2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)
Because usually there are no normal control cell lines, cancer cell lines can be examined only in... more Because usually there are no normal control cell lines, cancer cell lines can be examined only in a comparison between treatment and no-treatment conditions. Thus, characterization of cancer cell lines by themselves is impossible. To address this problem, one-class differential expression (DE) analysis, which can evaluate samples without a reference, is proposed here using tensor decomposition (TD)-based unsupervised feature extraction (FE) extended from recently proposed principal component analysis-based unsupervised FE. This one-class DE analysis was applied to multi-omics datasets of 26 lung adenocarcinoma cell lines. Enrichment analysis of selected genes identified multiple biological terms or concepts including signal recognition particles and nonsense-mediated decay (Reactome, Gene Ontology [GO] biological process), cadherin, poly(A) RNA binding (GO molecular function), eukaryotic translation initiation factors (Reactome), aberrant histone protein expression (Reactome and Human Protein Atlas [HPA]), and 163 transcription factors including E2F, PAX5, ARNT, AHR, and CREB, all of which are known to be related to non-small cell lung cancer and are expected to function cooperatively in lung adenocarcinoma oncogenesis. ,,,, These data not only indicate usefulness of one-class DE analysis using TD-based unsupervised FE but also point to new therapeutic targets in lung adenocarcinoma.
A simple tensor decomposition model was applied to the liver transcriptome analysis data to eluci... more A simple tensor decomposition model was applied to the liver transcriptome analysis data to elucidate the cause of cadmium-induced gene overexpression. In addition, we estimated the mechanism by which prenatal Cd exposure disrupts insulin metabolism in offspring. Numerous studies have reported on the toxicity of Cd. A liver transcriptome analysis revealed that Cd toxicity induces intracellular oxidative stress and mitochondrial dysfunction via changes in gene expression, which in turn induces endoplasmic reticulum-associated degradation via abnormal protein folding. However, the specific mechanisms underlying these effects remain unknown. In this study, we found that Cd-induced endoplasmic reticulum stress may promote increased expression of tumor necrosis factor-α (TNF-α). Based on the high expression of genes involved in the production of sphingolipids, it was also found that the accumulation of ceramide may induce intracellular oxidative stress through the overproduction of react...
ABSTRACTRNA-Seq data analysis of non-model organisms is often difficult because of the lack of a ... more ABSTRACTRNA-Seq data analysis of non-model organisms is often difficult because of the lack of a well-annotated genome. In model organisms, after short reads are mapped to the genome, it is possible to focus on the analysis of regions well-annotated regions. However, in non-model organisms, contigs can be generated by de novo assembling. This can result in a large number of transcripts, making it difficult to easily remove redundancy. A large number of transcripts can also lead to difficulty in the recognition of differentially expressed transcripts (DETs) between more than two experimental conditions, because P-values must be corrected by considering multiple comparison corrections whose effect is enhanced as the number of transcripts increases. Heavily corrected P-values often fail to take sufficiently small P-values as significant. In this study, we applied a recently proposed tensor decomposition (TD)-based unsupervised feature extraction (FE) to the RNA-seq data obtained for a ...
Although hypoxia is a critical factor that can drive the progression of various diseases, the mec... more Although hypoxia is a critical factor that can drive the progression of various diseases, the mechanism underlying hypoxia itself remains unclear. Recently, m6A has been proposed as an important factor driving hypoxia. Despite successful analyses, potential genes were not selected with statistical significance but were selected based solely on fold changes. Because the number of genes is large while the number of samples is small, it was impossible to select genes using conventional feature selection methods with statistical significance. In this study, we applied the recently proposed principal component analysis (PCA), tensor decomposition (TD), and kernel tensor decomposition (KTD)-based unsupervised feature extraction (FE) to a hypoxia data set. We found that PCA, TD, and KTD-based unsupervised FE could successfully identify a limited number of genes associated with altered gene expression and m6A profiles, as well as the enrichment of hypoxia-related biological terms, with impr...
