Science.gov

Sample records for chemical structure information

  1. Trends in information theory-based chemical structure codification.

    PubMed

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  2. Why relevant chemical information cannot be exchanged without disclosing structures

    NASA Astrophysics Data System (ADS)

    Filimonov, Dmitry; Poroikov, Vladimir

    2005-09-01

    Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of information contained in a training set. Suggestion that some relevant chemical information can be added to such training sets without disclosing chemical structures was generated at the recent ACS Symposium. We presented arguments that such safety exchange of relevant chemical information is impossible. Any relevant information about chemical structures can be used for search of either a particular compound itself or its close analogues. Risk of identifying such structures is enough to prevent pharma industry from relevant chemical information exchange.

  3. Mining chemical structural information from the drug literature.

    PubMed

    Banville, Debra L

    2006-01-01

    It is easier to find too many documents on a life science topic than to find the right information inside these documents. With the application of text data mining to biological documents, it is no surprise that researchers are starting to look at applications that mine out chemical information. The mining of chemical entities--names and structures--brings with it some unique challenges, which commercial and academic efforts are beginning to address. Ultimately, life science text data mining applications need to focus on the marriage of biological and chemical information.

  4. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  5. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  6. Classification of Chemicals Based On Structured Toxicity Information

    EPA Science Inventory

    Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-bas...

  7. Classification of Chemicals Based On Structured Toxicity Information

    EPA Science Inventory

    Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-bas...

  8. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    PubMed

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  9. Protein Structural Information Derived from NMR Chemical Shift with the Neural Network Program TALOS-N

    PubMed Central

    Shen, Yang; Bax, Ad

    2015-01-01

    Summary Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors and the artificial neural network based TALOS-N program has been trained to extract backbone and sidechain torsion angles from 1H, 15N and 13C shifts. The program is quite robust, and typically yields backbone torsion angles for more than 90% of the residues, and sidechain χ1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and 13Cβ nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations. PMID:25502373

  10. INTEGRATED CHEMICAL INFORMATION TECHNOLOGIES ...

    EPA Pesticide Factsheets

    A central regulatory mandate of the Environmental Protection Agency, spanning many Program Offices and issues, is to assess the potential health and environmental risks of large numbers of chemicals released into the environment, often in the absence of relevant test data. Models for predicting potential adverse effects of chemicals based primarily on chemical structure play a central role in prioritization and screening strategies yet are highly dependent and conditional upon the data used for developing such models. Hence, limits on data quantity, quality, and availability are considered by many to be the largest hurdles to improving prediction models in diverse areas of toxicology. Generation of new toxicity data for additional chemicals and endpoints, development of new high-throughput, mechanistically relevant bioassays, and increased generation of genomics and proteomics data that can clarify relevant mechanisms will all play important roles in improving future SAR prediction models. The potential for much greater immediate gains, across large domains of chemical and toxicity space, comes from maximizing the ability to mine and model useful information from existing toxicity data, data that represent huge past investment in research and testing expenditures. In addition, the ability to place newer “omics” data, data that potentially span many possible domains of toxicological effects, in the broader context of historical data is the means for opti

  11. Atmospheric Black Carbon: Chemical Bonding and Structural Information of Individual Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Gilles, M. K.; Tivanski, A. V.; Hopkins, R. J.; Marten, B. D.

    2006-12-01

    The formation of aerosols from both natural and anthropogenic sources affects the Earth's temperature and climate by altering the radiative properties of the atmosphere. Aerosols containing black carbon (BC) that are released into the atmosphere from the burning of biomass, natural fires and the combustion of coals, diesel and jet fuels, contribute a large positive component to this radiative forcing, thus causing a heating of the atmosphere. A distinct type of biomass burn aerosol referred to as "tar balls" has recently been reported in the literature and is characterized by a spherical morphology, high carbon content and ability to efficiently scatter and absorb light. At present, very little is known about the exact nature and variation of the range of BC aerosols in the atmosphere with regards to optical, chemical and physical properties. Additionally, the similarity of these aerosols to surrogates used in the laboratory as atmospheric mimics remains unclear. The local chemical bonding, structural ordering and carbon-to-oxygen ratios of a plethora of black carbon standard reference materials (BC SRMs), high molecular mass humic-like substances (HULIS) and atmospheric aerosols from a variety of sources are examined using scanning transmission X-ray microscopy (STXM) coupled with near edge X-ray absorption fine structure (NEXAFS) spectroscopy. STXM/NEXAFS enables single aerosol particles of diameter upwards of 100 nm to be studied, which allows the diversity of atmospheric aerosol collected during a variety of field missions to be assessed. We apply a semi-quantitative peak fitting method to the recorded NEXAFS spectral fingerprints allowing comparison of BC SRMs and HULIS to BC aerosol originating from anthropogenic combustion and biomass burning events. This method allows us to distinguish between anthropogenic combustion and biomass burn aerosol using both chemical bonding and structural ordering information. The STXM/NEXAFS technique has also been utilized to

  12. Chemical information science coverage in Chemical Abstracts.

    PubMed

    Wiggins, G

    1987-02-01

    For many years Chemical Abstracts has included in its coverage publications on chemical documentation or chemical information science. Although the bulk of those publications can be found in section 20 of Chemical Abstracts, many relevant articles were found scattered among 39 other sections of CA in 1984-1985. In addition to the scattering of references in CA, the comprehensiveness of Chemical Abstracts as a secondary source for chemical information science is called into question. Data are provided on the journals that contributed the most references on chemical information science and on the languages of publication of relevant articles.

  13. Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases

    PubMed Central

    Haan, Claude; Behrmann, Iris; Haan, Serge

    2010-01-01

    Abstract Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets. PMID:20132407

  14. Tautomerism in chemical information management systems

    NASA Astrophysics Data System (ADS)

    Warr, Wendy A.

    2010-06-01

    Tautomerism has an impact on many of the processes in chemical information management systems including novelty checking during registration into chemical structure databases; storage of structures; exact and substructure searching in chemical structure databases; and depiction of structures retrieved by a search. The approaches taken by 27 different software vendors and database producers are compared. It is hoped that this comparison will act as a discussion document that could ultimately improve databases and software for researchers in the future.

  15. EXPANDING CHEMICAL-TOXICITY INFORMATION ...

    EPA Pesticide Factsheets

    We find that the connection between structure and biological response is not symmetric, with biological response better at predicting chemical structure than vice versa. *ToxCast Toxicity Reference Database. We find that the connection between structure and biological response is not symmetric, with biological response better at predicting chemical structure than vice versa. *ToxCast Toxicity Reference Database.

  16. Adapting the structure of a neural network to extract chemical information. Application to structure-odour relationships.

    PubMed

    Chastrette, M; De Saint Laumer, J Y; Peyraud, J F

    1993-01-01

    Two types of neural networks were used to establish relationships between chemical structure and musk odour of 79 nitrobenzenic compounds. Substituents on the five free sites of the benzene ring (one position was always occupied by a t-butyl group) were described using three volume descriptors and three electronegativity descriptors. Musk odour was coded by a binary variable. First a classical network with two hidden layers containing six and three neurons was used. This network gave a better classification (94%) than that obtained by linear discriminant analysis (81%). The odour was then predicted using a leave-ten-out procedure, with 77% of correct prediction for the whole sample. Then a dual two-way network was built to mimic the symmetry of the problem (two sides on a molecule, two muskophore patterns). This network recognized both patterns already known to chemists and gave 99% of correct classifications by taking into account substitution in all positions. As a side benefit of the modified network structure it was possible to evaluate the influence of each of 19 substituents in each of the five possible positions.

  17. Extraction of structural and chemical information from high angle annular dark-field image by an improved peaks finding method.

    PubMed

    Yin, Wenhao; Huang, Rong; Qi, Ruijuan; Duan, Chungang

    2016-09-01

    With the development of spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM), high angle annular dark filed (HAADF) imaging technique has been widely applied in the microstructure characterization of various advanced materials with atomic resolution. However, current qualitative interpretation of the HAADF image is not enough to extract all the useful information. Here a modified peaks finding method was proposed to quantify the HAADF-STEM image to extract structural and chemical information. Firstly, an automatic segmentation technique including numerical filters and watershed algorithm was used to define the sub-areas for each atomic column. Then a 2D Gaussian fitting was carried out to determine the atomic column positions precisely, which provides the geometric information at the unit-cell scale. Furthermore, a self-adaptive integration based on the column position and the covariance of statistical Gaussian distribution were performed. The integrated intensities show very high sensitivity on the mean atomic number with improved signal-to-noise (S/N) ratio. Consequently, the polarization map and strain distributions were rebuilt from a HAADF-STEM image of the rhombohedral and tetragonal BiFeO3 interface and a MnO2 monolayer in LaAlO3 /SrMnO3 /SrTiO3 heterostructure was discerned from its neighbor TiO2 layers. Microsc. Res. Tech. 79:820-826, 2016. © 2016 Wiley Periodicals, Inc.

  18. Information Structure and Linguistic Structure.

    ERIC Educational Resources Information Center

    Zierer, Ernesto

    1972-01-01

    This document describes a format for analyzing the information content of sentences and the language patterns that accompany particular information content. The author writes in terms of information structures, each information structure having a corresponding linguistic structure composed of distinctive features. The information structure of a…

  19. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

    PubMed Central

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13C and 15N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13C–13C, 15N–13C, or 3D 15N–13C–13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C–13C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination. PMID:23625364

  20. Chemical Information: Print. Directed Study.

    ERIC Educational Resources Information Center

    Stone, Catherine C.

    This report provides a survey and evaluation of chemical information literature. Contained in this survey are an overview of the chemical literature field, comments on obtaining access to this literature and annotated bibliographies of primary, secondary, and tertiary sources as well as special topics. Primary sources include journals, patents,…

  1. Chemical Information: Print. Directed Study.

    ERIC Educational Resources Information Center

    Stone, Catherine C.

    This report provides a survey and evaluation of chemical information literature. Contained in this survey are an overview of the chemical literature field, comments on obtaining access to this literature and annotated bibliographies of primary, secondary, and tertiary sources as well as special topics. Primary sources include journals, patents,…

  2. An Integrated Chemical Information Program

    NASA Astrophysics Data System (ADS)

    Somerville, Arleen N.; Cardinal, Susan K.

    2003-05-01

    Chemical educators have long recognized the importance of teaching their students how to locate and use chemical information. Many articles have been written about stand-alone courses and about efforts that focus on teaching specific topics within a course or two. At the University of Rochester, however, chemical information instruction is integrated into courses throughout the undergraduate and graduate curriculum in a sequential manner. Students utilize their information-seeking skills in completing course work and then this information serves as the base on which to continuously build new skills. This article describes the program as implemented over four years, notes how the faculty and librarian work together in conjunction with student input, and depicts how the instruction contributes to the educational value of the courses.

  3. Chemical Information Literacy at a Liberal Arts College

    ERIC Educational Resources Information Center

    Greco, George E.

    2016-01-01

    Chemistry majors at Goucher College are now required to take a 1-credit course in their sophomore year entitled Chemical Information Literacy. Students in the course learn the structure and organization of the chemical literature, and how to carry out searches of various databases for topic, author, chemical compound, or structure. They learn…

  4. Chemical Information Literacy at a Liberal Arts College

    ERIC Educational Resources Information Center

    Greco, George E.

    2016-01-01

    Chemistry majors at Goucher College are now required to take a 1-credit course in their sophomore year entitled Chemical Information Literacy. Students in the course learn the structure and organization of the chemical literature, and how to carry out searches of various databases for topic, author, chemical compound, or structure. They learn…

  5. Image-Based Chemical Structure Determination.

    PubMed

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans

    2017-07-28

    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  6. Chemical Bonding and Structural Information of Black CarbonReference Materials and Individual Carbonaceous AtmosphericAerosols

    SciTech Connect

    Hopkins, Rebecca J.; Tivanski, Alexei V.; Marten, Bryan D.; Gilles, Mary K.

    2007-04-25

    The carbon-to-oxygen ratios and graphitic nature of a rangeof black carbon standard reference materials (BC SRMs), high molecularmass humic-like substances (HULIS) and atmospheric particles are examinedusing scanning transmission X-ray microscopy (STXM) coupled with nearedge X-ray absorption fine structure (NEXAFS) spectroscopy. UsingSTXM/NEXAFS, individual particles with diameter>100 nm are studied,thus the diversity of atmospheric particles collected during a variety offield missions is assessed. Applying a semi-quantitative peak fittingmethod to the NEXAFS spectra enables a comparison of BC SRMs and HULIS toparticles originating from anthropogenic combustion and biomass burns,thus allowing determination of the suitability of these materials forrepresenting atmospheric particles. Anthropogenic combustion and biomassburn particles can be distinguished from one another using both chemicalbonding and structural ordering information. While anthropogeniccombustion particles are characterized by a high proportion ofaromatic-C, the presence of benzoquinone and are highly structurallyordered, biomass burn particles exhibit lower structural ordering, asmaller proportion of aromatic-C and contain a much higher proportion ofoxygenated functional groups.

  7. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

    EPA Pesticide Factsheets

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

  8. Chemical Structural Aging Effects

    DTIC Science & Technology

    1974-10-01

    prediction 20 AIISTRPACT (Continue for reverse aid@ It necessary and lpentity 6v blockA moso&-, Aging studies have been conducted upon one batch of ANB - 3066...correlations can indeed be employed which will allow the use of accelerated surveillance to predict chemical aging rates of ANB -3066 under silo storage...3.2.2 Kinetic Analysis of Parameter Aging Changes 2-4 1.2. 1 Temperature and Strain Dependence of Aging Rates " 3.2.4 Comparison With Other ANB -3066

  9. Structuring the Information Gap.

    ERIC Educational Resources Information Center

    Edge, Julian

    1984-01-01

    Describes an information gap procedure to teach a new structure which requires students to look for and exchange information in order to complete a task in an English as a second language class. Illustrates the method with a set of materials and suggests ways for teachers to produce similar materials. (SED)

  10. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer

    PubMed Central

    Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

  11. 2007 Chemical Biological Information Systems

    DTIC Science & Technology

    2007-01-11

    Keynote – Mr. Jean Reed, Special Assistant to the Secretary of Defense for Chemical and Biological Defense Programs 9:45AM – 10:30AM BREAK (Exhibit Area...a-SiO2 are important adsorbents – many other materials are based on a silicate or aluminosilicate chemical composition 2. Pinto and Elliott, Phys...2007 Tom Harris, C. Dougherty, J. Sontowski, SAIC (harrist@saic.com) Jacques Moussafir, Julien Commanay, ARIA Technologies (jmoussafir@aria.fr

  12. ChemEx: information extraction system for chemical data curation.

    PubMed

    Tharatipyakul, Atima; Numnark, Somrak; Wichadakul, Duangdao; Ingsriswang, Supawadee

    2012-01-01

    Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx.

  13. Development of structure information from molecular topology for modeling chemical and biological properties: a tribute to the creativity of Lemont Burwell Kier on his 80th Birthday.

    PubMed

    Hall, Lowell H

    2012-06-01

    This review is a salute to Monty Kier's creativity. Emphasis is placed on creative aspects in the development of the representation of molecular topological structure information and the resultant formalisms: molecular connectivity and electrotopological state (E-State). Less attention is given to detailed analysis of individual papers and the generally well known books and book chapters. This discussion reveals creative paths that led to the concept of the atomic descriptors, simple connectivity delta, encoding local topology, and valence delta value which encodes valence electron information. The fundamental developments that led to the creation of molecular connectivity chi indices are described along with extensions to different chi and delta chi formalisms. Continued thinking about structure in the topological sense led to the development of the only valence state electronegativity formalism based entirely on structure, Kier-Hall electronegativity (KHE). That creation further inspired the development of the electronegativity/topology-based atomic intrinsic state along with perturbation terms that together give electrotopological state indices (E-State). Further creation led to atom and bond type E-State descriptors. All these developments are briefly illustrated with examples in QSAR, chemical similarity, and database searching.

  14. Classification and Dose-Response Characterization of Environmental Chemicals Based On Structured Toxicity Information From ToxRefDB

    EPA Science Inventory

    Thirty years and over a billion of today’s dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data, within the U.S. Environmental Protection Agency’s...

  15. A survey of chemical information systems

    NASA Technical Reports Server (NTRS)

    Dominick, Wayne D. (Editor); Shaikh, Aneesa Bashir

    1985-01-01

    A survey of the features, functions, and characteristics of a fairly wide variety of chemical information storage and retrieval systems currently in operation is given. The types of systems (together with an identification of the specific systems) addressed within this survey are as follows: patents and bibliographies (Derwent's Patent System; IFI Comprehensive Database; PULSAR); pharmacology and toxicology (Chemfile; PAGODE; CBF; HEEDA; NAPRALERT; MAACS); the chemical information system (CAS Chemical Registry System; SANSS; MSSS; CSEARCH; GINA; NMRLIT; CRYST; XTAL; PDSM; CAISF; RTECS Search System; AQUATOX; WDROP; OHMTADS; MLAB; Chemlab); spectra (OCETH; ASTM); crystals (CRYSRC); and physical properties (DETHERM). Summary characteristics and current trends in chemical information systems development are also examined.

  16. Chemical Data Reporting Fact Sheet: Basic Information

    EPA Pesticide Factsheets

    EPA collects information on the types and quantities of chemicals produced in the U.S under the Chemical Data Reporting (CDR) requirements. This fact sheet outlines key information about CDR, including what data are collected and how the data are used.

  17. Identification of Chemical Toxicity Using Ontology Information of Chemicals.

    PubMed

    Jiang, Zhanpeng; Xu, Rui; Dong, Changchun

    2015-01-01

    With the advance of the combinatorial chemistry, a large number of synthetic compounds have surged. However, we have limited knowledge about them. On the other hand, the speed of designing new drugs is very slow. One of the key causes is the unacceptable toxicities of chemicals. If one can correctly identify the toxicity of chemicals, the unsuitable chemicals can be discarded in early stage, thereby accelerating the study of new drugs and reducing the R&D costs. In this study, a new prediction method was built for identification of chemical toxicities, which was based on ontology information of chemicals. By comparing to a previous method, our method is quite effective. We hope that the proposed method may give new insights to study chemical toxicity and other attributes of chemicals.

  18. Network Centric Information Structure - Crisis Information Management

    DTIC Science & Technology

    2004-06-01

    information management during emergency and crisis. The paper presents a prioritized set of important information elements that would be of value during a crisis or a rescue mission. It suggests how the information should be collected, stored and distributed, and it suggests information distribution methods supporting a network centric information structure concept. The work is funded by Teleplan and the Norwegian Research

  19. The NIH-EPA Chemical Information System.

    ERIC Educational Resources Information Center

    Bernstein, Herbert J.; Andrews, Lawrence C.

    1979-01-01

    The NIH-EPA Chemical Information System (CIS) provides facilities useful for the characterization and identification of chemical substances in industrial, academic, regulatory, and emergency response environments. It is comprised of a variety of data bases, retrieval programs, and related processing and display programs with on-line interactive…

  20. Classification of Chemicals Based On Structured Toxicity ...

    EPA Pesticide Factsheets

    Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-based classifications of chemicals were performed as a model application of ToxRefDB. These endpoints will ultimately provide the anchoring toxicity information for the development of predictive models and biological signatures utilizing in vitro assay data. Utilizing query and structured data mining approaches, toxicity profiles were uniformly generated for greater than 300 chemicals. Based on observation rate, species concordance and regulatory relevance, individual and aggregated effects have been selected to classify the chemicals providing a set of predictable endpoints. ToxRefDB exhibits the utility of transforming unstructured toxicity data into structured data and, furthermore, into computable outputs, and serves as a model for applying such data to address modern toxicological problems.

  1. The PubChem chemical structure sketcher

    PubMed Central

    2009-01-01

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects. PMID:20298522

  2. The PubChem chemical structure sketcher.

    PubMed

    Ihlenfeldt, Wolf D; Bolton, Evan E; Bryant, Stephen H

    2009-12-17

    PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

  3. Mapping chemical structure-activity information of HAART-drug cocktails over complex networks of AIDS epidemiology and socioeconomic data of U.S. counties.

    PubMed

    Herrera-Ibatá, Diana María; Pazos, Alejandro; Orbegozo-Medina, Ricardo Alfredo; Romero-Durán, Francisco Javier; González-Díaz, Humberto

    2015-06-01

    Using computational algorithms to design tailored drug cocktails for highly active antiretroviral therapy (HAART) on specific populations is a goal of major importance for both pharmaceutical industry and public health policy institutions. New combinations of compounds need to be predicted in order to design HAART cocktails. On the one hand, there are the biomolecular factors related to the drugs in the cocktail (experimental measure, chemical structure, drug target, assay organisms, etc.); on the other hand, there are the socioeconomic factors of the specific population (income inequalities, employment levels, fiscal pressure, education, migration, population structure, etc.) to study the relationship between the socioeconomic status and the disease. In this context, machine learning algorithms, able to seek models for problems with multi-source data, have to be used. In this work, the first artificial neural network (ANN) model is proposed for the prediction of HAART cocktails, to halt AIDS on epidemic networks of U.S. counties using information indices that codify both biomolecular and several socioeconomic factors. The data was obtained from at least three major sources. The first dataset included assays of anti-HIV chemical compounds released to ChEMBL. The second dataset is the AIDSVu database of Emory University. AIDSVu compiled AIDS prevalence for >2300 U.S. counties. The third data set included socioeconomic data from the U.S. Census Bureau. Three scales or levels were employed to group the counties according to the location or population structure codes: state, rural urban continuum code (RUCC) and urban influence code (UIC). An analysis of >130,000 pairs (network links) was performed, corresponding to AIDS prevalence in 2310 counties in U.S. vs. drug cocktails made up of combinations of ChEMBL results for 21,582 unique drugs, 9 viral or human protein targets, 4856 protocols, and 10 possible experimental measures. The best model found with the original

  4. Effective communication of information about chemical hazards.

    PubMed

    Lee, T R

    1986-05-01

    Given that the best available means have been used to assess the risks arising from a chemical process or product, it is a crucial aspect of management to inform the employees and the public. This task of communicating may fall to industry, government, regulating authority, professional association or an environmental protection group. It requires some understanding of the public's perceptions of the risks involved and an ethical duty to try to modify attitudes judged to be either over-anxious or complacent. There is as yet no structured knowledge on communication about chemical hazards as such. Also, circumstances vary enormously. Hence, this paper deploys the general analytic framework constructed within social psychology and reviews the extensive experimental research (and some field studies) with the aim of providing understanding and some guidance. It considers the basic modelling of attitude change as induced by printed or verbal communications. The variables influencing the effectiveness of communications are divided into: the source (e.g. his/her credibility, power or attractiveness); the message (e.g. emotional versus logical; one-sided versus both-sided arguments); and modality or media effects (e.g. spoken versus written; the mass media; campaigns).

  5. [Chemical incidents and gathering information on toxicity].

    PubMed

    Yamamoto, Miyako; Morikawa, Kaoru

    2006-12-01

    Major cases of chemical incidents and information on chemical agents and chemical terrorist attacks are outlined. Since the late 1990s, major incidents occurred consecutively, such as two cases of sarin attack in 1994 and 1995, an oil spill from a Russian oil tanker in the Japan Sea in 1997, arsenic poisoning in Wakayama in 1998, the criticality incident at Tokai-Mura in 1999 in Japan, and terrorist attacks on September 11, 2001, in New York. The importance of crisis management and cooperation among relevant organizations has been emphasized. To provide information for an appropriate and quick response in emergencies, we prepared a Web portal site for information on chemicals including chemical agents, a chemical incident database, and links to relevant Web sites. In intentional cases of poisoning caused by toxic chemicals in Japan, 111 cases were collected mainly from a newspaper database (1984-1999). Many copy-cat poisonings occurred, especially in 1984-1985 and in 1998 just after an arsenic poisoning incident in Wakayama. Many cases occurred in the laboratories of institutes, universities, and hospitals where various types of chemicals are used.

  6. Structure validation in chemical crystallography

    PubMed Central

    Spek, Anthony L.

    2009-01-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

  7. Representation of chemical information in OASIS centralized 3D database for existing chemicals.

    PubMed

    Nikolov, Nikolai; Grancharov, Vanio; Stoyanova, Galya; Pavlov, Todor; Mekenyan, Ovanes

    2006-01-01

    The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of

  8. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  9. 77 FR 74685 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability Information... financial information, Chemical-terrorism Vulnerability Information (CVI), Sensitive Security Information... represents a national-level effort to minimize terrorism risk to such facilities. Its design...

  10. Structural and Chemical Biology of Terpenoid Cyclases

    PubMed Central

    2017-01-01

    The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function. PMID:28841019

  11. Structure factor in chemical sensorics

    SciTech Connect

    Gutman, E.E.; Belysheva, T.V.; Ryabtsev, S.V.; Chibirova, F.H.

    1996-12-31

    Additions of metals and metal oxides to semiconductor metal oxide films improve usually their gas sensitive sensor properties namely for detection of toxic and flammable gases. The aim of this work is the obtaining of new data and the elucidation of the role of the structure and the chemical nature of promoters in semiconductor gas sensorics. As examples, the authors consider the systems CO-SnO{sub 2} and O{sub 3}-In{sub 2}O{sub 3} sensors. The elaboration of mentioned sensors is aimed at the measurement of small gas constituent in Earth`s and Marth`s atmospheres.

  12. Chemical Biological Emergency Management Information System

    SciTech Connect

    2004-06-15

    CB-EMIS is designed to provide information and analysis to transit system operators and emergency responders in the event of a chemical attack on a subway system. The software inforporates detector data, video images, train data, meteorological data, and above- and below-ground plume dispersion models, hight of the liquid level.

  13. ChemEx: information extraction system for chemical data curation

    PubMed Central

    2012-01-01

    Background Manual chemical data curation from publications is error-prone, time consuming, and hard to maintain up-to-date data sets. Automatic information extraction can be used as a tool to reduce these problems. Since chemical structures usually described in images, information extraction needs to combine structure image recognition and text mining together. Results We have developed ChemEx, a chemical information extraction system. ChemEx processes both text and images in publications. Text annotator is able to extract compound, organism, and assay entities from text content while structure image recognition enables translation of chemical raster images to machine readable format. A user can view annotated text along with summarized information of compounds, organism that produces those compounds, and assay tests. Conclusions ChemEx facilitates and speeds up chemical data curation by extracting compounds, organisms, and assays from a large collection of publications. The software and corpus can be downloaded from http://www.biotec.or.th/isl/ChemEx. PMID:23282330

  14. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    SciTech Connect

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa; Tang, Ming; Harris, Jason B; Baudry, Jerome Y; Schuler, Mary A; Rienstra, Chad M

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  15. Factors Affecting Dissemination of Chemical Information

    ERIC Educational Resources Information Center

    Gushee, David E.

    1971-01-01

    That the value of information and, hence, the design of information systems, whether for a company, a university, a learned society, or an individual, is in the early stages of a significant change in structure is demonstrated in this paper. (5 references) (Author/NH)

  16. Fluidic microchemomechanical integrated circuits processing chemical information.

    PubMed

    Greiner, Rinaldo; Allerdissen, Merle; Voigt, Andreas; Richter, Andreas

    2012-12-07

    Lab-on-a-chip (LOC) technology has blossomed into a major new technology fundamentally influencing the sciences of life and nature. From a systemic point of view however, microfluidics is still in its infancy. Here, we present the concept of a microfluidic central processing unit (CPU) which shows remarkable similarities to early electronic Von Neumann microprocessors. It combines both control and execution units and, moreover, the complete power supply on a single chip and introduces the decision-making ability regarding chemical information into fluidic integrated circuits (ICs). As a consequence of this system concept, the ICs process chemical information completely in a self-controlled manner and energetically self-sustaining. The ICs are fabricated by layer-by-layer deposition of several overlapping layers based on different intrinsically active polymers. As examples we present two microchips carrying out long-term monitoring of critical parameters by around-the-clock sampling.

  17. Information Content of Turbulent Chemical Plumes

    NASA Astrophysics Data System (ADS)

    Webster, D. R.; Roberts, P. J. W.; Rahman, S.; Dasi, L. P.

    1999-11-01

    The rapid decrease in concentration contaminants released into the natural environment due to turbulent diffusion has traditionally been modeled based on time-averaged quantities. In contrast to the time-averaged concentration characteristics, the instantaneous characteristics and information content are poorly understood. Instantaneous peak levels are important in many contexts, including the impact of contaminants on organisms and the local ecosystem. The current work is motivated by the need to understand how aquatic organisms, such as blue crabs, search for and locate turbulent chemical odor plume sources. A fundamental question is what information is available to an animal or observer indicating its relative position to the plume source. In this study, the chemical plume is released iso-kinetically into a fully-developed, uniform open channel flow at 50 mm/s. Instantaneous concentration and velocity fields are simultaneously measured using planar laser induced fluorescence (PLIF) and digital particle tracking velocimetry (DPTV), respectively. In addition to the mean and variance, quantities of interest include intermittency, the temporal rise slope of chemical concentration and spatial correlations.

  18. 78 FR 16698 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-18

    ... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability Information... Collection Request, Chemical Facility Anti- Terrorism Standards (CFATS) Chemical-terrorism Vulnerability... minimize terrorism risk to such facilities. Its design and implementation balance maintaining...

  19. ACToR Chemical Structure processing using Open Source ...

    EPA Pesticide Factsheets

    ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

  20. The Indiana University Chemical Information Center Program of Chemical Literature Instruction.

    ERIC Educational Resources Information Center

    Wiggins, Gary

    1982-01-01

    Describes three chemical information science courses offered by Indiana University (IU) Department of Chemistry. Also describes goals and operation of IU's Chemical Information Center, created to implement online searching of chemical databases and to assume operation of the IU dissemination of information services based on Chemical Abstracts…

  1. The Indiana University Chemical Information Center Program of Chemical Literature Instruction.

    ERIC Educational Resources Information Center

    Wiggins, Gary

    1982-01-01

    Describes three chemical information science courses offered by Indiana University (IU) Department of Chemistry. Also describes goals and operation of IU's Chemical Information Center, created to implement online searching of chemical databases and to assume operation of the IU dissemination of information services based on Chemical Abstracts…

  2. Structure of the oxygen-evolving complex of photosystem II: information on the S(2) state through quantum chemical calculation of its magnetic properties.

    PubMed

    Pantazis, Dimitrios A; Orio, Maylis; Petrenko, Taras; Zein, Samir; Lubitz, Wolfgang; Messinger, Johannes; Neese, Frank

    2009-08-21

    Twelve structural models for the S(2) state of the oxygen-evolving complex (OEC) of photosystem II are evaluated in terms of their magnetic properties. The set includes ten models based on the 'fused twist' core topology derived by polarized EXAFS spectra and two related models proposed in recent mechanistic investigations. Optimized geometries and spin population analyses suggest that Mn(iii), which is most often identified with the manganese ion at site D, is always associated with a penta-coordinate environment, unless a chloride is directly ligated to the metal. Exchange coupling constants were determined by broken-symmetry density functional theory calculations and the complete spectrum of magnetic sublevels was obtained by direct diagonalization of the Heisenberg Hamiltonian. Seven models display a doublet ground state and are considered spectroscopic models for the ground state corresponding to the multiline signal (MLS) of the S(2) state of the OEC, whereas the remaining five models display a sextet ground state and could be related to the g = 4.1 signal of the S(2) state. It is found that the sign of the exchange coupling constant between the Mn centres at positions A and B of the cluster is directly related to the ground state multiplicity, implying that interconversion between the doublet and sextet can be induced by only small structural perturbations. The recently proposed quantum chemical method for the calculation of (55)Mn hyperfine coupling constants is subsequently applied to the S(2) MLS state models and the quantities that enter into the individual steps of the procedure (site-spin expectation values, intrinsic site isotropic hyperfine parameters and projected (55)Mn isotropic hyperfine constants) are analyzed and discussed in detail with respect to the structural and electronic features of each model. The current approach performs promisingly. It reacts sensitively to structural distortions and hence may be able to distinguish between different

  3. 75 FR 60444 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... technical information contact: Bernice Mudd, Information Management Division 7407M, Office of Chemical Safety Pollution Prevention, Environmental Protection Agency, 1200 Pennsylvania Ave., NW., Washington,...

  4. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 6 Domestic Security 1 2011-01-01 2011-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  5. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  6. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 6 Domestic Security 1 2013-01-01 2013-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  7. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 6 Domestic Security 1 2014-01-01 2014-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  8. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 6 Domestic Security 1 2012-01-01 2012-01-01 false Chemical-terrorism vulnerability information. 27... FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information. (a... that constitute Chemical-terrorism Vulnerability Information (CVI), as defined in § 27.400(b)....

  9. Current Research into Chemical and Textual Information Retrieval at the Department of Information Studies, University of Sheffield.

    ERIC Educational Resources Information Center

    Lynch, Michael F.; Willett, Peter

    1987-01-01

    Discusses research into chemical information and document retrieval systems at the University of Sheffield. Highlights include the use of cluster analysis methods for document retrieval and drug design, representation and searching of files of generic chemical structures, and the application of parallel computer hardware to information retrieval.…

  10. STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

    EPA Science Inventory

    Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

    Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

  11. STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

    EPA Science Inventory

    Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

    Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

  12. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  13. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  14. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.

