Surface Studies of Calcium Oxalate Dihydrate Single Crystals During Dissolution in the Presence of Urine

Single crystals of Calcium Oxalate Dihydrate (COD) were grown from solution under controlled release of the reacting ions. Dissolution of COD was studied at different pH levels and in different dilutions of urine. The descriptors of the contour were determined during dissolution of COD using a quantitative morphological technique. The shape parameters and surface ruggedness were determined from Fourier and fractal analysis. The results obtained give quantitative information on the dissolution kinetics and the surface geometry of COD crystals in normal and diluted urine. Dissolution inhibition and morphological changes of COD crystals during dissolution were attributed to selective adsorption of urine non-ionic macromolecules on the crystal stepped surface. Surface etching of COD was found to depend on urine dilution and time of incubation. The data obtained suggest that the geometric structure of the surface is likely to be a potential factor in understanding crystal aggregation in stone formation

Evaluation of the Surface Roughness of Cystine Stones Using a Visible Laser Diode Scattering Approach

To understand the processes of fragmentation and the chemical reactivity of solids, proper characterization of surface topography is crucial. This paper describes a non-destructive technique of quantifying the surface roughness of cystine renal stones, using visible laser diode scattering and fractal geometry. Fragments of cystine stones were mounted on microscope slides and coated by a carbon-sputtering apparatus. The slides were placed under a dynamic active-vision system, using a visible laser diode to measure three-dimensional surface coordinates. The data obtained were analyzed by fractal geometry. Surface fractal dimensions were determined by the variation method. The results showed that the surface of a compact-size sample can be evaluated quantitatively. The technique is valuable for the accurate presentation of surfaces in three dimensions

Structure of shells in complex networks

In a network, we define shell $\ell$ as the set of nodes at distance $\ell$ with respect to a given node and define $r_\ell$ as the fraction of nodes outside shell $\ell$. In a transport process, information or disease usually diffuses from a random node and reach nodes shell after shell. Thus, understanding the shell structure is crucial for the study of the transport property of networks. For a randomly connected network with given degree distribution, we derive analytically the degree distribution and average degree of the nodes residing outside shell $\ell$ as a function of $r_\ell$. Further, we find that $r_\ell$ follows an iterative functional form $r_\ell=\phi(r_{\ell-1})$, where $\phi$ is expressed in terms of the generating function of the original degree distribution of the network. Our results can explain the power-law distribution of the number of nodes $B_\ell$ found in shells with $\ell$ larger than the network diameter $d$, which is the average distance between all pairs of nodes. For real world networks the theoretical prediction of $r_\ell$ deviates from the empirical $r_\ell$. We introduce a network correlation function $c(r_\ell)\equiv r_{\ell+1}/\phi(r_\ell)$ to characterize the correlations in the network, where $r_{\ell+1}$ is the empirical value and $\phi(r_\ell)$ is the theoretical prediction. $c(r_\ell)=1$ indicates perfect agreement between empirical results and theory. We apply $c(r_\ell)$ to several model and real world networks. We find that the networks fall into two distinct classes: (i) a class of {\it poorly-connected} networks with $c(r_\ell)>1$, which have larger average distances compared with randomly connected networks with the same degree distributions; and (ii) a class of {\it well-connected} networks with $c(r_\ell)<1$

Bounded and unitary elements in pro-C^*-algebras

A pro-C^*-algebra is a (projective) limit of C^*-algebras in the category of topological *-algebras. From the perspective of non-commutative geometry, pro-C^*-algebras can be seen as non-commutative k-spaces. An element of a pro-C^*-algebra is bounded if there is a uniform bound for the norm of its images under any continuous *-homomorphism into a C^*-algebra. The *-subalgebra consisting of the bounded elements turns out to be a C^*-algebra. In this paper, we investigate pro-C^*-algebras from a categorical point of view. We study the functor (-)_b that assigns to a pro-C^*-algebra the C^*-algebra of its bounded elements, which is the dual of the Stone-\v{C}ech-compactification. We show that (-)_b is a coreflector, and it preserves exact sequences. A generalization of the Gelfand-duality for commutative unital pro-C^*-algebras is also presented.Comment: v2 (accepted