The diffusion-limited aggregation (DLA)[1] is currently of major interest in the field of physics... more The diffusion-limited aggregation (DLA)[1] is currently of major interest in the field of physics of pattern formation, because it is a simple model of several physical phenomena: metal leaves, viscous fingerings, and dielectric breakdown, etc. In all of the phenomena, growth probabilities depend on the gradient of a solution of the Laplace equation. DLA and these physical phenomena are known to show fractal patterns. Hence much effort has been made to obtain the fractal dimension d f of DLA. Remarkably, in some dimension analysis treatments [2,3], though the Laplace equation is not taken into account at all, the result (d f = 5/3) agrees with that of numerical simulations (d f = 1.7) [1]. The fact they make use of is that only trajectories of particles have fractal dimension d w of two. Here we notice a possibility that other trajectories with d w of two can also generate fractal patterns with the same d f as that of DLA. To clear up this point, we consider trajectories which are n...
To better understand the genes with altered expression caused by infection with the novel coronav... more To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened ...
Physica A: Statistical Mechanics and its Applications, 1996
Surface level instability when tube is injected into vibrating bed of powder, which was originall... more Surface level instability when tube is injected into vibrating bed of powder, which was originally found in experiments, is investigated numerically. We find that thicker (thiner) tube makes surface level inside tube higher (lower) than surface level outside tube. With fixed acceleration amplitude of vibration, surface level inside tube becomes higher as amplitude of vibration increases, which can be explained by considering the dependence upon strength of convective flow.
I propose a numerical model which describes the dynamical features of vibrated beds. It succeeds ... more I propose a numerical model which describes the dynamical features of vibrated beds. It succeeds in reproducing convective motion in vibrated beds which was observed by Faraday for the first time in 1831. In addition to this, this modeling can explain threshold value of instability and surface fluidization. Moreover, I numerically show vibrated bed without side wall can exhibit strong non-linear feature like turbulence or anomalous diffusion.
Simulations of vortex tube dynamics reveal that the non-Gaussian nature of turbulent fluctuation ... more Simulations of vortex tube dynamics reveal that the non-Gaussian nature of turbulent fluctuation originates in the effect of random advection. A similar non-Gaussian distribution is found numerically in a simplified statistical model of random advection. An analytical solution is obtained in the mean-field case.
DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins.... more DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. However, success rate of it is deeply dependent upon which pair of DNAs is employed for DNA shuffling. In this paper, we have used non-metric multidimensional scaling (nMDS) to select best pair of DNAs for it. It turns out that nMDS can sometimes choose better pairs of DNAs than hierarchical clustering which is frequently used to select the suitable pair of DNAs.
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, 2011
We have infer gene expression regulation via microRNA using both gene expression profile and targ... more We have infer gene expression regulation via microRNA using both gene expression profile and target gene tables during the differentiation from embryonic stem cell to neuronal cells. Comparison between obtained list of microRNA which regulates gene expression significantly and that of miRNAs whose expression level changes significantly results in significant overlap.
Background miRNA regulation of target genes and promoter methylation are known to be the primary ... more Background miRNA regulation of target genes and promoter methylation are known to be the primary mechanisms underlying the epigenetic regulation of gene expression. However, how these two processes cooperatively regulate gene expression has not been extensively studied. Methods Gene expression and promoter methylation profiles of 271 distinct human cell lines were obtained from gene expression omnibus. P-values that describe both miRNA-targeted-gene promoter methylaion and miRNA regulation of target genes were computed using the MiRaGE method proposed recently by the author. Results Significant changes in promoter methylation were associated with miRNA targeting. It was also found that miRNA-targeted-gene promoter hypomethylation was related to differential target gene expression; the genes with miRNA-targeted-gene promoter hypomethylation were downregulated during cell senescence and upregulated during cellular differentiation. Promoter hypomethylation was especially enhanced for genes targeted by miR-548 miRNAs, which are non-conserved, primate-specific miRNAs that are typically expressed at lower levels than the frequently investigated conserved miRNAs. Conclusions It was found that promoter methylation was affected by miRNA targeting. Furthermore, miRNA-targeted-gene promoter hypomethylation is suggested to facilitate gene regulation by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs).