  15. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  16. Survey of Ongoing Federal Chemical Information and Data Systems.

    ERIC Educational Resources Information Center

    Thompson (John I.) and Co., Washington, DC.

    The purpose of the survey was to collect data relating to (1) present usage of chemical information and data in the Federal community; (2) techniques and equipment now used in the acquisition, processing, and transmission of information and data; and (3) direction of plans for future chemical information services at ongoing systems. The scope of…

  17. Markov logic networks for optical chemical structure recognition.

    PubMed

    Frasconi, Paolo; Gabbrielli, Francesco; Lippi, Marco; Marinai, Simone

    2014-08-25

    Optical chemical structure recognition is the problem of converting a bitmap image containing a chemical structure formula into a standard structured representation of the molecule. We introduce a novel approach to this problem based on the pipelined integration of pattern recognition techniques with probabilistic knowledge representation and reasoning. Basic entities and relations (such as textual elements, points, lines, etc.) are first extracted by a low-level processing module. A probabilistic reasoning engine based on Markov logic, embodying chemical and graphical knowledge, is subsequently used to refine these pieces of information. An annotated connection table of atoms and bonds is finally assembled and converted into a standard chemical exchange format. We report a successful evaluation on two large image data sets, showing that the method compares favorably with the current state-of-the-art, especially on degraded low-resolution images. The system is available as a web server at http://mlocsr.dinfo.unifi.it.

  18. Chemical structure and dynamics: Annual report 1993

    SciTech Connect

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  19. Chemical structure and dynamics: Annual report 1996

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  20. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  1. Chemical structure and dynamics. Annual report 1995

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  2. Science Advisory Committee on Chemicals Basic Information

    EPA Pesticide Factsheets

    The SACC will provide independent scientific advice and recommendations to the EPA on the scientific basis for risk assessments, methodologies, and pollution prevention measures and approaches for chemicals regulated under the TSCA.

  3. Protein structure determination from NMR chemical shifts.

    PubMed

    Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

    2007-06-05

    NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

  4. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  5. Characteristics of comprehensive Chemical Industry Database CD-NET : Centered around chemical product information file

    NASA Astrophysics Data System (ADS)

    Takano, Hideo

    This paper describes Chemical Product Information File of Chemical Industry Database, CD-NET provided by Chemical Data Service Inc.. It defines "information" first, then explains file organization and presents how Chemical product Information File is located in CD-NET. Mentioning its complementary relation with JICST's JOIS-F the author defines the File as chemical product information for business purpose. All of the information items in the File emphasize that it is exactly a type of business and practical database. To distinguish general items from important items by product, all of the information is categorized into II classes by general chemical product and by area. The scope and emphasized items under each class are described in detail.

  6. THE IMPORTANCE OF SPATIAL ACCURACY FOR CHEMICAL INFORMATION MANAGEMENT

    EPA Science Inventory

    Information about chemicals can be critical to making timely decisions. The results of these decisions may not be realized for many years. In order to increase the value of chemical information and to create and utilize meaningful environmental models, the Environmental Prote...

  7. Chemical Information Instruction in Academe: Who Is Leading the Charge?

    ERIC Educational Resources Information Center

    Garritano, Jeremy R.; Culp, F. Bartow; Twiss-Brooks, Andrea

    2010-01-01

    Chemical information instruction (CII) has been recommended by the ACS Committee on Professional Training as a necessary component of the chemistry curriculum for both undergraduate and graduate students. Surveys conducted by the ACS Chemical Information Division (CINF) Education Committee in 1984 and 1993 showed the extent that CII had become…

  8. THE IMPORTANCE OF SPATIAL ACCURACY FOR CHEMICAL INFORMATION MANAGEMENT

    EPA Science Inventory

    Information about chemicals can be critical to making timely decisions. The results of these decisions may not be realized for many years. In order to increase the value of chemical information and to create and utilize meaningful environmental models, the Environmental Prote...

  9. Informational laws of genome structures

    PubMed Central

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-01-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

  10. Informational laws of genome structures

    NASA Astrophysics Data System (ADS)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  11. ASTM Data Banks and Chemical Information Sources

    ERIC Educational Resources Information Center

    Batik, Albert; Hale, Eleanor

    1972-01-01

    Among the data described are infrared indexes, mass spectral data, chromatographic data, X-ray emmission data, odor and taste threshold data, and thermodynamics data. This paper provides the chemical documentarian a complete reference source to a wide variety of analytical data. (Author/NH)

  12. ASTM Data Banks and Chemical Information Sources

    ERIC Educational Resources Information Center

    Batik, Albert; Hale, Eleanor

    1972-01-01

    Among the data described are infrared indexes, mass spectral data, chromatographic data, X-ray emmission data, odor and taste threshold data, and thermodynamics data. This paper provides the chemical documentarian a complete reference source to a wide variety of analytical data. (Author/NH)

  13. Valid Structure Diagrams and Chemical Gibberish

    ERIC Educational Resources Information Center

    Tauber, Stephen J.; Rankin, Kirk

    1972-01-01

    Chemical structure diagrams are considered as utterances in a written language. Two types of grammars are considered for this language: topological grammars and geometric grammars. The hypothesis is presented that compact computer storage may become accessible via grammars. (15 references) (Author/NH)

  14. Introducing Graduate Students to the Chemical Information Landscape: The Ongoing Evolution of a Graduate-Level Chemical Information Course

    ERIC Educational Resources Information Center

    Currano, Judith N.

    2016-01-01

    The University of Pennsylvania's doctoral chemistry curriculum has included a required course in chemical information since 1995. Twenty years later, the course has evolved from a loosely associated series of workshops on information resources to a holistic examination of the chemical literature and its place in the general research process. The…

  15. Introducing Graduate Students to the Chemical Information Landscape: The Ongoing Evolution of a Graduate-Level Chemical Information Course

    ERIC Educational Resources Information Center

    Currano, Judith N.

    2016-01-01

    The University of Pennsylvania's doctoral chemistry curriculum has included a required course in chemical information since 1995. Twenty years later, the course has evolved from a loosely associated series of workshops on information resources to a holistic examination of the chemical literature and its place in the general research process. The…

  16. Chemical Structure and Dynamics annual report 1997

    SciTech Connect

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

  17. Chemical hazard information profile of triphenyl phosphite

    SciTech Connect

    Faust, R.A.; Wiedow, M.A.; Daugherty, M.W.; Ross, R.H.; Leitzke, J.S.

    1986-12-01

    The only human study located showed that triphenyl phosphite applied to the skin in a 1:3 dilution with cold cream for 48 h caused slight irritation, and challenge with the compound 14 days later produced a moderate sensitization reaction. The most significant health effects described in experimental animals are those affecting the nervous system. In adult rats, subacute exposure to the chemical produced gross ataxia and spinal cord neuropathy which predominantly affected the lateral and ventral columns of the lumber and sacral regions. Other symptoms included hyperexcitability and agitation after several days, muscle wasting, asymmetric gait, and hind-limb paralysis. All animals developed tail rigidity with a kinky appearance, and some animals displayed a circling behavior. The compound appeared to only weakly inhibit acetylcholinesterase activity. Single oral doses of triphenyl phosphite Gallus domesticus produced ataxia, and spinal cord and peripheral nerve histopathology. Neurotoxicity in rats, cats, and chickens indicated that triphenyl phosphite caused two distinct stages of action. Rats given s.c. injections of the chemical exhibit rapidly-developing stage or fine or coarse tremors which disappeared after a few hours. The later stage, occurring several days after treatment, caused hyperexcitability, spasticity and incoordination, followed by partial flaccid paralysis of the extremities. 135 refs., 2 tabs.

  18. Chemical profiling of silicon nitride structures

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.

    1989-01-01

    X ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), and scanning electron microscopy (SEM) were used to study structural and chemical inhomogeneities in several electronic materials and device structures of relevance to radiation hard electronics. The systems studied include metal nitride oxide semiconductor (MNOS) structures, silicon oxynitride (SiO(x)N(y)) formed by the thermal nitridation of SiO2, and semiconductor on insulator (SOI) structures. Studies of MNOS structures suggest that the effect of H2 annealing is to make the Si3N4/SiO2 interface less abrupt by causing interdiffusion of silanol and silamine groups with subsequent oxynitride formation. Another effect of the annealing appears to be to relieve the strain at the SiO2/Si interface.

  19. Chemical structure and dynamics. Annual report 1994

    SciTech Connect

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  20. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  1. The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets.

    PubMed

    Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

    2015-01-01

    There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set

  2. Encoding information into precipitation structures

    NASA Astrophysics Data System (ADS)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  3. Quantum Information with Structured Light

    NASA Astrophysics Data System (ADS)

    Mirhosseini, Mohammad

    Quantum information science promises dramatic progress in a variety of fields such as cryptography, computation, and metrology. Although the proof-of-principle attempts for implementing quantum protocols have often relied on only a few qubits, the utilization of more sophisticated quantum systems is required for practical applications. In this thesis, we investigate the emerging role of high-dimensional optical states as a resource for encoding quantum information. We begin the first chapter with a review of orbital angular momentum (OAM) as a prime candidate for realizing multilevel quantum states and follow with a brief introduction to the quantum measurement theory. The second and the third chapters are dedicated to the application of OAM modes in quantum cryptography. In the second chapter, we discuss the challenges of projective measurement of OAM at the single-photon level, a crucial task required for quantum information processing. We then present our development of an efficient and accurate mode-sorting device that is capable of projectively measuring the orbital angular momentum of single photons. In the third chapter, we discuss the role of OAM modes in increasing the information capacity of quantum cryptography. We start this chapter by establishing the merits of encoding information on the quantum index of OAM modes in a free-space link. We then generalizing the BB-84 QKD protocol to the Hilbert space spanned by a finite number of OAM modes and outline our experimental realization. The last two chapters are dedicated to the tomography of structured light fields. We start the fourth chapter by applying the recently found method of direct measurement to the characterization of OAM superpositions. We find the quantum state in the Hilbert space spanned by 27 OAM modes by performing a weak measurement of orbital angular momentum (OAM) followed by a strong measurement of azimuthal angle. We then introduce the concept of compressive direct measurement (CDM

  4. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E.

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  5. Integrated chemical management system: A tool for managing chemical information at the Rocky Flats Environmental Technology Site

    SciTech Connect

    Costain, D.

    1995-07-01

    The Integrated Chemical Management System is a computer-based chemical information at the Rocky Flats Environmental Technology Site. Chemical containers are identified by bar code labels and information on the type, quantity and location of chemicals are tracked on individual data bases in separate buildings. Chemical inventories from multiple buildings are uploaded to a central sitewide chemical data base where reports are available from Product, Waste, and Chemical Use modules. Hazardous chemical information is provided by a separate Material Safety Data Sheet module and excess chemicals are traded between chemical owners and users with the aid of the Chemical Exchange Module.

  6. Construction of a Linux based chemical and biological information system.

    PubMed

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  7. Chemical Abstracts as a resource for health and safety-related chemical information.

    PubMed

    Moody, R L; Zahm, B C

    1980-02-01

    Documents relevant to the health and safety of the worker or consumer exposed to chemicals or radiation extend over the entire range of the chemical disciplines, and therefore pertinent information can appear throughout the Chemical Abstracts Service information systems. Access routes to such information in both CAS printed publications and computer-readable services are discussed. In the weekly issues of Chemical Abstracts, health and safety information can be accessed through the natural-language Keyword Index. Retrieval of pertinent information through the controlled headings of the CA Volume Indexes in conjunction with the Index Guide is also discussed. CA Selects, a set of current-awareness publications, is described as it pertains to the specialized areas of health and safety.

  8. Drop impact on chemically structured arrays

    NASA Astrophysics Data System (ADS)

    Mock, Ulrike; Michel, Tobias; Tropea, Cameron; Roisman, Ilia; Rühe, Jürgen

    2005-03-01

    We describe recent investigations on the impact behaviour of liquid drops onto chemically structured surfaces. The surface patterns were prepared via photochemical attachment of polymer molecules with different hydrophilicities using self-assembled monolayers of benzophenone bearing silanes. Immobilization of the polymer monolayers was followed by an ablation process to generate a chemical surface pattern. Impact experiments on systems consisting of very hydrophobic poly(perfluoroalkylethyl)acrylate coatings and hydrophilic areas show that within certain limitations the water drop has a strong tendency to reach the hydrophilic spots, even for inclined substrates. Impact experiments of drops on arrays of hydrophilic spots on the background of a perfluorinated polymer show that the drops spontaneously self-centre on the lithographically generated pattern. The obtained results suggest that the process can be used to circumvent some of the current problems in micro-array fabrication.

  9. Assessment of a Library Science Program Specializing in Chemical Information.

    ERIC Educational Resources Information Center

    Wiggins, Gary; Monnier, Cynthia

    1994-01-01

    Reports on a survey of Indiana University Master in Library Science (M.L.S.)-Chemical Information Specialist program graduates. Information includes graduates' educational background; the nature of first jobs and current positions held; and databases most frequently used. Graduates generally favored more training in computer skills, patent…

  10. Ice Cream Seminars for Graduate Students: Imparting Chemical Information Literacy

    ERIC Educational Resources Information Center

    Garritano, Jeremy R.

    2007-01-01

    This article provides information on a chemical information literacy program designed primarily for new graduate students. The full implementation of this program is discussed, including defining its purpose, topics covered, content presented, methods of marketing, and evaluation. The result is a series of voluntary seminars given biweekly…

  11. Ice Cream Seminars for Graduate Students: Imparting Chemical Information Literacy

    ERIC Educational Resources Information Center

    Garritano, Jeremy R.

    2007-01-01

    This article provides information on a chemical information literacy program designed primarily for new graduate students. The full implementation of this program is discussed, including defining its purpose, topics covered, content presented, methods of marketing, and evaluation. The result is a series of voluntary seminars given biweekly…

  12. Computerized management information systems and organizational structures

    NASA Technical Reports Server (NTRS)

    Zannetos, Z. S.; Sertel, M. R.

    1970-01-01

    The computerized management of information systems and organizational structures is discussed. The subjects presented are: (1) critical factors favoring centralization and decentralization of organizations, (2) classification of organizations by relative structure, (3) attempts to measure change in organization structure, and (4) impact of information technology developments on organizational structure changes.

  13. Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

    DOEpatents

    Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

    2015-01-13

    Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

  14. Weighted voting-based consensus clustering for chemical structure databases

    NASA Astrophysics Data System (ADS)

    Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.

  15. Insight into Amyloid Structure Using Chemical Probes

    PubMed Central

    Reinke, Ashley A.; Gestwicki, Jason E.

    2011-01-01

    Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

  16. Computational analysis of RNA structures with chemical probing data

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed. PMID:25687190

  17. Using chemical shifts to determine structural changes in proteins upon complex formation.

    PubMed

    Cavalli, Andrea; Montalvao, Rinaldo W; Vendruscolo, Michele

    2011-08-04

    Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the determination of the structures of protein complexes is that the changes in the chemical shifts upon binding tend to be rather limited and indeed often smaller than the standard errors made in the predictions of chemical shifts corresponding to given structures. We present a procedure that, despite this problem, enables one to use of chemical shifts to determine accurately the conformational changes that take place upon complex formation.

  18. Chemical biology at the crossroads of molecular structure and mechanism.

    PubMed

    Doudna, Jennifer A

    2005-11-01

    Chemical insight into biological function is the holy grail of structural biology. Small molecules are central players as building blocks, effectors and probes of macromolecular structure and function.

  19. The publication speed of information in bibliographic chemical databases.

    PubMed

    Dióspatonyi, I; Horvai, G; Braun, T

    2001-01-01

    The quality of bibliographic databases depends very much on the reliably fast follow-up of the pertinent literature. We have studied this quality feature of two important chemical bibliographic databases: Chemical Abstracts (CA) and Analytical Abstracts (AA). The follow-up rate (speed of information) of these databases has been determined with respect to 10 core journals in analytical chemistry. On the average the performance of Chemical Abstracts has been good over the past decade, while the formerly poor performance of Analytical Abstracts has improved considerably. Some quite unexpected nonuniformities can, however, still be detected in the publication time distributions of both databases.

  20. The origin and dynamic evolution of chemical information transfer

    PubMed Central

    Steiger, Sandra; Schmitt, Thomas; Schaefer, H. Martin

    2011-01-01

    Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general. PMID:21177681

  1. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

    Emberson, R.; Hovius, N.; Hsieh, M.; Galy, A.

    2013-12-01

    Material eroded from active mountain belts can spend extended periods in depositional structures within the mountain catchments before reaching its final destination. This can be in the form of colluvial fills, debris fans, or alluvial valley fills and terraces. The existence of these landforms is testament to the catastrophic nature of the events that lead to their formation. Sourced by landslides or debris flows, the material that forms them is in many cases either unweathered or incompletely weathered (e.g. Hsieh and Chyi 2010). Due to their porosity and permeability, these deposits likely serve as locations for extensive chemical weathering within bedrock landscapes. Recent studies considering the weathering flux from active mountain belts (e.g. Calmels et al. 2011) have distinguished between shallow and deep groundwater in terms of the contribution to the solute budget from a catchment; in this study we have attempted to more tightly constrain the sources of these groundwater components in the context of the previously mentioned depositional structures. We have collected water samples from a large number of sites within the Chen-you-lan catchment (370 km2) in central west Taiwan to elucidate the location of chemical weathering as well as how the sourcing of weathering products varies depending on the meteorological conditions. Central Taiwan has good attributes for this work considering both the extremely active tectonics and tropical climate, (including extensive cyclonic activity) which stimulate both extensive physical erosion (Dadson et al. 2003) and chemical weathering (Calmels et al. 2011). The Chen-you-lan catchment in particular contains some of the largest alluvial deposits inside the Taiwan mountain belt (Hsieh and Chyi 2010). Our preliminary results suggest that weathering within intramontane deposits may be a significant source of solutes, with the hyporheic systems within mountain rivers of particular import. This input of solutes occurs over

  2. Applications of the Cambridge Structural Database in chemical education.

    PubMed

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  3. Applications of the Cambridge Structural Database in chemical education1

    PubMed Central

    Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

    2010-01-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  4. [International Chemical Safety Cards: information source on hazards caused by chemical substances].

    PubMed

    Pakulska, Daria; Czerczak, Sławomir

    2007-01-01

    International Chemical Safety Cards (ICSC) are produced by the International Programme on Chemical Safety (IPCS) in collaboration with the European Commission and various IPCS-participating institutions in different countries. ICSCs disseminate essential information on chemicals to promote their safe production, transport and use. Application of standard terminology along with relevant criteria facilitates the comparison of risk related to different chemicals, which makes the cards a successful hazard-communication tool. Translation of the cards into various languages all over the world reflects the range of their growing use. A multi-stage compilation of information contained in ICSCs, based on the most up-to-date world literature and professional databases, assures its reliability. Their concise form makes them easy in everyday use as a source of information on chemical safety. The range of information contained in ICSCs corresponds to that provided by Material Safety Data Sheets (MSDS), however, the former are more concise and simpler. Although ICSCs have no legal status they may complement a 16-point MSDSs and help in the implementation of labeling and classification of chemicals according to the Globally Harmonized System.

  5. Real-time interactive data mining for chemical imaging information: application to automated histopathology

    PubMed Central

    2013-01-01

    Background Vibrational spectroscopic imaging is now used in several fields to acquire molecular information from microscopically heterogeneous systems. Recent advances have led to promising applications in tissue analysis for cancer research, where chemical information can be used to identify cell types and disease. However, recorded spectra are affected by the morphology of the tissue sample, making identification of chemical structures difficult. Results Extracting features that can be used to classify tissue is a cumbersome manual process which limits this technology from wide applicability. In this paper, we describe a method for interactive data mining of spectral features using GPU-based manipulation of the spectral distribution. Conclusions This allows researchers to quickly identify chemical features corresponding to cell type. These features are then applied to tissue samples in order to visualize the chemical composition of the tissue without the use of chemical stains. PMID:23651487

  6. Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia.

    PubMed

    Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

    2015-01-01

    Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation. The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

  7. Communication and re-use of chemical information in bioscience

    PubMed Central

    Murray-Rust, Peter; Mitchell, John BO; Rzepa, Henry S

    2005-01-01

    The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective. PMID:16026614

  8. Communication and re-use of chemical information in bioscience.

    PubMed

    Murray-Rust, Peter; Mitchell, John B O; Rzepa, Henry S

    2005-07-18

    The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.

  9. Introducing Chemistry Undergraduate Students to Online Chemical Information Retrieval.

    ERIC Educational Resources Information Center

    Wolman, Yecheskel

    1985-01-01

    The results of manual and online searching are compared during a unit on online chemical information retrieval taught at Hebrew University. Strategies and results obtained are provided for student searches on the synthesis of vitamin K(3) from 2-methylnaphthalene and polywater. (JN)

  10. Support from Afar: Using Chemical Safety Information on the Internet.

    ERIC Educational Resources Information Center

    Stuart, Ralph

    One of the major challenges facing people committed to Teaching Safety in High Schools, Colleges, and Universities is keeping up with both the wide range of relevant technical information about potential hazards (ranging from fire protection to chemical hazards to biological issues) and the ever-changing world of safety regulations and standards.…

  11. Informing Workers of Chemical Hazards: The OSHA Hazard Communication Standard.

    ERIC Educational Resources Information Center

    American Chemical Society, Washington, DC.

    Practical information on how to implement a chemical-related safety program is outlined in this publication. Highlights of the federal Occupational Safety and Health Administrations (OSHA) Hazard Communication Standard are presented and explained. These include: (1) hazard communication requirements (consisting of warning labels, material safety…

  12. Chemical Information in Scirus and BASE (Bielefeld Academic Search Engine)

    ERIC Educational Resources Information Center

    Bendig, Regina B.

    2009-01-01

    The author sought to determine to what extent the two search engines, Scirus and BASE (Bielefeld Academic Search Engines), would be useful to first-year university students as the first point of searching for chemical information. Five topics were searched and the first ten records of each search result were evaluated with regard to the type of…

  13. Chemical Information in Scirus and BASE (Bielefeld Academic Search Engine)

    ERIC Educational Resources Information Center

    Bendig, Regina B.

    2009-01-01

    The author sought to determine to what extent the two search engines, Scirus and BASE (Bielefeld Academic Search Engines), would be useful to first-year university students as the first point of searching for chemical information. Five topics were searched and the first ten records of each search result were evaluated with regard to the type of…

  14. Haz-Map: Information on Hazardous Chemicals and Occupational Diseases

    MedlinePlus

    ... Processes Symptoms/Findings Haz-Map®: Information on Hazardous Chemicals and Occupational Diseases by Jay A. Brown, M.D., M.P.H. Hazardous Agents Occupational Diseases High Risk Jobs Non-Occupational Activities Industries Job Tasks Processes Symptoms/Findings Customer Service: tehip@ ...

  15. Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

    PubMed

    Yabuzaki, Junko

    2017-01-01

    To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp.

  16. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    EPA Science Inventory

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  17. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    EPA Science Inventory

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  18. Typography, Color, and Information Structure.

    ERIC Educational Resources Information Center

    Keyes, Elizabeth

    1993-01-01

    Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

  19. Typography, Color, and Information Structure.

    ERIC Educational Resources Information Center

    Keyes, Elizabeth

    1993-01-01

    Focuses on how typography and color complement and differ from each other in signaling an underlying content structure; the synergism between typography, color, and page layout (use of white space) that aids audience understanding and use; and the characteristics of typography and of color that are most important in these contexts. (SR)

  20. Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells.

    PubMed

    Wagler, Patrick F; Tangen, Uwe; Maeke, Thomas; McCaskill, John S

    2012-07-01

    The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells. Copyright © 2012 Elsevier Ireland Ltd. All rights

  1. Orchestration of Molecular Information through Higher Order Chemical Recognition

    NASA Astrophysics Data System (ADS)

    Frezza, Brian M.

    Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.

  2. Information Structure, Grammar and Strategy in Discourse

    ERIC Educational Resources Information Center

    Stevens, Jon

    2013-01-01

    This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

  3. A Grammar Library for Information Structure

    ERIC Educational Resources Information Center

    Song, Sanghoun

    2014-01-01

    This dissertation makes substantial contributions to both the theoretical and computational treatment of information structure, with an eye toward creating natural language processing applications such as multilingual machine translation systems. The aim of the present dissertation is to create a grammar library of information structure for the…

  4. A Grammar Library for Information Structure

    ERIC Educational Resources Information Center

    Song, Sanghoun

    2014-01-01

    This dissertation makes substantial contributions to both the theoretical and computational treatment of information structure, with an eye toward creating natural language processing applications such as multilingual machine translation systems. The aim of the present dissertation is to create a grammar library of information structure for the…

  5. Information Handling, Organizational Structure, and Power.

    ERIC Educational Resources Information Center

    Buckland, Michael K.

    1989-01-01

    Uses examples from military strategic communications to demonstrate that organizational structures and the distribution of power within organizational structures adapt to changes in information handling capability. It is concluded that delegation and decentralization can be viewed as indicative of inadequate information handling and that improved…

  6. Information Structure, Grammar and Strategy in Discourse

    ERIC Educational Resources Information Center

    Stevens, Jon

    2013-01-01

    This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

  7. Mapping of protein structural ensembles by chemical shifts.

    PubMed

    Baskaran, Kumaran; Brunner, Konrad; Munte, Claudia E; Kalbitzer, Hans Robert

    2010-10-01

    Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.

  8. Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

    NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

  9. Managing major chemical accidents in China: towards effective risk information.

    PubMed

    He, Guizhen; Zhang, Lei; Lu, Yonglong; Mol, Arthur P J

    2011-03-15

    Chemical industries, from their very inception, have been controversial due to the high risks they impose on safety of human beings and the environment. Recent decades have witnessed increasing impacts of the accelerating expansion of chemical industries and chemical accidents have become a major contributor to environmental and health risks in China. This calls for the establishment of an effective chemical risk management system, which requires reliable, accurate and comprehensive data in the first place. However, the current chemical accident-related data system is highly fragmented and incomplete, as different responsible authorities adopt different data collection standards and procedures for different purposes. In building a more comprehensive, integrated and effective information system, this article: (i) reviews and assesses the existing data sources and data management, (ii) analyzes data on 976 recorded major hazardous chemical accidents in China over the last 40 years, and (iii) identifies the improvements required for developing integrated risk management in China. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View.

    PubMed

    López-Rosa, Sheila; Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Soriano-Correa, Catalina; Dehesa, Jésus S

    2016-12-05

    The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy-like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three-dimensional space (IT-3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT-3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para-aminobenzoic acid than to the theoretically designed analogues. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Teaching Chemical Information in a Liberal Arts Curriculum

    NASA Astrophysics Data System (ADS)

    Ricker, Alison Scott; Thompson, Robert Q.

    1999-11-01

    We first offered Chemical Information as a one-credit, semester-long course in 1993 and have continued to team-teach it each fall. We offer this summary of our course as a model that might be adapted in other settings, acknowledging that no single course can adequately prepare chemists for the many challenges involved in finding, evaluating, and utilizing chemical information. The focus on information retrieval, evaluation, and presentation in a separate course has worked well for us, successfully integrating concepts of information literacy in a chemical context. We cover a wide array of topics, beginning with print and electronic resources on our campus and moving quickly to databases and other sources on the Internet. Searching CA Online via STN Express and STN Easy is emphasized more than any other single source. We have described the course in some detail elsewhere and give here a synopsis of our current approach and significant changes in the course over the last two years.

  12. Finding Chemical Structures Corresponding to a Set of Coordinates in Chemical Descriptor Space.

    PubMed

    Miyao, Tomoyuki; Funatsu, Kimito

    2017-08-01

    When chemical structures are searched based on descriptor values, or descriptors are interpreted based on values, it is important that corresponding chemical structures actually exist. In order to consider the existence of chemical structures located in a specific region in the chemical space, we propose to search them inside training data domains (TDDs), which are dense areas of a training dataset in the chemical space. We investigated TDDs' features using diverse and local datasets, assuming that GDB11 is the chemical universe. These two analyses showed that considering TDDs gives higher chance of finding chemical structures than a random search-based method, and that novel chemical structures actually exist inside TDDs. In addition to those findings, we tested the hypothesis that chemical structures were distributed on the limited areas of chemical space. This hypothesis was confirmed by the fact that distances among chemical structures in several descriptor spaces were much shorter than those among randomly generated coordinates in the training data range. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Structures and Stabilization Mechanisms in Chemically Stabilized Ceramics

    NASA Astrophysics Data System (ADS)

    Gai-Boyes, Pratibha L.; Saltzberg, Michael A.; Vega, Alexander

    1993-09-01

    Structural complexities and disorder in chemically stabilized cristobalites (CSC), which are room temperature silica-based ceramics, prepared by a wet chemical route, are described. CSC displays many of the structural characteristics of the high temperature cristobalite, elucidated by HREM and X-ray diffraction. In-situ electron diffraction and NMR results suggest that the disorder is structural and is static.

  14. ChemDataExtractor: A Toolkit for Automated Extraction of Chemical Information from the Scientific Literature.

    PubMed

    Swain, Matthew C; Cole, Jacqueline M

    2016-10-24

    The emergence of "big data" initiatives has led to the need for tools that can automatically extract valuable chemical information from large volumes of unstructured data, such as the scientific literature. Since chemical information can be present in figures, tables, and textual paragraphs, successful information extraction often depends on the ability to interpret all of these domains simultaneously. We present a complete toolkit for the automated extraction of chemical entities and their associated properties, measurements, and relationships from scientific documents that can be used to populate structured chemical databases. Our system provides an extensible, chemistry-aware, natural language processing pipeline for tokenization, part-of-speech tagging, named entity recognition, and phrase parsing. Within this scope, we report improved performance for chemical named entity recognition through the use of unsupervised word clustering based on a massive corpus of chemistry articles. For phrase parsing and information extraction, we present the novel use of multiple rule-based grammars that are tailored for interpreting specific document domains such as textual paragraphs, captions, and tables. We also describe document-level processing to resolve data interdependencies and show that this is particularly necessary for the autogeneration of chemical databases since captions and tables commonly contain chemical identifiers and references that are defined elsewhere in the text. The performance of the toolkit to correctly extract various types of data was evaluated, affording an F-score of 93.4%, 86.8%, and 91.5% for extracting chemical identifiers, spectroscopic attributes, and chemical property attributes, respectively; set against the CHEMDNER chemical name extraction challenge, ChemDataExtractor yields a competitive F-score of 87.8%. All tools have been released under the MIT license and are available to download from http://www.chemdataextractor.org .

  15. Chemical structure of odorants and perceptual similarity in ants.

    PubMed

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity.

  16. Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

    PubMed Central

    Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

    2012-01-01

    Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

  17. Progressively Fostering Students' Chemical Information Skills in a Three-Year Chemical Engineering Program in France

    ERIC Educational Resources Information Center

    Gozzi, Christel; Arnoux, Marie-Jose´; Breuzard, Jere´my; Marchal, Claire; Nikitine, Clémence; Renaudat, Alice; Toulgoat, Fabien

    2016-01-01

    Literature searches are essential for scientists. Thus, courses on how to do a good literature search have been integrated in studies at CPE Lyon for many years. Recently, we modified our pedagogical approach in order to initiate students progressively in the search for chemical information. In addition, this new teaching organization is now based…

  18. Progressively Fostering Students' Chemical Information Skills in a Three-Year Chemical Engineering Program in France

    ERIC Educational Resources Information Center

    Gozzi, Christel; Arnoux, Marie-Jose´; Breuzard, Jere´my; Marchal, Claire; Nikitine, Clémence; Renaudat, Alice; Toulgoat, Fabien

    2016-01-01

    Literature searches are essential for scientists. Thus, courses on how to do a good literature search have been integrated in studies at CPE Lyon for many years. Recently, we modified our pedagogical approach in order to initiate students progressively in the search for chemical information. In addition, this new teaching organization is now based…

  19. Chemical Safety: Emergency Response Community Views on the Adequacy of Federally Required Chemical Information

    DTIC Science & Technology

    2002-07-01

    chemicals facilities to provide such information: the Emergency Planning and Community Right-to-Know Act of 1986 (EPCRA) and the Clean Air Act Amendments of...management plans with the Environmental Protection Agency (EPA), at least every 5 years. The Clean Air Act also requires that these plans be submitted to state

  20. Automated Physico-Chemical Cell Model Development through Information Theory

    SciTech Connect

    Peter J. Ortoleva

    2005-11-29

    The objective of this project was to develop predictive models of the chemical responses of microbial cells to variations in their surroundings. The application of these models is optimization of environmental remediation and energy-producing biotechnical processes.The principles on which our project is based are as follows: chemical thermodynamics and kinetics; automation of calibration through information theory; integration of multiplex data (e.g. cDNA microarrays, NMR, proteomics), cell modeling, and bifurcation theory to overcome cellular complexity; and the use of multiplex data and information theory to calibrate and run an incomplete model. In this report we review four papers summarizing key findings and a web-enabled, multiple module workflow we have implemented that consists of a set of interoperable systems biology computational modules.

