Cell Petri Net Concepts

Based on the Petri net definitions and theorems already formalized in [8], with this article, we developed the concept of "Cell Petri Nets". It is based on [9]. In a cell Petri net we introduce the notions of colors and colored states of a Petri net, connecting mappings for linking two Petri nets, firing rules for transitions, and the synthesis of two or more Petri nets.Mitsuru Jitsukawa - Chiba-ken Asahi-shi, Kotoda 2927-13 289-2502 JapanPauline Kawamoto - Shinshu University, Nagano, JapanYasunari Shidama - Shinshu University, Nagano, JapanYatsuka Nakamura - Shinshu University, Nagano, Japa

Formulation of Cell Petri Nets

Based on the Petri net definitions and theorems already formalized in the Mizar article [13], in this article we were able to formalize the definition of cell Petri nets. It is based on [12]. Colored Petri net has already been defined in [11]. In addition, the conditions of the firing rule and the colored set to this definition, that defines the cell Petri nets are further extended to CPNT.i further. The synthesis of two Petri nets was introduced in [11] and in this work the definition is extended to produce the synthesis of a family of colored Petri nets. Specifically, the extension to a CPNT family is performed by specifying how to link the outbound transitions of each colored Petri net to the place elements of other nets to form a neighborhood relationship. Finally, the activation of colored Petri nets was formalized.Jitsukawa Mitsuru - Shinshu University Nagano, JapanKawamoto Pauline N. - Shinshu University Nagano, JapanShidama Yasunari - Shinshu University Nagano, JapanGrzegorz Bancerek. König’s theorem. Formalized Mathematics, 1(3):589-593, 1990.Grzegorz Bancerek. Free term algebras. Formalized Mathematics, 20(3):239-256, 2012. doi:10.2478/v10037-012-0029-6.Grzegorz Bancerek. The fundamental properties of natural numbers. Formalized Mathematics, 1(1):41-46, 1990.Grzegorz Bancerek. The ordinal numbers. Formalized Mathematics, 1(1):91-96, 1990.Czesław Bylinski. Functions and their basic properties. Formalized Mathematics, 1(1): 55-65, 1990.Czesław Bylinski. Functions from a set to a set. Formalized Mathematics, 1(1):153-164, 1990.Czesław Bylinski. The modification of a function by a function and the iteration of the composition of a function. Formalized Mathematics, 1(3):521-527, 1990.Czesław Bylinski. Partial functions. Formalized Mathematics, 1(2):357-367, 1990.Czesław Bylinski. Some basic properties of sets. Formalized Mathematics, 1(1):47-53, 1990.Agata Darmochwał. Finite sets. Formalized Mathematics, 1(1):165-167, 1990.Mitsuru Jitsukawa, Pauline N. Kawamoto, Yasunari Shidama, and Yatsuka Nakamura. Cell Petri net concepts. Formalized Mathematics, 17(1):37-42, 2009. doi:10.2478/v10037-009-0004-z.Pauline N. Kawamoto and Yatsuka Nakamura. On Cell Petri Nets. Journal of Applied Functional Analysis, 1996.Pauline N. Kawamoto, Yasushi Fuwa, and Yatsuka Nakamura. Basic Petri net concepts. Formalized Mathematics, 3(2):183-187, 1992.Krzysztof Retel. Properties of first and second order cutting of binary relations. Formalized Mathematics, 13(3):361-365, 2005.Andrzej Trybulec. Domains and their Cartesian products. Formalized Mathematics, 1(1): 115-122, 1990.Andrzej Trybulec. Many sorted sets. Formalized Mathematics, 4(1):15-22, 1993.Michał J. Trybulec. Integers. Formalized Mathematics, 1(3):501-505, 1990.Zinaida Trybulec. Properties of subsets. Formalized Mathematics, 1(1):67-71, 1990.Edmund Woronowicz. Relations and their basic properties. Formalized Mathematics, 1 (1):73-83, 1990

Analysis and Synthesis of Head Motionfor Life like Conversational Agents

This study aims to investigate which and what motions of lifelike conversational agents play essential role to make the agents natural. Some preliminary experimental results and future plan are shown. Embodying conversational agents is intended to imitate paralinguistic channel or back channel which plays important role in human-human conversation. Although there have been not a few lifelike conversational agents developed, appearance and behaviour of the agents are far from being natural, and merits of embodying have not been realized that much. One of the main reasons is the lack of natural motions of the agents, including the motion of head, mouth, eyes and eye brows. To improve the quality of these motions, several pioneering works have been reported [1–3]. To tackle the problem, the present study was started conducting a subjective test of head motion and analysis of head motion using signal processing techniques

