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Search Results: 1 - 10 of 5150 matches for " Naoki Sato "
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Scientific élan Vital: Entropy Deficit or Inhomogeneity as a Unified Concept of Driving Forces of Life in Hierarchical Biosphere Driven by Photosynthesis
Naoki Sato
Entropy , 2012, DOI: 10.3390/e14020233
Abstract: Life is considered something different from non-living things, but no single driving force can account for all the different aspects of life, which consists of different levels of hierarchy, such as metabolism, cell physiology, multi-cellular development and organization, population dynamics, ecosystem, and evolution. Although free energy is evidently the driving force in biochemical reactions, there is no established relationship between metabolic energy and spatiotemporal organization of living organisms, or between metabolic energy and genetic information. Since Schr?dinger pointed out the importance of exporting entropy in maintaining life, misunderstandings of entropy notion have been obstacles in constructing a unified view on the driving forces of life. Here I present a simplified conceptual framework for unifying driving forces of life at various different levels of hierarchy. The key concept is “entropy deficit”, or simply, ‘inhomogeneity’, which is defined as the difference of maximal possible entropy and actual entropy. This is equivalent to information content in genetic information and protein structure, and is also defined similarly for non-homogeneous structures in ecosystems and evolution. Entropy deficit or inhomogeneoity is a unified measure of all driving forces of life, which could be considered a scientific equivalent to ‘élan vital’ of Bergson.
Enzymes involved in organellar DNA replication in photosynthetic eukaryotes
Takashi Moriyama,Naoki Sato
Frontiers in Plant Science , 2014, DOI: 10.3389/fpls.2014.00480
Abstract: Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.
A Stochastic Model of Inward Diffusion in Magnetospheric Plasmas
Naoki Sato,Zensho Yoshida
Physics , 2014, DOI: 10.1088/1751-8113/48/20/205501
Abstract: The inward diffusion of particles, often observed in magnetospheric plasmas (either naturally created stellar ones or laboratory devices) creates a spontaneous density gradient, which seemingly contradicts the entropy principle. We construct a theoretical model of diffusion that can explain the inward diffusion in a dipole magnetic field. The key is the identification of the proper coordinates on which an appropriate diffusion operator can be formulated. The effective phase space is foliated by the adiabatic invariants; on the symplectic leaf, the invariant measure (by which the entropy must be calculated) is distorted, by the inhomogeneous magnetic field, with respect to the conventional Lebesgue measure of the natural phase space. The collision operator is formulated to be consistent to the ergodic hypothesis on the symplectic leaf, i.e., the resultant diffusion must diminish gradients on the proper coordinates. The non-orthogonality of the cotangent vectors of the configuration space causes a coupling between the perpendicular and parallel diffusions, which is derived by applying Ito's formula of changing variables. The model has been examined by numerical simulations. We observe the creation of a peaked density profile that mimics radiation belts in planetary magnetospheres as well as laboratory experiments.
Renormalization procedure for random tensor networks and the canonical tensor model
Naoki Sasakura,Yuki Sato
Physics , 2015, DOI: 10.1093/ptep/ptv049
Abstract: We discuss a renormalization procedure for random tensor networks, and show that the corresponding renormalization-group flow is given by the Hamiltonian vector flow of the canonical tensor model, which is a discretized model of quantum gravity. The result is the generalization of the previous one concerning the relation between the Ising model on random networks and the canonical tensor model with N=2. We also prove a general theorem which relates discontinuity of the renormalization-group flow and the phase transitions of random tensor networks.
Ising model on random networks and the canonical tensor model
Naoki Sasakura,Yuki Sato
Physics , 2014, DOI: 10.1093/ptep/ptu049
Abstract: We introduce a statistical system on random networks of trivalent vertices for the purpose of studying the canonical tensor model, which is a rank-three tensor model in the canonical formalism. The partition function of the statistical system has a concise expression in terms of integrals, and has the same symmetries as the kinematical ones of the canonical tensor model. We consider the simplest non-trivial case of the statistical system corresponding to the Ising model on random networks, and find that its phase diagram agrees with what is implied by regrading the Hamiltonian vector field of the canonical tensor model with N = 2 as a renormalization group flow. Along the way, we obtain an explicit exact expression of the free energy of the Ising model on random networks in the thermodynamic limit by the Laplace method. This paper provides a new example connecting a model of quantum gravity and a random statistical system.
Exact Free Energies of Statistical Systems on Random Networks
Naoki Sasakura,Yuki Sato
Physics , 2014, DOI: 10.3842/SIGMA.2014.087
Abstract: Statistical systems on random networks can be formulated in terms of partition functions expressed with integrals by regarding Feynman diagrams as random networks. We consider the cases of random networks with bounded but generic degrees of vertices, and show that the free energies can be exactly evaluated in the thermodynamic limit by the Laplace method, and that the exact expressions can in principle be obtained by solving polynomial equations for mean fields. As demonstrations, we apply our method to the ferromagnetic Ising models on random networks. The free energy of the ferromagnetic Ising model on random networks with trivalent vertices is shown to exactly reproduce that of the ferromagnetic Ising model on the Bethe lattice. We also consider the cases with heterogeneity with mixtures of orders of vertices, and derive the known formula of the Curie temperature.