  1. Approaches to Chemical and Biochemical Information and Signal Processing

    NASA Astrophysics Data System (ADS)

    Privman, Vladimir

    2012-02-01

    We outline models and approaches for error control required to prevent buildup of noise when ``gates'' and other ``network elements'' based on (bio)chemical reaction processes are utilized to realize stable, scalable networks for information and signal processing. We also survey challenges and possible future research. [4pt] [1] Control of Noise in Chemical and Biochemical Information Processing, V. Privman, Israel J. Chem. 51, 118-131 (2010).[0pt] [2] Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic, V. Privman, J. Halamek, M. A. Arugula, D. Melnikov, V. Bocharova and E. Katz, J. Phys. Chem. B 114, 14103-14109 (2010).[0pt] [3] Towards Biosensing Strategies Based on Biochemical Logic Systems, E. Katz, V. Privman and J. Wang, in: Proc. Conf. ICQNM 2010 (IEEE Comp. Soc. Conf. Publ. Serv., Los Alamitos, California, 2010), pages 1-9.

  2. Management and High-rank Utilization of Chemical Information

    NASA Astrophysics Data System (ADS)

    Sasaki, Shinichi

    This is the record of Special Lecture at the 24th Annual Meeting on Information Science and Technology. Firstly, lecturer outlined the production way and a general utilization of database on 13C and H magnetic resonance spectrum, which is produced by his group. In order to make higher the rank of utilization for this kind of factual database, he described three new systems such as CHEMICS, TUTORS and AIPHOS.

  3. A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL).

    PubMed

    Trepalin, Sergei V; Yarkov, Alexander V; Pletnev, Igor V; Gakh, Andrei A

    2006-03-29

    A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI).

  4. Feature Selection for Chemical Sensor Arrays Using Mutual Information

    PubMed Central

    Wang, X. Rosalind; Lizier, Joseph T.; Nowotny, Thomas; Berna, Amalia Z.; Prokopenko, Mikhail; Trowell, Stephen C.

    2014-01-01

    We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays. PMID:24595058

  5. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    PubMed

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  6. The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

    PubMed Central

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA). PMID:21991315

  7. DSSTox EPA Integrated Risk Information System Structure ...

    EPA Pesticide Factsheets

    EPA's Integrated Risk Information System (IRIS) database was developed and is maintained by EPA's Office of Research and Developement, National Center for Environmental Assessment. IRIS is a database of human health effects that may result from exposure to various substances found in the environment. The information in IRIS is intended for those without extensive training in toxicology, but with some knowledge of sciences. IRIS chemical files contain descriptive and quantitative information in oral reference doses and inhalation reference concentrations and hazard identification, oral slope factors, and oral and inhalation unit risks for carcinogenic effects.

  8. The Structure of the Chemical Processing Industries.

    ERIC Educational Resources Information Center

    Russell, T. W. F.

    1979-01-01

    Described is a graduate and senior level course utilizing the case study approach in chemical engineering at the University of Delaware that stresses the function and economics of the chemical processing industry. A history of the course development, course outline, and teaching methods used are included. (BT)

  9. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

    NASA Astrophysics Data System (ADS)

    Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

    We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

  10. Identification of structure-activity relationships from screening a structurally compact DNA-encoded chemical library.

    PubMed

    Franzini, Raphael M; Ekblad, Torun; Zhong, Nan; Wichert, Moreno; Decurtins, Willy; Nauer, Angela; Zimmermann, Mauro; Samain, Florent; Scheuermann, Jörg; Brown, Peter J; Hall, Jonathan; Gräslund, Susanne; Schüler, Herwig; Neri, Dario

    2015-03-23

    Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA-encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL-100K, a DNA-encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA-sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate-specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small-molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.

  11. Accurate protein structure modeling using sparse NMR data and homologous structure information.

    PubMed

    Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

    2012-06-19

    While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

  12. Providing citizens with information about health effects of hazardous chemicals

    SciTech Connect

    Hadden, S.G.

    1989-06-01

    Passage of the Emergency Planning and Community Right-to-Know Act of 1986, also known as Superfund Amendments and Reauthorization Act Title III has extended the need for conveying information about the health effects of chemicals from the workplace to the community generally. Material Safety Data Sheets (MSDSs) constitute the primary source of health effects information under Title III although they were originally intended for workers. MSDSs are both too technical for many citizens and fail to address citizen concerns and questions. An alternative format is proposed that meets the criticisms of MSDSs. The alternative format may also be appropriate as supplementary information for workers, although it would not fulfill the requirements of the Occupational Safety and Health Administration Hazard Communication Standard.

  13. Structural Transformations in Chemically Modified Graphene

    DTIC Science & Technology

    2012-07-16

    unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 graphene oxide (GO) [13], chemical vapor deposition ( CVD ) onto transition metals [14...significantly. Here we focus on the mechanical aspects of graphene materials primarily using multilayer GO, but we also use single-layer CVD graphene grown on...pressure CVD growth on Cu foils [16] and subsequently transfer graphene from Cu using wet chemical approaches [14]. This includes the use of a poly

  14. Information Access in Complex, Poorly Structured Information Spaces

    DTIC Science & Technology

    1990-02-01

    distributed and made available through News creates a serious information overload. The conceptual framework behind this research effort explores (a...is willing to generate it, whose structure is it?). The innovative system building effort (instantiating the conceptual framework as well as

  15. How to add chemical abstracts service registry numbers and structures to databases via chemical names comparison

    PubMed

    Krebs; Jordis

    2000-03-01

    For the conversion of nonstructural chemical databases to structure databases, a series of algorithms to find the closest match between existing names to names in a reference database are described. On the basis of the best match, new fields such as the Chemical Abstracts Service Registry Number (CASRN) or structures were added to the database.

  16. Structural Information Retention in Visual Art Processing.

    ERIC Educational Resources Information Center

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  17. Structural Information Retention in Visual Art Processing.

    ERIC Educational Resources Information Center

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  18. Advanced Data Structure and Geographic Information Systems

    NASA Technical Reports Server (NTRS)

    Peuquet, D. (Principal Investigator)

    1984-01-01

    The current state of the art in specified areas of Geographic Information Systems GIS technology is examined. Study of the question of very large, efficient, heterogeneous spatial databases is required in order to explore the potential application of remotely sensed data for studying the long term habitability of the Earth. Research includes a review of spatial data structures and storage, development of operations required by GIS, and preparation of a testbed system to compare Vaster data structure with NASA's Topological Raster Structure.

  19. A probabilistic model for secondary structure prediction from protein chemical shifts.

    PubMed

    Mechelke, Martin; Habeck, Michael

    2013-06-01

    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Copyright © 2013 Wiley Periodicals, Inc.

  20. Entering new publication territory in chemoinformatics and chemical information science.

    PubMed

    Bajorath, Jürgen

    2015-01-01

    The F1000Research publishing platform offers the opportunity to launch themed article collections as a part of its dynamic publication environment. The idea of article collections is further expanded through the generation of publication channels that focus on specific scientific areas or disciplines. This editorial introduces the Chemical Information Science channel of F1000Research designed to collate high-quality publications and foster a culture of open peer review. Articles will be selected by guest editor(s) and a group of experts, the channel Editorial Board, and subjected to open peer review.

  1. Development of the Structural Materials Information Center

    SciTech Connect

    Oland, C.B.; Naus, D.J.

    1990-01-01

    The US Nuclear Regulatory Commission has initiated a Structural Aging Program at the Oak Ridge National Laboratory to identify potential structural safety issues related to continued service of nuclear power plants and to establish criteria for evaluating and resolving these issues. One of the tasks in this program focuses on the establishment of a Structural Materials Information Center where data and information on the time variation of concrete and other structural material properties under the influence of pertinent environmental stressors and aging factors are being collected and assembled into a data base. This data base will be used to assist in the prediction of potential long-term deterioration of critical structural components in nuclear power plants and to establish limits on hostile environmental exposure for these structures and materials. Two complementary data base formats have been developed. The Structural Materials Handbook is an expandable, hard-copy reference document that contains complete sets of data and information for selected portland cement concrete, metallic reinforcement, prestressing tendon, and structural steel materials. Baseline data, reference properties and environmental information are presented in the handbook as tables, notes and graphs. The handbook, which will be published in four volumes, serves as the information source for the electronic data base. The Structural Materials Electronic Data Base is accessible by an IBM-compatible personal computer and provides an efficient means for searching the various data base files to locate materials with similar properties. Properties will be reported in the International System of Units (SI) and in customary units whenever possible. 7 refs., 3 figs., 4 tabs.

  2. Neurotropic Effects in Relation to Chemical Structure.

    DTIC Science & Technology

    ANTISPASMODIC AGENTS, *MOLECULAR STRUCTURE), (*ANALGESICS + ANTIPYRETICS, MOLECULAR STRUCTURE), (*POLYCYCLIC COMPOUNDS, SYNTHESIS(CHEMISTRY...TOXICITY, ANTISPASMODIC AGENTS), MUSCLE RELAXANTS, BIOASSAY, MOLECULAR ISOMERISM, POLYCYCLIC COMPOUNDS, ANHYDRIDES, AMINES, CARBOXYLIC ACIDS, AMIDES, ANTHRACENES, PHENOLS, NAPHTHALENES

  3. Influence of chemical structure on carbon isotope composition of lignite

    NASA Astrophysics Data System (ADS)

    Erdenetsogt, Bat-Orshikh; Lee, Insung; Ko, Yoon-Joo; Mungunchimeg, Batsaikhan

    2017-04-01

    structure, is less than that of isotopically light methane. Coal is made up of complex macromolecules and this complexity influences the changes in carbon isotope composition during coalification. This study provides some information on the changes in the carbon isotope composition of lignite. However, further detailed investigation is required to reveal the relationships between δ13C value and chemical structure changes at certain levels of coal maturation.

  4. Fan organs of crayfish enhance chemical information flow.

    PubMed

    Breithaupt, T

    2001-04-01

    Animals as well as autonomous robots need to acquire environmental signals in order to adjust their activity in time and space. Some information is accessible to the sensors only as a result of specific behaviors for stimulus acquisition. Due to the slow rate of molecular diffusion, dispersal of chemical stimuli depends on fluid flow. Aquatic crustaceans can generate directed water currents by specialized appendages. Here I describe the crayfish fan organs, which are feathered flagella of the mouthparts, and their activity in sending and receiving chemical signals in environments with stagnant flow conditions. During the power-stroke, the fan opens and displaces water; during the return stroke, it collapses and thereby minimizes drag. These organs can create a variety of flow fields including water jets, and in many different directions. Bilateral upward fanning draws water horizontally from all directions toward the anterior chemoreceptors. Unilateral upward fanning draws water from only one side towards the body. The versatility of the crayfish fan organ makes it a candidate for biomimetic reconstruction and use in autonomous robots that can search chemical sources.

  5. Chemical Structure Search on the World Wide Web.

    ERIC Educational Resources Information Center

    Inlenfeldt, Wolf-D.

    Chemists have been very active in utilizing the World Wide Web as an information distribution medium and much interesting scientific chemical information is already offered on it. Various classical text-based search engines have made locating information on the Web easier. However, keyword-based searches are often insufficient for chemists…

  6. Information structure expectations in sentence comprehension

    PubMed Central

    Carlson, Katy; Dickey, Michael Walsh; Frazier, Lyn; Clifton, Charles

    2009-01-01

    In English, new information typically appears late in the sentence, as does primary accent. Because of this tendency, perceivers might expect the final constituent or constituents of a sentence to contain informational focus. This expectation should in turn affect how they comprehend focus-sensitive constructions such as ellipsis sentences. Results from four experiments on sluicing sentences (e.g., The mobster implicated the thug, but we can’t find out who else) suggest that perceivers do prefer to place focus late in the sentence, though that preference can be mitigated by prosodic information (pitch accents, Experiment 2) or syntactic information (clefted sentences, Experiment 3) indicating that focus is located elsewhere. Furthermore, it is not necessarily the direct object, but the informationally-focused constituent that is the preferred antecedent (Experiment 4). Expectations regarding the information structure of a sentence, which are only partly cancelable by means of overt focus markers, may explain persistent biases in ellipsis resolution. PMID:18609404

  7. Information Structure: Linguistic, Cognitive, and Processing Approaches

    PubMed Central

    Arnold, Jennifer E.; Kaiser, Elsi; Kahn, Jason M.; Kim, Lucy Kyoungsook

    2013-01-01

    Language form varies as a result of the information being communicated. Some of the ways in which it varies include word order, referential form, morphological marking, and prosody. The relevant categories of information include the way a word or its referent have been used in context, for example whether a particular referent has been previously mentioned or not, and whether it plays a topical role in the current utterance or discourse. We first provide a broad review of linguistic phenomena that are sensitive to information structure. We then discuss several theoretical approaches to explaining information structure: information status as a part of the grammar; information status as a representation of the speaker’s and listener’s knowledge of common ground and/or the knowledge state of other discourse participants; and the optimal systems approach. These disparate approaches reflect the fact that there is little consensus in the field about precisely which information status categories are relevant, or how they should be represented. We consider possibilities for future work to bring these lines of work together in explicit psycholinguistic models of how people encode information status and use it for language production and comprehension. PMID:26150905

  8. Progress and challenges for chemical probing of RNA structure inside living cells

    PubMed Central

    Kubota, Miles; Tran, Catherine; Spitale, Robert C

    2016-01-01

    Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges. PMID:26575240

  9. Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

    PubMed Central

    Hay, Mark E.

    2012-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

  10. Structuring medication related activities for information management.

    PubMed

    Luukkonen, Irmeli; Mykkänen, Juha; Kivekäs, Eija; Saranto, Kaija

    2014-01-01

    Medication treatment and the related information management are central parts of a patient's health care. As a cross-organizational and cooperative process, medication information management is a complex domain for development activities. We studied medication activities and related information management in a regional project in order to produce a shared broad picture of its processes and to understand the main issues and the needs for improvement. In this paper we provide a summary of the findings in a structured form, based on a six-dimensioned framework for design and analysis of activities and processes.

  11. 77 FR 22559 - Proposed Information Collection; Comment Request; Chemical Weapons Convention Provisions of the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-16

    ... Bureau of Industry and Security Proposed Information Collection; Comment Request; Chemical Weapons...) 482-4895, Lawrence.Hall@bis.doc.gov . SUPPLEMENTARY INFORMATION: I. Abstract The Chemical Weapons... weapons (CW). The CWC prohibits the use, development, production, acquisition, stockpiling, retention,...

  12. Profiling differences in chemical composition of brain structures using Raman spectroscopy.

    PubMed

    Daković, Marko; Stojiljković, Aleksandra S; Bajuk-Bogdanović, Danica; Starčević, Ana; Puškaš, Laslo; Filipović, Branislav; Uskoković-Marković, Snežana; Holclajtner-Antunović, Ivanka

    2013-12-15

    Raman spectroscopy enables non-invasive investigation of chemical composition of biological tissues. Due to similar chemical composition, the analysis of Raman spectra of brain structures and assignment of their spectral features to chemical constituents presents a particular challenge. In this study we demonstrate that standard and independent component analysis of Raman spectra is capable of assessment of differences in chemical composition between functionally related gray and white matter structures. Our results show the ability of Raman spectroscopy to successfully depict variation in chemical composition between structurally similar and/or functionally connected brain structures. The observed differences were attributed to variations in content of proteins and lipids in these structures. Independent component analysis enabled separation of contributions of major constituents in spectra and revealed spectral signatures of low-concentration metabolites. This provided finding of discrepancies between structures of striatum as well as between white matter structures. Raman spectroscopy can provide information about variations in contents of major chemical constituents in brain structures, while the application of independent component analysis performed on obtained spectra can help in revealing minute differences between closely related brain structures.

  13. Michigan Occupational Information System (MOIS) Structured Search.

    ERIC Educational Resources Information Center

    Michigan State Board of Education, Lansing.

    This guide leads users through a structured search of the Michigan Occupational Information System (MOIS). It is intended to help the user prepare a profile of interests and preferences that will be used in career exploration. The booklet asks the user to make choices in seven categories and to enter the responses on the MOIS Search Worksheet. The…

  14. Management Information Systems and Organizational Structure.

    ERIC Educational Resources Information Center

    Cox, Bruce B.

    1987-01-01

    Discusses the context within which office automation takes place by using the models of the Science of Creative Intelligence and Transcendental Meditation. Organizational structures are compared to the phenomenon of the "collective consciousness" and the development of automated information systems from manual methods of organizational…

  15. The Cognitive Dimensions of Information Structures.

    ERIC Educational Resources Information Center

    Green, T. R. G.

    1994-01-01

    Describes a set of terms (viscosity, hidden dependencies, imposes guess-ahead, abstraction level, and secondary notation) intended as a set of discussion tools for nonspecialists to converse about the structural features of a range of information artifacts. Explains the terms using spreadsheets as an example. (SR)

  16. The Cognitive Dimensions of Information Structures.

    ERIC Educational Resources Information Center

    Green, T. R. G.

    1994-01-01

    Describes a set of terms (viscosity, hidden dependencies, imposes guess-ahead, abstraction level, and secondary notation) intended as a set of discussion tools for nonspecialists to converse about the structural features of a range of information artifacts. Explains the terms using spreadsheets as an example. (SR)

  17. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  18. New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

    PubMed

    Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

    2013-07-01

    Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

  19. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field

    PubMed Central

    Nielsen, Jakob T.; Eghbalnia, Hamid R.; Nielsen, Niels Chr.

    2011-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field. PMID:22293396

  20. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field.

    PubMed

    Nielsen, Jakob T; Eghbalnia, Hamid R; Nielsen, Niels Chr

    2012-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field.

  1. Nematic films at chemically structured surfaces

    NASA Astrophysics Data System (ADS)

    Silvestre, N. M.; Telo da Gama, M. M.; Tasinkevych, M.

    2017-02-01

    We investigate theoretically the morphology of a thin nematic film adsorbed at flat substrate patterned by stripes with alternating aligning properties, normal and tangential respectively. We construct a simple ‘exactly-solvable’ effective interfacial model where the liquid crystal distortions are accounted for via an effective interface potential. We find that chemically patterned substrates can strongly deform the nematic-air interface. The amplitude of this substrate-induced undulations increases with decreasing average film thickness and with increasing surface pattern pitch. We find a regime where the interfacial deformation may be described in terms of a material-independent universal scaling function. Surprisingly, the predictions of the effective interfacial model agree semi-quantitatively with the results of the numerical solution of a full model based on the Landau-de Gennes theory coupled to a square-gradient phase field free energy functional for a two phase system.

  2. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    PubMed

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  3. Informational technologies in modern educational structure

    NASA Astrophysics Data System (ADS)

    Fedyanin, A. B.

    2017-01-01

    The article represents the structure of informational technologies complex that is applied in modern school education, describes the most important educational methods, shows the results of their implementation. It represents the forms and methods of educational process informative support usage, examined in respects of different aspects of their using that take into account also the psychological features of students. A range of anxious facts and dangerous trends connected with the usage and distribution of the informational technologies that are to be taken into account in the educational process of informatization is also indicated in the article. Materials of the article are based on the experience of many years in operation and development of the informational educational sphere on the basis of secondary school of the physics and mathematics specialization.

  4. Chemical Profiling of Silicon Nitride Structures

    DTIC Science & Technology

    1989-06-01

    Zip Can*) 7b ADORESSC, State. anid 71PCoaej 4.800 Oak Grove Drive ?asadena CA 91103 Hanscom AFB MA 01721-S-COC 3a NAM );: ION SPCNSOR!NG 130 OFItSYMBOL...I Chapter 2: Studies of Metal -Nitride-Oxide-Semiconductor (MNOS) Structures ................................ 12 Chapter 3...3 88 II. SO Formed by Ion Implantation .......................................................... 8 89 Ill. SO

  5. Information processing for aerospace structural health monitoring

    NASA Astrophysics Data System (ADS)

    Lichtenwalner, Peter F.; White, Edward V.; Baumann, Erwin W.

    1998-06-01

    Structural health monitoring (SHM) technology provides a means to significantly reduce life cycle of aerospace vehicles by eliminating unnecessary inspections, minimizing inspection complexity, and providing accurate diagnostics and prognostics to support vehicle life extension. In order to accomplish this, a comprehensive SHM system will need to acquire data from a wide variety of diverse sensors including strain gages, accelerometers, acoustic emission sensors, crack growth gages, corrosion sensors, and piezoelectric transducers. Significant amounts of computer processing will then be required to convert this raw sensor data into meaningful information which indicates both the diagnostics of the current structural integrity as well as the prognostics necessary for planning and managing the future health of the structure in a cost effective manner. This paper provides a description of the key types of information processing technologies required in an effective SHM system. These include artificial intelligence techniques such as neural networks, expert systems, and fuzzy logic for nonlinear modeling, pattern recognition, and complex decision making; signal processing techniques such as Fourier and wavelet transforms for spectral analysis and feature extraction; statistical algorithms for optimal detection, estimation, prediction, and fusion; and a wide variety of other algorithms for data analysis and visualization. The intent of this paper is to provide an overview of the role of information processing for SHM, discuss various technologies which can contribute to accomplishing this role, and present some example applications of information processing for SHM implemented at the Boeing Company.

  6. Earth's interdependent thermal, structural, and chemical evolution

    NASA Astrophysics Data System (ADS)

    Hofmeister, A.; Criss, R. E.

    2012-12-01

    The popular view that 30-55% of Earth's global power is primordial, with deep layers emanating significant power, rests on misunderstandings and models that omit magmatism and outgassing. These processes link Earth's chemical and thermal evolution, while creating layers, mainly because magmas transport latent heat and radioactive isotopes rapidly upwards. We link chemistry to heat flow, measured and theoretical, to understand the interior layering and workings. Quasi-steady state conditions describe most of Earth's history: (1) Accretion was cold and was not a source of deep heat. (2) Friction during core formation cannot have greatly heated the interior (thermodynamics plus buoyancy). (3) Conduction is the governing microscopic mechanism in the deep Earth. (4) Using well-constrained values of thermal conductivity (k), we find that homogeneously distributed radionuclides provide extremely high internal temperature (T) under radial symmetry. Moreover, for any given global power, sequestering heat producing elements into the upper mantle reduces Earth's central temperature by a factor of 10 from a homogeneous distribution. Hence, (5) core formation was a major cooling event. From modern determinations of k(T) we provide a reference conductive geotherm. Present-day global power of 30 TW from heat flux measurements and sequestering of heat producing elements in the upper mantle and transition zone, produces nearly isothermal T = 5300 K below 670 km, which equals experimentally determined freezing of pure Fe0 at the inner core boundary. Core freezing buffers the interior temperatures, while the Sun constrains the surface temperature, providing steady state conditions: Earth's deep interior is isothermal due to these constraints, low flux and high k. Our geotherms point to a stagnant lower mantle and convection above 670 km. Rotational flattening cracks the brittle lithosphere, providing paths for buoyant magmas to ascend. Release of latent heat augments the conductive

  7. Chemical Source Localization Fusing Concentration Information in the Presence of Chemical Background Noise.

    PubMed

    Pomareda, Víctor; Magrans, Rudys; Jiménez-Soto, Juan M; Martínez, Dani; Tresánchez, Marcel; Burgués, Javier; Palacín, Jordi; Marco, Santiago

    2017-04-20

    We present the estimation of a likelihood map for the location of the source of a chemical plume dispersed under atmospheric turbulence under uniform wind conditions. The main contribution of this work is to extend previous proposals based on Bayesian inference with binary detections to the use of concentration information while at the same time being robust against the presence of background chemical noise. For that, the algorithm builds a background model with robust statistics measurements to assess the posterior probability that a given chemical concentration reading comes from the background or from a source emitting at a distance with a specific release rate. In addition, our algorithm allows multiple mobile gas sensors to be used. Ten realistic simulations and ten real data experiments are used for evaluation purposes. For the simulations, we have supposed that sensors are mounted on cars which do not have among its main tasks navigating toward the source. To collect the real dataset, a special arena with induced wind is built, and an autonomous vehicle equipped with several sensors, including a photo ionization detector (PID) for sensing chemical concentration, is used. Simulation results show that our algorithm, provides a better estimation of the source location even for a low background level that benefits the performance of binary version. The improvement is clear for the synthetic data while for real data the estimation is only slightly better, probably because our exploration arena is not able to provide uniform wind conditions. Finally, an estimation of the computational cost of the algorithmic proposal is presented.

  8. Chemical Source Localization Fusing Concentration Information in the Presence of Chemical Background Noise †

    PubMed Central

    Pomareda, Víctor; Magrans, Rudys; Jiménez-Soto, Juan M.; Martínez, Dani; Tresánchez, Marcel; Burgués, Javier; Palacín, Jordi; Marco, Santiago

    2017-01-01

    We present the estimation of a likelihood map for the location of the source of a chemical plume dispersed under atmospheric turbulence under uniform wind conditions. The main contribution of this work is to extend previous proposals based on Bayesian inference with binary detections to the use of concentration information while at the same time being robust against the presence of background chemical noise. For that, the algorithm builds a background model with robust statistics measurements to assess the posterior probability that a given chemical concentration reading comes from the background or from a source emitting at a distance with a specific release rate. In addition, our algorithm allows multiple mobile gas sensors to be used. Ten realistic simulations and ten real data experiments are used for evaluation purposes. For the simulations, we have supposed that sensors are mounted on cars which do not have among its main tasks navigating toward the source. To collect the real dataset, a special arena with induced wind is built, and an autonomous vehicle equipped with several sensors, including a photo ionization detector (PID) for sensing chemical concentration, is used. Simulation results show that our algorithm, provides a better estimation of the source location even for a low background level that benefits the performance of binary version. The improvement is clear for the synthetic data while for real data the estimation is only slightly better, probably because our exploration arena is not able to provide uniform wind conditions. Finally, an estimation of the computational cost of the algorithmic proposal is presented. PMID:28425926

  9. Toxics Release Inventory Chemical Hazard Information Profiles (TRI-CHIP) Dataset

    EPA Pesticide Factsheets

    The Toxics Release Inventory (TRI) Chemical Hazard Information Profiles (TRI-CHIP) dataset contains hazard information about the chemicals reported in TRI. Users can use this XML-format dataset to create their own databases and hazard analyses of TRI chemicals. The hazard information is compiled from a series of authoritative sources including the Integrated Risk Information System (IRIS). The dataset is provided as a downloadable .zip file that when extracted provides XML files and schemas for the hazard information tables.

  10. Miniature photoacoustic chemical sensor using microelectromechanical structures

    NASA Astrophysics Data System (ADS)

    Pellegrino, Paul M.; Polcawich, Ronald G.; Firebaugh, Samara L.

    2004-08-01

    Photoacoustic spectroscopy is a useful monitoring technique that is well suited for trace gas detection. The technique also possesses favorable detection characteristics when the system dimensions are scaled to a micro-system design. The objective of present work is to incorporate two strengths of the Army Research Laboratory (ARL), piezoelectric microelectromechanical systems (MEMS) and chemical and biological sensing into a monolithic MEMS photoacoustic trace gas sensor. A miniaturized macro-cell design was studied as a means to examine performance and design issues as the photoacoustics is scaled to a dimension approaching the MEMS level. Performance of the macro-cell was tested using standard organo-phosphate nerve gas simulants, Dimethyl methyl phosphonate (DMMP) and Diisoprpyl methyl phosphonate (DIMP). Current MEMS work centered on fabrication of a multi-layer cell subsystem to be incorporated in the full photoacoustic device. Preliminary results were very positive for the macro-cell sensitivity (ppb levels) and specificity indicating that the scaled cell maintains sensitivity. Several bonding schemes for a three-dimension MEMS photoacoustic cavity were investigated with initial results of a low temperature AuSn bond proving most feasible.

  11. Information transfer in community structured multiplex networks

    NASA Astrophysics Data System (ADS)

    Solé Ribalta, Albert; Granell, Clara; Gómez, Sergio; Arenas, Alex

    2015-08-01

    The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

  12. Chemical structure indexing of toxicity data on the internet: moving toward a flat world.

    PubMed

    Richard, Ann M; Gold, Lois Swirsky; Nicklaus, Marc C

    2006-05-01

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database.

  13. Prediction of chemical carcinogenicity from molecular structure.

    PubMed

    Sun, Hongmao

    2004-01-01

    Carcinogens represent a serious threat to human health. In vivo determination of carcinogenicity is time-consuming and expensive, thus in silico models to predict chemical carcinogenicity are highly desirable for virtual screening of compound libraries of both pharmaceutically and other commercially interesting molecules. In the present study, a PLS-DA (partial least squares discriminant analysis) model was developed to predict carcinogenicities in each of four rodent models: male mouse (MM), female mouse (FM), male rat (MR), and female rat (FR). The data set that was used contained over 520 compounds from both the NTP and the FDA databases. All the models were built from the same molecular descriptor system, which is based on atom typing [Sun, H. J. Chem. Inf. Comput. Sci. 2004, 44, 748-757], enabling the comparison of atomic contributions to carcinogenicity with respect to species and gender. Using four components, the models were able to achieve excellent fitting and prediction, with r(2) = 0.987 and q(2) = 0.944 for MM, r(2) = 0.985 and q(2) = 0.950 for FM, r(2) = 0.989 and q(2) = 0.962 for MR, and r(2) = 0.990 and q(2) = 0.965 for FR. The models were further validated by response permutation testing and external validation, and the results indicated that the models were both statistically significant and predictive. Variable influence on projection (VIP) analysis identified the key atom types and fragments that contributed to carcinogenicities and response differences across species and gender.

  14. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  15. Structural analysis of photosystem I polypeptides using chemical crosslinking.

    PubMed

    Armbrust, T S; Odom, W R; Guikema, J A

    1994-07-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  16. THE INVESTIGATION OF STRUCTURAL PROPERTIES AND CHEMICAL TRANSFORMATIONS OF CARBAZOLE AND SOME OF ITS DERIVATIVES

    DTIC Science & Technology

    AZOLES, ALKYL RADICALS, AMIDES, CHEMICAL RADICALS, CHEMICAL REACTIONS , GLYCINE, HETEROCYCLIC COMPOUNDS, METHYL RADICALS, MOLECULAR STRUCTURE, ULTRAVIOLET SPECTROPHOTOMETERS, ULTRAVIOLET SPECTROSCOPY.

  17. How to optimize shape-based virtual screening: choosing the right query and including chemical information.

    PubMed

    Kirchmair, Johannes; Distinto, Simona; Markt, Patrick; Schuster, Daniela; Spitzer, Gudrun M; Liedl, Klaus R; Wolber, Gerhard

    2009-03-01

    Shape-based molecular similarity approaches have been established as important and popular virtual screening techniques. Recent applications have shown successful screening campaigns using different parameters and query selection. It is common sense that pure volume overlap scoring (or "shape-based screening") under-represents chemical or pharmacophoric information of a molecule. Using the "Directory of Useful Decoys" (DUD) as a benchmark set, we systematically evaluate how (i) the choice of query conformations, (ii) the selection of the active compound to be used as a query structure, and (iii) the inclusion of chemical information (i.e., the pharmacophoric properties of the query molecule) affect screening performance. Varying these parameters bears remarkable potential for improvements and delivers the best screening performance reported using these tools so far. From these insights, guidelines on how to reach optimum performance during virtual screening are developed.

  18. Information and hierarchical structure in financial markets

    NASA Astrophysics Data System (ADS)

    Mantegna, R. N.

    1999-09-01

    I investigate the information content present in the time series of stock prices of a portfolio of stocks traded in a financial market. By investigating the correlation coefficient between pairs of stocks I provide a working definition of a generalized distance between the stocks of the portfolio. This generalized distance is used to obtain an ultrametric distance matrix between the stocks. The ultrametric structure of the portfolio investigated has associated a taxonomy which is meaningful from an economic point of view.

  19. A new conceptual structure for travel information.

    PubMed

    Verhoef, L W

    1993-08-01

    This paper describes how to improve dynamic transport timetables. Mostly, such information as departure time, gate number, platform number, intermediate stops, and delays is arranged per flight or train. Each train or flight has one line or one column. A field observation of passengers using such a system showed that presenting information in this fashion is not optimal. Of passengers, 38% were unable to find the correct departure time. We analysed the performance of passengers. This analysis suggested that the information should not be arranged per train or flight but per destination. Each train or flight has one line or one column. An empirical comparison supported this conclusion. When a destination-based structure was used, the number of correct answers was 16% higher, the delay of each passenger was 75% less, and the time needed to search for a train decreased by 42%.

  20. Structural damage detection using information fusion technique

    NASA Astrophysics Data System (ADS)

    Guo, H. Y.

    2006-07-01

    In order to precisely identify the multiple damage locations of a structure, an information fusion technique is proposed in this paper. First, the frequency data and the mode shape data are regarded as two different information sources, and local decisions can be obtained using the multiple damage location assurance criterion (MDLAC) method and the frequency change damage detection method (FCDDM), respectively. Then, the local decisions are sent to a fusion centre. In the fusion centre, three main fusion approaches are applied to integrate all the local decisions. Finally, a global decision is acquired. The measurement errors are also taken into account in the fusion process. The numerical example and analysis demonstrate that the identification results of the three information fusion methods are better than those of the MDLAC method and the frequency change damage detection method.

