを理論的に解釈する.
A numerical calculation scheme for stress and its consistent tangent moduli with hyper-dual numbers(HDN) Ogden-type hyperelastic material model was proposed. The main advantage of this is that once the framework coded, any can be implemented by only re-coding strain energy density function. In scheme, new differentiation method eigenvalue eigenvector symmetric matrices HDN were proposed calculate in non-real part analytically using real part, case all eigenvalues are not multiple root. We...