Remarks on Bootstrap Percolation in Metric Networks

We examine bootstrap percolation in d-dimensional, directed metric graphs in the context of recent measurements of firing dynamics in 2D neuronal cultures. There are two regimes, depending on the graph size N. Large metric graphs are ignited by the occurrence of critical nuclei, which initially occupy an infinitesimal fraction, f_* -> 0, of the graph and then explode throughout a finite fraction. Smaller metric graphs are effectively random in the sense that their ignition requires the initial ignition of a finite, unlocalized fraction of the graph, f_* >0. The crossover between the two regimes is at a size N_* which scales exponentially with the connectivity range \lambda like_* \sim \exp\lambda^d. The neuronal cultures are finite metric graphs of size N \simeq 10^5-10^6, which, for the parameters of the experiment, is effectively random since N<< N_*. This explains the seeming contradiction in the observed finite f_* in these cultures. Finally, we discuss the dynamics of the firing front

Deposition of tin oxide, iridium and iridium oxide films by metal-organic chemical vapor deposition for electrochemical wastewater treatment

In this research, the specific electrodes were prepared by metal-organic chemical vapor deposition (MOCVD) in a hot-wall CVD reactor with the presence of O2 under reduced pressure. The Ir protective layer was deposited by using (Methylcyclopentadienyl) (1,5-cyclooctadiene) iridium (I), (MeCp)Ir(COD), as precursor. Tetraethyltin (TET) was used as precursor for the deposition of SnO2 active layer. The optimum condition for Ir film deposition was at 300 °C, 125 of O2/(MeCp)Ir(COD) molar ratio and 12 Torr of total pressure. While that of SnO2 active layer was at 380 °C, 1200 of O2/TET molar ratio and 15 Torr of total pressure. The prepared SnO2/Ir/Ti electrodes were tested for anodic oxidation of organic pollutant in a simple three-electrode electrochemical reactor using oxalic acid as model solution. The electrochemical experiments indicate that more than 80% of organic pollutant was removed after 2.1 Ah/L of charge has been applied. The kinetic investigation gives a two-step process for organic pollutant degradation, the kinetic was zero-order and first-order with respect to TOC of model solution for high and low TOC concentrations, respectively

High performance computing and communications grand challenges program

The so-called protein folding problem has numerous aspects, however it is principally concerned with the {ital de novo} prediction of three-dimensional (3D) structure from the protein primary amino acid sequence, and with the kinetics of the protein folding process. Our current project focuses on the 3D structure prediction problem which has proved to be an elusive goal of molecular biology and biochemistry. The number of local energy minima is exponential in the number of amino acids in the protein. All current methods of 3D structure prediction attempt to alleviate this problem by imposing various constraints that effectively limit the volume of conformational space which must be searched. Our Grand Challenge project consists of two elements: (1) a hierarchical methodology for 3D protein structure prediction; and (2) development of a parallel computing environment, the Protein Folding Workbench, for carrying out a variety of protein structure prediction/modeling computations. During the first three years of this project, we are focusing on the use of two proteins selected from the Brookhaven Protein Data Base (PDB) of known structure to provide validation of our prediction algorithms and their software implementation, both serial and parallel. Both proteins, protein L from {ital peptostreptococcus magnus}, and {ital streptococcal} protein G, are known to bind to IgG, and both have an {alpha} {plus} {beta} sandwich conformation. Although both proteins bind to IgG, they do so at different sites on the immunoglobin and it is of considerable biological interest to understand structurally why this is so. 12 refs., 1 fig