Thermal equilibrium of non-neutral plasma in dipole magnetic field
Naoki Sato,Norikazu Kasaoka,Zensho Yoshida
Physics , 2015, DOI: 10.1063/1.4917474
Abstract: Self-organization of a long-lived structure is one of the remarkable characteristics of macroscopic systems governed by long-range interactions. In a homogeneous magnetic field, a non-neutral plasma creates a "thermal equilibrium" which is a Boltzmann distribution on a rigidly rotating frame. Here, we study how a non-neutral plasma self-organizes in inhomogeneous magnetic field; as a typical system we consider a dipole magnetic field. In this generalized setting, the plasma exhibits its fundamental mechanism that determines the relaxed state. The scale hierarchy of adiabatic invariants is the determinant; the Boltzmann distribution under the topological constraint by the robust adiabatic invariants (hence, the homogeneous distribution with respect to the fragile invariant) is the relevant relaxed state, which turns out to be a rigidly rotating clump of particles (just same as in a homogeneous magnetic field), while the density is no longer homogeneous.
One Case of Suspected Angiostenosis Revealed by MRA Following Carotid Endarterectomy Due to a Rare Cause  [PDF]
Yuji Endo, Naoki Sato, Hidekazu Takahashi, Mamoru Ota, Toshihito Ishikawa, Katsuhiro Endo, Kenichi Ebihara
Open Journal of Modern Neurosurgery (OJMN) , 2018, DOI: 10.4236/ojmn.2018.83023
Abstract: We herein report on a case in which magnetic resonance angiography (MRA) following carotid endarterectomy revealed the appearance of angiostenosis due to an artifact of metallic powder, which was thought to have come from an old surgical instrument. The patient was a 77-year-old male. Carotid endarterectomy (CEA) was performed for stenosis in the internal carotid artery of his left neck (82%). Upon observing a decline in renal function following CEA surgery, a postoperative cervical MRA revealed the appearance of high-grade stenosis at the common carotid artery on which surgery was performed. No stenosis was revealed upon carotid ultrasonography and angiography. In the original MRA image, an orbicular low intensity area was observed in concordance with the narrow segment. 3D computed tomography (3D-CT) revealed a metallic finding, suggesting it was an artifact caused by metal powder. Close inspection of the metal surgical instruments used during surgery revealed slight damage to a suture snare which had been used for 30 years. Going forward, it is necessary to pay attention to old surgical instruments, introduce a system by which the number of years and the frequency of use of each surgical instrument can be learned, and replace them with new equipment as necessary.
Functional performance levels of strength and power needed for independence in 80-year-old individuals  [PDF]
Mieko Shimada, Yoshiaki Nomura, Yasuo Kimura, Naoki Nakagawa, Hiroshi Nagayama, Mitsumasa Tazawa, Tamotsu Sato, Daisuke Inaba, Masami Yonemitsu, Yutaka Yoshitake
Open Journal of Epidemiology (OJEpi) , 2012, DOI: 10.4236/ojepi.2012.23010
Abstract: Background: The ability to climb stairs (ascending and descending stair without using a handrail) and rise from a chair (rising from chairs without using an elbow rest) are among the most important measures of physical function for ADL evaluation for the independent living, and assessed by the questioners on many epidemiological studies in elderly. But little is known about the relationship between the self-reported performance level of the tasks and lower leg strength and power in very elderly people. The purpose of this study was to ascertain the relationship between the self-reported performance level of two tasks and the lower leg function in community-dwelling 80-year-old population. Methods: Out of 994 persons who were 80 years old living in Morioka City, Iwate Prefecture, Japan, 607 individuals (236 men and 371 women) underwent a physical fitness test that included measurements of leg extensor power and knee extensor strength. The ability to climb up stair and to rise from a chair was assessed by self- reported questionnaire which was ranked in three levels. The area under the receiver-operating characteristic (ROC) curve (AUC) was used to evaluate the measurements. Results: The cut-off points for the leg extensor power of subjects who could completely perform the stair-climbing and chair-rising functions were determined to be approximately 8.6 watt/kg body mass for men and 5.6 watt/kg body mass for women. In addition, the cut-off points for the knee extensor strength of subjects who could completely perform the stair-climbing and chair-rising functions were determined to be approximately 0.97 kg/kg body mass for men and 0.84 kg/kg body mass for women. Conclusions: From a practical viewpoint, the present study suggested that the cut-off points of leg extensor power and knee extensor strength can be used as targets in simple self-reported questionnaires to help in screening for mobility in 80-year-old population
Actin-Independent Behavior and Membrane Deformation Exhibited by the Four-Transmembrane Protein M6a
Yasufumi Sato, Naoki Watanabe, Nanae Fukushima, Sakura Mita, Tatsumi Hirata
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0026702
Abstract: M6a is a four-transmembrane protein that is abundantly expressed in the nervous system. Previous studies have shown that over-expression of this protein induces various cellular protrusions, such as neurites, filopodia, and dendritic spines. In this detailed characterization of M6a-induced structures, we found their varied and peculiar characteristics. Notably, the M6a-induced protrusions were mostly devoid of actin filaments or microtubules and exhibited free random vibrating motion. Moreover, when an antibody bound to M6a, the membrane-wrapped protrusions were suddenly disrupted, leading to perturbation of the surrounding membrane dynamics involving phosphoinositide signaling. During single-molecule analysis, M6a exhibited cytoskeleton-independent movement and became selectively entrapped along the cell perimeter in an actin-independent manner. These observations highlight the unusual characteristics of M6a, which may have a significant yet unappreciated role in biological systems.
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