  1. Basic Information for the Review of New Chemicals

    EPA Pesticide Factsheets

    Mandated by section 5 of the Toxic Substances Control Act (TSCA), EPA's New Chemicals program helps manage the potential risk to human health and the environment from chemicals new to the marketplace.

  2. STATISTICAL DATA ON CHEMICAL COMPOUNDS.

    DTIC Science & Technology

    DATA STORAGE SYSTEMS, FEASIBILITY STUDIES, COMPUTERS, STATISTICAL DATA , DOCUMENTS, ARMY...CHEMICAL COMPOUNDS, INFORMATION RETRIEVAL), (*INFORMATION RETRIEVAL, CHEMICAL COMPOUNDS), MOLECULAR STRUCTURE, BIBLIOGRAPHIES, DATA PROCESSING

  3. Forgotten topological index of chemical structure in drugs.

    PubMed

    Gao, Wei; Siddiqui, Muhammad Kamran; Imran, Muhammad; Jamil, Muhammad Kamran; Farahani, Mohammad Reza

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs.

  4. Chemical composition in relation with biomass ash structure

    NASA Astrophysics Data System (ADS)

    Holubcik, Michal; Jandacka, Jozef

    2014-08-01

    Biomass combustion can be more complicated like combustion of fossil fuels because it is necessary to solve problems with lower ash melting temperature. It can cause a lot of problems during combustion process. Chemical composition of biomass ash has great impact on sinters and slags creation in ash because it affects structure of heated ash. In this paper was solved relation between chemical composition and structure of heated ash from three types of biomass (spruce wood, miscanthus giganteus and wheat straw). Amount of SiO2, CaO, MgO, Al2O3 and K2O was determined. Structure of heated ash was optically determined after heating to 1000 °C or 1200 °C. Results demonstrated that chemical composition has strong effect on structure and color of heated ash.

  5. Enhancing retinal images by extracting structural information

    NASA Astrophysics Data System (ADS)

    Molodij, G.; Ribak, E. N.; Glanc, M.; Chenegros, G.

    2014-02-01

    High-resolution imaging of the retina has significant importance for science: physics and optics, biology, and medicine. The enhancement of images with poor contrast and the detection of faint structures require objective methods for assessing perceptual image quality. Under the assumption that human visual perception is highly adapted for extracting structural information from a scene, we introduce a framework for quality assessment based on the degradation of structural information. We implemented a new processing technique on a long sequence of retinal images of subjects with normal vision. We were able to perform a precise shift-and-add at the sub-pixel level in order to resolve the structures of the size of single cells in the living human retina. Last, we quantified the restoration reliability of the distorted images using an improved quality assessment. To that purpose, we used the single image restoration method based on the ergodic principle, which has originated in solar astronomy, to deconvolve aberrations after adaptive optics compensation.

  6. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

  7. Chemical Tagging Can Work: Identification of Stellar Phase-space Structures Purely by Chemical-abundance Similarity

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Casey, Andrew R.; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel; Hasselquist, Sten; Ho, Anna Y. Q.; Holtzman, Jon A.; Majewski, Steven R.; Martell, Sarah L.; Mészáros, Szabolcs; Nidever, David L.; Shetrone, Matthew

    2016-12-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were, in fact, born together (in the same molecular cloud) long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ˜ {10}5 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space, and we recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at the survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon the prospects for future data sets appear very good.

  8. Students' Chemical Information Project, October 1967 - September 1968. Final Report: Part I.

    ERIC Educational Resources Information Center

    Callaghan, A.; And Others

    Since 1966 the Chemical Society Research Unit in Information Dissemination and Retrieval at the University of Nottingham has been evaluating the use of "Chemical Titles" (CT) and "Chemical-Biological Activities" (CBAC) as current awareness services. Early results of this evaluation led to the Students' Chemical Information…

  9. Extracting and connecting chemical structures from text sources using chemicalize.org.

    PubMed

    Southan, Christopher; Stracz, Andras

    2013-04-23

    Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and

  10. Structuring Broadcast Audio for Information Access

    NASA Astrophysics Data System (ADS)

    Gauvain, Jean-Luc; Lamel, Lori

    2003-12-01

    One rapidly expanding application area for state-of-the-art speech recognition technology is the automatic processing of broadcast audiovisual data for information access. Since much of the linguistic information is found in the audio channel, speech recognition is a key enabling technology which, when combined with information retrieval techniques, can be used for searching large audiovisual document collections. Audio indexing must take into account the specificities of audio data such as needing to deal with the continuous data stream and an imperfect word transcription. Other important considerations are dealing with language specificities and facilitating language portability. At Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI), broadcast news transcription systems have been developed for seven languages: English, French, German, Mandarin, Portuguese, Spanish, and Arabic. The transcription systems have been integrated into prototype demonstrators for several application areas such as audio data mining, structuring audiovisual archives, selective dissemination of information, and topic tracking for media monitoring. As examples, this paper addresses the spoken document retrieval and topic tracking tasks.

  11. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information... to complete and submit a Top-Screen process, which may be completed through a secure Department...

  12. New Chemical Information Bulletin: Exemptions for Research and Development and Test Marketing

    EPA Pesticide Factsheets

    EPA has received numerous questions about the scope of the exemption for R&D, under TSCA section 5(h)(3). This New Chemical Information Bulletin provides more specific guidance to manufacturers and processors of new chemical substances.

  13. Chemical structures and characteristics of animal manures and composts during composting and assessment of maturity indices

    PubMed Central

    Huang, Jieying; Yu, Zixuan; Gao, Hongjian; Yan, Xiaoming; Chang, Jiang; Wang, Chengming; Hu, Jingwei

    2017-01-01

    Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different. PMID:28604783

  14. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  15. Quality of Chemical Safety Information in Printing Industry

    PubMed Central

    Tsai, Chung-Jung; Mao, I-Fang; Ting, Jo-Yu; Young, Chi-Hsien; Lin, Jhih-Sian; Li, Wei-Lun

    2016-01-01

    Objectives: Employees in printing industries can be exposed to multiple solvents in their work environment. The objectives of this study were to investigate the critical components of chemical solvents by analyzing the components of the solvents and collecting the Safety data sheets (SDSs), and to evaluate the hazard communication implementation status in printing industries. Method: About 152 printing-related industries were recruited by area-stratified random sampling and included 23 plate-making, 102 printing and 27 printing-assistance companies in Taiwan. We analyzed company questionnaires (n = 152), SDSs (n = 180), and solvents (n = 20) collected from this sample of printing-related companies. Results: Analytical results indicated that benzene and ethylbenzene, which were carcinogen and possibly carcinogen, were detectable in the cleaning solvents, and the detection rate were 54.5% (concentrations: <0.011–0.035 wt%) and 63.6% (concentrations: <0.011–6.22 wt%), respectively; however, neither compound was disclosed in the SDS for the solvents. Several other undisclosed components, including methanol, isopropanol and n-butanol, were also identified in the printing inks, fountain solutions and dilution solvents. We noted that, of the companies we surveyed, only 57.2% had a hazard communication program, 61.8% had SDSs on file and 59.9% provided employee safety and health training. We note that hazard communication programs were missing or ineffective in almost half of the 152 printing industries surveyed. Conclusions: Current safety information of solvents components in printing industries was inadequate, and many hazardous compounds were undisclosed in the SDSs of the solvents or the labels of the containers. The implementation of hazard communications in printing industries was still not enough for protecting the employees’ safety and health. PMID:26568584

  16. Quality of Chemical Safety Information in Printing Industry.

    PubMed

    Tsai, Chung-Jung; Mao, I-Fang; Ting, Jo-Yu; Young, Chi-Hsien; Lin, Jhih-Sian; Li, Wei-Lun

    2016-04-01

    Employees in printing industries can be exposed to multiple solvents in their work environment. The objectives of this study were to investigate the critical components of chemical solvents by analyzing the components of the solvents and collecting the Safety data sheets (SDSs), and to evaluate the hazard communication implementation status in printing industries. About 152 printing-related industries were recruited by area-stratified random sampling and included 23 plate-making, 102 printing and 27 printing-assistance companies in Taiwan. We analyzed company questionnaires (n = 152), SDSs (n = 180), and solvents (n = 20) collected from this sample of printing-related companies. Analytical results indicated that benzene and ethylbenzene, which were carcinogen and possibly carcinogen, were detectable in the cleaning solvents, and the detection rate were 54.5% (concentrations: <0.011-0.035 wt%) and 63.6% (concentrations: <0.011-6.22 wt%), respectively; however, neither compound was disclosed in the SDS for the solvents. Several other undisclosed components, including methanol, isopropanol and n-butanol, were also identified in the printing inks, fountain solutions and dilution solvents. We noted that, of the companies we surveyed, only 57.2% had a hazard communication program, 61.8% had SDSs on file and 59.9% provided employee safety and health training. We note that hazard communication programs were missing or ineffective in almost half of the 152 printing industries surveyed. Current safety information of solvents components in printing industries was inadequate, and many hazardous compounds were undisclosed in the SDSs of the solvents or the labels of the containers. The implementation of hazard communications in printing industries was still not enough for protecting the employees' safety and health. © The Author 2015. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

  17. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

    Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

  18. Chemical Information Literacy: pK[subscript a] Values--Where Do Students Go Wrong?

    ERIC Educational Resources Information Center

    Flynn, Alison B.; Amellal, Delphine G.

    2016-01-01

    Chemical information literacy is an essential skillset for navigating, evaluating, and using the wealth of print and online information. Accordingly, efforts are underway to improve students' acquisition and mastery of this skillset. However, less is known about students' abilities related to finding and using chemical information to solve…

  19. Chemical Information Literacy: pK[subscript a] Values--Where Do Students Go Wrong?

    ERIC Educational Resources Information Center

    Flynn, Alison B.; Amellal, Delphine G.

    2016-01-01

    Chemical information literacy is an essential skillset for navigating, evaluating, and using the wealth of print and online information. Accordingly, efforts are underway to improve students' acquisition and mastery of this skillset. However, less is known about students' abilities related to finding and using chemical information to solve…

  20. Prediction of Harmful Human Health Effects of Chemicals from Structure

    NASA Astrophysics Data System (ADS)

    Cronin, Mark T. D.

    There is a great need to assess the harmful effects of chemicals to which man is exposed. Various in silico techniques including chemical grouping and category formation, as well as the use of (Q)SARs can be applied to predict the toxicity of chemicals for a number of toxicological effects. This chapter provides an overview of the state of the art of the prediction of the harmful effects of chemicals to human health. A variety of existing data can be used to obtain information; many such data are formalized into freely available and commercial databases. (Q)SARs can be developed (as illustrated with reference to skin sensitization) for local and global data sets. In addition, chemical grouping techniques can be applied on "similar" chemicals to allow for read-across predictions. Many "expert systems" are now available that incorporate these approaches. With these in silico approaches available, the techniques to apply them successfully have become essential. Integration of different in silico approaches with each other, as well as with other alternative approaches, e.g., in vitro and -omics through the development of integrated testing strategies, will assist in the more efficient prediction of the harmful health effects of chemicals

  1. A Chemical Information Literacy Program for First-Year Students

    ERIC Educational Resources Information Center

    Gawalt, Ellen S.; Adams, Barbara

    2011-01-01

    The ability to navigate and understand the chemical literature is integral to the scientific research process. Learning these skills is therefore an important, though often overwhelming, part of an undergraduate chemical education. We describe an inquiry-based program designed to help chemistry students begin to learn to search and read the…

  2. 77 FR 61600 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-10

    ........... 08/28/2012 11/25/2012 Chryso, Inc....... (G) Cement (G) Amine acetate. additive. Degree of... polymer, hydrolyzed, sodium salts. P-12-0543........ 08/30/2012 11/27/2012 Shell chemical LP. (S) Chemical...]carbamate and 2-propanol, peroxydisulfuric acid ( 2O2)sodium salt (1:2)- initiated. P-12-0267 09/06/2012 08...

  3. A Chemical Information Literacy Program for First-Year Students

    ERIC Educational Resources Information Center

    Gawalt, Ellen S.; Adams, Barbara

    2011-01-01

    The ability to navigate and understand the chemical literature is integral to the scientific research process. Learning these skills is therefore an important, though often overwhelming, part of an undergraduate chemical education. We describe an inquiry-based program designed to help chemistry students begin to learn to search and read the…

  4. Shot detection combining Bayesian and structural information

    NASA Astrophysics Data System (ADS)

    Han, Seung H.; Kweon, In-So

    2000-12-01

    There are a number of shots in a video, each of which has boundary types, such as cut, fade, dissolve and wipe. Many previous approaches can find the cut boundary without difficulty. However, most of them often produce false alarms for the videos with large motions of camera and objects. We propose a shot boundary detection method combining Bayesian and structural information. In the Bayesian approach, a probability distribution function models each transition type, e.g., normal, abrupt, gradual transition, and also models shot length. But inseparability between those distributions causes unwanted results and degrades the precision. In this paper, we demonstrate that the shape of the filtered frame difference, called the structural information, provides an important cue to distinguish fade and dissolve effects form cut effects and gradual changes caused by motion of camera and objects. The proposed method has been tested for a few golf video segments and shown good performances in detecting fade and dissolve effects as well as cut.

  5. Understanding chemical expansion in perovskite-structured oxides.

    PubMed

    Marrocchelli, Dario; Perry, Nicola H; Bishop, Sean R

    2015-04-21

    In this work, chemical expansion in perovskite oxides was characterized in detail, motivated, inter alia, by a desire to understand the lower chemical expansion coefficients observed for perovskites in comparison to fluorite-structured oxides. Changes in lattice parameter and in local atomic arrangements taking place during compositional changes of perovskites, i.e., stoichiometric expansion, were investigated by developing an empirical model and through molecular dynamics and density functional theory atomistic simulations. An accurate empirical expression for predicting lattice constants of perovskites was developed, using a similar approach to previous reports. From this equation, analytical expressions relating chemical expansion coefficients to separate contributions from the cation and anion sublattices, assuming Shannon ionic radii, were developed and used to isolate the effective radius of an oxygen vacancy, rV. Using both experimental and simulated chemical expansion coefficient data, rV for a variety of perovskite compositions was estimated, and trends in rV were studied. In most cases, rV was slightly smaller than or similar to the radius of an oxide ion, but larger than in the fluorite structured materials. This result was in good agreement with the atomistic simulations, showing contractive relaxations of the closest oxide ions towards the oxygen vacancy. The results indicate that the smaller chemical expansion coefficients of perovskites vs. fluorites are largely due to the smaller change in cation radii in perovskites, given that the contraction around the oxygen vacancy appears to be less in this structure. Limitations of applicability for the model are discussed.

  6. Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

    PubMed Central

    Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

    2016-01-01

    Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields. PMID:27156575

  7. Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

    2016-05-01

    Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields.

  8. Hidden structures of information transport underlying spiral wave dynamics

    NASA Astrophysics Data System (ADS)

    Ashikaga, Hiroshi; James, Ryan G.

    2017-01-01

    A spiral wave is a macroscopic dynamics of excitable media that plays an important role in several distinct systems, including the Belousov-Zhabotinsky reaction, seizures in the brain, and lethal arrhythmia in the heart. Because the spiral wave dynamics can exhibit a wide spectrum of behaviors, its precise quantification can be challenging. Here we present a hybrid geometric and information-theoretic approach to quantifying the spiral wave dynamics. We demonstrate the effectiveness of our approach by applying it to numerical simulations of a two-dimensional excitable medium with different numbers and spatial patterns of spiral waves. We show that, by defining the information flow over the excitable medium, hidden coherent structures emerge that effectively quantify the information transport underlying the spiral wave dynamics. Most importantly, we find that some coherent structures become more clearly defined over a longer observation period. These findings provide validity with our approach to quantitatively characterize the spiral wave dynamics by focusing on information transport. Our approach is computationally efficient and is applicable to many excitable media of interest in distinct physical, chemical, and biological systems. Our approach could ultimately contribute to an improved therapy of clinical conditions such as seizures and cardiac arrhythmia by identifying potential targets of interventional therapies.

  9. Domain theoretic structures in quantum information theory

    NASA Astrophysics Data System (ADS)

    Feng, Johnny

    2011-12-01

    In this thesis, we continue the study of domain theoretic structures in quantum information theory initiated by Keye Martin and Bob Coecke in 2002. The first part of the thesis is focused on exploring the domain theoretic properties of qubit channels. We discover that the Scott continuous qubit channels are exactly those that are unital or constant. We then prove that the unital qubit channels form a continuous dcpo, and identify various measurements on them. We show that Holevo capacity is a measurement on unital qubit channels, and discover the natural measurement in this setting. We find that qubit channels also form a continuous dcpo, but capacity fails to be a measurement. In the second part we focus on the study of exact dcpos, a domain theoretic structure, closely related to continuous dcpos, possessed by quantum states. Exact dcpos admit a topology, called the exact topology, and we show that the exact topology has an order theoretic characterization similar to the characterization of the Scott topology on continuous dcpos. We then explore the connection between exact and continuous dcpos; first, by identifying an important set of points, called the split points, that distinguishes between exact and continuous structures; second, by exploring a continuous completion of exact dcpos, and showing that we can recover the exact topology from the Scott topology of the completion.

  10. Tangent Sphere Model. An Analog to Chemical Structure.

    ERIC Educational Resources Information Center

    Schultz, Ethel L.

    1986-01-01

    Discusses the use of the Tangent Sphere Model (TSM) in introducing chemical structure to beginning chemistry students at both the secondary school and college levels. Describes various applications of the use of such models, including instruction of the atom's kernel and valence electrons. (TW)

  11. The Chemical Structure and Acid Deterioration of Paper.

    ERIC Educational Resources Information Center

    Hollinger, William K., Jr.

    1984-01-01

    Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

  12. Rule-Based Classification of Chemical Structures by Scaffold.

    PubMed

    Schuffenhauer, Ansgar; Varin, Thibault

    2011-08-01

    Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.

  13. Exposure Levels for Chemical Threat Compounds; Information to Facilitate Chemical Incident Response

    SciTech Connect

    Hauschild, Veronique; Watson, Annetta Paule

    2013-01-01

    Exposure Standards, Limits and Guidelines for Chemical Threat Compunds ABSTRACT Exposure criteria for chemical warfare (CW) agents and certain toxic industrial chemicals (TICs) used as CW agents (such as chlorine fill in an improvised explosive device) have been developed for protection of the civilian general public, civilian employees in chemical agent processing facilities and deployed military populations. In addition, compound-specific concentrations have been developed to serve as how clean is clean enough clearance criteria guiding facility recovery following chemical terrorist or other hazardous release events. Such criteria are also useful to verify compound absence, identify containment boundaries and expedite facility recovery following chemical threat release. There is no single right value or concentration appropriate for all chemical hazard control applications. It is acknowledged that locating and comparing the many sources of CW agent and TIC exposure criteria has not been previously well-defined. This paper summarizes many of these estimates and assembles critical documentation regarding their derivation and use.

  14. Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

    PubMed

    Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

    2017-08-25

    The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. PACSY, a relational database management system for protein structure and chemical shift analysis.

    PubMed

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

  16. Occupational and Qualification Structures in the Field of Environmental Protection in the Metal and Chemical Industries in the United Kingdom.

    ERIC Educational Resources Information Center

    European Centre for the Development of Vocational Training, Berlin (Germany).

    A study analyzed the occupational structure and qualifications associated with the field of environmental protection in the metal and chemical industries in the United Kingdom. The analysis included nine case studies based on interviews with firms in the chemicals and metals sectors. Information was gathered within an analytical framework that…

  17. Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model

    PubMed Central

    Fernández, Victoria; Guzmán-Delgado, Paula; Graça, José; Santos, Sara; Gil, Luis

    2016-01-01

    The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing toward the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth. PMID:27066059

  18. Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model.

    PubMed

    Fernández, Victoria; Guzmán-Delgado, Paula; Graça, José; Santos, Sara; Gil, Luis

    2016-01-01

    The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing toward the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth.

  19. A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions

    NASA Astrophysics Data System (ADS)

    Hawthorne, Frank C.

    2012-11-01

    Here, I describe a theoretical approach to the structure and chemical composition of minerals based on their bond topology. This approach allows consideration of many aspects of minerals and mineral behaviour that cannot be addressed by current theoretical methods. It consists of combining the bond topology of the structure with aspects of graph theory and bond-valence theory (both long range and short range), and using the moments approach to the electronic energy density-of-states to interpret topological aspects of crystal structures. The structure hierarchy hypothesis states that higher bond-valence polyhedra polymerize to form the (usually anionic) structural unit, the excess charge of which is balanced by the interstitial complex (usually consisting of large low-valence cations and (H2O) groups). This hypothesis may be justified within the framework of bond topology and bond-valence theory, and may be used to hierarchically classify oxysalt minerals. It is the weak interaction between the structural unit and the interstitial complex that controls the stability of the structural arrangement. The principle of correspondence of Lewis acidity-basicity states that stable structures will form when the Lewis-acid strength of the interstitial complex closely matches the Lewis-base strength of the structural unit, and allows us to examine the factors that control the chemical composition and aspects of the structural arrangements of minerals. It also provides a connection between a structure, the speciation of its constituents in aqueous solution and its mechanism of crystallization. The moments approach to the electronic energy density-of-states provides a link between the bond topology of a structure and its thermodynamic properties, as indicated by correlations between average anion coordination number and reduced enthalpy of formation from the oxides for [6]Mg{/m [4]}Si n O( m+2 n) and MgSO4(H2O) n .

  20. 78 FR 20101 - Access to Confidential Business Information by Chemical Abstract Services

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-03

    ... AGENCY Access to Confidential Business Information by Chemical Abstract Services AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: EPA expects to authorize its contractor, Chemical Abstract... chemicals. Since other entities may also be interested, the Agency has not attempted to describe all...

  1. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Information regarding security risk for a chemical facility. 27.200 Section 27.200 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200...

  2. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 6 Domestic Security 1 2014-01-01 2014-01-01 false Information regarding security risk for a chemical facility. 27.200 Section 27.200 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200...

  3. 40 CFR 711.5 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... information must be reported. 711.5 Section 711.5 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.5 Chemical... File at the beginning of a submission period described in § 711.20, unless the chemical substance is...

  4. 40 CFR 711.5 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... information must be reported. 711.5 Section 711.5 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.5 Chemical... File at the beginning of a submission period described in § 711.20, unless the chemical substance is...

  5. 40 CFR 711.5 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... information must be reported. 711.5 Section 711.5 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.5 Chemical... File at the beginning of a submission period described in § 711.20, unless the chemical substance is...

  6. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

    nanomaterial with lateral dimensions in the hundreds of microns if not larger, with a corresponding atomic vertical thickness poses significant difficulties. Graphene's unique structure is dominated by surface area or potentially hybridized interfaces; consequently, the true realization of this remarkable nanomaterial in device constructs relies on engineering graphene interfaces at the surface in order to controllably mold the electronic structure. Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy and the transmission mode analogue scanning transmission X-ray microscopy (STXM) are particularly useful tools to study the unoccupied states of graphene and graphene interfaces. In addition, polarized NEXAFS and STXM studies provide information on surface orientation, bond sterics, and the extent of substrate alignment before and after interfacial hybridization. The work presented in this dissertation is fundamentally informed by NEXAFS and STXM measurements on graphene/metal, graphene/dielectric, and graphene/organic interfaces. We start with a general review of the electronic structure of freestanding graphene and graphene interfaces in Chapter 1. In Chapter 2, we investigate freestanding single-layer graphene via STXM and NEXAFS demonstrating that electronic structure heterogeneities from synthesis and processing are ubiquitous in 2-dimensional graphene. We show the mapping of discrete charge transfer regions as a result of doped impurities that decorate the surfaces of graphene and that transfer processing imparts local electronic corrugations or ripples. In corroboration with density functional theory, definitive assignments to the spectral features, global steric orientations of the localized domains, and quantitative charge transfer schemes are evidenced. In the following chapters, we deliberately (Chapter 3) incorporate substitutional nitrogen into reduced graphene oxide to induce C--N charge redistribution and improve global conductivity, (Chapter 4

  7. Electrical and structural properties of chemically modified graphene sheets

    NASA Astrophysics Data System (ADS)

    Dikin, Dmitriy A.; Jung, Inhwa; Ruoff, Rodney S.

    2009-03-01

    The chemical exfoliation of graphite through oxidation and then dispersion in a solvent is one of the methods of achieving scalable production of single graphene sheets. We use this method for making chemically modified graphene (CMG) sheets with tunable electronic properties, which can be placed flat on any surface or dispersed in various matrices. CMG sheets share some similarities with pristine graphene and with carbon nanotubes, e.g. tunable electron- and hole-type conductivity is observed in single CMG sheets just above the percolation threshold. CMGs may also be considered as a template for a bottom up development of a new class of materials. We have performed electrical measurements of individual CMG sheets and will discuss their electronic properties and the possible mechanisms of the charge transport in relation to their atomic structure and chemical composition.

  8. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    ERIC Educational Resources Information Center

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  9. The Impact of Computers on the Retrieval and Utilization of Chemical Information.

    ERIC Educational Resources Information Center

    Lawrence, Barbara

    The use of computers in retrieving bibliographic chemical information is traced through the SDI, batch, and online modes, and related changes are noted in such areas as data base availability, cost, software, and amount of user control. The impact of these changes on both the quality and quantity of chemical information use is discussed, as well…

  10. The Impact of Computers on the Retrieval and Utilization of Chemical Information.

    ERIC Educational Resources Information Center

    Lawrence, Barbara

    The use of computers in retrieving bibliographic chemical information is traced through the SDI, batch, and online modes, and related changes are noted in such areas as data base availability, cost, software, and amount of user control. The impact of these changes on both the quality and quantity of chemical information use is discussed, as well…

  11. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    ERIC Educational Resources Information Center

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  12. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information..., funding, and other matters bearing on the effectiveness of the security, safety and emergency response... 6 Domestic Security 1 2012-01-01 2012-01-01 false Information regarding security risk for a...

  13. (Sub)structure Searches in Databases Containing Generic Chemical Structure Representations.

    ERIC Educational Resources Information Center

    Schoch-Grubler, Ursula

    1990-01-01

    Reviews three database systems available for searching generic chemical structure representations: (1) Derwent's Chemical Code System; (2) IDC's Gremas System; and (3) Derwent's Markush DARC System. Various types of searches are described, features desirable to users are discussed, and comparison searches are described that measured recall and…

  14. 77 FR 5096 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-01

    .... producing packaging films. P-12-0089 12/06/2011 03/04/2012 Brueggemann (G) Zinc is a (S) Process Chemical U... in polymers.. P-12-0104 12/14/2011 03/12/2012 CBI (G) The product (G) Mixture of can be used as isomers of a dye for condensation papers, wood. products of substituted diazotized aminoanilines....

  15. 75 FR 60447 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... with 1-propene, paint additive. maleated. P-10-0429 06/24/10 09/21/10 CBI (G) Lithographic inks (G...) Chemical (G) Sodium bromide intermediate for mda complex. manufacturing polyurethane rubber elastomer for..., Inc. (G) Resin additive (G) Unsaturated polyester resin. P-10-0437 07/07/10 10/04/10 CBI (S) Coatings...

  16. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  17. Optical disk toxic information online system at Sumitomo Chemical Co. through telecommunication network in Japan

    NASA Astrophysics Data System (ADS)

    Kishida, Fumio; Omodaka, Hisakata; Ishihara, Koichiro; Yamada, Yoshinori; Kato, Hiromi

    Toxicity data about several hundred chemicals, handled and commercialized by Sumitomo Chemical Co., have been collected and estimated. These data are stored in an optical disk filing system "sanfile 8500D". Because the system is mounted with a keyword input panel "Word selecter", information retrieval system is simplified but precised. Online system through telecommunication network is extended between Sumitomo Chemical's works, laboratories, and others. Image informations are mailed from installed facsimili in sanfile 8500D directly.

  18. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  19. Bridging the Implementation Gap through Chemical and Materials Information Management

    DTIC Science & Technology

    2011-05-01

    Information • Consistent data management with common data connectivity • Customized interfaces & tools – intuitive user experience • Track materials to components • Target implementation strategies

  20. Information Structures in Nash and Leader-Follower Strategies.

    DTIC Science & Technology

    1981-01-01

    The role of information structures in some Nash and Leader - Follower games is examined. By preserving the information structure of the full order...classes of Leader - Follower games. Decision-dependent information structure is employed in both Nash games and optimal coordination problems and two...the solutions of both the stochastic optimal coordination problem with decision-dependent information structure and the stochastic Leader - Follower team

  1. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

  2. Characterization of iron-phosphate-silicate chemical garden structures.

    PubMed

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  3. The Stepping Stone Approach to Teaching Chemical Information Skills

    ERIC Educational Resources Information Center

    Yeagley, Andrew A.; Porter, Sarah E. G.; Rhoten, Melissa C.; Topham, Benjamin J.

    2016-01-01

    Information literacy is of paramount importance to any successful research program. Information techniques and skills should be infused throughout a student's undergraduate curriculum rather than being the focus of a single course. To this end, we have created several courses, beginning in the first year, where students review current scientific…

  4. The Stepping Stone Approach to Teaching Chemical Information Skills

    ERIC Educational Resources Information Center

    Yeagley, Andrew A.; Porter, Sarah E. G.; Rhoten, Melissa C.; Topham, Benjamin J.

    2016-01-01

    Information literacy is of paramount importance to any successful research program. Information techniques and skills should be infused throughout a student's undergraduate curriculum rather than being the focus of a single course. To this end, we have created several courses, beginning in the first year, where students review current scientific…

  5. Electronic and chemical structure of metal-silicon interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, P. J.; Grunthaner, F. J.

    1984-01-01

    This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

  6. Chemical and structural effects of base modifications in messenger RNA

    NASA Astrophysics Data System (ADS)

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles.

  7. Information diffusion in structured online social networks

    NASA Astrophysics Data System (ADS)

    Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

    2015-05-01

    Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

  8. Chemical compatibility of structural materials in alkali metals

    SciTech Connect

    Natesan, K.; Rink, D.L.; Haglund, R.

    1995-04-01

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments.

  9. Correlating the structural, chemical, and optical properties at nanometer resolution

    NASA Astrophysics Data System (ADS)

    Gu, L.; Özdöl, V. B.; Sigle, W.; Koch, C. T.; Srot, V.; van Aken, P. A.

    2010-01-01

    Valence electron spectroscopic imaging (VESI) techniques, taking advantages of the energy-losses suffered by inelastic scattering of the fast electrons in the transmission electron microscope, offer an inherently high spatial resolution to characterize the electronic structure of materials close to the Fermi level. Here we demonstrate that the combination of an electron monochromator and a highly dispersive imaging energy filter, which has become available only recently, allows reliable measurements of local bandgaps on the nanometer scale. In addition, the correlations of structural, chemical, and optical properties can be revealed via VESI using monochromated electrons with a high spatial resolution.

  10. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

    Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.

  11. CAS Online: A New Source of Substance Information from Chemical Abstracts Service.

    ERIC Educational Resources Information Center

    Farmer, Nick A.; O'Hara, Michael P.

    1980-01-01

    Describes features of a new type of chemical database which provides the ability to search for substances sharing particular structural characteristics. Search concepts are examined in detail, and menu selection of "screens," system commands, and interpretation of results (which appear in the form of chemical bond structures) are…

  12. CAS Online: A New Source of Substance Information from Chemical Abstracts Service.

    ERIC Educational Resources Information Center

    Farmer, Nick A.; O'Hara, Michael P.

    1980-01-01

    Describes features of a new type of chemical database which provides the ability to search for substances sharing particular structural characteristics. Search concepts are examined in detail, and menu selection of "screens," system commands, and interpretation of results (which appear in the form of chemical bond structures) are…

  13. Application of chemical structure and bonding of actinide oxide materials for forensic science

    SciTech Connect

    Wilkerson, Marianne Perry

    2010-01-01

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO{sub 2} (An: U, Pu) to form non-stoichiometric species described as AnO{sub 2+x}. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  14. Exposure levels for chemical threat compounds: information to facilitate chemical incident response.

    PubMed

    Hauschild, Veronique D; Watson, Annetta

    2013-01-01

    Although not widely known, a robust set of peer-reviewed public health and occupational exposure levels presently exist for key chemical warfare agents (CWAs) and certain acutely toxic industrial chemicals (TICs) identified as terrorist attack threats. Familiarity with these CWA and TIC exposure levels and their historic applications has facilitated emergency management decision-making by public and environmental health decision-makers. Specifically, multiple air, soil, and water exposure levels for CWAs and TICs summarized here have been extensively peer-reviewed and published; many have been recognized and are in use by federal and state health agencies as criteria for hazard zone prediction and assessment, occupational safety, and "how clean is clean enough" decisions. The key, however, is to know which criteria are most appropriate for specific decisions. While public safety is critical, high levels of concern often associated with perceived or actual proximity to extremely toxic chemical agents could result in overly cautious decisions that generate excessive delays, expenditure of scarce resources, and technological difficulties. Rapid selection of the most appropriate chemical exposure criteria is recommended to avoid such problems and expedite all phases of chemical incident response and recovery.

