Fundamental Cycle of a Periodic Box-Ball System

We investigate a soliton cellular automaton (Box-Ball system) with periodic boundary conditions. Since the cellular automaton is a deterministic dynamical system that takes only a finite number of states, it will exhibit periodic motion. We determine its fundamental cycle for a given initial state.Comment: 28 pages, 6 figure

ECO-friendly distributed routing protocol for reducing network energy consumption

Abstract—The growth of Internet traffic has led to an increase in energy consumption by network equipment such as routers and switches. Consequently, energy consumption is becoming a key environmental, social, political and cost issue. Focusing on energy consumption by Internet Service Provider networks, the energy bottleneck is routers. Thus, it is imperative for us to reduce the energy consumption of routers. In this paper, we propose a new ECO-friendly distributed routing protocol (ECO-RP) based on OSPF. In our proposal, an ECO-RP entity periodically checks the amount of traffic forwarded by the ECO-RP entity. Moreover, an ECO-RP entity floods information on the amount of traffic to other entities such as the OSPF Link State Advertisement. This allows each ECO-RP entity to obtain information on traffic in the network, and to dynamically change OSPF link weights based on the information. For example, when the amount of overall network traffic is small, the entity changes link weights so that the traffic can be routed only through a subset of routers, and unneeded routers can shift into sleep mode. Several simulation studies, which assume two ECO-RP enabled networks, are conducted. The result shows that the proposed protocol is able to reduce energy consumption by about 18.5% at maximum without network congestion. I

Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease

Kidneys are enlarged by aberrant proliferation of tubule epithelial cells leading to the formation of numerous cysts, nephron loss, and interstitial fibrosis in polycystic kidney disease (PKD). Pioglitazone (PIO), a PPAR-γ agonist, decreased cell proliferation, interstitial fibrosis, and inflammation, and ameliorated PKD progression in PCK rats (Am. J. Physiol.-Renal, 2011). To explore genetic mechanisms involved, changes in global gene expression were analyzed. By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 downregulated gene ontology biological process gene sets and six of the top 20 curated gene set canonical pathways identified to be downregulated by PIOtreatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes downregulated by PIO treatment. Immunohistochemical analysis revealed that the gene product of this enzyme was highly expressed in PCK kidneys and decreased by PIO. These data show that PIO alters the expression of genes involved in cell cycle progression, cell proliferation, and fatty acid metabolism

Osteoclasts adapt to physioxia perturbation through DNA demethylation

Oxygen plays an important role in diverse biological processes. However, since quantitation of the partial pressure of cellular oxygen in vivo is challenging, the extent of oxygen perturbation in situ and its cellular response remains underexplored. Using two-photon phosphorescence lifetime imaging microscopy, we determine the physiological range of oxygen tension in osteoclasts of live mice. We find that oxygen tension ranges from 17.4 to 36.4 mmHg, under hypoxic and normoxic conditions, respectively. Physiological normoxia thus corresponds to 5% and hypoxia to 2% oxygen in osteoclasts. Hypoxia in this range severely limits osteoclastogenesis, independent of energy metabolism and hypoxia-inducible factor activity. We observe that hypoxia decreases ten-eleven translocation (TET) activity. Tet2/3 cooperatively induces Prdm1 expression via oxygen-dependent DNA demethylation, which in turn activates NFATc1 required for osteoclastogenesis. Taken together, our results reveal that TET enzymes, acting as functional oxygen sensors, regulate osteoclastogenesis within the physiological range of oxygen tension, thus opening new avenues for research on in vivo response to oxygen perturbation.Nishikawa K., Seno S., Yoshihara T., et al. Osteoclasts adapt to physioxia perturbation through DNA demethylation. EMBO Reports 22, e53035 (2021); https://doi.org/10.15252/embr.202153035

Mitochondrial Abnormality Facilitates Cyst Formation in Autosomal Dominant Polycystic Kidney Disease

ABSTRACT Autosomal dominant polycystic kidney disease (ADPKD) constitutes the most inherited kidney disease. Mutations in the PKD1 and PKD2 genes, encoding the polycystin 1 and polycystin 2 Ca2+ ion channels, respectively, result in tubular epithelial cell-derived renal cysts. Recent clinical studies demonstrate oxidative stress to be present early in ADPKD. Mitochondria comprise the primary reactive oxygen species source and also their main effector target; however, the pathophysiological role of mitochondria in ADPKD remains uncharacterized. To clarify this function, we examined the mitochondria of cyst-lining cells in ADPKD model mice (Ksp-Cre PKD1flox/flox) and rats (Han:SPRD Cy/+), demonstrating obvious tubular cell morphological abnormalities. Notably, the mitochondrial DNA copy number and peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) expression were decreased in ADPKD model animal kidneys, with PGC-1α expression inversely correlated with oxidative stress levels. Consistent with these findings, human ADPKD cyst-derived cells with heterozygous and homozygous PKD1 mutation exhibited morphological and functional abnormalities, including increased mitochondrial superoxide. Furthermore, PGC-1α expression was suppressed by decreased intracellular Ca2+ levels via calcineurin, p38 mitogen-activated protein kinase (MAPK), and nitric oxide synthase deactivation. Moreover, the mitochondrion-specific antioxidant MitoQuinone (MitoQ) reduced intracellular superoxide and inhibited cyst epithelial cell proliferation through extracellular signal-related kinase/MAPK inactivation. Collectively, these results indicate that mitochondrial abnormalities facilitate cyst formation in ADPKD

Occlusal disharmony induces BDNF level in rat submandibular gland

Objectives: Brain-derived neurotrophic factor (BDNF), which is produced in rat submandibular gland, is one of the most abundant neurotrophins in the central nervous system. It is generally accepted that occlusal disharmony causes stress. The purpose of the present study was to investigate whether occlusal disharmony-induced chronic stress affects BDNF levels and morphology in rat submandibular gland. Design: Eight wks old male Wistar rats (n = 21) were randomly divided into three groups of 7 rats. In a control (C) group, the rats received no treatment for 8 wks. In a molar cusp-less (OD) group, maxillary molar cusps were cut off with a dental turbine at baseline and kept for 8 wks. In a molar cusp-less + recovered cusp (OR) group, maxillary molar cusps were cut off and then were recovered after 4 wks using resin material. After the experimental period, expression of BDNF mRNA and protein as well as histological findings were evaluated in the submandibular glands. The comparisons between the groups were made using the Mann-Whitney U test with Bonferroni correction. Results: The OD group showed a significant increase in submandibular gland BDNF mRNA and protein expression after 8 wks, and plasma adrenocorticotropic hormone and corticosterone levels increased in a time-dependent manner. There were no significant differences in BDNF expression in the submandibular glands and in levels of plasma adrenocorticotropic hormone and corticosterone between the OR and C groups. Conclusions: These results indicate that psychological stress induced by occlusal disharmony reversibly induces BDNF expression in the rat submandibular gland