Fluid turbulence is analysed with a lattice model which requires relatively small number of degre... more Fluid turbulence is analysed with a lattice model which requires relatively small number of degrees of freedom. The lattice model employs vortex tube representation and can reproduce characteristic features in turbulence; Kolmogorov's inertial range is observed, probability distribution functions of local velocities are close to a Gaussian, exponential-like distributions appear in local vorticity, relative velocities and local velocity through a high-pass filter. Coherent structures consisted of vortex tubes are also observed. The model also provides new mechanism which generates non-Gaussian distributions.
Journal of Physics A: Mathematical and General, 1988
The author calculates the fractal dimensions of self-avoiding walks (SAW) on Sierpinski carpets w... more The author calculates the fractal dimensions of self-avoiding walks (SAW) on Sierpinski carpets with the bond-moving-type renormalisation. The results suggest that carpets with the same fractal dimension of the random walk have almost the same fractal dimension of SAW within the approximation.
Distribution functions of relative velocities among particles in a vibrated bed of powder are stu... more Distribution functions of relative velocities among particles in a vibrated bed of powder are studied both numerically and theoretically. In the solid phase where granular particles remain near their local stable states, the probability distribution is Gaussian. On the other hand, in the fluidized phase, where the particles can exchange their positions, the distribution clearly deviates from Gaussian. This is interpreted with two analogies; aggregation processes and soft-to-hard turbulence transition in thermal convection. The non-Gaussian distribution is well-approximated by the t-distribution which is derived theoretically by considering the effect of clustering by inelastic collisions in the former analogy.
A set of hard spheres with tangential inelastic collision is found to reproduce observations of r... more A set of hard spheres with tangential inelastic collision is found to reproduce observations of real and numerical granular matter. After time is scaled so as to cancel energy dissipation due to inelastic collisions out, inelastically colliding hard spheres in two dimensional space come to have 1/f α fluctuation of total energy, non-Gaussian distribution of displacement vectors, and convective motion of spheres, which hard spheres with elastic collision, a conventional model of granular matter, cannot reproduce.
Numerical modeling of convection of powder was performed. Convection of powder occurs when a stro... more Numerical modeling of convection of powder was performed. Convection of powder occurs when a strong vertical vibration is applied. When the control parameter, the acceleration amplitude r, exceeds some critical value rc, convection and heaping start. In our simulation, the powder is modeled with a discrete elementary method but without rotation and with isotropic linear visco-elastic interaction. The convectionis reproduced and rc turns out to be about the gravity acceleration g, which agrees with experimental findings. Another remarkable phenomena, surface fluidization,is also reproduced and the critical value rc again agrees with experimental findings. It is suggested that this convection is caused by the instability of powder induced by the elastic interaction.
IEEE Journal of Selected Topics in Signal Processing, 2021
To better understand the genes with altered expression caused by infection with the novel coronav... more To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened with an in silico method to identify candidate drugs for treating COVID-19.
2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)
Because usually there are no normal control cell lines, cancer cell lines can be examined only in... more Because usually there are no normal control cell lines, cancer cell lines can be examined only in a comparison between treatment and no-treatment conditions. Thus, characterization of cancer cell lines by themselves is impossible. To address this problem, one-class differential expression (DE) analysis, which can evaluate samples without a reference, is proposed here using tensor decomposition (TD)-based unsupervised feature extraction (FE) extended from recently proposed principal component analysis-based unsupervised FE. This one-class DE analysis was applied to multi-omics datasets of 26 lung adenocarcinoma cell lines. Enrichment analysis of selected genes identified multiple biological terms or concepts including signal recognition particles and nonsense-mediated decay (Reactome, Gene Ontology [GO] biological process), cadherin, poly(A) RNA binding (GO molecular function), eukaryotic translation initiation factors (Reactome), aberrant histone protein expression (Reactome and Human Protein Atlas [HPA]), and 163 transcription factors including E2F, PAX5, ARNT, AHR, and CREB, all of which are known to be related to non-small cell lung cancer and are expected to function cooperatively in lung adenocarcinoma oncogenesis. ,,,, These data not only indicate usefulness of one-class DE analysis using TD-based unsupervised FE but also point to new therapeutic targets in lung adenocarcinoma.