  15. Chemical and physical structures of proteinoids and related polyamino acids

    NASA Astrophysics Data System (ADS)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  16. Chemical structure analysis of starch and cellulose derivatives.

    PubMed

    Mischnick, Petra; Momcilovic, Dane

    2010-01-01

    Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch and cellulose cause the products resulting from their modification to display high complexity. Chemical composition analysis of these mixtures is therefore a challenging task. Detailed knowledge on substitution patterns is fundamental for understanding structure-property relationships in modified cellulose and starch, and thus also for the improvement of reproducibility and rational design of properties. Substitution patterns resulting from kinetically or thermodynamically controlled reactions show certain preferences for the three available hydroxyl functions in (1→4)-linked glucans. Spurlin, seventy years ago, was the first to describe this in an idealized model, and nowadays this model has been extended and related to the next hierarchical levels, namely, the substituent distribution in and over the polymer chains. This structural complexity, with its implications for data interpretation, and the analytical approaches developed for its investigation are outlined in this article. Strategies and methods for the determination of the average degree of substitution (DS), monomer composition, and substitution patterns at the polymer level are presented and discussed with respect to their limitations and interpretability. Nuclear magnetic resonance spectroscopy, chromatography, capillary electrophoresis, and modern mass spectrometry (MS), including tandem MS, are the main instrumental techniques employed, in combination with appropriate sample preparation by chemical and enzymatic methods.

  17. Understanding Networks of Computing Chemical Droplet Neurons Based on Information Flow.

    PubMed

    Gruenert, Gerd; Gizynski, Konrad; Escuela, Gabi; Ibrahim, Bashar; Gorecki, Jerzy; Dittrich, Peter

    2015-11-01

    In this paper, we present general methods that can be used to explore the information processing potential of a medium composed of oscillating (self-exciting) droplets. Networks of Belousov-Zhabotinsky (BZ) droplets seem especially interesting as chemical reaction-diffusion computers because their time evolution is qualitatively similar to neural network activity. Moreover, such networks can be self-generated in microfluidic reactors. However, it is hard to track and to understand the function performed by a medium composed of droplets due to its complex dynamics. Corresponding to recurrent neural networks, the flow of excitations in a network of droplets is not limited to a single direction and spreads throughout the whole medium. In this work, we analyze the operation performed by droplet systems by monitoring the information flow. This is achieved by measuring mutual information and time delayed mutual information of the discretized time evolution of individual droplets. To link the model with reality, we use experimental results to estimate the parameters of droplet interactions. We exemplarily investigate an evolutionary generated droplet structure that operates as a NOR gate. The presented methods can be applied to networks composed of at least hundreds of droplets.

  18. 75 FR 11414 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-10

    ... Best Sanitizers, Inc. (S) Surfactant (S) Palm oil, mixed D- glucose and oleic acid, candida bombicola... comments to docket ID number EPA-HQ-OPPT- 2010-0171. EPA's policy is that all comments received will be..., and be free of any defects or viruses. For additional information about EPA's public docket, visit...

  19. The chemical structure and the crystalline structures of Bombyx mori silk fibroin.

    PubMed

    Lotz, B; Colonna Cesari, F

    1979-01-01

    Some recent data (i.e. published in the last ten years) on the chemical and crystalline structures of B. mori silk are reviewed. The main emphasis is put on the crystallizable portion of silk fibroin, including its chemical constitution and its molecular conformation (at the crystallographic unit-cell level) in the two crystalline modifications : the beta pleated sheet and the silk I structures. The structural aspects are based on a discussion of X-ray and electron diffraction data, and on conformational energy analyses of a model (Ala-Gly)n polypeptide of silk fibroin.

  20. Linear complexions: Confined chemical and structural states at dislocations.

    PubMed

    Kuzmina, M; Herbig, M; Ponge, D; Sandlöbes, S; Raabe, D

    2015-09-04

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  1. Atomically Resolved Structural and Chemical Investigation of Single MXene Sheets.

    PubMed

    Karlsson, Linda H; Birch, Jens; Halim, Joseph; Barsoum, Michel W; Persson, Per O Å

    2015-08-12

    The properties of two-dimensional (2D) materials depend strongly on the chemical and electrochemical activity of their surfaces. MXene, one of the most recent additions to 2D materials, shows great promise as an energy storage material. In the present investigation, the chemical and structural properties of individual Ti3C2 MXene sheets with associated surface groups are investigated at the atomic level by aberration corrected STEM-EELS. The MXene sheets are shown to exhibit a nonuniform coverage of O-based surface groups which locally affect the chemistry. Additionally, native point defects which are proposed to affect the local surface chemistry, such as oxidized titanium adatoms (TiOx), are identified and found to be mobile.

  2. Chemically Resolved Structure of the Sn/Ge(111) Surface

    NASA Astrophysics Data System (ADS)

    Lee, Tien-Lin; Warren, Samantha; Cowie, Bruce C. C.; Zegenhagen, Jörg

    2006-02-01

    The structure and chemical states of the Sn/Ge(111) surface are characterized by x-ray standing waves combined with photoemission. For the room temperature 3×3 phase two chemical components, approximately 0.4 eV apart, are observed for both Sn 3d and 4d core levels. Our model-independent, x-ray standing wave analysis shows unambiguously that the two components originate from Sn adatoms located at two different heights separated vertically by 0.23 Å, in favor of a model composed of a fluctuating Sn layer. Contrary to the most accepted scenario, the stronger Sn 3d and 4d components, which appear at the lower binding-energy sides and account for 2/3 of the Sn adatoms, are identified to be associated with the higher Sn position, manifesting their filled valence state character.

  3. SYBYL line notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries.

    PubMed

    Homer, R Webster; Swanson, Jon; Jilek, Robert J; Hurst, Tad; Clark, Robert D

    2008-12-01

    SYBYL line notation (SLN) is a powerful way to represent molecular structures, reactions, libraries of structures, molecular fragments, formulations, molecular queries, and reaction queries. Nearly any chemical structure imaginable, including macromolecules, pharmaceuticals, catalysts, and even combinatorial libraries can be represented as an SLN string. The language provides a rich syntax for database queries comparable to SMARTS. It provides full Markush, R-Group, reaction, and macro atom capabilities in a single unified notation. It includes the ability to specify 3D conformations and 2D depictions. All the information necessary to recreate the structure in a modeling or drawing package is present in a single, concise string of ASCII characters. This makes SLN ideal for structure communication over global computer networks between applications sitting at remote sites. Unlike SMILES and its derivatives, SLN accomplishes this within a single unified syntax. Structures, queries, compounds, reactions, and virtual libraries can all be represented in a single notation.

  4. Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

    PubMed

    Camilloni, Carlo; De Simone, Alfonso; Vranken, Wim F; Vendruscolo, Michele

    2012-03-20

    One of the major open challenges in structural biology is to achieve effective descriptions of disordered states of proteins. This problem is difficult because these states are conformationally highly heterogeneous and cannot be represented as single structures, and therefore it is necessary to characterize their conformational properties in terms of probability distributions. Here we show that it is possible to obtain highly quantitative information about particularly important types of probability distributions, the populations of secondary structure elements (α-helix, β-strand, random coil, and polyproline II), by using the information provided by backbone chemical shifts. The application of this approach to mammalian prions indicates that for these proteins a key role in molecular recognition is played by disordered regions characterized by highly conserved polyproline II populations. We also determine the secondary structure populations of a range of other disordered proteins that are medically relevant, including p53, α-synuclein, and the Aβ peptide, as well as an oligomeric form of αB-crystallin. Because chemical shifts are the nuclear magnetic resonance parameters that can be measured under the widest variety of conditions, our approach can be used to obtain detailed information about secondary structure populations for a vast range of different protein states.

  5. Sources of toxicity and exposure information for identifying chemicals of high concern to children

    SciTech Connect

    Stone, Alex; Delistraty, Damon

    2010-11-15

    Due to the large number of chemicals in commerce without adequate toxicity characterization data, coupled with an ineffective federal policy for chemical management in the United States, many states are grappling with the challenge to identify toxic chemicals that may pose a risk to human health and the environment. Specific populations (e.g., children, elderly) are particularly sensitive to these toxic chemicals. In 2008, the Children's Safe Product Act (CSPA) was passed in Washington State. The CSPA included specific requirements to identify High Priority Chemicals (HPCs) and Chemicals of High Concern to Children (CHCCs). To implement this legislation, a methodology was developed to identify HPCs from authoritative scientific and regulatory sources on the basis of toxicity criteria. Another set of chemicals of concern was then identified from authoritative sources, based on their potential exposure to children. Exposure potential was evaluated by identifying chemicals detected in biomonitoring studies (i.e., human tissues), as well as those present in residential exposure media (e.g., indoor air, house dust, drinking water, consumer products). Accordingly, CHCCs were defined as HPCs that also appear in biomonitoring studies or relevant exposure media. For chemicals with unique Chemical Abstracts Service (CAS) numbers, we identified 2044 HPCs and 2219 chemicals with potential exposure to children, resulting in 476 CHCCs. The process of chemical identification is dynamic, so that chemicals may be added or subtracted as new information becomes available. Although beyond the scope of this paper, the 476 CHCCs will be prioritized in a more detailed assessment, based on the strength and weight of evidence of toxicity and exposure data. Our approach was developed to be flexible which allows the addition or removal of specific sources of toxicity or exposure information, as well as transparent to allow clear identification of inputs. Although the methodology was

  6. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    PubMed

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign .

  7. A structured strategy for assessing chemical risks, suitable for small and medium-sized enterprises.

    PubMed

    Balsat, A; de Graeve, J; Mairiaux, P

    2003-10-01

    A previous study carried out in 20 Belgian companies, especially small and medium-sized enterprises (SMEs), showed that prevention advisors did not use any structured approaches to assess chemical risk. They used their personal judgement and the information contained in manufacturers' Safety Data Sheets to assess the risk. The purpose of the Regetox network is to provide companies with a global approach for assessing chemical health risks. The structured approach proposed consists of two successive steps of increasing complexity. For the first step, we chose a method developed by the INRS (France), the 'ranking of potential risk', which allows the safety officer or staff member to identify hazards and to set priorities among all the supplied products used in the workplace. For the second step, we applied the COSHH method and EASE model established by the UK Health & Safety Executive for assessing 'chemical risk by reference to occupational exposure limits'. The INRS and COSHH Essentials methods were chosen because they define hazards using R-phrases of the European classification system and assess the exposure by using simple information that is easy to collect in the workplace and toxicological databases. A feasibility study conducted in two enterprises shows the usefulness of this approach. In addition to the intrinsic limitations of the methods, the approach showed some limitations related to the inaccuracy of the manufactured safety data sheets and to the collection of the basic information needed for ranking potential risks. The use of the Regetox approach needs training of prevention advisors and a strategy involving employers, staff members and workers in collecting basic information and managing chemical risks. Under these conditions, Regetox seems to be a useful tool for chemical risk assessment in SMEs.

  8. 75 FR 32760 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ... general industrial derived from the use. pyrolysis of rubber tire shreds P-10-0368 05/03/10 07/31/10 CBI...) Tire pyrolysis general industrial oil or tire-derived use oil P-10-0370 05/04/10 08/01/10 CBI (G... use pyrolysis of rubber tire shreds In Table II of this unit, EPA provides the following information...

  9. Temporal and Statistical Information in Causal Structure Learning

    ERIC Educational Resources Information Center

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  10. Temporal and Statistical Information in Causal Structure Learning

    ERIC Educational Resources Information Center

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  11. Exploring the Global Structure of "Information Books."

    ERIC Educational Resources Information Center

    Pappas, Christine C.

    Children's "information books" are usually illustrated books on one topic, typically identified by the title. For example, "Squirrels" tells all about the characteristics and behaviors of squirrels. An exploration of what does or does not constitute an information book using five specific questions about the genre yields an…

  12. Ideologically Structured Information Exchange among Environmental Groups

    ERIC Educational Resources Information Center

    Lhotka, Laura; Bailey, Conner; Dubois, Mark

    2008-01-01

    We use social network analysis to test the hypothesis that group ideology affects information exchange among environmental groups. The analysis is based on interviews with leaders of 136 environmental groups in Alabama. This paper adds to the literature on resource mobilization among social movement organizations by exploring information exchange…

  13. Crystal structure and chemical bonding of Mg3Ru2.

    PubMed

    Pöttgen, Rainer; Hlukhyy, Viktor; Baranov, Aleksey; Grin, Yuri

    2008-07-07

    Mg 3Ru 2 was prepared by a reaction between the elements in the ideal ratio in a sealed tantalum ampule. Its beta-manganese type crystal structure was refined on the basis of the single-crystal data: space group P4 132, a = 693.52(6) pm, wR2 = 0.024, 168 F (2) values, and 10 parameters. The magnesium (CN = 14) and ruthenium (CN = 12) atoms are completely ordered on the 12d and 8c sites of the crystal structure of beta-manganese. Both environments can be considered as Frank-Kasper related polyhedra. A periodic nodal surface P4 132(110) pi (1) P4 132 separates the magnesium and ruthenium positions in two different labyrinths, suggesting different chemical interactions within different parts of the structural motif. Analysis of the chemical bonding with the electron localizability indicator (ELI-D) reveals covalently interacting three-bonded ruthenium atoms, forming a 3D network. The network interacts with the magnesium substructure by multicenter bonds.

  14. Equity and Information: Information Regulation, Environmental Justice, and Risks from Toxic Chemicals

    ERIC Educational Resources Information Center

    Shapiro, Marc D.

    2005-01-01

    Decreases over time in pounds of industrial chemical emissions have led to concerns that nonminority, higher-income communities have benefited disproportionately in reductions in risk. Toxic chemical release data, modeled for toxicity and dispersion in square kilometer units across 45 states, are used to test six sets of hypotheses of potential…

  15. Equity and Information: Information Regulation, Environmental Justice, and Risks from Toxic Chemicals

    ERIC Educational Resources Information Center

    Shapiro, Marc D.

    2005-01-01

    Decreases over time in pounds of industrial chemical emissions have led to concerns that nonminority, higher-income communities have benefited disproportionately in reductions in risk. Toxic chemical release data, modeled for toxicity and dispersion in square kilometer units across 45 states, are used to test six sets of hypotheses of potential…

  16. 75 FR 68809 - Agency Information Collection Activities: Importation Bond Structure

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-09

    ... Information Collection Activities: Importation Bond Structure AGENCY: U.S. Customs and Border Protection...: Importation Bond Structure. This is a proposed extension and revision of an information collection that was...: Importation Bond Structure. OMB Number: 1651-0050. Form Numbers: 301 and 5297. Abstract: Bonds are used...

  17. Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

    SciTech Connect

    Elrod, D.W.

    1992-01-01

    Computational neural networks (CNNs) are a computational paradigm inspired by the brain's massively parallel network of highly interconnected neurons. The power of computational neural networks derives not so much from their ability to model the brain as from their ability to learn by example and to map highly complex, nonlinear functions, without the need to explicitly specify the functional relationship. Two central questions about CNNs were investigated in the context of predicting chemical reactions: (1) the mapping properties of neural networks and (2) the representation of chemical information for use in CNNs. Chemical reactivity is here considered an example of a complex, nonlinear function of molecular structure. CNN's were trained using modifications of the back propagation learning rule to map a three dimensional response surface similar to those typically observed in quantitative structure-activity and structure-property relationships. The computational neural network's mapping of the response surface was found to be robust to the effects of training sample size, noisy data and intercorrelated input variables. The investigation of chemical structure representation led to the development of a molecular structure-based connection-table representation suitable for neural network training. An extension of this work led to a BE-matrix structure representation that was found to be general for several classes of reactions. The CNN prediction of chemical reactivity and regiochemistry was investigated for electrophilic aromatic substitution reactions, Markovnikov addition to alkenes, Saytzeff elimination from haloalkanes, Diels-Alder cycloaddition, and retro Diels-Alder ring opening reactions using these connectivity-matrix derived representations. The reaction predictions made by the CNNs were more accurate than those of an expert system and were comparable to predictions made by chemists.

  18. Chemical and structural effects of base modifications in messenger RNA

    PubMed Central

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification — the epitranscriptome — is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles. PMID:28102265

  19. Information resources for assessing health effects from chemical exposure: Office of pesticides programs

    SciTech Connect

    Fenner-Crisp, P.

    1990-12-31

    The US Environmental Protection Agency (EPA) Office of Pesticide Programs is trying to develop a complete picture of a chemical`s toxicity and exposure profile. It is also important to share information in the office`s files because of pesticides, particularly as a consequence of agricultural use, find their way into places not necessarily intended.

  20. 40 CFR 710.25 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Chemical substances for which information must be reported. 710.25 Section 710.25 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS 2002 Inventory Update...

  1. 40 CFR 710.45 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Chemical substances for which information must be reported. 710.45 Section 710.45 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL INVENTORY REGULATIONS Inventory Update Reporting...

  2. 75 FR 68370 - Agency Information Collection Activities: Office of Infrastructure Protection; Chemical Security...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-05

    ... Infrastructure Protection; Chemical Security Awareness Training Program AGENCY: National Protection and Programs... currently approved information collection request (ICR) for the Chemical Security Awareness Training Program. DHS previously published this ICR in the Federal Register on August 27, 2010 at 75 FR 52768, for a...

  3. IMPROVING THE ENVIRONMENTAL PERFORMANCE OF CHEMICAL PROCESSES THROUGH THE USE OF INFORMATION TECHNOLOGY

    EPA Science Inventory

    Efforts are currently underway at the USEPA to develop information technology applications to improve the environmental performance of the chemical process industry. These efforts include the use of genetic algorithms to optimize different process options for minimal environmenta...

  4. 77 FR 59891 - Proposed Information Collection; Comment Request; Chemical Weapons Convention Declaration and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-01

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Bureau of Industry and Security Proposed Information Collection; Comment Request; Chemical Weapons Convention Declaration and Report Handbook and Forms AGENCY: Bureau of Industry and Security. ACTION: Notice...

  5. IMPROVING THE ENVIRONMENTAL PERFORMANCE OF CHEMICAL PROCESSES THROUGH THE USE OF INFORMATION TECHNOLOGY

    EPA Science Inventory

    Efforts are currently underway at the USEPA to develop information technology applications to improve the environmental performance of the chemical process industry. These efforts include the use of genetic algorithms to optimize different process options for minimal environmenta...

  6. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  7. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  8. Chemical and structural diversity of siRNA molecules.

    PubMed

    Nawrot, Barbara; Sipa, Katarzyna

    2006-01-01

    Short interfering RNAs (siRNAs) are 21-23 nt long double-stranded oligoribonucleotides which in mammalian cells exhibit a potency for sequence-specific gene silencing via an RNA interference (RNAi) pathway. It has been already proven that exogenous, chemically synthesized siRNA molecules are effective inhibitors of gene expression and are widely applied for analysis of protein function and proteomics-based target identification. Moreover, since their discovery siRNA molecules have been implemented as potential candidates for therapeutic applications. Variously modified siRNA molecules containing sugar modifications (2'-OMe, -F, -O-allyl, -amino, orthoesters and LNA analogues), internucleotide phospodiester bond modifications (phosphorothioates, boranophosphates), base modifications (s(2)U) as well as 3'-terminal cholesterol-conjugated constructs were investigated as potential candidates for effective inhibition of gene expression. This chapter reviews an impact of chemical and structural modifications of siRNA molecules on their serum and thermal stability, cellular and in vivo activity, cellular uptake, biodistribution and cytotoxicity. Functional analysis of chemically modified siRNA molecules allows for better understanding of the mechanism of the RNA interference process as well as demonstrates immense efforts in optimizing in vivo potency of siRNA molecules for RNAi-based drug design.

  9. Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates.

    PubMed

    Southan, Christopher; Williams, Antony J; Ekins, Sean

    2013-01-01

    There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this.

  10. Multivariate chemical mapping of antibiotics and identification of structurally representative substances.

    PubMed

    Papa, Ester; Fick, Jerker; Lindberg, Richard; Johansson, Magnus; Gramatica, Paola; Andersson, Patrik L

    2007-03-01

    Antibiotics used in human and veterinary medicine have been found in samples from diverse environments in many parts of the world. To assess the environmental risks associated with them, data regarding their toxicity, occurrence, and fate are needed, but gathering such data is time-consuming and expensive. An efficient approach to address these difficulties would be to select a small subset of antibiotics with a wide variation in chemical characteristics, perform experimental tests on this subset, and then extrapolate the results to larger numbers of antibiotics, including the most potentially hazardous compounds. To assess the potential utility of such an approach, a set of 92 antibiotics for human use was studied and their structural properties were described with 24 chemical descriptors that included information on their steric, lipophilic, and electronic properties. Principal component analysis in combination with statistical experimental design was used to map the chemical diversity of the antibiotics and to select a small subset, a "training set", of 20 antibiotics. The chemical representativity of the training set was assessed in a quantitative structure-activity model established to predict ultimate biodegradation. The selected antibiotics showed to cover the chemical variation of the studied antibiotics and are suggested for use in future testing programs to assess antibiotics' fate and effects in the environment.

  11. Chemical Structural Novelty: On-Targets and Off-Targets

    PubMed Central

    Yera, Emmanuel R.; Cleves, Ann. E.; Jain, Ajay N.

    2011-01-01

    Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3D similarity, or their combination. For prediction of primary targets, the benefit of 3D over 2D was relatively small, but for prediction of off-targets, the added benefit was large. In addition to assessing prediction, the relationship between chemical similarity and pharmacological novelty was studied. Drug pairs that shared high 3D similarity but low 2D similarity (i.e. a novel scaffold) were shown to be much more likely to exhibit pharmacologically relevant differences in terms of specific protein target modulation. PMID:21916467

  12. Chemical probes for higher-order structure in RNA.

    PubMed Central

    Peattie, D A; Gilbert, W

    1980-01-01

    Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved. Images PMID:6159633

  13. A quantum chemical method for rapid optimization of protein structures.

    PubMed

    Wada, Mitsuhito; Sakurai, Minoru

    2005-01-30

    A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear-scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements.

  14. Structured pedigree information for distributed fusion systems

    NASA Astrophysics Data System (ADS)

    Arambel, Pablo O.

    2008-04-01

    One of the most critical challenges in distributed data fusion is the avoidance of information double counting (also called "data incest" or "rumor propagation"). This occurs when a node in a network incorporates information into an estimate - e.g. the position of an object - and the estimate is injected into the network. Other nodes fuse this estimate with their own estimates, and continue to propagate estimates through the network. When the first node receives a fused estimate from the network, it does not know if it already contains its own contributions or not. Since the correlation between its own estimate and the estimate received from the network is not known, the node can not fuse the estimates in an optimal way. If it assumes that both estimates are independent from each other, it unknowingly double counts the information that has already being used to obtain the two estimates. This leads to overoptimistic error covariance matrices. If the double-counting is not kept under control, it may lead to serious performance degradation. Double counting can be avoided by propagating uniquely tagged raw measurements; however, that forces each node to process all the measurements and precludes the propagation of derived information. Another approach is to fuse the information using the Covariance Intersection (CI) equations, which maintain consistent estimates irrespective of the cross-correlation among estimates. However, CI does not exploit pedigree information of any kind. In this paper we present an approach that propagates multiple covariance matrices, one for each uncorrelated source in the network. This is a way to compress the pedigree information and avoids the need to propagate raw measurements. The approach uses a generalized version of the Split CI to fuse different estimates with appropriate weights to guarantee the consistency of the estimates.

  15. Structural damage and chemical contaminants on reprocessed arthroscopic shaver blades.

    PubMed

    Kobayashi, Masahiko; Nakagawa, Yasuaki; Okamoto, Yukihiro; Nakamura, Shinichiro; Nakamura, Takashi

    2009-02-01

    In response to socioeconomic pressure to cut budgets in medicine, single-use surgical instruments are often reprocessed despite potential biological hazard. To evaluate the quality and contaminants of reprocessed shaver blades. Reprocessed shaver blades have mechanical damage and chemical contamination. Controlled laboratory study. Seven blades and 3 abraders were reprocessed 1 time or 3 times and then were assessed. In the first part of the study, structural damage on the blades after 3 reprocessings was compared to that after 1 reprocessing using optical microscopy. In the second part, surface damage was observed using optical microscopy and scanning electron microscopy; elemental and chemical analyses of contaminants found by the microscopy were performed using scanning electron microscopy/energy dispersive x-ray spectroscopy, scanning Auger microscopy, and Fourier transform infrared spectroscopy. Optical microscopic examination revealed abrasion on the surface of the inner blade and cracks on the inner tube after 1 reprocessing. These changes were more evident after 3 reprocessings. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the blade reprocessed once showed contaminants containing calcium, carbon, oxygen, and silicon, and Fourier transform infrared spectroscopy demonstrated biological protein consisting mainly of collagen, some type of salts, and polycarbonate used in plastic molding. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the reprocessed abrader revealed contaminants containing carbon, calcium, phosphorous, and oxygen, and Fourier transform infrared spectroscopy showed H2O, hydroxyapatite, and hydroxyl proteins. Scanning Auger microscopy showed that the tin-nickel plating on the moving blade and abrader was missing in some locations. This is the first study to evaluate both mechanical damage and chemical contaminants containing collagen, hydroxyapatite, and salts

  16. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels.

    PubMed

    Kim, Eunkyoung; Liu, Yi; Ben-Yoav, Hadar; Winkler, Thomas E; Yan, Kun; Shi, Xiaowen; Shen, Jana; Kelly, Deanna L; Ghodssi, Reza; Bentley, William E; Payne, Gregory F

    2016-10-01

    The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.

  17. Designing ionic liquids: the chemical structure role in the toxicity.

    PubMed

    Ventura, Sónia P M; Gonçalves, Ana M M; Sintra, Tânia; Pereira, Joana L; Gonçalves, Fernando; Coutinho, João A P

    2013-01-01

    Ionic liquids (ILs) are a novel class of solvents with interesting physicochemical properties. Many different applications have been reported for ILs as alternatives to organic solvents in chemical and bioprocesses. Despite the argued advantage of having low vapor pressure, even the most hydrophobic ILs show some degree of solubility in water, allowing their dispersion into aquatic systems and raising concerns on its pollutant potential. Moreover, nowadays most widespread notion concerning the ILs toxicity is that there is a direct relationship with their hydrophobicity/lipophilicity. This work aims at enlarging the currently limited knowledge on ILs toxicity by addressing negative impacts in aquatic ecosystems and investigating the possibility of designing hydrophobic ILs of low ecotoxicity, by the manipulation of their chemical structures. The impact of aromaticity on the toxicity of different cations (pyridinium, piperidinium, pyrrolidinium and imidazolium) and hydrophobic anions (bis(trifluoromethylsulfonyl)imide [NTf(2)] and hexafluorophosphate [PF(6)]) was analysed. Concomitantly, several imidazolium-based ILs of the type [C( n )C( m )C( j )im][NTf(2)] were also studied to evaluate the effects of the position of the alkyl chain on the ILs' toxicity. For that purpose, standard assays were performed using organisms of different trophic levels, Vibrio fischeri, Pseudokirchneriella subcapitata and Daphnia magna, allowing to evaluate the consistency of the structure-activity relationships across different biological targets. The results here reported suggest the possibility of designing ILs with an enhanced hydrophobic character and lower toxicity, by elimination of their aromatic nature.

  18. The chemical structure of the Hawaiian mantle plume.

    PubMed

    Ren, Zhong-Yuan; Ingle, Stephanie; Takahashi, Eiichi; Hirano, Naoto; Hirata, Takafumi

    2005-08-11

    The Hawaiian-Emperor volcanic island and seamount chain is usually attributed to a hot mantle plume, located beneath the Pacific lithosphere, that delivers material sourced from deep in the mantle to the surface. The shield volcanoes of the Hawaiian islands are distributed in two curvilinear, parallel trends (termed 'Kea' and 'Loa'), whose rocks are characterized by general geochemical differences. This has led to the proposition that Hawaiian volcanoes sample compositionally distinct, concentrically zoned, regions of the underlying mantle plume. Melt inclusions, or samples of local magma 'frozen' in olivine phenocrysts during crystallization, may record complexities of mantle sources, thereby providing better insight into the chemical structure of plumes. Here we report the discovery of both Kea- and Loa-like major and trace element compositions in olivine-hosted melt inclusions in individual, shield-stage Hawaiian volcanoes--even within single rock samples. We infer from these data that one mantle source component may dominate a single lava flow, but that the two mantle source components are consistently represented to some extent in all lavas, regardless of the specific geographic location of the volcano. We therefore suggest that the Hawaiian mantle plume is unlikely to be compositionally concentrically zoned. Instead, the observed chemical variation is probably controlled by the thermal structure of the plume.

  19. DSSTox and Chemical Information Technologies in Support of PredictiveToxicology

    EPA Science Inventory

    The EPA NCCT Distributed Structure-Searchable Toxicity (DSSTox) Database project initially focused on the curation and publication of high-quality, standardized, chemical structure-annotated toxicity databases for use in structure-activity relationship (SAR) modeling. In recent y...

  20. DSSTox and Chemical Information Technologies in Support of PredictiveToxicology

    EPA Science Inventory

    The EPA NCCT Distributed Structure-Searchable Toxicity (DSSTox) Database project initially focused on the curation and publication of high-quality, standardized, chemical structure-annotated toxicity databases for use in structure-activity relationship (SAR) modeling. In recent y...

  1. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    PubMed

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Observability and Information Structure of Nonlinear Systems,

    DTIC Science & Technology

    1985-10-01

    defined by Shannon and used as a measure of mut.:al infor-mation between event x. and y4. If p(x.l IY.) I I(x., y.) xil -in (1/p(x.)) =- JInp (x.) (2...entropy H(x,y) in a similar way as H(x,y) = - fx,yp(xiy)lnp(x,y)cdlY, = -E[ JInp (x,y)]. (3-13) With the above definitions, mutual information between x...Observabiity of Nonlinear Systems, Eng. Cybernetics, Volume 1, pp 338-345, 1972. 18. Sen , P., Chidambara, M.R., Observability of a Class of Nonli-.ear

  3. Informational biopolymer structure in early living forms.

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Mclaughlin, P. J.; Barker, W. C.; Hunt, L. T.

    1972-01-01

    Some studies devoted to the search in various organisms for 'relics' of the biochemical nature of ancient organisms, preserved by the conservative nature of the evolutionary process in all living species, are reviewed. Investigations of five families of informational molecules constituting such 'relics' in very diverse organisms are reported. They include: cytochrome c, ferredoxin, trypsin, transfer ribonucleic acid (RNA), and 5S ribosomal RNA. It is shown that, even from these few informational molecules, some interesting inferences about early living organisms can be drawn.

  4. Infochemistry and infofuses for the chemical storage and transmission of coded information.

    PubMed

    Thomas, Samuel W; Chiechi, Ryan C; LaFratta, Christopher N; Webb, Michael R; Lee, Andrew; Wiley, Benjamin J; Zakin, Mitchell R; Walt, David R; Whitesides, George M

    2009-06-09

    This article describes a self-powered system that uses chemical reactions--the thermal excitation of alkali metals--to transmit coded alphanumeric information. The transmitter (an "infofuse") is a strip of the flammable polymer nitrocellulose patterned with alkali metal ions; this pattern encodes the information. The wavelengths of 2 consecutive pulses of light represent each alphanumeric character. While burning, infofuses transmit a sequence of pulses (at 5-20 Hz) of atomic emission that correspond to the sequence of metallic salts (and therefore to the encoded information). This system combines information technology and chemical reactions into a new area--"infochemistry"--that is the first step toward systems that combine sensing and transduction of chemical signals with multicolor transmission of alphanumeric information.

  5. A bibliometric study on chemical information and computer sciences focusing on literature of JCICS.

    PubMed

    Onodera, N

    2001-01-01

    A bibliometric approach was used to survey the state-of-the-art of research in the field of chemical information and computer sciences (CICS). By examining the CA database for the articles abstracted under the subsection "Chemical information, documentation, and data processing", Journal of Chemical Information and Computer Sciences (JCICS) was identified to have been the top journal in this subsection for the last 30 years. Based on this result, CA subsections and controlled index terms given to JCICS articles were analyzed to see trends in subjects and topics in the CICS field during the last two decades. These analyses revealed that the subjects of research in CICS have diversified from traditional information science and computer applications to chemistry to "molecular information sciences". The SCISEARCH database was used to grasp interdependency between JCICS and other key journals and also the international nature of JCICS in its publications and citedness.

  6. Infochemistry and infofuses for the chemical storage and transmission of coded information

    PubMed Central

    Thomas, Samuel W.; Chiechi, Ryan C.; LaFratta, Christopher N.; Webb, Michael R.; Lee, Andrew; Wiley, Benjamin J.; Zakin, Mitchell R.; Walt, David R.; Whitesides, George M.