Pre-torsors and Galois comodules over mixed distributive laws

We study comodule functors for comonads arising from mixed distributive laws. Their Galois property is reformulated in terms of a (so-called) regular arrow in Street's bicategory of comonads. Between categories possessing equalizers, we introduce the notion of a regular adjunction. An equivalence is proven between the category of pre-torsors over two regular adjunctions $(N_A,R_A)$ and $(N_B,R_B)$ on one hand, and the category of regular comonad arrows $(R_A,\xi)$ from some equalizer preserving comonad ${\mathbb C}$ to $N_BR_B$ on the other. This generalizes a known relationship between pre-torsors over equal commutative rings and Galois objects of coalgebras.Developing a bi-Galois theory of comonads, we show that a pre-torsor over regular adjunctions determines also a second (equalizer preserving) comonad ${\mathbb D}$ and a co-regular comonad arrow from ${\mathbb D}$ to $N_A R_A$, such that the comodule categories of ${\mathbb C}$ and ${\mathbb D}$ are equivalent.Comment: 34 pages LaTeX file. v2: a few typos correcte

Fractal Analysis of Protein Potential Energy Landscapes

The fractal properties of the total potential energy V as a function of time t are studied for a number of systems, including realistic models of proteins (PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the exponent \gamma, is almost independent of temperature and increases with time, more slowly the larger the protein. Perhaps the most striking observation of this study is the apparent universality of the fractal dimension, which depends only weakly on the type of molecular system. We explain this behavior by assuming that fractality is caused by a self-generated dynamical noise, a consequence of intermode coupling due to anharmonicity. Global topological features of the potential energy landscape are found to have little effect on the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure

Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6A

Human herpesvirus-6A (HHV-6A) and 6B (HHV-6B) are two closely related betaherpesviruses that are associated with various diseases including seizures and encephalitis. The HHV-6A/B genomes have been shown to be present in an integrated state in the telomeres of latently infected cells. In addition, integration of HHV-6A/B in germ cells has resulted in individuals harboring this inherited chromosomally integrated HHV-6A/B (iciHHV-6) in every cell of their body. Until now, the viral transcriptome and the epigenetic modifications that contribute to the silencing of the integrated virus genome remain elusive. In the current study, we used a patient-derived iciHHV-6A cell line to assess the global viral gene expression profile by RNA-seq, and the chromatin profiles by MNase-seq and ChIP-seq analyses. In addition, we investigated an in vitro generated cell line (293-HHV-6A) that expresses GFP upon the addition of agents commonly used to induce herpesvirus reactivation such as TPA. No viral gene expression including miRNAs was detected from the HHV-6A genomes, indicating that the integrated virus is transcriptionally silent. Intriguingly, upon stimulation of the 293-HHV-6A cell line with TPA, only foreign promoters in the virus genome were activated, while all HHV-6A promoters remained completely silenced. The transcriptional silencing of latent HHV-6A was further supported by MNase-seq results, which demonstrate that the latent viral genome resides in a highly condensed nucleosome-associated state. We further explored the enrichment profiles of histone modifications via ChIP-seq analysis. Our results indicated that the HHV-6 genome is modestly enriched with the repressive histone marks H3K9me3/H3K27me3 and does not possess the active histone modifications H3K27ac/H3K4me3. Overall, these results indicate that HHV-6 genomes reside in a condensed chromatin state, providing insight into the epigenetic mechanisms associated with the silencing of the integrated HHV-6A genome

The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages

<p>Abstract</p> <p>Background</p> <p>The transcription factors of the LSF/Grainyhead (GRH) family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, <it>Grainyhead </it>(GRH) homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression.</p> <p>Results</p> <p>To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (<it>Nematostella vectensis</it>, <it>Vallicula multiformis</it>, <it>Trichoplax adhaerens</it>, and <it>Amphimedon queenslandica</it>), a choanoflagellate (<it>Monosiga brevicollis</it>) and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1) the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2) the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae <it>Volvox carteri </it>and <it>Chlamydomonas reinhardtii </it>or the amoebozoan <it>Dictyostelium purpureum</it>. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone <it>Nematostella</it>, with one locus encoding a DNA binding domain and the other locus encoding the dimerization domain.</p> <p>Conclusions</p> <p>In metazoans, LSF and GRH proteins play a number of roles that are essential to achieving and maintaining multicellularity. It is now clear that this protein family already existed in the unicellular ancestor of animals, choanoflagellates, and fungi. However, the diversification of distinct LSF and GRH subfamilies appears to be a metazoan invention. Given the conserved role of GRH in maintaining epithelial integrity in vertebrates, insects, and nematodes, it is noteworthy that the evolutionary origin of Grh appears roughly coincident with the evolutionary origin of the epithelium.</p

Dynamical chaos and power spectra in toy models of heteropolymers and proteins

The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the way in which a separation between the twin trajectories behaves in time. This observation allows one to determine the size of a folding funnel in good folders. We study the energy landscapes of the toy models by determining the power spectra and fractal characteristics of the dependence of the potential energy on time. For good folders, folding and unfolding trajectories have distinctly different correlated behaviors at low frequencies.Comment: 8 pages, 9 EPS figures, Phys. Rev. E (in press