A simple tensor decomposition model was applied to the liver transcriptome analysis data to eluci... more A simple tensor decomposition model was applied to the liver transcriptome analysis data to elucidate the cause of cadmium-induced gene overexpression. In addition, we estimated the mechanism by which prenatal Cd exposure disrupts insulin metabolism in offspring. Numerous studies have reported on the toxicity of Cd. A liver transcriptome analysis revealed that Cd toxicity induces intracellular oxidative stress and mitochondrial dysfunction via changes in gene expression, which in turn induces endoplasmic reticulum-associated degradation via abnormal protein folding. However, the specific mechanisms underlying these effects remain unknown. In this study, we found that Cd-induced endoplasmic reticulum stress may promote increased expression of tumor necrosis factor-α (TNF-α). Based on the high expression of genes involved in the production of sphingolipids, it was also found that the accumulation of ceramide may induce intracellular oxidative stress through the overproduction of react...
ABSTRACTRNA-Seq data analysis of non-model organisms is often difficult because of the lack of a ... more ABSTRACTRNA-Seq data analysis of non-model organisms is often difficult because of the lack of a well-annotated genome. In model organisms, after short reads are mapped to the genome, it is possible to focus on the analysis of regions well-annotated regions. However, in non-model organisms, contigs can be generated by de novo assembling. This can result in a large number of transcripts, making it difficult to easily remove redundancy. A large number of transcripts can also lead to difficulty in the recognition of differentially expressed transcripts (DETs) between more than two experimental conditions, because P-values must be corrected by considering multiple comparison corrections whose effect is enhanced as the number of transcripts increases. Heavily corrected P-values often fail to take sufficiently small P-values as significant. In this study, we applied a recently proposed tensor decomposition (TD)-based unsupervised feature extraction (FE) to the RNA-seq data obtained for a ...
Although hypoxia is a critical factor that can drive the progression of various diseases, the mec... more Although hypoxia is a critical factor that can drive the progression of various diseases, the mechanism underlying hypoxia itself remains unclear. Recently, m6A has been proposed as an important factor driving hypoxia. Despite successful analyses, potential genes were not selected with statistical significance but were selected based solely on fold changes. Because the number of genes is large while the number of samples is small, it was impossible to select genes using conventional feature selection methods with statistical significance. In this study, we applied the recently proposed principal component analysis (PCA), tensor decomposition (TD), and kernel tensor decomposition (KTD)-based unsupervised feature extraction (FE) to a hypoxia data set. We found that PCA, TD, and KTD-based unsupervised FE could successfully identify a limited number of genes associated with altered gene expression and m6A profiles, as well as the enrichment of hypoxia-related biological terms, with impr...
The diffusion-limited aggregation (DLA)[1] is currently of major interest in the field of physics... more The diffusion-limited aggregation (DLA)[1] is currently of major interest in the field of physics of pattern formation, because it is a simple model of several physical phenomena: metal leaves, viscous fingerings, and dielectric breakdown, etc. In all of the phenomena, growth probabilities depend on the gradient of a solution of the Laplace equation. DLA and these physical phenomena are known to show fractal patterns. Hence much effort has been made to obtain the fractal dimension d f of DLA. Remarkably, in some dimension analysis treatments [2,3], though the Laplace equation is not taken into account at all, the result (d f = 5/3) agrees with that of numerical simulations (d f = 1.7) [1]. The fact they make use of is that only trajectories of particles have fractal dimension d w of two. Here we notice a possibility that other trajectories with d w of two can also generate fractal patterns with the same d f as that of DLA. To clear up this point, we consider trajectories which are n...
To better understand the genes with altered expression caused by infection with the novel coronav... more To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened ...