    2009-01-01

    This article describes a self-powered system that uses chemical reactions—the thermal excitation of alkali metals—to transmit coded alphanumeric information. The transmitter (an “infofuse”) is a strip of the flammable polymer nitrocellulose patterned with alkali metal ions; this pattern encodes the information. The wavelengths of 2 consecutive pulses of light represent each alphanumeric character. While burning, infofuses transmit a sequence of pulses (at 5–20 Hz) of atomic emission that correspond to the sequence of metallic salts (and therefore to the encoded information). This system combines information technology and chemical reactions into a new area—“infochemistry”—that is the first step toward systems that combine sensing and transduction of chemical signals with multicolor transmission of alphanumeric information. PMID:19470465

  7. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  8. Nature of the binding interaction for 50 structurally diverse chemicals with rat estrogen receptors.

    PubMed

    Laws, Susan C; Yavanhxay, S; Cooper, Ralph L; Eldridge, J Charles

    2006-11-01

    This study was conducted to characterize the estrogen receptor (ER)-binding affinities of 50 chemicals selected from among the high production volume chemicals under the U.S. EPA's (U.S. Environmental Protection Agency's) Toxic Substances Control Act inventory. The chemicals were evaluated using the rat uterine cytosolic (RUC) ER-competitive binding assay, with secondary analysis using Lineweaver-Burk plots and slope replots to confirm true competitive inhibition and to determine an experimental K(i). Data from these ER-competitive binding assays represent the types of competitive binding curves that can be obtained when screening chemicals with broad structural diversity. True competitive inhibition was observed in 17 of 50 chemicals. Binding affinities were much lower than that of estradiol (E(2)) with K(i) concentrations ranging from 0.6 to 373 microM as compared with that of E(2) (0.77 nM). Other chemicals that appeared to displace radiolabeled E(2) binding to ER were, in fact, found not to be competitive inhibitors in the secondary K(i) experiments. These seven chemicals likely altered the stability of the assay by changing the buffer pH, denaturing ER, or disrupting the ER-binding kinetics. Thus, several conditions that may confound interpretation of RUC ER-binding assay data are illustrated. For another group of eight chemicals, neither an IC(50) nor K(i) could be determined due to solubility constraints. These chemicals exhibited slight (20-40%) inhibition at concentrations of 10-100 microM, suggesting that they could be competitors at very high concentrations, yet K(i) experiments were not possible as the limit of chemical solubility in the aqueous assay buffer was well above the IC(50). An additional 18 of the 50 chemicals were classified as nonbinders because in concentrations up to 100 microM they produced essentially no displacement of radiolabeled E(2). These results show that although the ER-competitive binding assay is a valuable tool for screening

  9. Structured Requirements Determination for Information Resources Management

    DTIC Science & Technology

    1988-12-01

    50 The User’s Manual .............................................................. 51 V . Conclusions and Recommendations...8 v L.st of Fieres Figure Page 1. The Organizational Information System...externalize concepts and propositions, and to negotiate meanings between users and designers (Novak & Gowin , 1984:20). An example concept map is shown in

  10. THz-Raman: accessing molecular structure with Raman spectroscopy for enhanced chemical identification, analysis, and monitoring

    NASA Astrophysics Data System (ADS)

    Heyler, Randy A.; Carriere, James T. A.; Havermeyer, Frank

    2013-05-01

    Structural analysis via spectroscopic measurement of rotational and vibrational modes is of increasing interest for many applications, since these spectra can reveal unique and important structural and behavioral information about a wide range of materials. However these modes correspond to very low frequency (~5cm-1 - 200cm-1, or 150 GHz-6 THz) emissions, which have been traditionally difficult and/or expensive to access through conventional Raman and Terahertz spectroscopy techniques. We report on a new, inexpensive, and highly efficient approach to gathering ultra-low-frequency Stokes and anti-Stokes Raman spectra (referred to as "THz-Raman") on a broad range of materials, opening potential new applications and analytical tools for chemical and trace detection, identification, and forensics analysis. Results are presented on explosives, pharmaceuticals, and common elements that show strong THz-Raman spectra, leading to clear discrimination of polymorphs, and improved sensitivity and reliability for chemical identification.

  11. Phase structure rewrite systems in information retrieval

    NASA Technical Reports Server (NTRS)

    Klingbiel, P. H.

    1985-01-01

    Operational level automatic indexing requires an efficient means of normalizing natural language phrases. Subject switching requires an efficient means of translating one set of authorized terms to another. A phrase structure rewrite system called a Lexical Dictionary is explained that performs these functions. Background, operational use, other applications and ongoing research are explained.

  12. Phase structure rewrite systems in information retrieval

    NASA Technical Reports Server (NTRS)

    Klingbiel, P. H.

    1985-01-01

    Operational level automatic indexing requires an efficient means of normalizing natural language phrases. Subject switching requires an efficient means of translating one set of authorized terms to another. A phrase structure rewrite system called a Lexical Dictionary is explained that performs these functions. Background, operational use, other applications and ongoing research are explained.

  13. Nuclear spins and moments: Fundamental structural information

    SciTech Connect

    Semmes, P.B.

    1991-01-01

    Predictions for the low energy structure of well deformed odd-A Pm and Sm nuclei in the A {approx} 130 region are given, based on the particle-rotor model. Distinctive magnetic dipole properties (static moments and transition rates) are expected for certain Nilsson configurations, and comparisons to recent data are made for {sup 133}Pm, {sup 135}Sm and {sup 133}Sm.

  14. Nuclear spins and moments: Fundamental structural information

    SciTech Connect

    Semmes, P.B.

    1991-12-31

    Predictions for the low energy structure of well deformed odd-A Pm and Sm nuclei in the A {approx} 130 region are given, based on the particle-rotor model. Distinctive magnetic dipole properties (static moments and transition rates) are expected for certain Nilsson configurations, and comparisons to recent data are made for {sup 133}Pm, {sup 135}Sm and {sup 133}Sm.

  15. Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

    PubMed Central

    Batke, Monika; Gütlein, Martin; Partosch, Falko; Gundert-Remy, Ursula; Helma, Christoph; Kramer, Stefan; Maunz, Andreas; Seeland, Madeleine; Bitsch, Annette

    2016-01-01

    Interest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g., the European Union's Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database, and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural, and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT) approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (< 5). We discuss the limitations of the

  16. 78 FR 17680 - Information Collection Request; Chemical Facility Anti-Terrorism Standards Personnel Surety Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... SECURITY Information Collection Request; Chemical Facility Anti-Terrorism Standards Personnel Surety...-Terrorism Standards (CFATS) Personnel Surety Program pursuant to 6 CFR 27.230(a)(12)(iv). \\1\\ A 60-day... Register notice, the Department submitted an Information Collection Request about the CFATS Personnel...

  17. CHEMICAL STRUCTURES IN COAL: GEOCHEMICAL EVIDENCE FOR THE PRESENCE OF MIXED STRUCTURAL COMPONENTS.

    USGS Publications Warehouse

    Hatcher, P.G.; Breger, I.A.; Maciel, G.E.; Szeverenyi, N.M.

    1983-01-01

    The purpose of this paper is to summarize work on the chemical structural components of coal, comparing them with their possible plant precursors in modern peat. Solid-state **1**3C nuclear magnetic resonance (NMR), infrared spectroscopy (IR), elemental analysis and, in some cases, individual compound analyses formed the bases for these comparisons.

  18. Drug repositioning by applying 'expression profiles' generated by integrating chemical structure similarity and gene semantic similarity.

    PubMed

    Tan, Fujian; Yang, Ruizhi; Xu, Xiaoxue; Chen, Xiujie; Wang, Yunfeng; Ma, Hongzhe; Liu, Xiangqiong; Wu, Xin; Chen, Yuelong; Liu, Lei; Jia, Xiaodong

    2014-05-01

    Drug repositioning, also known as drug repurposing or reprofiling, is the process of finding new indications for established drugs. Because drug repositioning can reduce costs and enhance the efficiency of drug development, it is of paramount importance in medical research. Here, we present a systematic computational method to identify potential novel indications for a given drug. This method utilizes some prior knowledge such as 3D drug chemical structure information, drug-target interactions and gene semantic similarity information. Its prediction is based on another form of 'expression profile', which contains scores ranging from -1 to 1, reflecting the consensus response scores (CRSs) between each drug of 965 and 1560 proteins. The CRS integrates chemical structure similarity and gene semantic similarity information. We define the degree of similarity between two drugs as the absolute value of their correlation coefficients. Finally, we establish a drug similarity network (DSN) and obtain 33 modules of drugs with similar modes of action, determining their common indications. Using these modules, we predict new indications for 143 drugs and identify previously unknown indications for 42 drugs without ATC codes. This method overcomes the instability of gene expression profiling derived from experiments due to experimental conditions, and predicts indications for a new compound feasibly, requiring only the 3D structure of the compound. In addition, the high literature validation rate of 71.8% also suggests that our method has the potential to discover novel drug indications for existing drugs.

  19. BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.

    PubMed

    Hamdalla, Mai A; Mandoiu, Ion I; Hill, Dennis W; Rajasekaran, Sanguthevar; Grant, David F

    2013-03-25

    The structural identification of unknown biochemical compounds in complex biofluids continues to be a major challenge in metabolomics research. Using LC/MS, there are currently two major options for solving this problem: searching small biochemical databases, which often do not contain the unknown of interest or searching large chemical databases which include large numbers of nonbiochemical compounds. Searching larger chemical databases (larger chemical space) increases the odds of identifying an unknown biochemical compound, but only if nonbiochemical structures can be eliminated from consideration. In this paper we present BioSM; a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSM identifies endogenous mammalian biochemical structures with high accuracy. In a leave-one-out cross validation experiment, BioSM correctly predicted 95% of 1388 Kyoto Encyclopedia of Genes and Genomes (KEGG) compounds as endogenous mammalian biochemicals using 1565 scaffolds. Analysis of two additional biological data sets containing 2330 human metabolites (HMDB) and 2416 plant secondary metabolites (KEGG) resulted in biochemical annotations of 89% and 72% of the compounds, respectively. When a data set of 3895 drugs (DrugBank and USAN) was tested, 48% of these structures were predicted to be biochemical. However, when a set of synthetic chemical compounds (Chembridge and Chemsynthesis databases) were examined, only 29% of the 458,207 structures were predicted to be biochemical. Moreover, BioSM predicted that 34% of 883,199 randomly selected compounds from PubChem were biochemical. We then expanded the scaffold list to 3927 biochemical compounds and reevaluated the above data sets to determine whether scaffold number influenced model performance

  20. Digital Learning Characteristics and Principles of Information Resources Knowledge Structuring

    ERIC Educational Resources Information Center

    Belichenko, Margarita; Davidovitch, Nitza; Kravchenko, Yuri

    2017-01-01

    Analysis of principles knowledge representation in information systems led to the necessity of improving the structuring knowledge. It is caused by the development of software component and new possibilities of information technologies. The article combines methodological aspects of structuring knowledge and effective usage of information…

  1. Teaching Text Structure: Examining the Affordances of Children's Informational Texts

    ERIC Educational Resources Information Center

    Jones, Cindy D.; Clark, Sarah K.; Reutzel, D. Ray

    2016-01-01

    This study investigated the affordances of informational texts to serve as model texts for teaching text structure to elementary school children. Content analysis of a random sampling of children's informational texts from top publishers was conducted on text structure organization and on the inclusion of text features as signals of text…

  2. Teaching Text Structure: Examining the Affordances of Children's Informational Texts

    ERIC Educational Resources Information Center

    Jones, Cindy D.; Clark, Sarah K.; Reutzel, D. Ray

    2016-01-01

    This study investigated the affordances of informational texts to serve as model texts for teaching text structure to elementary school children. Content analysis of a random sampling of children's informational texts from top publishers was conducted on text structure organization and on the inclusion of text features as signals of text…

  3. The Interaction of Information Structure and Syntactic Representation in Chinese

    ERIC Educational Resources Information Center

    Hsu, Yu-Yin

    2013-01-01

    This dissertation concerns the interaction of syntax and information structure in Mandarin Chinese and puts the theoretical assumption of parallelism between clauses and noun phrases to the test. It examines and validates the information structural status of the object phrases preposed to clause-internal positions. I argue that Rizzi's (1997)…

  4. Evolution of polymer photovoltaic performances from subtle chemical structure variations.

    PubMed

    Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

    2012-11-21

    Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency.

  5. Quantitative Survey and Structural Classification of Fracking Chemicals Reported in Unconventional Gas Exploitation

    NASA Astrophysics Data System (ADS)

    Elsner, Martin; Schreglmann, Kathrin

    2015-04-01

    Few technologies are being discussed in such controversial terms as hydraulic fracturing ("fracking") in the recovery of unconventional gas. Particular concern regards the chemicals that may return to the surface as a result of hydraulic fracturing. These are either "fracking chemicals" - chemicals that are injected together with the fracking fluid to optimize the fracturing performance or geogenic substances which may turn up during gas production, in the so-called produced water originating from the target formation. Knowledge about them is warranted for several reasons. (1) Monitoring. Air emissions are reported to arise from well drilling, the gas itself or condensate tanks. In addition, potential spills and accidents bear the danger of surface and shallow groundwater contaminations. Monitoring strategies are therefore warranted to screen for "indicator" substances of potential impacts. (2) Chemical Analysis. To meet these analytical demands, target substances must be defined so that adequate sampling approaches and analytical methods can be developed. (3) Transformation in the Subsurface. Identification and classification of fracking chemicals (aromatics vs. alcohols vs. acids, esters, etc.) is further important to assess the possibility of subsurface reactions which may potentially generate new, as yet unidentified transformation products. (4) Wastewater Treatment. For the same reason chemical knowledge is important for optimized wastewater treatment strategies. (5) Human and Ecosystem Health. Knowledge of the most frequent fracking chemicals is further essential for risk assessment (environmental behavior, toxicity) (6) Public Discussions. Finally, an overview of reported fracking chemicals can provide unbiased scientific into current public debates and enable critical reviews of Green Chemistry approaches. Presently, however, such information is not readily available. We aim to close this knowledge gap by providing a quantitative overview of chemical

  6. Chemical structure determines target organ carcinogenesis in rats

    PubMed Central

    Carrasquer, C. A.; Malik, N.; States, G.; Qamar, S.; Cunningham, S.L.; Cunningham, A.R.

    2012-01-01

    SAR models were developed for 12 rat tumour sites using data derived from the Carcinogenic Potency Database. Essentially, the models fall into two categories: Target Site Carcinogen – Non-Carcinogen (TSC-NC) and Target Site Carcinogen – Non-Target Site Carcinogen (TSC-NTSC). The TSC-NC models were composed of active chemicals that were carcinogenic to a specific target site and inactive ones that were whole animal non-carcinogens. On the other hand, the TSC-NTSC models used an inactive category also composed of carcinogens but to any/all other sites but the target site. Leave one out validations produced an overall average concordance value for all 12 models of 0.77 for the TSC-NC models and 0.73 for the TSC-NTSC models. Overall, these findings suggest that while the TSC-NC models are able to distinguish between carcinogens and non-carcinogens, the TSC-NTSC models are identifying structural attributes that associate carcinogens to specific tumour sites. Since the TSC-NTSC models are composed of active and inactive compounds that are genotoxic and non-genotoxic carcinogens, the TSC-NTSC models may be capable of deciphering non-genotoxic mechanisms of carcinogenesis. Together, models of this type may also prove useful in anticancer drug development since they essentially contain chemicals moieties that target specific tumour site. PMID:23066888

  7. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    PubMed Central

    Lee, H. V.; Hamid, S. B. A.; Zain, S. K.

    2014-01-01

    Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

  8. Chemical and structural analyses of titanium plates retrieved from patients.

    PubMed

    Pinto, C M S A; Asprino, L; de Moraes, M

    2015-08-01

    The aim of this study was to evaluate the microscopic structure and chemical composition of titanium bone plates and screws retrieved from patients with a clinical indication and to relate the results to the clinical conditions associated with the removal of these devices. Osteosynthesis plates and screws retrieved from 30 patients between January 2010 and September 2013 were studied by metallographic, gas, and energy dispersive X-ray (EDX) analyses and the medical records of these patients were reviewed. Forty-eight plates and 238 screws were retrieved. The time elapsed between plate and screw insertion and removal ranged between 11 days and 10 years. Metallographic analysis revealed that all the plates were manufactured from commercially pure titanium (CP-Ti). The screw samples analyzed consisted of Ti-6Al-4V alloy, except four samples, which consisted of CP-Ti. Titanium plates studied by EDX analysis presented greater than 99.7% titanium by mass. On gas analysis of Ti-6Al-4V screws, three samples were outside the standard values. One CP-Ti screw sample and one plate sample also presented an oxygen analysis value above the standard. The results indicated that the physical properties and chemical compositions of the plates and screws did not correspond with the need to remove these devices or the time of retention.

  9. Lincosamides: Chemical structure, biosynthesis, mechanism of action, resistance, and applications.

    PubMed

    Spížek, Jaroslav; Řezanka, Tomáš

    2017-06-01

    Lincomycin and its derivatives are antibiotics exhibiting biological activity against bacteria, especially Gram-positive ones, and also protozoans. Lincomycin and its semi-synthetic chlorinated derivative clindamycin are widely used in clinical practice. Both antibiotics are bacteriostatic, inhibiting protein synthesis in sensitive bacteria; however, at higher concentrations, they may be bactericidal. Clindamycin is usually much more active than lincomycin in the treatment of bacterial infections, in particular those caused by anaerobic species; it can also be used for the treatment of important protozoal diseases, e.g. malaria, most effectively in combination with other antibiotic or non-antibiotic antimicrobials (primaquine, fosfidomycin, benzoyl peroxide). Chemical structures of lincosamide antibiotics and the biosynthesis of lincomycin and its genetic control have been summarized and described. Resistance to lincomycin and clindamycin may be caused by methylation of 23S ribosomal RNA, modification of the antibiotics by specific enzymes or active efflux from the bacterial cell. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Tailoring Surface Chemical Properties Using Electronic Structure Theory

    NASA Astrophysics Data System (ADS)

    Norskov, Jens

    2012-02-01

    Electronic structure methods based on density functional theory have reached a level of sophistication where they can be used to describe complete catalytic reactions on transition metal surfaces. This opens the possibility that computational methods can be used to tailor surfaces with desired chemical properties. Recent progress in this direction for transition metal catalysts will be discussed. A series of concepts will be introduced to describe and understand trends in reactivity from one metal surface to the next. It is shown how these concepts can be used to identify the factors determining the catalytic activity of a given transition metal surface, and how this can form the basis for screening of a large number of metals and alloys for catalytic properties.

  11. Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications.

    PubMed

    Li-Beisson, Yonghua; Nakamura, Yuki; Harwood, John

    2016-01-01

    Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism.

  12. Hybrid carrageenans: isolation, chemical structure, and gel properties.

    PubMed

    Hilliou, Loic

    2014-01-01

    Hybrid carrageenan is a special class of carrageenan with niche application in food industry. This polysaccharide is extracted from specific species of seaweeds belonging to the Gigartinales order. This chapter focuses on hybrid carrageenan showing the ability to form gels in water, which is known in the food industry as weak kappa or kappa-2 carrageenan. After introducing the general chemical structure defining hybrid carrageenan, the isolation of the polysaccharide will be discussed focusing on the interplay between seaweed species, extraction parameters, and the hybrid carrageenan chemistry. Then, the rheological experiments used to determine the small and large deformation behavior of gels will be detailed before reviewing the relationships between gel properties and hybrid carrageenan chemistry.

  13. Structural simplification of chemical reaction networks in partial steady states.

    PubMed

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

    PubMed

    Astakhov, Vadim

    2009-01-01

    Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

  15. Community structure detection based on the neighbor node degree information

    NASA Astrophysics Data System (ADS)

    Tang, Li-Ying; Li, Sheng-Nan; Lin, Jian-Hong; Guo, Qiang; Liu, Jian-Guo

    2016-11-01

    Community structure detection is of great significance for better understanding the network topology property. By taking into account the neighbor degree information of the topological network as the link weight, we present an improved Nonnegative Matrix Factorization (NMF) method for detecting community structure. The results for empirical networks show that the largest improved ratio of the Normalized Mutual Information value could reach 63.21%. Meanwhile, for synthetic networks, the highest Normalized Mutual Information value could closely reach 1, which suggests that the improved method with the optimal λ can detect the community structure more accurately. This work is helpful for understanding the interplay between the link weight and the community structure detection.

  16. Automated extraction of information from the literature on chemical-CYP3A4 interactions.

    PubMed

    Feng, Chunlai; Yamashita, Fumiyoshi; Hashida, Mitsuru

    2007-01-01

    A text mining system is presented for automatically extracting information from the literature on chemical-CYP3A4 interactions (i.e., substrate, induction, inhibition). The system identifies chemicals and CYP3A4 forms according to a combination of name dictionaries and context features. In addition, it transforms sentences into multiple simple clauses each containing a single event and extracts information on chemical-CYP3A4 interactions using a simple but effective pattern matching method based on the order of three keywords (chemicals, CYP3A4, key verbs). Using this system, 2990 relations including 2700 identified interactions with CYP3A4 for 600 chemicals were extracted from a corpus of 2900 PubMed abstracts. In an evaluation test using 100 randomly selected abstracts, it achieved 87.4% recall and 92.3% precision for identification of the chemical name and 85.2% recall and 92.0% precision for the extraction of chemical-CYP3A4 interactions, respectively. This system will be applicable to interactions of chemicals with any functional proteins, such as enzymes and transporters, simply by changing the list of key verbs.

  17. Interplay between chemical reactions and transport in structured spaces

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2005-07-01

    The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C1,C2,…,CN and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate λ . Tubes connecting containers allow for the exchange of chemicals with the transport rate D . A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

  18. Thiaminylated adenine nucleotides. Chemical synthesis, structural characterization and natural occurrence.

    PubMed

    Frédérich, Michel; Delvaux, David; Gigliobianco, Tiziana; Gangolf, Marjorie; Dive, Georges; Mazzucchelli, Gabriel; Elias, Benjamin; De Pauw, Edwin; Angenot, Luc; Wins, Pierre; Bettendorff, Lucien

    2009-06-01

    Thiamine and its three phosphorylated derivatives (mono-, di- and triphosphate) occur naturally in most cells. Recently, we reported the presence of a fourth thiamine derivative, adenosine thiamine triphosphate, produced in Escherichia coli in response to carbon starvation. Here, we show that the chemical synthesis of adenosine thiamine triphosphate leads to another new compound, adenosine thiamine diphosphate, as a side product. The structure of both compounds was confirmed by MS analysis and 1H-, 13C- and 31P-NMR, and some of their chemical properties were determined. Our results show an upfield shifting of the C-2 proton of the thiazolium ring in adenosine thiamine derivatives compared with conventional thiamine phosphate derivatives. This modification of the electronic environment of the C-2 proton might be explained by a through-space interaction with the adenosine moiety, suggesting U-shaped folding of adenosine thiamine derivatives. Such a structure in which the C-2 proton is embedded in a closed conformation can be located using molecular modeling as an energy minimum. In E. coli, adenosine thiamine triphosphate may account for 15% of the total thiamine under energy stress. It is less abundant in eukaryotic organisms, but is consistently found in mammalian tissues and some cell lines. Using HPLC, we show for the first time that adenosine thiamine diphosphate may also occur in small amounts in E. coli and in vertebrate liver. The discovery of two natural thiamine adenine compounds further highlights the complexity and diversity of thiamine biochemistry, which is not restricted to the cofactor role of thiamine diphosphate.

  19. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem.

    PubMed

    Kim, Sunghwan; Thiessen, Paul A; Bolton, Evan E; Bryant, Stephen H

    2015-07-01

    PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)-a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system.

  20. Axiomatic Evaluation Method and Content Structure for Information Appliances

    ERIC Educational Resources Information Center

    Guo, Yinni

    2010-01-01

    Extensive studies have been conducted to determine how best to present information in order to enhance usability, but not what information is needed to be presented for effective decision making. Hence, this dissertation addresses the factor structure of the nature of information needed for presentation and proposes a more effective method than…

  1. Information Architecture and the Comic Arts: Knowledge Structure and Access

    ERIC Educational Resources Information Center

    Farmer, Lesley S. J.

    2015-01-01

    This article explains information architecture, focusing on comic arts' features for representing and structuring knowledge. Then it details information design theory and information behaviors relative to this format, also noting visual literacy. Next , applications of comic arts in education are listed. With this background, several research…

  2. Axiomatic Evaluation Method and Content Structure for Information Appliances

    ERIC Educational Resources Information Center

    Guo, Yinni

    2010-01-01

    Extensive studies have been conducted to determine how best to present information in order to enhance usability, but not what information is needed to be presented for effective decision making. Hence, this dissertation addresses the factor structure of the nature of information needed for presentation and proposes a more effective method than…

  3. THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

    EPA Science Inventory

    Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

  4. THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

    EPA Science Inventory

    Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

  5. Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules.

    PubMed

    Wassermann, Anne Mai; Lounkine, Eugen; Glick, Meir

    2013-03-25

    Virtual screening using bioactivity profiles has become an integral part of currently applied hit finding methods in pharmaceutical industry. However, a significant drawback of this approach is that it is only applicable to compounds that have been biologically tested in the past and have sufficient activity annotations for meaningful profile comparisons. Although bioactivity data generated in pharmaceutical institutions are growing on an unprecedented scale, the number of biologically annotated compounds still covers only a minuscule fraction of chemical space. For a newly synthesized compound or an isolated natural product to be biologically characterized across multiple assays, it may take a considerable amount of time. Consequently, this chemical matter will not be included in virtual screening campaigns based on bioactivity profiles. To overcome this problem, we herein introduce bioturbo similarity searching that uses chemical similarity to map molecules without biological annotations into bioactivity space and then searches for biologically similar compounds in this reference system. In benchmark calculations on primary screening data, we demonstrate that our approach generally achieves higher hit rates and identifies structurally more diverse compounds than approaches using chemical information only. Furthermore, our method is able to discover hits with novel modes of inhibition that traditional 2D and 3D similarity approaches are unlikely to discover. Test calculations on a set of natural products reveal the practical utility of the approach for identifying novel and synthetically more accessible chemical matter.

  6. Structural and Optical Study of Chemical Bath Deposited Nano-Structured CdS Thin Films

    NASA Astrophysics Data System (ADS)

    Kumar, Suresh; Sharma, Dheeraj; Sharma, Pankaj; Sharma, Vineet; Barman, P. B.; Katyal, S. C.

    2011-12-01

    CdS is commonly used as window layer in polycrystalline solar cells. The paper presents a structural and optical study of CdS nano-structured thin films. High quality CdS thin films are grown on commercial glass by means of chemical bath deposition. It involves an alkaline solution of cadmium salt, a complexant, a chalcogen source and a non-ionic surfactant. The films have been prepared under various process parameters. The chemically deposited films are annealed to estimate its effect on the structural and optical properties of films. These films (as -deposited and annealed) have been characterized by means of XRD, SEM and UV-Visible spectrophotometer. XRD of films show the nano-crystalline nature. The energy gap of films is found to be of direct in nature.

  7. Extracting Structural information from Galaxy Images

    NASA Astrophysics Data System (ADS)

    Hayes, Wayne B.; Davis, D.

    2010-05-01

    The amount of data from sky images is large and growing. About 1 million galaxies can be discerned in the Sloan Digital Sky Survey (SDSS). The Large Synoptic Survey Telescope (LSST) is being built and will scan the entire sky repeatedly, providing images of millions of galaxies and petabytes of data every night. The Joint Dark Energy Mission (JDEM) is a proposed orbiting satellite that will repeatedly map the entire sky from orbit, providing images of perhaps billions of galaxies. Unfortunately, given an image of a spiral galaxy, there does not exist an automated vision algorithm that can even tell us which direction the spiral arms wind, much less count them or provide any other quantitative information about them. To wit, the largest galaxy classification project is the Galaxy Zoo, in which thousands of human volunteers classify images by eye over the web. Although valuable, such human classifications will provide only limited objective quantitative measurements, and will soon be overwhelmed with more data than humans can handle. However, such information would prove an invaluable source for astronomers and cosmologists to test current theories of galaxy formation and cosmic evolution (which can now be simulated with high accuracy on large computers, producing copious predictions that cannot be tested due to a lack of objective, quantitative observational data). In this talk, I will report on preliminary results from dynamical grammars and other machine learning and vision techniques to "parse" images of galaxies, starting us on the road towards producing quantitative data that will be useful for astronomers to test theories.

  8. Designing allosteric control into enzymes by chemical rescue of structure.

    PubMed

    Deckert, Katelyn; Budiardjo, S Jimmy; Brunner, Luke C; Lovell, Scott; Karanicolas, John

    2012-06-20

    Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a β-glycosidase enzyme (β-gly) and W492G in a β-glucuronidase enzyme (β-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of β-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of β-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate β-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

  9. Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

    SciTech Connect

    Deckert, Katelyn; Budiardjo, S. Jimmy; Brunner, Luke C.; Lovell, Scott; Karanicolas, John

    2012-08-07

    Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a {beta}-glycosidase enzyme ({beta}-gly) and W492G in a {beta}-glucuronidase enzyme ({beta}-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of {beta}-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of {beta}-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate {beta}-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

  10. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    EPA Science Inventory

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  11. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    EPA Science Inventory

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  12. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    PubMed

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments.

  13. Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts

    PubMed Central

    Kumar, Arun. V.; Ali, Rehana F.M.; Cao, Yu; Krishnan, V.V.

    2015-01-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue’s averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80 % accuracy measured by Matthew Correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with > 90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094

  14. Chemical Structures at the Desktop: Integrating Drawing Tools with On-Line Registry Files.

    ERIC Educational Resources Information Center

    Baumgras, Jan L.; Rogers, Anne E.

    1995-01-01

    Examines and reviews the ability of various software packages and database systems to recognize and process chemical structures generated by chemical drawing packages, especially the ability of relational database management systems to recognize and process chemical structures from a variety of sources. The need for better standard representations…

  15. Limitations of Structural Superlubricity: Chemical Bonds versus Contact Size.

    PubMed

    Dietzel, Dirk; Brndiar, Ján; Štich, Ivan; Schirmeisen, André

    2017-08-22

    Structural superlubricity describes the state of virtually frictionless sliding if two atomically flat interfaces are incommensurate, that is, they share no common periodicity. Despite the exciting prospects of this low friction phenomenon, there are physical limitations to the existence of this state. Theory predicts that the contact size is one fundamental limit, where the critical size threshold mainly depends on the interplay between lateral contact compliance and interface interaction energies. Here we provide experimental evidence for this size threshold by measuring the sliding friction force of differently sized antimony particles on MoS2. We find that superlubric sliding with the characteristic linear decrease of shear stress with contact size prevails for small particles with contact areas below 15 000 nm(2). Larger particles, however, show a transition toward constant shear stress behavior. In contrast, Sb particles on graphite show superlubricity over the whole size range. Ab initio simulations reveal that the chemical interaction energies for Sb/MoS2 are much stronger than for Sb/HOPG and can therefore explain the different friction properties as well as the critical size thresholds. These limitations must be considered when designing low friction contacts based on structural superlubricity concepts.

  16. Information structuring improves recall of emergency discharge information: a randomized clinical trial.

    PubMed

    Ackermann, Selina; Ghanim, Leyla; Heierle, Anette; Hertwig, Ralph; Langewitz, Wolf; Mata, Rui; Bingisser, Roland

    2017-07-01

    This article examines the extent to which structuring Emergency Department discharge information improves the ability to recall that information, and whether such benefits interact with relevant prior knowledge. Using three samples of students with different levels of prior medical knowledge, we investigated the amount of information recalled after structured vs. non-structured presentation of information. Across all student samples, the structured discharge information led to a relative increase in recalled items of 17% compared to non-structured discharge information (M = 9.70, SD = 4.96 vs. M = 8.31, SD = 4.93). In the sample with least medical knowledge, however, the structured discharge information resulted in a relative increase in recall by 42% (M = 8.12 vs. M = 5.71). These results suggest that structuring discharge information can be a useful tool to improve recall of information and is likely to be most beneficial for patient populations with lower levels of medical knowledge.

  17. Review of the Literature on Determinants of Chemical Hazard Information Recall among Workers and Consumers

    PubMed Central

    Sathar, Farzana; Dalvie, Mohamed Aqiel; Rother, Hanna-Andrea

    2016-01-01

    In many low and middle income countries (LMIC), workers’ and consumers’ only access to risk and hazard information in relation to the chemicals they use or work with is on the chemical label and safety data sheet. Recall of chemical hazard information is vital in order for label warnings and precautionary information to promote effective safety behaviors. A literature review, therefore, was conducted on determinants of chemical hazard information recall among workers and consumers globally. Since comprehension and recall are closely linked, the determinants of both were reviewed. Literature was reviewed from both online and print peer reviewed journals for all study designs and countries. This review indicated that the level of education, previous training and the inclusion of pictograms on the hazard communication material are all factors that contribute to the recall of hazard information. The influence of gender and age on recall is incongruent and remains to be explored. More research is required on the demographic predictors of the recall of hazard information, the effect of design and non-design factors on recall, the effect of training on the recall among low literate populations and the examining of different regions or contexts. PMID:27258291

  18. Review of the Literature on Determinants of Chemical Hazard Information Recall among Workers and Consumers.

    PubMed

    Sathar, Farzana; Dalvie, Mohamed Aqiel; Rother, Hanna-Andrea

    2016-05-31

    In many low and middle income countries (LMIC), workers' and consumers' only access to risk and hazard information in relation to the chemicals they use or work with is on the chemical label and safety data sheet. Recall of chemical hazard information is vital in order for label warnings and precautionary information to promote effective safety behaviors. A literature review, therefore, was conducted on determinants of chemical hazard information recall among workers and consumers globally. Since comprehension and recall are closely linked, the determinants of both were reviewed. Literature was reviewed from both online and print peer reviewed journals for all study designs and countries. This review indicated that the level of education, previous training and the inclusion of pictograms on the hazard communication material are all factors that contribute to the recall of hazard information. The influence of gender and age on recall is incongruent and remains to be explored. More research is required on the demographic predictors of the recall of hazard information, the effect of design and non-design factors on recall, the effect of training on the recall among low literate populations and the examining of different regions or contexts.