Ferritin is secreted via 2 distinct nonclassical vesicular pathways

Ferritin turnover plays a major role in tissue iron homeostasis, and ferritin malfunction is associated with impaired iron homeostasis and neurodegenerative diseases. In most eukaryotes, ferritin is considered an intracellular protein that stores iron in a nontoxic and bioavailable form. In insects, ferritin is a classically secreted protein and plays a major role in systemic iron distribution. Mammalian ferritin lacks the signal peptide for classical endoplasmic reticulum–Golgi secretion but is found in serum and is secreted via a nonclassical lysosomal secretion pathway. This study applied bioinformatics and biochemical tools, alongside a protein trafficking mouse models, to characterize the mechanisms of ferritin secretion. Ferritin trafficking via the classical secretion pathway was ruled out, and a 2:1 distribution of intracellular ferritin between membrane-bound compartments and the cytosol was observed, suggesting a role for ferritin in the vesicular compartments of the cell. Focusing on nonclassical secretion, we analyzed mouse models of impaired endolysosomal trafficking and found that ferritin secretion was decreased by a BLOC-1 mutation but increased by BLOC-2, BLOC-3, and Rab27A mutations of the cellular trafficking machinery, suggesting multiple export routes. A 13-amino-acid motif unique to ferritins that lack the secretion signal peptide was identified on the BC-loop of both subunits and plays a role in the regulation of ferritin secretion. Finally, we provide evidence that secretion of iron-rich ferritin was mediated via the multivesicular body–exosome pathway. These results enhance our understanding of the mechanism of ferritin secretion, which is an important piece in the puzzle of tissue iron homeostasis

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits

The International Grid (iGrid): Empowering Global Research Community Networking Using High Performance International Internet Services

The Electronic Visualization Laboratory (EVL) at the University of Illinois at Chicago and Indiana University collaborated on a major research demonstration at the IEEE/ACM Supercomputing '98 (SC'98) conference in Orlando, Florida, November 7-13, 1998, to showcase the evolution and importance of global research community networking. Collaborators worked together to solve complex computational problems using advanced high-speed networks to access geographically-distributed computing, storage, and display resources. It is the collection of computing and communication resources that we refer to as the International Grid (iGrid). This paper presents an overview of the grid testbed, some of the underlying technologies used to enable distributed computing and collaborative problem solving, and descriptions of the applications. It concludes with recommendations for the future of global research community networking, based on the experiences of iGrid participants from the USA, Australia, Canada, Germany, Japan, The Netherlands, Russia, Switzerland, Singapore, and Taiwan

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

IHMCIF (github.com/ihmwg/IHMCIF) is a data information framework that supports archiving and disseminating macromolecular structures determined by integrative or hybrid modeling (IHM), and making them Findable, Accessible, Interoperable, and Reusable (FAIR). IHMCIF is an extension of the Protein Data Bank Exchange/macromolecular Crystallographic Information Framework (PDBx/mmCIF) that serves as the framework for the Protein Data Bank (PDB) to archive experimentally determined atomic structures of biological macromolecules and their complexes with one another and small molecule ligands (e.g., enzyme cofactors and drugs). IHMCIF serves as the foundational data standard for the PDB-Dev prototype system, developed for archiving and disseminating integrative structures. It utilizes a flexible data representation to describe integrative structures that span multiple spatiotemporal scales and structural states with definitions for restraints from a variety of experimental methods contributing to integrative structural biology. The IHMCIF extension was created with the benefit of considerable community input and recommendations gathered by the Worldwide Protein Data Bank (wwPDB) Task Force for Integrative or Hybrid Methods (wwpdb.org/task/hybrid). Herein, we describe the development of IHMCIF to support evolving methodologies and ongoing advancements in integrative structural biology. Ultimately, IHMCIF will facilitate the unification of PDB-Dev data and tools with the PDB archive so that integrative structures can be archived and disseminated through PDB

Rosseland and Planck Mean Opacities for Protoplanetary Discs

In this paper, we present mean gas and dust opacities relevant to the physical conditions typical of protoplanetary discs. As the principal absorber for temperatures below ~1,500 K, we consider spherical and aggregate dust particles of various sizes, chemical structure, and porosity, consisting of ice, organics, troilite, silicates, and iron. For higher temperatures, ions, atoms, molecules, and electrons are included as the main opacity sources. Rosseland and Planck mean opacities are calculated for temperatures between 5 K and 10,000 K and gas densities ranging from 10^{-18} g/ccm to 10^{-7} g/ccm. The dependence on the adopted model of dust grains is investigated. We compare our results with recent opacity tables and show how different opacity models affect the calculated hydrodynamical structure of accretion discs.Comment: 12 pages, 4 figures, to be published in A&A, 200