Physica A: Statistical Mechanics and its Applications, 1996
Surface level instability when tube is injected into vibrating bed of powder, which was originall... more Surface level instability when tube is injected into vibrating bed of powder, which was originally found in experiments, is investigated numerically. We find that thicker (thiner) tube makes surface level inside tube higher (lower) than surface level outside tube. With fixed acceleration amplitude of vibration, surface level inside tube becomes higher as amplitude of vibration increases, which can be explained by considering the dependence upon strength of convective flow.
I propose a numerical model which describes the dynamical features of vibrated beds. It succeeds ... more I propose a numerical model which describes the dynamical features of vibrated beds. It succeeds in reproducing convective motion in vibrated beds which was observed by Faraday for the first time in 1831. In addition to this, this modeling can explain threshold value of instability and surface fluidization. Moreover, I numerically show vibrated bed without side wall can exhibit strong non-linear feature like turbulence or anomalous diffusion.
Simulations of vortex tube dynamics reveal that the non-Gaussian nature of turbulent fluctuation ... more Simulations of vortex tube dynamics reveal that the non-Gaussian nature of turbulent fluctuation originates in the effect of random advection. A similar non-Gaussian distribution is found numerically in a simplified statistical model of random advection. An analytical solution is obtained in the mean-field case.
DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins.... more DNA shuffling is widely used for optimizing complex properties contained within DNA and proteins. However, success rate of it is deeply dependent upon which pair of DNAs is employed for DNA shuffling. In this paper, we have used non-metric multidimensional scaling (nMDS) to select best pair of DNAs for it. It turns out that nMDS can sometimes choose better pairs of DNAs than hierarchical clustering which is frequently used to select the suitable pair of DNAs.
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, 2011
We have infer gene expression regulation via microRNA using both gene expression profile and targ... more We have infer gene expression regulation via microRNA using both gene expression profile and target gene tables during the differentiation from embryonic stem cell to neuronal cells. Comparison between obtained list of microRNA which regulates gene expression significantly and that of miRNAs whose expression level changes significantly results in significant overlap.
Background miRNA regulation of target genes and promoter methylation are known to be the primary ... more Background miRNA regulation of target genes and promoter methylation are known to be the primary mechanisms underlying the epigenetic regulation of gene expression. However, how these two processes cooperatively regulate gene expression has not been extensively studied. Methods Gene expression and promoter methylation profiles of 271 distinct human cell lines were obtained from gene expression omnibus. P-values that describe both miRNA-targeted-gene promoter methylaion and miRNA regulation of target genes were computed using the MiRaGE method proposed recently by the author. Results Significant changes in promoter methylation were associated with miRNA targeting. It was also found that miRNA-targeted-gene promoter hypomethylation was related to differential target gene expression; the genes with miRNA-targeted-gene promoter hypomethylation were downregulated during cell senescence and upregulated during cellular differentiation. Promoter hypomethylation was especially enhanced for genes targeted by miR-548 miRNAs, which are non-conserved, primate-specific miRNAs that are typically expressed at lower levels than the frequently investigated conserved miRNAs. Conclusions It was found that promoter methylation was affected by miRNA targeting. Furthermore, miRNA-targeted-gene promoter hypomethylation is suggested to facilitate gene regulation by miRNAs that are not strongly expressed (e.g., miR-548 miRNAs).
Fluid turbulence is analysed with a lattice model which requires relatively small number of degre... more Fluid turbulence is analysed with a lattice model which requires relatively small number of degrees of freedom. The lattice model employs vortex tube representation and can reproduce characteristic features in turbulence; Kolmogorov's inertial range is observed, probability distribution functions of local velocities are close to a Gaussian, exponential-like distributions appear in local vorticity, relative velocities and local velocity through a high-pass filter. Coherent structures consisted of vortex tubes are also observed. The model also provides new mechanism which generates non-Gaussian distributions.
Journal of Physics A: Mathematical and General, 1988
The author calculates the fractal dimensions of self-avoiding walks (SAW) on Sierpinski carpets w... more The author calculates the fractal dimensions of self-avoiding walks (SAW) on Sierpinski carpets with the bond-moving-type renormalisation. The results suggest that carpets with the same fractal dimension of the random walk have almost the same fractal dimension of SAW within the approximation.