  19. Automated extraction of information on chemical-P-glycoprotein interactions from the literature.

    PubMed

    Yoshida, Shuya; Yamashita, Fumiyoshi; Ose, Atsushi; Maeda, Kazuya; Sugiyama, Yuichi; Hashida, Mitsuru

    2013-10-28

    Knowledge of the interactions between drugs and transporters is important for drug discovery and development as well as for the evaluation of their clinical safety. We recently developed a text-mining system for the automatic extraction of information on chemical-CYP3A4 interactions from the literature. This system is based on natural language processing and can extract chemical names and their interaction patterns according to sentence context. The present study aimed to extend this system to the extraction of information regarding chemical-transporter interactions. For this purpose, the key verb list designed for cytochrome P450 enzymes was replaced with that for known drug transporters. The performance of the system was then tested by examining the accuracy of information on chemical-P-glycoprotein (P-gp) interactions extracted from randomly selected PubMed abstracts. The system achieved 89.8% recall and 84.2% precision for the identification of chemical names and 71.7% recall and 78.6% precision for the extraction of chemical-P-gp interactions.

  20. Lessons learned in building a global information network on chemicals (GINC).

    PubMed

    Kaminuma, Tsuguchika

    2005-09-01

    The Global Information Network on Chemicals (GINC) was a project to construct a worldwide information network linking international, national, and other organizations working for the safe management of chemicals. Proposed in 1993, the project started the next year and lasted almost 10 years. It was begun as a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP), and later endorsed by the Intergovernmental Forum on Chemical Safety (IFCS). Asia, particularly East Asia and the Pacific islands, was chosen as the feasibility study region. The author's group then at the National Institute of Health Sciences (NIHS) of Japan led this initiative and hosted numerous meetings. At these meetings, tutorial sessions for communicating chemical safety expertise and emerging new information technologies relevant to the safe management of chemicals were offered. Our experience with this project, particularly the Web-based system and the tutorial sessions, may be of use to others involved with Web-based instruction and the training of chemical safety specialists from both developed and developing countries.

  1. Lessons learned in building a global information network on chemicals (GINC)

    SciTech Connect

    Kaminuma, Tsuguchika . E-mail: kaminuma@cbi.or.jp

    2005-09-01

    The Global Information Network on Chemicals (GINC) was a project to construct a worldwide information network linking international, national, and other organizations working for the safe management of chemicals. Proposed in 1993, the project started the next year and lasted almost 10 years. It was begun as a joint project of World Health Organization (WHO), International Labor Organization (ILO), and United Nations Environment Program (UNEP), and later endorsed by the Intergovernmental Forum on Chemical Safety (IFCS). Asia, particularly East Asia and the Pacific islands, was chosen as the feasibility study region. The author's group then at the National Institute of Health Sciences (NIHS) of Japan led this initiative and hosted numerous meetings. At these meetings, tutorial sessions for communicating chemical safety expertise and emerging new information technologies relevant to the safe management of chemicals were offered. Our experience with this project, particularly the Web-based system and the tutorial sessions, may be of use to others involved with Web-based instruction and the training of chemical safety specialists from both developed and developing countries.

  2. Temporal and statistical information in causal structure learning.

    PubMed

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-03-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical system that operated probabilistically. Participants of all ages preferentially relied on the temporal pattern of events in their inferences, even if this conflicted with statistical information. In Experiments 2 and 3, participants observed a series of interventions on the system, which in these experiments operated deterministically. In Experiment 2, participants found it easier to use temporal pattern information than statistical information provided as a result of interventions. In Experiment 3, in which no temporal pattern information was provided, children from 6- to 7-years-old, but not younger children, were able to use intervention information to make causal chain judgments, although they had difficulty when the structure was a common cause. The findings suggest that participants, and children in particular, may find it more difficult to use statistical information than temporal pattern information because of its demands on information processing resources. However, there may also be an inherent preference for temporal information. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  3. yaInChI: modified InChI string scheme for line notation of chemical structures.

    PubMed

    Cho, Y S; No, K T; Cho, K-H

    2012-01-01

    A modified InChI (International Chemical Identifier) string scheme, yaInChI (yet another InChI), is suggested as a method for including the structural information of a given molecule, making it straightforward and more easily readable. The yaInChI theme is applicable for checking the structural identity with higher sensitivity and generating three-dimensional (3-D) structures from the one-dimensional (1-D) string with less ambiguity than the general InChI method. The modifications to yaInChI provide non-rotatable single bonds, stereochemistry of organometallic compounds, allene and cumulene, and parity of atoms with a lone pair. Additionally, yaInChI better preserves the original information of the given input file (SDF) using the protonation information, hydrogen count +1, and original bond type, which are not considered or restrictively considered in InChI and SMILES. When yaInChI is used to perform a duplication check on a 3D chemical structure database, Ligand.Info, it shows more discriminating power than InChI. The structural information provided by yaInChI is in a compact format, making it a promising solution for handling large chemical structure databases.

  4. Extracting Information about Model Structure from Observations

    NASA Astrophysics Data System (ADS)

    Nearing, Grey; Gupta, Hoshin

    2013-04-01

    We propose an expectation-maximization (EM) approach to adapting the state-transition component of a hidden Markov model. The state-transition simulator is emulated by sparse Gaussian process regression (sgpr; Snelson and Ghahramani 2006), and the expectation step consists of Bayesian smoothing of the emulator state conditional on observations taken according to a known observation function. After smoothing, maximum likelihood sgpr hyperparameters and pseudo-inputs are estimated. Expectation and maximization steps are iterated until convergence of the state estimates. The method results in a posterior emulator of the state-transition model rather than an input-output relationship developed by traditional neural network and regression approaches. This allows for a direct comparison between prior and posterior state-transition response surfaces, which can facilitate subjective and/or objective evaluations of model deficiencies. The method was tested on a simple rainfall-runoff simulator by assimilating daily observations of streamflow using the ensemble Kalman smoother (Evensen and van Leeuwen, 2000). The Nash-Sutcliffe efficiency of predictions made by the emulator for the simulation period containing observations increased monotonically after each maximization step for a total increase of 0.72 to 0.98. Similarly, the efficiency of the trained emulator increased from 0.60 to 0.80 during a validation period not used for training. We calculated the Kullback-Leibler divergence between prior and posterior response surfaces and from this identified missing or incorrect conceptual model components. Major changes to the model structure during EM training included an addition of a process which mimicked drainage, prolonged infiltration after a rainfall event, and a change in the slope of the runoff ratio function which served to increase runoff only during high precipitation events. Snelson, E., & Ghahramani, Z. (Eds.) (2006). Sparse Gaussian Processes using Pseudo

  5. Structure and chemical composition of layers adsorbed at interfaces with champagne.

    PubMed

    Aguié-Béghin, V; Adriaensen, Y; Péron, N; Valade, M; Rouxhet, P; Douillard, R

    2009-11-11

    The structure and the chemical composition of the layer adsorbed at interfaces involving champagne have been investigated using native champagne, as well as ultrafiltrate (UFch) and ultraconcentrate (UCch) obtained by ultrafiltration with a 10(4) nominal molar mass cutoff. The layer adsorbed at the air/liquid interface was examined by surface tension and ellipsometry kinetic measurements. Brewster angle microscopy demonstrated that the layer formed on polystyrene by adsorption or drop evaporation was heterogeneous, with a domain structure presenting similarities with the layer adsorbed at the air/liquid interface. The surface chemical composition of polystyrene with the adlayer was determined by X-ray photoelectron spectroscopy (XPS). The contribution of champagne constituents varied according to the liquid (native, UFch, and UCch) and to the procedure of adlayer formation (evaporation, adsorption, and adsorption + rinsing). However, their chemical composition was not significantly influenced either by ultrafiltration or by the procedure of deposition on polystyrene. Modeling this composition in terms of classes of model compounds gave approximately 35% (w/w) of proteins and 65% (w/w) of polysaccharides. In the adlayer, the carboxyl groups or esters represent about 18% of carbon due to nonpolypeptidic compounds, indicating the presence of either uronic acids in the complex structure of pectic polysaccharides or of polyphenolic esters. This structural and chemical information and its relationship with the experimental procedures indicate that proteins alone cannot be used as a realistic model for the macromolecules forming the adsorption layer of champagne. Polysaccharides, the other major macromolecular components of champagne wine, are assembled with proteins at the interfaces, in agreement with the heterogeneous character of the adsorbed layer at interfaces.

  6. SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES.

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  7. A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  8. A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  9. SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES.

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  10. Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

    PubMed

    Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

    2015-12-01

    First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

  11. Perspective: On the relevance of slower-than-femtosecond time scales in chemical structural-dynamics studies.

    PubMed

    Coppens, Philip

    2015-03-01

    A number of examples illustrate structural-dynamics studies of picosecond and slower photo-induced processes. They include molecular rearrangements and excitations. The information that can be obtained from such studies is discussed. The results are complementary to the information obtained from femtosecond studies. The point is made that all pertinent time scales should be covered to obtain comprehensive insight in dynamic processes of chemical and biological importance.

  12. DNA codes and information: formal structures and relational causes.

    PubMed

    Sternberg, Richard V

    2008-09-01

    Recently the terms "codes" and "information" as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are higher-order informational structures that obviate any "DNA-centric" reductionism. In addition to the implications that are discussed, this approach validates the array of coding systems now recognized in molecular biology.

  13. Information and telecommunication system for monitoring of hydraulic engineering structures

    NASA Astrophysics Data System (ADS)

    Pavlycheva, Nadezhda K.; Akhmetgaleeva, Railia R.; Muslimov, Eduard R.; Murav'eva, Elena V.; Peplov, Artem A.; Sibgatulina, Dina S.

    2016-03-01

    In this article, we present the information and telecommunications system that allows to carry out real-time monitoring of the quality and quantity of hydraulic engineering structures in order to reduce the risk of emergencies caused by environmental damage.

  14. Plasmonic photoluminescence for recovering native chemical information from surface-enhanced Raman scattering

    PubMed Central

    Lin, Kai-Qiang; Yi, Jun; Zhong, Jin-Hui; Hu, Shu; Liu, Bi-Ju; Liu, Jun-Yang; Zong, Cheng; Lei, Zhi-Chao; Wang, Xiang; Aizpurua, Javier; Esteban, Rubén; Ren, Bin

    2017-01-01

    Surface-enhanced Raman scattering (SERS) spectroscopy has attracted tremendous interests as a highly sensitive label-free tool. The local field produced by the excitation of localized surface plasmon resonances (LSPRs) dominates the overall enhancement of SERS. Such an electromagnetic enhancement is unfortunately accompanied by a strong modification in the relative intensity of the original Raman spectra, which highly distorts spectral features providing chemical information. Here we propose a robust method to retrieve the fingerprint of intrinsic chemical information from the SERS spectra. The method is established based on the finding that the SERS background originates from the LSPR-modulated photoluminescence, which contains the local field information shared also by SERS. We validate this concept of retrieval of intrinsic fingerprint information in well controlled single metallic nanoantennas of varying aspect ratios. We further demonstrate its unambiguity and generality in more complicated systems of tip-enhanced Raman spectroscopy (TERS) and SERS of silver nanoaggregates. PMID:28348368

  15. Toxicological information on chemicals published in the Russian language: Contribution to REACH and 3Rs.

    PubMed

    Sihtmäe, Mariliis; Dubourguier, Henri-Charles; Kahru, Anne

    2009-07-28

    This review is reporting on the current situation of publicly available toxicological and ecotoxicological information on chemicals published in Russian language in various libraries, databases as well as in the Internet. This information can be beneficial for the new EU chemical policy REACH and for the development of intelligent testing strategies (involving also QSAR and QAAR) that enable a significant increase in the use of non-testing information for regulatory decision making, thus minimizing the need for animal testing according to the 3R's strategy. Currently, the access to this information is limited due to the language barrier and low level of digitalization of respective journals and books. Fortunately, on-line translation services are overcoming language barriers already now.

  16. Nepheline structural and chemical dependence on melt composition

    SciTech Connect

    Marcial, José; Crum, Jarrod; Neill, Owen; McCloy, John

    2016-02-01

    Nepheline crystallizes upon slow-cooling in some melts concentrated in Na2O and Al2O3, which can result in a residual glass phase of low chemical durability. Nepheline can incorporate many components often found in high-level waste radioactive borosilicate glass, including glass network ions (e.g., Si, Al, Fe), alkali metals (e.g., Cs, K, Na, and possibly Li), alkaline-earth metals (e.g., Ba, Sr, Ca, Mg), and transition metals (e.g., Mn, and possibly Cr, Zn, Ni). When crystallized from melts of different compositions, nepheline chemistry varies as a function of starting glass composition. Five simulated high level nuclear waste borosilicate glasses shown to crystallize large fractions of nepheline on slow cooling, were selected for study. These melts constituted a range of Al2O3, B2O3, CaO, Na2O, K2O, Fe2O3, and SiO2 compositions. Compositional analyses of nepheline crystals in glass by electron probe micro-analysis (EPMA) indicate that boron is unlikely to be present in any significant concentration, if at all, in nepheline. Also, several models are presented for calculating the fraction of vacancies in the nepheline structure.

  17. Structural a priori information in near-infrared optical tomography

    NASA Astrophysics Data System (ADS)

    Dehghani, Hamid; Carpenter, Colin M.; Yalavarthy, Phaneendra K.; Pogue, Brian W.; Culver, Joseph P.

    2007-02-01

    Recent interest in the use of dual modality imaging in the field of optical Near Infrared (NIR) Tomography has increased, specifically with use of structural information, from for example, MRI. Although MRI images provide high resolution structural information about tissue, they lack the contrast and functional information needed to investigate physiology, whereas NIR data has been established as a high contrast imaging modality, but one which suffers from low resolution. To this effect, the use of dual modality data has been shown to increase the qualitative and quantitative accuracy of clinical information that can be obtained from tissue. Results so far have indicated that providing accurate apriori structural information is available, such dual modality imaging techniques can be used for the detection and characterization of breast cancer in-vivo, as well as the investigation of brain function and physiology in both human and small animal studies. Although there has been much interest and research into the best suitable and robust use of a-priori structural information within the reconstruction of optical properties of tissue, little work has been done into the investigation of how much accuracy is needed from the structural MRI images in order to obtain the most clinically reliable information. In this paper, we will present and demonstrate the two most common application of a-priori information into image reconstruction, namely soft and hard priori. The effect of inaccuracies of the a-priori structural information within the reconstructed NIR images are presented showing that providing that the error of the a-priori information is within 20% in terms of size and location, adequate NIR images can be reconstructed.

  18. Chemical and Materials Information Management to Achieve Sustainable Engineering and Design for the 21st Century

    DTIC Science & Technology

    2011-11-01

    Approved for Public Release ; Distribution Unlimited Chemical and Materials Information Management to Achieve Sustainable Engineering and Design for...Data Sources Solution – Distributed Information System Logistics Sustainability Approved for Public Release ; Distribution Unlimited • Single point...currently valid OMB control number. 1. REPORT DATE NOV 2011 2. REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4. TITLE AND SUBTITLE

  19. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files

    ERIC Educational Resources Information Center

    Adamson, George W.; And Others

    1973-01-01

    A major problem in the design of screening systems for substructure searches of chemical structure files is the development of a methodology for selection of an optimal set of structural characteristics to act as screens. Distributions of several structural characteristics of the Chemical Abstracts Service Registry System are summarized. (13…

  20. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files

    ERIC Educational Resources Information Center

    Adamson, George W.; And Others

    1973-01-01

    A major problem in the design of screening systems for substructure searches of chemical structure files is the development of a methodology for selection of an optimal set of structural characteristics to act as screens. Distributions of several structural characteristics of the Chemical Abstracts Service Registry System are summarized. (13…

  1. Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

    PubMed

    Otero, Toribio F

    2017-01-18

    In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (Ea), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. Ea, k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

  2. How much information do extinction and backscattering measurements contain about the chemical composition of atmospheric aerosol?

    NASA Astrophysics Data System (ADS)

    Kahnert, Michael; Andersson, Emma

    2017-03-01

    We theoretically and numerically investigate the problem of assimilating multiwavelength lidar observations of extinction and backscattering coefficients of aerosols into a chemical transport model. More specifically, we consider the inverse problem of determining the chemical composition of aerosols from these observations. The main questions are how much information the observations contain to determine the particles' chemical composition, and how one can optimize a chemical data assimilation system to make maximum use of the available information. We first quantify the information content of the measurements by computing the singular values of the scaled observation operator. From the singular values we can compute the number of signal degrees of freedom, Ns, and the reduction in Shannon entropy, H. As expected, the information content as expressed by either Ns or H grows as one increases the number of observational parameters and/or wavelengths. However, the information content is strongly sensitive to the observation error. The larger the observation error variance, the lower the growth rate of Ns or H with increasing number of observations. The right singular vectors of the scaled observation operator can be employed to transform the model variables into a new basis in which the components of the state vector can be partitioned into signal-related and noise-related components. We incorporate these results in a chemical data assimilation algorithm by introducing weak constraints that restrict the assimilation algorithm to acting on the signal-related model variables only. This ensures that the information contained in the measurements is fully exploited, but not overused. Numerical tests show that the constrained data assimilation algorithm provides a solution to the inverse problem that is considerably less noisy than the corresponding unconstrained algorithm. This suggests that the restriction of the algorithm to the signal-related model variables suppresses

  3. CMB topography and electrical conductivity as additional constraints for the lowermost mantle thermo-chemical structure

    NASA Astrophysics Data System (ADS)

    Deschamps, F.; Yin, Y.; Tackley, P. J.

    2013-12-01

    A variety of seismic observations, including tomographic models, indicate that the lowermost mantle is strongly heterogeneous. Seismic observations further support a thermo-chemical origin for the large scale heterogeneities. In particular, the large low-shear wave velocity provinces (LLSVP) observed by global tomographic images are better explained by a combination of thermal and chemical anomalies. Despite the accuracy of seismic information, uncertainties and trade-off still prevent the determination of a detailed lower mantle thermo-chemical structure. For instance, the nature of chemical heterogeneities and the exact role played by the post-perovskite phase transition are still debated. Additional constraints are needed to discriminate between the possible models of structure and dynamics of the lower mantle. Here, we consider two potential additional constraints, the electrical conductivity and the dynamic topography at the core-mantle boundary (CMB). Unlike density and seismic velocities, electrical conductivity increases with temperature. In addition, it strongly varies with the iron and silicate content. Using appropriate mineral physics data, we calculated a 3D distribution of electrical conductivity in lower mantle from the thermo-chemical structure inferred by probabilistic tomography, which maps iron and silicate excess in the LLSVP. In the lowermost mantle, we observe a belt of high conductivity, with maximum values around 20 S/m located in the LLSVP. Such a belt may trigger electric currents in the lowermost mantle and induce magnetic field variations with period of one year or more. It may thus be seen by global models of electrical conductivity. Unfortunately, such models do not sample yet regions deeper than 2000 km. A second, independent constraint we explored is the dynamic topography at the CMB. We used stagYY to calculate the dynamic topography associated with several models of thermo-chemical convection, and observe strong differences

  4. Information on Quantifiers and Argument Structure in English Learner's Dictionaries.

    ERIC Educational Resources Information Center

    Lee, Thomas Hun-tak

    1993-01-01

    Lexicographers have been arguing for the inclusion of abstract and complex grammatical information in dictionaries. This paper examines the extent to which information about quantifiers and the argument structure of verbs is encoded in English learner's dictionaries. The Oxford Advanced Learner's Dictionary (1989), the Longman Dictionary of…

  5. Structured Information Management Using New Techniques for Processing Text.

    ERIC Educational Resources Information Center

    Gibb, Forbes; Smart, Godfrey

    1990-01-01

    Describes the development of a software system, SIMPR (Structured Information Management: Processing and Retrieval), that will process documents by indexing them and classifying their subjects. Topics discussed include information storage and retrieval, file inversion techniques, modelling the user, natural language searching, automatic indexing,…

  6. Structured Information Management Using New Techniques for Processing Text.

    ERIC Educational Resources Information Center

    Gibb, Forbes; Smart, Godfrey

    1990-01-01

    Describes the development of a software system, SIMPR (Structured Information Management: Processing and Retrieval), that will process documents by indexing them and classifying their subjects. Topics discussed include information storage and retrieval, file inversion techniques, modelling the user, natural language searching, automatic indexing,…

  7. Capturing business requirements for the Swedish national information structure.

    PubMed

    Kajbjer, Karin; Johansson, Catharina

    2009-01-01

    As a subproject for the National Information Structure project of the National Board of Health and Welfare, four different stakeholder groups were used to capture business requirements. These were: Subjects of care, Health professionals, Managers/Research and Industry. The process is described with formulating goal models, concept, process and information models.

  8. Quantitative structure-activity relationship models of chemical transformations from matched pairs analyses.

    PubMed

    Beck, Jeremy M; Springer, Clayton

    2014-04-28

    The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

  9. Quantitative Survey and Structural Classification of Hydraulic Fracturing Chemicals Reported in Unconventional Gas Production.

    PubMed

    Elsner, Martin; Hoelzer, Kathrin

    2016-04-05

    Much interest is directed at the chemical structure of hydraulic fracturing (HF) additives in unconventional gas exploitation. To bridge the gap between existing alphabetical disclosures by function/CAS number and emerging scientific contributions on fate and toxicity, we review the structural properties which motivate HF applications, and which determine environmental fate and toxicity. Our quantitative overview relied on voluntary U.S. disclosures evaluated from the FracFocus registry by different sources and on a House of Representatives ("Waxman") list. Out of over 1000 reported substances, classification by chemistry yielded succinct subsets able to illustrate the rationale of their use, and physicochemical properties relevant for environmental fate, toxicity and chemical analysis. While many substances were nontoxic, frequent disclosures also included notorious groundwater contaminants like petroleum hydrocarbons (solvents), precursors of endocrine disruptors like nonylphenols (nonemulsifiers), toxic propargyl alcohol (corrosion inhibitor), tetramethylammonium (clay stabilizer), biocides or strong oxidants. Application of highly oxidizing chemicals, together with occasional disclosures of putative delayed acids and complexing agents (i.e., compounds designed to react in the subsurface) suggests that relevant transformation products may be formed. To adequately investigate such reactions, available information is not sufficient, but instead a full disclosure of HF additives is necessary.

  10. Chemicals and Structural Foams to Neutralize or Defeat Anti-Personnel Mines

    DTIC Science & Technology

    1990-10-01

    AD-A256 739 Report# CTI/DAAK7089/002 II 711 _Comprehensive ITechnologies International CHEMICALS AND STRUCTURAL FOAMS II TO NEUTRALIZE OR DEFEAT...CTI/DAAK7089/002 _Cornprehensive Technologies - International CHEMICALS AND STRUCTURAL FOAMS TO NEUTRALIZE OR DEFEAT ANTI-PERSONNEL MINES TECHNICAL...study and analysis of chemical and structural foam products to determine if current technology could be used to defeat/ neutralize anti-personnel

  11. Incorporating Chemical Information Instruction and Environmental Science into the First-Year Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Landolt, R. G.

    2006-01-01

    The chemical information instruction and environmental science which is incorporated into a first-year organic chemistry laboratory is presented. The students are charged with devised search strategies, conducting online searches and limiting the project scope to ocean systems. The laboratory serves to provide for search strategy development…

  12. 76 FR 7841 - Agency Information Collection Activities; Proposed Collections; Toxic Chemical Release Reporting...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-11

    ... AGENCY Agency Information Collection Activities; Proposed Collections; Toxic Chemical Release Reporting... codes other than SIC codes 20 through 39): 212111, 212112, 212113 (correspond to SIC 12, Coal Mining (except 1241)); or 212221, 212222, 212231, 212234, 212299 (correspond to SIC 10, Metal Mining (except 1011...

  13. The Effect of Peer Review on Information Literacy Outcomes in a Chemical Literature Course

    ERIC Educational Resources Information Center

    Zwicky, David A.; Hands, Michael D.

    2016-01-01

    This article describes the use of peer review in a writing project involving upper-level chemistry students in a chemical literature course, with the goal of improving student performance in meeting information literacy outcomes. Students were asked to find articles on a topic of their choice over the course of a semester and assemble the results…

  14. Compilation of Physicochemical and Toxicological Information About Hydraulic Fracturing-Related Chemicals (Draft Database)

    EPA Science Inventory

    The purpose of this product is to make accessible the information about the 1,173 hydraulic fracturing-related chemicals that were listed in the external review draft of the Hydraulic Fracturing Drinking Water Assessment that was released recently. The product consists of a serie...

  15. Educational and Commercial Utilization of a Chemical Information Center, Four Year Summary.

    ERIC Educational Resources Information Center

    Williams, Martha E.; And Others

    The major objective of the IITRI Computer Search Center is to educate and link industry, academia, and government institutions to chemical and other scientific information systems and sources. The Center was developed to meet this objective and is in full operation providing services to users from a variety of machine-readable data bases with…

  16. Four-Year Summary, Educational and Commercial Utilization of a Chemical Information Center, Part II.

    ERIC Educational Resources Information Center

    Schipma, Peter B., Ed.

    The major objective of the Illinois Institute of Technology Retrieval Institute (IITRI) Computer Search Center (CSC) is to educate and link industry, academia, and government institutions to chemical and other scientific information systems and sources. The CSC is in full operation providing services to users from a variety of machine-readable…

  17. Four-Year Summary, Educational and Commercial Utilization of a Chemical Information Center. Part I.

    ERIC Educational Resources Information Center

    Schipma, Peter B., Ed.

    The major objective of the Illinois Institute of Technology (IIT) Computer Search Center (CSC) is to educate and link industry, academia, and government institutions to chemical and other scientific information systems and sources. The CSC is in full operation providing services to users from a variety of machine-readable data bases with minimal…

  18. Toward a Modern Secondary Information System for Chemistry and Chemical Engineering

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1975

    1975-01-01

    Describes the information processing system employed by Chemical Abstracts Service which utilizes computers to organize material from the data base, convert it to the appropriate type face and format, and photocompose it in a form suitable for conversion to offset printing plates. (GS)

  19. On the evolving open peer review culture for chemical information science.

    PubMed

    Walters, W Patrick; Bajorath, Jürgen

    2015-01-01

    Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science channel of F1000Research.

  20. Compilation of Physicochemical and Toxicological Information About Hydraulic Fracturing-Related Chemicals (Draft Database)

    EPA Science Inventory

    The purpose of this product is to make accessible the information about the 1,173 hydraulic fracturing-related chemicals that were listed in the external review draft of the Hydraulic Fracturing Drinking Water Assessment that was released recently. The product consists of a serie...

  1. The Effect of Peer Review on Information Literacy Outcomes in a Chemical Literature Course

    ERIC Educational Resources Information Center

    Zwicky, David A.; Hands, Michael D.

    2016-01-01

    This article describes the use of peer review in a writing project involving upper-level chemistry students in a chemical literature course, with the goal of improving student performance in meeting information literacy outcomes. Students were asked to find articles on a topic of their choice over the course of a semester and assemble the results…

  2. Toward a Modern Secondary Information System for Chemistry and Chemical Engineering

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1975

    1975-01-01

    Describes the information processing system employed by Chemical Abstracts Service which utilizes computers to organize material from the data base, convert it to the appropriate type face and format, and photocompose it in a form suitable for conversion to offset printing plates. (GS)

  3. Incorporating Chemical Information Instruction and Environmental Science into the First-Year Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Landolt, R. G.

    2006-01-01

    The chemical information instruction and environmental science which is incorporated into a first-year organic chemistry laboratory is presented. The students are charged with devised search strategies, conducting online searches and limiting the project scope to ocean systems. The laboratory serves to provide for search strategy development…

  4. The chemical structure of the Main-Belt

    NASA Astrophysics Data System (ADS)

    Carry, Benoit; DeMeo, Francesca

    2015-08-01

    The asteroid main belt between Mars and Jupiter holds evidences from the early Solar System history. The original chemical stratification of the accretion disk has been scrambled by planetary migrations, resulting in a radial mixing of compositions. Since the 1970s, spectral surveys have characterized the surface compositions of the largest members first, then of smaller bodies, slowly tapering into the size-frequency distribution. These surveys led to major discoveries, including the succession of dominating taxonomic classes along heliocentric distances, stained by the presence of interlopers in this over-arching structure. In the 2000s, these results have sustained the emergence of the current paradigm of Solar System formation: the Nice model, in which planets migrated from their formation locations to their current orbits.Since then, all-sky surveys in the visible and mid-infrared, the Sloan Digital Sky Survey and NASA WISE mission, have observed tens of thousands of asteroids, allowing characterization of their surface composition and estimation of their diameter. Simultaneously, our knowledge on asteroid density greatly improved: the sample of density determinations presented a tenfold increase. Such a rich dataset opened the possibility to scrutinize asteroid compositions to smaller sizes and to study the distribution of material in the main belt by mass, rather than by numbers. The picture resulting from these data go back over the previous view, and the few interlopers seem to be rule. The large scale structure seen on the largest bodies holds, but mixing increases at smaller sizes. This detailed picture supports the main results from recent dynamical models of planetary migration and radial mixing of smaller bodies, albeit several observed structures remain yet to be explained: numerous primitive D-type in the inner belt, apparently missing mantle counterpart (A-types) to the crustal and iron core-like (V- and M-types) material.Observational evidences

  5. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    SciTech Connect

    Sadtler, Bryce F

    2009-05-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or

  6. Chemical Industry Corrosion Management: A Comprehensive Information System (ASSET 2). Final Report

    SciTech Connect

    John, Randy C.; Young, Arthur L.; Pelton, Arthur D.; Thompson, William T.; Wright, Ian G.

    2008-10-10

    The research sponsored by this project has greatly expanded the ASSET corrosion prediction software system to produce a world-class technology to assess and predict engineering corrosion of metals and alloys corroding by exposure to hot gases. The effort included corrosion data compilation from numerous industrial sources and data generation at Shell Oak Ridge National Laboratory and several other companies for selected conditions. These data were organized into groupings representing various combinations of commercially available alloys and corrosion by various mechanisms after acceptance via a critical screening process to ensure the data were for alloys and conditions, which were adequately well defined, and of sufficient repeatability. ASSET is the largest and most capable, publicly-available technology in the field of corrosion assessment and prediction for alloys corroding by high temperature processes in chemical plants, hydrogen production, energy conversion processes, petroleum refining, power generation, fuels production and pulp/paper processes. The problems addressed by ASSET are: determination of the likely dominant corrosion mechanism based upon information available to the chemical engineers designing and/or operating various processes and prediction of engineering metal losses and lifetimes of commercial alloys used to build structural components. These assessments consider exposure conditions (metal temperatures, gas compositions and pressures), alloy compositions and exposure times. Results of the assessments are determination of the likely dominant corrosion mechanism and prediction of the loss of metal/alloy thickness as a function of time, temperature, gas composition and gas pressure. The uses of these corrosion mechanism assessments and metal loss predictions are that the degradation of processing equipment can be managed for the first time in a way which supports efforts to reduce energy consumption, ensure structural integrity of equipment

  7. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP MODELS FOR PREDICTION OF ESTROGEN RECEPTOR BINDING AFFINITY OF STRUCTURALLY DIVERSE CHEMICALS

    EPA Science Inventory

    The demonstrated ability of a variety of structurally diverse chemicals to bind to the estrogen receptor has raised the concern that chemicals in the environment may be causing adverse effects through interference with nuclear receptor pathways. Many structure-activity relationsh...

  8. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Thillai Govindaraja, S.; Jose, Sujin P.; Mohan, S.

    2014-07-01

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G**, high level 6-311++G** and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors.

  9. Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

    PubMed

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  10. Integrating Epistemological Perspectives on Chemistry in Chemical Education: The Cases of Concept Duality, Chemical Language, and Structural Explanations

    NASA Astrophysics Data System (ADS)

    Kaya, Ebru; Erduran, Sibel

    2013-07-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ( Foundations of Chemistry 1:225-238, 1999) notion of concept duality, Jacob's ( HYLE-International Journal for Philosophy of Chemistry 7:31-50, 2001) descriptions of chemical language and Goodwin's ( Foundations of Chemistry 10:117-127, 2008) explication of structural explanations in organic chemistry to highlight the particular ways in which chemical knowledge is structured. We use examples of textbooks and curricula to illustrate that even though the mentioned aspects of are relevant to and are covered in educational contexts, the philosophical dimensions of this coverage is absent in textbooks and curricula. The emphasis in the use of these features of chemical knowledge seems to be more on the conceptual definitions rather than on their "epistemological nature". We argue that chemical education will be improved through the inclusion of the philosophical perspectives in chemistry teaching and learning by highlighting the specific ways in which chemical knowledge functions.

  11. Access and use of information resources in assessing health risks from chemical exposure: Proceedings

    SciTech Connect

    Not Available

    1990-12-31

    Health risk assessment is based on access to comprehensive information about potentially hazardous agents in question. Relevant information is scattered throughout the literature, and often is not readily accessible. To be useful in assessment efforts, emerging scientific findings, risk assess parameters, and associated data must be compiled and evaluated systemically. The US Environmental Protection Agency (EPA) and Oak Ridge National Laboratory (ORNL) are among the federal agencies heavily involved in this effort. This symposium was a direct response by EPA and ORNL to the expressed needs of individuals involved in assessing risks from chemical exposure. In an effort to examine the state of the risk assessment process, the availability of toxicological information, and the future development and transfer of this information, the symposium provided an excellent cadre of speakers and participants from state and federal agencies, academia and research laboratories to address these topics. This stimulating and productive gathering discussed concerns associated with (1) environmental contamination by chemicals; (2) laws regulating chemicals; (3) information needs and resources; (4) applications; (5) challenges and priorities; and (6)future issues. Individual reports are processed separately for the data bases.

  12. Chemical Structure of Lipid A Isolated from Flavobacterium meningosepticum Lipopolysaccharide

    PubMed Central

    Kato, Hitomi; Haishima, Yuji; Iida, Takatoshi; Tanaka, Akira; Tanamoto, Ken-ichi

    1998-01-01

    The chemical structure of the lipid A of the lipopolysaccharide component isolated from Flavobacterium meningosepticum IFO 12535 was elucidated. Methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid A: a β (1→6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid A’s, and a 2-amino-6-O-(2,3-diamino-2,3-dideoxy-β-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. Both backbones were α-glycosidically phosphorylated in position 1, and the hydroxyl groups at positions 4, 4′, and 6′ were unsubstituted. Liquid secondary ion-mass spectrometry revealed a pseudomolecular ion at m/z 1673 [M-H]− as a major monophosphoryl lipid A component carrying five acyl groups. Fatty acid analysis showed that the lipid A contained 1 mol each of amide-linked (R)-3-OH iC17:0, ester-linked (R)-3-OH iC15:0, amide-linked (R)-3-O-(iC15:0)-iC17:0, and both amide- and ester-linked (R)-3-OH C16:0. Fatty acid distribution analyses using several mass spectrometry determinations demonstrated that the former two constituents were distributed on positions 2 and 3 of the reducing terminal unit of the backbones and that the latter two were attached to the 2′ and 3′ positions in the nonreducing terminal residue. PMID:9683486

  13. 40 CFR 711.6 - Chemical substances for which information is not required.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... reaction is totally polymeric in structure. (2) Microorganisms. Any combination of chemical substances that...), light straight-run. 64741-47-5 Natural gas condensates (petroleum). 64741-49-7 Condensates (petroleum), vacuum tower. 64741-50-0 Distillates (petroleum), light paraffinic. 64741-51-1 Distillates (petroleum...

  14. Complementary molecular information changes our perception of food web structure.

    PubMed

    Wirta, Helena K; Hebert, Paul D N; Kaartinen, Riikka; Prosser, Sean W; Várkonyi, Gergely; Roslin, Tomas

    2014-02-04

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host-parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them.

  15. Complementary molecular information changes our perception of food web structure

    PubMed Central

    Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

    2014-01-01

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

  16. Structural and chemical derivatization of graphene for electronics and sensing

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    Graphene - a single atom thick two dimensional sheet of sp 2 bonded carbon atoms arranged in a honeycomb lattice - has shown great promise for both fundamental research & applications because of its unique electrical, optical, thermal, mechanical and chemical properties. Derivatization of graphene unlocks a plethora of novel properties unavailable to their pristine parent "graphene". In this dissertation we have synthesized various structural and chemical derivatives of graphene; characterized them in detail; and leveraged their exotic properties for diverse applications. We have synthesized protein/DNA/ethylenediamine functionalized derivatives of graphene via a HATU catalyzed amide reaction of primary-amine-containing moieties with graphene oxide (GO) -- an oxyfunctional graphene derivative. In contrast to non-specificity of graphene, this functionalization of GO has enabled highly specific interactions with analytes. Devices fabricated from the protein (concanavalin -- A) and DNA functionalized graphene derivatives were demonstrated to enable label-free, specific detection of bacteria and DNA molecules, respectively, with single quanta sensitivity. Room temperature electrical characterization of the sensors showed a generation of ˜ 1400 charge carriers for single bacterium attachment and an increase of 5.6 X 1012 charge carriers / cm2 for attachment of a single complementary strand of DNA. This work has shown for the first time the viability of graphene for bio-electronics and sensing at single quanta level. Taking the bio-interfacing of graphene to the next level, we demonstrate the instantaneous swaddling of a single live bacterium (Bacillus subtilis ) with several hundred sq. micron (˜ 600 mum2) areal protein-functionalized graphene sheets. The atomic impermeability and high yield strength of graphene resulted in hermetic compartmentalization of bacteria. This enabled preservation of the dimensional and topological characteristics of the bacterium against

  17. Structures and chemical properties of silicene: unlike graphene.

    PubMed

    Jose, Deepthi; Datta, Ayan

    2014-02-18

    The discovery of graphene and its remarkable and exotic properties have aroused interest in other elements and molecules that form 2D atomic layers, such as metal chalcogenides, transition metal oxides, boron nitride, silicon, and germanium. Silicene and germanene, the Si and Ge counterparts of graphene, have interesting fundamental physical properties with potential applications in technology. For example, researchers expect that silicene will be relatively easy to incorporate within existing silicon-based electronics. In this Account, we summarize the challenges and progress in the field of silicene research. Theoretical calculations have predicted that silicene possesses graphene-like properties such as massless Dirac fermions that carry charge and the quantum spin Hall effect. Researchers are actively exploring the physical and chemical properties of silicene and tailoring it for wide variety of applications. The symmetric buckling in each of the six-membered rings of silicene differentiates it from graphene and imparts a variety of interesting properties with potential technological applications. The pseudo-Jahn-Teller (PJT) distortion breaks the symmetry and leads to the buckling in silicenes. In graphene, the two sublattice structures are equivalent, which does not allow for the opening of the band gap by an external electric field. However, in silicene where the neighboring Si atoms are displaced alternatively perpendicular to the plane, the intrinsic buckling permits a band gap opening in silicene in the presence of external electric field. Silicene's stronger spin orbit coupling than graphene has far reaching applications in spintronic devices. Because silicon prefers sp(3) hybridization over sp(2), hydrogenation is much easier in silicene. The hydrogenation of silicene to form silicane opens the band gap and increases the puckering angle. Lithiation can suppress the pseudo-Jahn-Teller distortion in silicene and hence can flatten silicene's structure

  18. Probing the water on chemically heterogeneous surface: interfacial-structural analysis for surface charge distribution

    NASA Astrophysics Data System (ADS)

    Shin, Sucheol; Willard, Adam

    We introduce the novel method for predicting the charge distribution of chemically heterogeneous surface, but reconstructed from the perspective of the interfacial water molecules. Our approach is to analyze the response of water to a disordered surface and infer from that response the heterogeneous distribution of surface charge. We accomplish this using a framework that is based on a probabilistic description of water's interfacial molecular structure and maximum likelihood estimation. This framework allows to deduce the apparent charge that is most congruently represented by the set of water configurations over the particular region of a surface. We demonstrate that the estimated charge distribution is consistent to the actual distribution for a static model substrate and hence that our method can be applied to investigate a dynamic fluctuating substrate such as the surface of a hydrated protein. This novel technique provides the useful information that can reflect the influence of fluctuations in the structure of biomolecule.

  19. Chemical and structural characterization of boron carbide powders and ceramics

    NASA Astrophysics Data System (ADS)

    Kuwelkar, Kanak Anant

    Boron carbide is the material of choice for lightweight armor applications due to its extreme hardness, high Young's modulus and low specific weight. The homogeneity range in boron carbide extends from 9 to 20 at% carbon with the solubility limits not uniquely defined in literature. Over the homogeneity range, the exact lattice positions of boron and carbon atoms have not been unambiguously established, and this topic has been the consideration of significant debate over the last 60 years. The atomic configuration and positions of the boron and carbon atoms play a key role in the crystal structure of the boron carbide phases. Depending on the atomic structure, boron carbide exhibits different mechanical properties which may alter its ballistic performance under extreme dynamic conditions. This work focusses on refinement and development of analytical and chemical methods for an accurate determination of the boron carbide stoichiometry. These methods were then utilized to link structural changes of boron carbide across the solubility range to variations in mechanical properties. After an extensive assessment of the currently employed characterization techniques, it was discerned that the largest source of uncertainty in the determination of the boron carbide stoichiometry was found to arise from the method utilized to evaluate the free carbon concentration. To this end, a modified spiking technique was introduced for free carbon determination where curve fitting techniques were employed to model the asymmetry of the 002 free carbon diffraction peak based on the amorphous, disordered and graphitic nature of carbon. A relationship was then established between the relative intensities of the carbon and boron carbide peaks to the percentage of added carbon and the free-carbon content was obtained by extrapolation. Samples with varying chemistry and high purity were synthesized across the solubility range by hot pressing mixtures of amorphous boron and boron carbide

  20. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms.

    PubMed

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J; Le Thi Thu, Huong; Torres, F Javier; Zambrano, Cesar H; Muñiz Olite, Jorge L; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M

    2016-05-27

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel's Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

  1. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    PubMed Central

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  2. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

    EPA Science Inventory

    Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors ...

  3. A computer-Based System for Handling Chemical Nomenclature and Structural Representations

    ERIC Educational Resources Information Center

    Rowlett, Russell J.; Tate, Fred A.

    1972-01-01

    Among other improvements in chemical nomenclature used in the Chemical Registry System, Chemical Abstracts Service intends to standardize the fundamental principles for naming cyclic structures so that procedures for the derivation of ring names can become more amenable to computer generation and translation. (Author/NH)

  4. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

    EPA Science Inventory

    Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors ...

  5. A computer-Based System for Handling Chemical Nomenclature and Structural Representations

    ERIC Educational Resources Information Center

    Rowlett, Russell J.; Tate, Fred A.

    1972-01-01

    Among other improvements in chemical nomenclature used in the Chemical Registry System, Chemical Abstracts Service intends to standardize the fundamental principles for naming cyclic structures so that procedures for the derivation of ring names can become more amenable to computer generation and translation. (Author/NH)

  6. Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set.

    PubMed

    Klimenko, Kyrylo; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2016-08-22

    Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set, providing an association of antiviral compounds to seven broadly defined antiviral activity classes. Generative topographic mapping (GTM) subjected to evolutionary tuning was then used to produce maps of the antiviral chemical space, providing an optimal separation of compound families associated with the different antiviral classes. The ability to pinpoint the specific spots occupied (responsibility patterns) on a map by various classes of antiviral compounds opened the way for a GTM-supported search for privileged structural motifs, typical for each antiviral class. The privileged locations of antiviral classes were analyzed in order to highlight underlying privileged common structural motifs. Unlike in classical medicinal chemistry, where privileged structures are, almost always, predefined scaffolds, privileged structural motif detection based on GTM responsibility patterns has the decisive advantage of being able to automatically capture the nature ("resolution detail"-scaffold, detailed substructure, pharmacophore pattern, etc.) of the relevant structural motifs. Responsibility patterns were found to represent underlying structural motifs of various natures-from very fuzzy (groups of various "interchangeable" similar scaffolds), to the classical scenario in medicinal chemistry (underlying motif actually being the scaffold), to very precisely defined motifs (specifically substituted scaffolds).

  7. Effect of chemical composition and density of the pelvic structure in intracavitary brachytherapy dosimetry

    NASA Astrophysics Data System (ADS)

    Chávez-Aguilera, N.; Torres-García, E.; Mitsoura, E.

    2011-03-01

    High dose rate (HDR) and low dose rate (LDR) intracavitary brachytherapies dosimetry in clinical practice are typically performed by commercial treatment planning systems. However, these systems do not fully consider the heterogeneities present in the real structure of the patient. The aim of this work is to obtain isodose curves and surfaces around the usual array of sources used in LDR ( 137Cs) and HDR ( 192Ir) intracavitary brachytherapy by Monte Carlo simulation, considering the real anatomic structure, density and chemical composition of media and tissues from the female pelvic region. The structural information was obtained from computed tomography images in the DICOM format. A voxel phantom (VP) was developed to perform ionizing radiation transport, considering the gamma spectrum of 137Cs and 192Ir. The absorbed dose was computed within each voxel of 2×2×3 mm 3. Four materials were considered in the VP—air, fat, muscle tissue and bone; however, one material per voxel was defined. Results show and quantify the effect of density and chemical composition of the medium on the absorbed dose distribution. According to them, the treatment planning systems underestimate the absorbed dose by 8% approximately for both radionuclides. In a heterogeneous medium, the absorbed dose distribution of 192Ir is more irregular than that of 137Cs but spatially better defined.

  8. Nanometer-resolved chemical analyses of femtosecond laser-induced periodic surface structures on titanium

    NASA Astrophysics Data System (ADS)

    Kirner, Sabrina V.; Wirth, Thomas; Sturm, Heinz; Krüger, Jörg; Bonse, Jörn

    2017-09-01

    The chemical characteristics of two different types of laser-induced periodic surface structures (LIPSS), so-called high and low spatial frequency LIPSS (HSFL and LSFL), formed upon irradiation of titanium surfaces by multiple femtosecond laser pulses in air (30 fs, 790 nm, 1 kHz), are analyzed by various optical and electron beam based surface analytical techniques, including micro-Raman spectroscopy, energy dispersive X-ray analysis, X-ray photoelectron spectroscopy, and Auger electron spectroscopy. The latter method was employed in a high-resolution mode being capable of spatially resolving even the smallest HSFL structures featuring spatial periods below 100 nm. In combination with an ion sputtering technique, depths-resolved chemical information of superficial oxidation processes was obtained, revealing characteristic differences between the two different types of LIPSS. Our results indicate that a few tens of nanometer shallow HSFL are formed on top of a ˜150 nm thick graded superficial oxide layer without sharp interfaces, consisting of amorphous TiO2 and partially crystallized Ti2O3. The larger LSFL structures with periods close to the irradiation wavelength originate from the laser-interaction with metallic titanium. They are covered by a ˜200 nm thick amorphous oxide layer, which consists mainly of TiO2 (at the surface) and other titanium oxide species of lower oxidation states underneath.

  9. Proposal for a new tomographic device providing information on the chemical properties of a body section

    SciTech Connect

    Gatti, E.; Rehak, P.; Kemmer, J.

    1986-02-27

    A system to analyze the chemical properties of a region of tissue located deep inside the human body without having to access it is proposed. The method is based on a high precision detection of x-rays or ..gamma..-rays (photons) from an external source Compton scattered from the tissue under inspection. The method provides chemical information of plane regions lying not too deep inside the body (<6 cm). The amount of radiation absorbed by the body is about the same as needed for a standard x-ray tomography. The exposure time is estimated to be shorter than 10 minutes. 37 refs., 13 figs.

  10. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    SciTech Connect

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  11. Information resources for assessing health effects from chemical exposure: Challenges, priorities, and future issues

    SciTech Connect

    Seigel, S.

    1990-12-31

    Issues related to developing information resources for assessing the health effects from chemical exposure include the question of how to address the individual political issues relevant to identifying and determining the timeliness, scientific credibility, and completeness of such kinds of information resources. One of the important ways for agencies to share information is through connection tables. This type of software is presently being used to build information products for some DHHS agencies. One of the challenges will be to convince vendors of data of the importance of trying to make data files available to communities that need them. In the future, information processing will be conducted with neural networks, object-oriented database management systems, and fuzzy-set technologies, and meta analysis techniques.

  12. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    PubMed

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  13. ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2016-01-01

    Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

  14. Light Scattering from Systems with Chemical Oscillations and Dissipative Structures.

    DTIC Science & Technology

    splitting in the chemical lines and dispersive (non-Lorentzian) contributions. Two model reaction mechanisms, the Volterra - Lotka model and the Prigogine-Lefever model, are examined in detail. (Author)

  15. Prediction of the rodent carcinogenicity of organic compounds from their chemical structures using the FALS method.

    PubMed Central

    Moriguchi, I; Hirano, H; Hirono, S

    1996-01-01

    Fuzzy adaptive least-squares (FALS), a pattern recognition method recently developed in our laboratory for correlating structure with activity rating, was used to generate quantitative structure-activity relationship (QSAR) models on the carcinogenicity of organic compounds of several chemical classes. Using the predictive models obtained from the chemical class-based FALS QSAR approach, the rodent carcinogenicity or noncarcinogenicity of a group of organic chemicals currently being tested by the U.S. National Toxicology Program was estimated from their chemical structures. PMID:8933054

  16. Correlating structural order with structural rearrangement in dusty plasma liquids: can structural rearrangement be predicted by static structural information?

    PubMed

    Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

    2012-11-09

    Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

  17. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

    PubMed

    Bae, Juhee; Watson, Benjamin

    2014-12-01

    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator.

  18. An Event-Related Potentials Study of Mental Rotation in Identifying Chemical Structural Formulas

    ERIC Educational Resources Information Center

    Huang, Chin-Fei; Liu, Chia-Ju

    2012-01-01

    The purpose of this study was to investigate how mental rotation strategies affect the identification of chemical structural formulas. This study conducted event-related potentials (ERPs) experiments. In addition to the data collected in the ERPs, a Chemical Structure Conceptual Questionnaire and interviews were also admin-istered for data…

  19. Interaction between Syntactic Structure and Information Structure in the Processing of a Head-Final Language

    ERIC Educational Resources Information Center

    Koizumi, Masatoshi; Imamura, Satoshi

    2017-01-01

    The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two…

  20. Interaction between Syntactic Structure and Information Structure in the Processing of a Head-Final Language

    ERIC Educational Resources Information Center

    Koizumi, Masatoshi; Imamura, Satoshi

    2017-01-01

    The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two…

  1. The smell of change: warming affects species interactions mediated by chemical information.

    PubMed

    Sentis, Arnaud; Ramon-Portugal, Felipe; Brodeur, Jacques; Hemptinne, Jean-Louis

    2015-10-01

    Knowledge of how temperature influences an organism's physiology and behaviour is of paramount importance for understanding and predicting the impacts of climate change on species' interactions. While the behaviour of many organisms is driven by chemical information on which they rely on to detect resources, conspecifics, natural enemies and competitors, the effects of temperature on infochemical-mediated interactions remain largely unexplored. Here, we experimentally show that temperature strongly influences the emission of infochemicals by ladybeetle larvae, which, in turn, modifies the oviposition behaviour of conspecific females. Temperature also directly affects female perception of infochemicals and their oviposition behaviour. Our results suggest that temperature-mediated effects on chemical communication can influence flows across system boundaries (e.g. immigration and emigration) and thus alter the dynamics and stability of ecological networks. We therefore argue that investigating the effects of temperature on chemical communication is a crucial step towards a better understanding of the functioning of ecological communities facing rapid environmental changes.

  2. Transient Dissipation and Structural Costs of Physical Information Transduction

    NASA Astrophysics Data System (ADS)

    Boyd, Alexander B.; Mandal, Dibyendu; Riechers, Paul M.; Crutchfield, James P.

    2017-06-01

    A central result that arose in applying information theory to the stochastic thermodynamics of nonlinear dynamical systems is the information-processing second law (IPSL): the physical entropy of the Universe can decrease if compensated by the Shannon-Kolmogorov-Sinai entropy change of appropriate information-carrying degrees of freedom. In particular, the asymptotic-rate IPSL precisely delineates the thermodynamic functioning of autonomous Maxwellian demons and information engines. How do these systems begin to function as engines, Landauer erasers, and error correctors? We identify a minimal, and thus inescapable, transient dissipation of physical information processing, which is not captured by asymptotic rates, but is critical to adaptive thermodynamic processes such as those found in biological systems. A component of transient dissipation, we also identify an implementation-dependent cost that varies from one physical substrate to another for the same information processing task. Applying these results to producing structured patterns from a structureless information reservoir, we show that "retrodictive" generators achieve the minimal costs. The results establish the thermodynamic toll imposed by a physical system's structure as it comes to optimally transduce information.

  3. National measures under the chemical weapons convention to protect confidential business information and compensate for its loss

    SciTech Connect

    Tanzman, E.A.; Kellman, B.

    1995-07-01

    This report contains a discussion presented at the Regional Seminar on the National Authority and the Chemical Weapons Convention. Measures to protect confidential business information and compensation for information which has not been sufficiently protected is discussed.

  4. Designing quantum information processing via structural physical approximation

    NASA Astrophysics Data System (ADS)

    Bae, Joonwoo

    2017-10-01

    In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of quantum mechanics is more restrictive than classical systems, identified to a specific form of dynamics, that is, unitary transformations and, consequently, positive and completely positive maps to subsystems. This also characterizes classes of disallowed transformations on quantum systems, among which positive but not completely maps are of particular interest as they characterize entangled states, a general resource in quantum information processing. Structural physical approximation offers a systematic way of approximating those non-physical maps, positive but not completely positive maps, with quantum channels. Since it has been proposed as a method of detecting entangled states, it has stimulated fundamental problems on classifications of positive maps and the structure of Hermitian operators and quantum states, as well as on quantum measurement such as quantum design in quantum information theory. It has developed efficient and feasible methods of directly detecting entangled states in practice, for which proof-of-principle experimental demonstrations have also been performed with photonic qubit states. Here, we present a comprehensive review on quantum information processing with structural physical approximations and the related progress. The review mainly focuses on properties of structural physical approximations and their applications toward practical information applications.

  5. Designing quantum information processing via structural physical approximation.

    PubMed

    Bae, Joonwoo

    2017-10-01

    In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of quantum mechanics is more restrictive than classical systems, identified to a specific form of dynamics, that is, unitary transformations and, consequently, positive and completely positive maps to subsystems. This also characterizes classes of disallowed transformations on quantum systems, among which positive but not completely maps are of particular interest as they characterize entangled states, a general resource in quantum information processing. Structural physical approximation offers a systematic way of approximating those non-physical maps, positive but not completely positive maps, with quantum channels. Since it has been proposed as a method of detecting entangled states, it has stimulated fundamental problems on classifications of positive maps and the structure of Hermitian operators and quantum states, as well as on quantum measurement such as quantum design in quantum information theory. It has developed efficient and feasible methods of directly detecting entangled states in practice, for which proof-of-principle experimental demonstrations have also been performed with photonic qubit states. Here, we present a comprehensive review on quantum information processing with structural physical approximations and the related progress. The review mainly focuses on properties of structural physical approximations and their applications toward practical information applications.

  6. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    PubMed

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  7. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

    PubMed Central

    Galdeano, Carles; Ciulli, Alessio

    2017-01-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity. PMID:27193077

  8. Neural network recognition of chemical class information in mobility spectra obtained at high temperatures

    NASA Technical Reports Server (NTRS)

    Bell, S.; Nazarov, E.; Wang, Y. F.; Rodriguez, J. E.; Eiceman, G. A.

    2000-01-01

    A minimal neural network was applied to a large library of high-temperature mobility spectra drawn from 16 chemical classes including 154 substances with 2000 spectra at various concentrations. A genetic algorithm was used to create a representative subset of points from the mobility spectrum as input to a cascade-type back-propagation network. This network demonstrated that significant information specific to chemical class was located in the spectral region near the reactant ions. This network failed to generalize the solution to unfamiliar compounds necessitating the use of complete spectra in network processing. An extended back-propagation network classified unfamiliar chemicals by functional group with a mean for average values of 0.83 without sulfides and 0.79 with sulfides. Further experiments confirmed that chemical class information was resident in the spectral region near the reactant ions. Deconvolution of spectra demonstrated the presence of ions, merged with the reactant ion peaks that originated from introduced samples. The ability of the neural network to generalize the solution to unfamiliar compounds suggests that these ions are distinct and class specific.

  9. Neural network recognition of chemical class information in mobility spectra obtained at high temperatures

    NASA Technical Reports Server (NTRS)

    Bell, S.; Nazarov, E.; Wang, Y. F.; Rodriguez, J. E.; Eiceman, G. A.

    2000-01-01

    A minimal neural network was applied to a large library of high-temperature mobility spectra drawn from 16 chemical classes including 154 substances with 2000 spectra at various concentrations. A genetic algorithm was used to create a representative subset of points from the mobility spectrum as input to a cascade-type back-propagation network. This network demonstrated that significant information specific to chemical class was located in the spectral region near the reactant ions. This network failed to generalize the solution to unfamiliar compounds necessitating the use of complete spectra in network processing. An extended back-propagation network classified unfamiliar chemicals by functional group with a mean for average values of 0.83 without sulfides and 0.79 with sulfides. Further experiments confirmed that chemical class information was resident in the spectral region near the reactant ions. Deconvolution of spectra demonstrated the presence of ions, merged with the reactant ion peaks that originated from introduced samples. The ability of the neural network to generalize the solution to unfamiliar compounds suggests that these ions are distinct and class specific.

  10. Informational Complexity and Functional Activity of RNA Structures

    PubMed Central

    Carothers, James M.; Oestreich, Stephanie C.; Davis, Jonathan H.

    2004-01-01

    Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an ∼1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers. PMID:15099096

  11. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    PubMed

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors. © 2014 Society for Laboratory Automation and Screening.

  12. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-02

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  13. The Relationship Between Chemical Structure and Dielectric Properties of Plasma-Enhanced Chemical Vapor Deposited Polymer Thin Films (Postprint)

    DTIC Science & Technology

    2007-01-01

    Materials Sci & Tech Applications, LLC) N. Venkatasubramanian and John T. Grant (University of Dayton) Kurt Eyink, Jesse Enlow, and Timothy J. Bunning...structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films Hao Jiang b,⁎, Lianggou Hong b, N. Venkatasubramanian c

  14. Knowledge Structures, Social Information Processing, and Children's Aggressive Behavior

    PubMed Central

    Burks, Virginia Salzer; Laird, Robert D.; Dodge, Kenneth A.; Pettit, Gregory S.; Bates, John E.

    2009-01-01

    Although a multitude of factors may be involved in the development of children's violent behavior, the actual aggressive act is preceded by a decision-making process that serves as the proximal control mechanism. The primary goal of this longitudinal study was to understand the nature of this proximal control mechanism involved in children's aggressive acts by focusing on two aspects of social cognitions: social information processing and stored knowledge (i.e., internal knowledge structures that are the latent memories of past events). It was hypothesized that: (1) children with hostile knowledge structures will display more biased patterns of aggressive social information processing than children whose knowledge structures are less hostile and negative; (2) children who display hostile knowledge structures will behave in chronically aggressive ways; and (3) the development of hostile knowledge structures and hostile patterns of social information processing contribute to the stability of aggressive behavior and thus partially mediate the relation between early and later aggressive behavior. 585 boys and girls (19% African-American) were followed from kindergarten through eighth grade. Results from this investigation support the hypotheses and are discussed in terms of the significance of the inclusion of knowledge structures in our theories of the mental processes involved in children's violent behaviour. PMID:20011226

  15. Erratum to "Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment"

    NASA Astrophysics Data System (ADS)

    Loague, Keith; Green, Richard E.; Giambelluca, Thomas W.; Liang, Tony C.; Yost, Russell S.

    2016-11-01

    A simple mobility index, when combined with a geographic information system, can be used to generate rating maps which indicate qualitatively the potential for various organic chemicals to leach to groundwater. In this paper we investigate the magnitude of uncertainty associated with pesticide mobility estimates as a result of data uncertainties. Our example is for the Pearl Harbor Basin, Oahu, Hawaii. The two pesticides included in our analysis are atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) and diuron [3-(3,4-dichlorophenyl)-1,1-dimethylarea]. The mobility index used here is known as the Attenuation Factor (AF); it requires soil, hydrogeologic, climatic, and chemical information as input data. We employ first-order uncertainty analysis to characterize the uncertainty in estimates of AF resulting from uncertainties in the various input data. Soils in the Pearl Harbor Basin are delineated at the order taxonomic category for this study. Our results show that there can be a significant amount of uncertainty in estimates of pesticide mobility for the Pearl Harbor Basin. This information needs to be considered if future decisions concerning chemical regulation are to be based on estimates of pesticide mobility determined from simple indices.

  16. Efficiency of 22 online databases in the search for physicochemical, toxicological and ecotoxicological information on chemicals.

    PubMed

    Guerbet, Michel; Guyodo, Gaetan

    2002-03-01

    The objective of this study was to evaluate the efficiency of 22 free online databases that could be used for an exhaustive search of physicochemical, toxicological and/or ecotoxicological information about various chemicals. Twenty-two databases with free access on the Internet were referenced. We then selected 27 major physicochemical, toxicological and ecotoxicological criteria and 14 compounds belonging to seven different chemical classes which were used to interrogate all the databases. Two indices were successively calculated to evaluate the efficiency with taking or not taking account of their specialization. More than 50% of the 22 databases 'knew' all of the 14 chemicals, but the quantity of information provided is very different from one to the other and most are poorly documented. Two categories clearly appear with specialized and non-specialized databases. The HSDB database is the most efficient general database to be searched first, because it is well documented for most of the 27 criteria. However, some specialized databases (i.e. EXTOXNET, SOLVEDB, etc.) must be searched secondarily to find additional information.

  17. Erratum to "Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment".

    PubMed

    Loague, Keith; Green, Richard E; Giambelluca, Thomas W; Liang, Tony C; Yost, Russell S

    2016-11-01

    A simple mobility index, when combined with a geographic information system, can be used to generate rating maps which indicate qualitatively the potential for various organic chemicals to leach to groundwater. In this paper we investigate the magnitude of uncertainty associated with pesticide mobility estimates as a result of data uncertainties. Our example is for the Pearl Harbor Basin, Oahu, Hawaii. The two pesticides included in our analysis are atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) and diuron [3-(3,4-dichlorophenyl)-1,1-dimethylarea]. The mobility index used here is known as the Attenuation Factor (AF); it requires soil, hydrogeologic, climatic, and chemical information as input data. We employ first-order uncertainty analysis to characterize the uncertainty in estimates of AF resulting from uncertainties in the various input data. Soils in the Pearl Harbor Basin are delineated at the order taxonomic category for this study. Our results show that there can be a significant amount of uncertainty in estimates of pesticide mobility for the Pearl Harbor Basin. This information needs to be considered if future decisions concerning chemical regulation are to be based on estimates of pesticide mobility determined from simple indices.

  18. Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment

    NASA Astrophysics Data System (ADS)

    Loague, Keith; Green, Richard E.; Giambelluca, Thomas W.; Liang, Tony C.; Yost, Russell S.

    1990-01-01

    A simple mobility index, when combined with a geographic information system, can be used to generate rating maps which indicate qualitatively the potential for various organic chemicals to leach to groundwater. In this paper we investigate the magnitude of uncertainty associated with pesticide mobility estimates as a result of data uncertainties. Our example is for the Pearl Harbor Basin, Oahu, Hawaii. The two pesticides included in our analysis are atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) and diuron [3-(3,4-dichlorophenyul)-1,1-dimethylarea]. The mobility index used here is known as the Attenuation Factor ( AF); it requires soil, hydrogeologic, climatic and chemical information as input data. We employ first-order uncertainty analysis to characterize the uncertainty in estimates of AF resulting from uncertainties in the various input data. Soils in the Pearl Harbor Basin are delineated at the order taxonomic category for this study. Our results show that there can be a significant amount of uncertainty in estimates of pesticide mobility for the Pearl Harbor Basin. This information needs to be considered if future decisions concerning chemical regulation are to be based on estimates of pesticide mobility determined from simple indices.

  19. Information-theoretical noninvasive damage detection in bridge structures

    NASA Astrophysics Data System (ADS)

    Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

    2016-11-01

    Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.

  20. Information-theoretical noninvasive damage detection in bridge structures.

    PubMed

    Sudu Ambegedara, Amila; Sun, Jie; Janoyan, Kerop; Bollt, Erik

    2016-11-01

    Damage detection of mechanical structures such as bridges is an important research problem in civil engineering. Using spatially distributed sensor time series data collected from a recent experiment on a local bridge in Upper State New York, we study noninvasive damage detection using information-theoretical methods. Several findings are in order. First, the time series data, which represent accelerations measured at the sensors, more closely follow Laplace distribution than normal distribution, allowing us to develop parameter estimators for various information-theoretic measures such as entropy and mutual information. Second, as damage is introduced by the removal of bolts of the first diaphragm connection, the interaction between spatially nearby sensors as measured by mutual information becomes weaker, suggesting that the bridge is "loosened." Finally, using a proposed optimal mutual information interaction procedure to prune away indirect interactions, we found that the primary direction of interaction or influence aligns with the traffic direction on the bridge even after damaging the bridge.