Spatial chaos and complexity in the intracellular space of cancer and normal cells

BACKGROUND: One of the most challenging problems in biological image analysis is the quantification of the dynamical mechanism and complexity of the intracellular space. This paper investigates potential spatial chaos and complex behavior of the intracellular space of typical cancer and normal cell images whose structural details are revealed by the combination of scanning electron microscopy and focused ion beam systems. Such numerical quantifications have important implications for computer modeling and simulation of diseases. METHODS: Cancer cell lines derived from a human head and neck squamous cell carcinoma (SCC-61) and normal mouse embryonic fibroblast (MEF) cells produced by focused ion beam scanning electron microscopes were used in this study. Spatial distributions of the organelles of cancer and normal cells can be analyzed at both short range and long range of the bounded dynamical system of the image space, depending on the orientations of the spatial cell. A procedure was designed for calculating the largest Lyapunov exponent, which is an indicator of the potential chaotic behavior in intracellular images. Furthermore, the sample entropy and regularity dimension were applied to measure the complexity of the intracellular images. RESULTS: Positive values of the largest Lyapunov exponents (LLEs) of the intracellular space of the SCC-61 were obtained in different spatial orientations for both long-range and short-range models, suggesting the chaotic behavior of the cell. The MEF has smaller positive values of LLEs in the long range than those of the SCC-61, and zero vales of the LLEs in the short range analysis, suggesting a non-chaotic behavior. The intracellular space of the SCC-61 is found to be more complex than that of the MEF. The degree of complexity measured in the spatial distribution of the intracellular space in the diagonal direction was found to be approximately twice larger than the complexity measured in the horizontal and vertical directions. CONCLUSION: Initial findings are promising for characterizing different types of cells and therefore useful for studying cancer cells in the spatial domain using state-of-the-art imaging technology. The measures of the chaotic behavior and complexity of the spatial cell will help computational biologists gain insights into identifying associations between the oscillation patterns and spatial parameters of cells, and appropriate model for simulating cancer cell signaling networks for cancer treatment and new drug discovery

Biochemical Analysis of Dimethyl Suberimidate-crosslinked Yeast Nucleosomes

Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we provide a detailed protocol for the use of DMS to analyze yeast nucleosomes

Outcome Independence of Entanglement in One-Way Computation

We show that the various intermediate states appearing in the process of one-way computation at a given step of measurement are all equivalent modulo local unitary transformations. This implies, in particular, that all those intermediate states share the same entanglement irrespective of the measurement outcomes, indicating that the process of one-way computation is essentially unique with respect to local quantum operations.Comment: 6 pages, 4 figure

forall x (UBC Edition)

This is an open-access introductory logic textbook, prepared by Jonathan Ichikawa, based on P.D. Magnus's forallx. This (v2.0, July 2020) is intended as a stable, ready-for-teaching edition

Neutrino mass constraint from CMB and its degeneracy with other cosmological parameters

We show that the cosmic microwave background (CMB) data of WMAP can give subelectronvolt limit on the neutrino mass: m_nu < 0.63 eV (95% CL). We also investigate its degeneracy with other cosmological parameters. In particular, we show the Hubble constant derived from the WMAP data decreases considerably when the neutrino mass is a few times 0.1 eV.Comment: 3 pages, 2 figures, prepared for the TAUP2007 Proceeding

An asymmetric centromeric nucleosome

Nucleosomes contain two copies of each core histone, held together by a naturally symmetric, homodimeric histone H3-H3 interface. This symmetry has complicated efforts to determine the regulatory potential of this architecture. Through molecular design and in vivo selection, we recently generated obligately heterodimeric H3s, providing a powerful tool for discovery of the degree to which nucleosome symmetry regulates chromosomal functions in living cells (Ichikawa et al., 2017). We now have extended this tool to the centromeric H3 isoform (Cse4/CENP-A) in budding yeast. These studies indicate that a single Cse4 N- or C-terminal extension per pair of Cse4 molecules is sufficient for kinetochore function, and validate previous experiments indicating that an octameric centromeric nucleosome is required for viability in this organism. These data also support the generality of the H3 asymmetric interface for probing general questions in chromatin biology

An Analysis of the Quantum Penny Flip Game using Geometric Algebra

We analyze the quantum penny flip game using geometric algebra and so determine all possible unitary transformations which enable the player Q to implement a winning strategy. Geometric algebra provides a clear visual picture of the quantum game and its strategies, as well as providing a simple and direct derivation of the winning transformation, which we demonstrate can be parametrized by two angles. For comparison we derive the same general winning strategy by conventional means using density matrices.Comment: 8 Pages, 1 Figure, accepted for publication in the Journal of Physical Society of Japa

The oscillation effects on thermalization of the neutrinos in the universe with low reheating temperature

We study how the oscillations of the neutrinos affect their thermalization process during the reheating period with temperature O(1) MeV in the early universe. We follow the evolution of the neutrino density matrices and investigate how the predictions of big bang nucleosynthesis vary with the reheating temperature. For the reheating temperature of several MeV, we find that including the oscillations makes different predictions, especially for $^4$He abundance. Also, the effects on the lower bound of the reheating temperature from cosmological observations are discussed.Comment: 24 pages, 8 figures; references and explanatory comments added, conclusion unchange

Solving the cosmic lithium problems with primordial late-decaying particles

We investigate the modifications to predictions for the abundances of light elements from standard Big-Bang nucleosynthesis when exotic late-decaying particles with lifetimes exceeding ~1 sec are prominent in the early Universe. Utilising a model-independent analysis of the properties of these long-lived particles, we identify the parameter space associated with models that are consistent with all observational data and hence resolve the much discussed discrepancies between observations and theoretical predictions for the abundances of Li^7 and Li^6.Comment: 6 pages, 3 figures, submitted to Physical Review D; minor changes to reference