Biphasic Aire expression in early embryos and in medullary thymic epithelial cells before end-stage terminal differentiation

The roles of autoimmune regulator (Aire)–expressing medullary thymic epithelial cells (mTECs) in the organization of the thymic microenvironment for establishing self-tolerance are enigmatic. We sought to monitor the production and maintenance of Aire-expressing mTECs by a fate-mapping strategy in which bacterial artificial chromosome transgenic (Tg) mice expressing Cre recombinase under the control of the Aire regulatory element were crossed with a GFP reporter strain. We found that, in addition to its well recognized expression within mature mTECs, Aire was expressed in the early embryo before emergence of the three germ cell layers. This observation may help to explain the development of ectodermal dystrophy often seen in patients with AIRE deficiency. With the use of one Tg line in which Cre recombinase expression was confined to mTECs, we found that Aire+CD80high mTECs further progressed to an Aire−CD80intermediate stage, suggesting that Aire expression is not constitutive from after its induction until cell death but instead is down-regulated at the beginning of terminal differentiation. We also demonstrated that many mTECs of Aire-expressing lineage are in close contact with thymic dendritic cells. This close proximity may contribute to transfer of tissue-restricted self-antigens expressed by mTECs to professional antigen-presenting cells

Cytotoxic T Lymphocytes Regenerated from iPS Cells Have Therapeutic Efficacy in a Patient-Derived Xenograft Solid Tumor Model

Current adoptive T cell therapies conducted in an autologous setting are costly, time consuming, and depend on the quality of the patient's T cells. To address these issues, we developed a strategy in which cytotoxic T lymphocytes (CTLs) are regenerated from iPSCs that were originally derived from T cells and succeeded in regenerating CTLs specific for the WT1 antigen, which exhibited therapeutic efficacy in a xenograft model of leukemia. In this study, we extended our strategy to solid tumors. The regenerated WT1-specific CTLs had a strong therapeutic effect in orthotopic xenograft model using a renal cell carcinoma (RCC) cell line. To make our method more generally applicable, we developed an allogeneic approach by transducing HLA-haplotype homozygous iPSCs with WT1-specific TCR α/β genes that had been tested clinically. The regenerated CTLs antigen-specifically suppressed tumor growth in a patient-derived xenograft model of RCC, demonstrating the feasibility of our strategy against solid tumors

Pharmacokinetics of Intravitreal Vancomycin and Ceftazidime in Silicone Oil-Filled Macaque Eyes.

Purpose:This study evaluated the pharmacokinetics of intravitreal vancomycin and ceftazidime in the aqueous humor of macaque eyes filled with silicone oil in the vitreous cavity.Methods:Intravitreal vancomycin (1 mg/0.1 mL) and ceftazidime (2 mg/0.1 mL) were injected into four normal macaque eyes, four vitrectomized aphakic macaque eyes, and four previously vitrectomized aphakic macaque eyes filled with silicone oil (silicone oil-filled eyes). Aqueous humor samples (0.1 mL) were obtained just before injection and at 2 and 5 hours and 1, 2, 3, 5, 7, and 10 days after injection. In each group, corneal endothelial cell density (ECD) measurements and electroretinogram (ERG) recordings were obtained before injection and after 1 month.Results:The half-lives of vancomycin in the aqueous humor of normal, vitrectomized, and silicone oil-filled eyes were 29.4, 21.1, and 6.8 hours, respectively, and those of ceftazidime were 20.4, 5.2, and 3.1 hours, respectively. The maximum vancomycin aqueous humor concentrations of normal, vitrectomized, and silicone oil-filled eyes were 151.4, 205.6, and 543.5 µg/mL, respectively, and the maximum ceftazidime aqueous humor concentrations are 64.6, 260.0, and 1176.3 µg/mL, respectively. There was no change in ECD, and ERG was not declined after intravitreal injection in all groups.Conclusions:The half-lives of vancomycin and ceftazidime in the aqueous humor were shorter in silicone oil-filled eyes than in normal and vitrectomized eyes. High antibiotic concentrations in silicone oil-filled eyes seemed to be well tolerated.Translational Relevance:This study aids in estimating how often an antibiotic should be intravitreally injected for endophthalmitis of silicone oil-filled eyes

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution