環境権と地方自治の役割-八王子市の緑化行政をモデルとして-

Articledepartmental bulletin pape

SBML Level 3: an extensible format for the exchange and reuse of biological models

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution

SBML Level 3: an extensible format for the exchange and reuse of biological models

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.journal articl

<判例研究>共同企業体の構成員の和議申立ておよび和議開始決定の前後にわたって他の構成員が取得した求償権をもってする相殺の可否

2000-06-30departmental bulletin pape

平成13年度国立学校等技術専門職員研修報告 : 物理・化学コース

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Study on Cyber Information Security

departmental bulletin pape

A lincRNA connected to cell mortality and epigenetically-silenced in most common human cancers

<p>Immortality is an essential characteristic of human carcinoma cells. We recently developed an efficient, reproducible method that immortalizes human mammary epithelial cells (HMEC) in the absence of gross genomic changes by targeting 2 critical senescence barriers. Consistent transcriptomic changes associated with immortality were identified using microarray analysis of isogenic normal finite pre-stasis, abnormal finite post-stasis, and immortal HMECs from 4 individuals. A total of 277 genes consistently changed in cells that transitioned from post-stasis to immortal. Gene ontology analysis of affected genes revealed biological processes significantly altered in the immortalization process. These immortalization-associated changes showed striking similarity to the gene expression changes seen in The Cancer Genome Atlas (TCGA) clinical breast cancer data. The most dramatic change in gene expression seen during the immortalization step was the downregulation of an unnamed, incompletely annotated transcript that we called <i>MORT</i>, for mortality, since its expression was closely associated with the mortal, finite lifespan phenotype. We show here that <i>MORT</i> (<i>ZNF667-AS1</i>) is expressed in all normal finite lifespan human cells examined to date and is lost in immortalized HMEC. <i>MORT</i> gene silencing at the mortal/immortal boundary was due to DNA hypermethylation of its CpG island promoter. This epigenetic silencing is also seen in human breast cancer cell lines and in a majority of human breast tumor tissues. The functional importance of DNA hypermethylation in <i>MORT</i> gene silencing is supported by the ability of 5-aza-2′-deoxycytidine to reactivate <i>MORT</i> expression. Analysis of TCGA data revealed deregulation of <i>MORT</i> expression due to DNA hypermethylation in 15 out of the 17 most common human cancers. The epigenetic silencing of <i>MORT</i> in a large majority of the common human cancers suggests a potential fundamental role in cellular immortalization during human carcinogenesis.</p

The highly stable 1,6-methanotetradehydro-[26]-, -[28]-, -[30]-, -[32]-, -[34]-, and -[38]-annulenes. Limiting ring size for dia- and para-tropicity

The title annulenes have been synthesized and their 1H n.m.r. spectra indicate that the [28]- and [34]-annulenes as well as the lower-membered ones can sustain a ring current

Evaluation of intercellular lipid lamellae in the stratum corneum by polarized microscopy

BackgroundIntercellular lipids contain a lamellar structure that glows in polarized images. It could be expected that the intercellular lipid content be estimated from the luminance values calculated from polarized images of stratum corneum strips. Therefore, we attempted to develop a method for simple and rapid evaluation of the intercellular lipid content through a procedure. Herein, we demonstrated a relationship between the luminance value and the amount of ceramides, one of the main components of intercellular lipids.Materials and methodsThe stratum corneum was collected from the forearm using slides with a pure rubber-based adhesive, which did not produce unnecessary luminescence under polarizing conditions. Images were analyzed using luminance indices. The positive secondary ion peak images were obtained using the time of flight-secondary ion mass spectrometry; the polarized and brightfield images were obtained using a polarized microscope. The ceramide and protein amount was measured by high-performance liquid chromatography and bicinchoninic acid protein assay after microscope imaging. Images and quantitative values were used to construct evaluation models based on a convolutional neural network (CNN).ResultsThere was a correlation between the highlighted areas of the polarized image to overlap with the area where ceramide-derived peak was detected. Evaluation of the CNN-based model of the polarized images predicted the amount of ceramides per unit of stratum corneum.ConclusionThe method proposed in the study enabled a large number of specimens to provide a simple, rapid, and efficient evaluation of the intercellular lipid content.journal articl