Distribution functions of relative velocities among particles in a vibrated bed of powder are stu... more Distribution functions of relative velocities among particles in a vibrated bed of powder are studied both numerically and theoretically. In the solid phase where granular particles remain near their local stable states, the probability distribution is Gaussian. On the other hand, in the fluidized phase, where the particles can exchange their positions, the distribution clearly deviates from Gaussian. This is interpreted with two analogies; aggregation processes and soft-to-hard turbulence transition in thermal convection. The non-Gaussian distribution is well-approximated by the t-distribution which is derived theoretically by considering the effect of clustering by inelastic collisions in the former analogy.
A set of hard spheres with tangential inelastic collision is found to reproduce observations of r... more A set of hard spheres with tangential inelastic collision is found to reproduce observations of real and numerical granular matter. After time is scaled so as to cancel energy dissipation due to inelastic collisions out, inelastically colliding hard spheres in two dimensional space come to have 1/f α fluctuation of total energy, non-Gaussian distribution of displacement vectors, and convective motion of spheres, which hard spheres with elastic collision, a conventional model of granular matter, cannot reproduce.
Numerical modeling of convection of powder was performed. Convection of powder occurs when a stro... more Numerical modeling of convection of powder was performed. Convection of powder occurs when a strong vertical vibration is applied. When the control parameter, the acceleration amplitude r, exceeds some critical value rc, convection and heaping start. In our simulation, the powder is modeled with a discrete elementary method but without rotation and with isotropic linear visco-elastic interaction. The convectionis reproduced and rc turns out to be about the gravity acceleration g, which agrees with experimental findings. Another remarkable phenomena, surface fluidization,is also reproduced and the critical value rc again agrees with experimental findings. It is suggested that this convection is caused by the instability of powder induced by the elastic interaction.
IEEE Journal of Selected Topics in Signal Processing, 2021
To better understand the genes with altered expression caused by infection with the novel coronav... more To better understand the genes with altered expression caused by infection with the novel coronavirus strain SARS-CoV-2 causing COVID-19 infectious disease, a tensor decomposition (TD)-based unsupervised feature extraction (FE) approach was applied to a gene expression profile dataset of the mouse liver and spleen with experimental infection of mouse hepatitis virus, which is regarded as a suitable model of human coronavirus infection. TD-based unsupervised FE selected 134 altered genes, which were enriched in protein-protein interactions with orf1ab, polyprotein, and 3C-like protease that are well known to play critical roles in coronavirus infection, suggesting that these 134 genes can represent the coronavirus infectious process. We then selected compounds targeting the expression of the 134 selected genes based on a public domain database. The identified drug compounds were mainly related to known antiviral drugs, several of which were also included in those previously screened with an in silico method to identify candidate drugs for treating COVID-19.
We have numerically investigated coexistence phases of optimal velocity model which appear when h... more We have numerically investigated coexistence phases of optimal velocity model which appear when homogeneous stat.es become unstable, When instability increases, distance between cars in congestion phase which is one of coexistence phases becomes very smalL In such situation a few new phases appear, i.e. passing phase, congestion phase with zero distance between cars, and spatially modulated phase.
—Wilms tumor is one of lethal child renal cancers , for which no known disease causing mechanisms... more —Wilms tumor is one of lethal child renal cancers , for which no known disease causing mechanisms exist. In this paper, we tried to identify possible disease causing microRNA(miRNA)-mRNA pairs (interactions) by analyzing (partially matched) miRNA/mRNA gene expression profiles with the recently proposed principal component analysis based unsupervised feature extraction. It successfully identified multiple miRNA-mRNA pairs whose biological natures are convincing. Correlation coefficients between miRNA and mRNA expression in matched parts of profiles turned out to be significantly negative. Constructed miRNA-mRNA network will be a key to understand Wilms tumor causing mechanisms.
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Papers by Y-h. Taguchi