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. 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...

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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,…

  14. 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.

  15. 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…

  16. 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.

  17. 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

  18. 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)

  19. 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.

  20. 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.

  1. 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.

  2. 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…

  3. 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.

  4. 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

  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. 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.

  7. 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.

  8. 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

  9. 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... chemical facilities. On April 9, 2007, the Department issued an Interim Final Rule (IFR), implementing...

  10. 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)

  11. 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.

  12. 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.

  13. 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

  14. 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…

  15. 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,...

  16. 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.…

  17. 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

  18. 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...

  19. 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)

  20. 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. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information....

  1. 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. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information....

  2. 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. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information....

  3. 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. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information....

  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. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Other § 27.400 Chemical-terrorism vulnerability information....

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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...

  16. 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…

  17. 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)

  18. 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)

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. 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).

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 77 FR 21769 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-11

    ... application for a test marketing exemption (TME), and to publish in the Federal Register periodic status... Federal Register periodic status reports on the new chemicals under review and the receipt of NOCs to... Table I. of this unit, EPA provides the following information (to the extent that such information...

  12. 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…

  13. 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…

  14. 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.

  15. 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

  16. 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

  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 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

  20. Application Specific Chemical Information Microprocessor (ASCI mu P)

    DTIC Science & Technology

    2016-06-13

    Application Specific Chemical Information Microprocessor (ASCI µP) David Fries U. South Florida, Marine Science Dept, 140 7TH Ave So. St. Petersburg...00-00-1999 to 00-00-1999 4. TITLE AND SUBTITLE Application Specific Chemical Information Microprocessor (ASCI μP) 5a. CONTRACT NUMBER 5b. GRANT...NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND

  1. 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.

  2. 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

  3. [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.

  4. 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

  5. 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.

  6. 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…

  7. 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…

  8. 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.…

  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. 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...

  11. 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)

  12. 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…

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 77 FR 59891 - Proposed Information Collection; Comment Request; Chemical Weapons Convention Declaration and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-01

    ... Bureau of Industry and Security Proposed Information Collection; Comment Request; Chemical Weapons...@bis.doc.gov . SUPPLEMENTARY INFORMATION: ] I. Abstract The Chemical Weapons Convention Implementation Act of 1998 and Commerce Chemical Weapons Convention Regulations (CWCR) specify the...

  1. 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 .

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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…

  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. 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

  9. 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).

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  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. 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…

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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…

  1. 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

  2. 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.

  3. 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

  4. 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,...

  5. 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…

  6. 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…

  7. 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)

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Exploiting syntactic and semantics information for chemical-disease relation extraction.

    PubMed

    Zhou, Huiwei; Deng, Huijie; Chen, Long; Yang, Yunlong; Jia, Chen; Huang, Degen

    2016-01-01

    Identifying chemical-disease relations (CDR) from biomedical literature could improve chemical safety and toxicity studies. This article proposes a novel syntactic and semantic information exploitation method for CDR extraction. The proposed method consists of a feature-based model, a tree kernel-based model and a neural network model. The feature-based model exploits lexical features, the tree kernel-based model captures syntactic structure features, and the neural network model generates semantic representations. The motivation of our method is to fully utilize the nice properties of the three models to explore diverse information for CDR extraction. Experiments on the BioCreative V CDR dataset show that the three models are all effective for CDR extraction, and their combination could further improve extraction performance.Database URL:http://www.biocreative.org/resources/corpora/biocreative-v-cdr-corpus/.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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…

  8. 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.

  9. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 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...

  10. 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...

  11. 76 FR 76963 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-09

    .... feedstock. P-12-0022 10/24/2011 1/21/2012 CBI (G) The new (G) Complex chemical will strontium be used as a... needed. ] P-12-0023 10/24/2011 1/21/2012 CBI (G) The new (G) Complex chemical will strontium be used as a... needed. P-12-0024 10/24/2011 1/21/2012 CBI (G) The new (G) Complex chemical will strontium be used as...

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 75 FR 71688 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ... terminated urethane adhesive. The polymer. predicted volume for every application is same for all 6 chemical... polymer. predicted volume for every application is same for all 6 chemical substances. The production is... polyurethane terminated urethane adhesive. The polymer. predicted volume for every application is same for...

  18. 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…

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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)

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. 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…

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

    MedlinePlus

    ... Occupational Activities Industries Job Tasks Processes Symptoms/Findings Customer Service: tehip@teh.nlm.nih.gov Specialized Information Services ... Health Disclaimer Notice Privacy Last Updated: July 2016 Customer Service: tehip@teh.nlm.nih.gov Specialized Information Services ...

  10. 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

  11. 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.

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

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 6 Domestic Security 1 2012-01-01 2012-01-01 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...

  13. 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...

  14. 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 .

  15. 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

  16. 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…

  17. 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…

  18. 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…

  19. 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

  20. 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.

  1. (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…

  2. 75 FR 39520 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-09

    ... receipt of a premanufacture notice (PMN) or an application for a test marketing exemption (TME), and to... to publish a notice of receipt of a PMN or an application for a TME and to publish periodic status... Manufacturer/Importer Use Chemical P-10-0406 05/28/10 08/25/10 CBI (G) Polymer used to (G) Alkene...

  3. 75 FR 32760 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ... application and in a destructive use as a reactant P-10-0361 04/30/10 07/28/10 CBI (G) Organic (G) Substituted... receipt of a premanufacture notice (PMN) or an application for a test marketing exemption (TME), and to... receipt of a PMN or an application for a TME and to publish periodic status reports on the chemicals...

  4. 75 FR 32751 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ... receipt of a premanufacture notice (PMN) or an application for a test marketing exemption (TME), and to... receipt of a PMN or an application for a TME and to publish periodic status reports on the chemicals under... (S) Dodecanedioic make foam insulation acid, polymer with 1,6-hexanediol ] P-10-0237 02/18/10...

  5. 76 FR 35886 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    .... P-11-0345 4/25/2011 7/23/2011 CBI (G) An organic chemical (G) Heterocyclic organic intermediate for...-dimethyl ester, polymer with 1,2-ethanediol and 1,2,3-propanetriol, ester with methyl--hydroxypoly(oxy-1,2...-benzenedicarboxylic fabric washes. acid, 1,4-dimethyl ester, polymer with 1,2-propanediol, ester with...

  6. 77 FR 56639 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-13

    ... notice end Manufacturer/ Use Chemical date date importer P-12-0488 08/01/2012 10/29/2012 CBI (G) Additive... 10/29/2012 CBI (G) Additive to (G) Hydroxy polyurethane containing oil, foam. polymer with alkylene.../2012 CBI (G) Additive to (G) Alkanol, polyurethane oxybis-, foam. polymer with aromatic...

  7. 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

  8. 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.

  9. 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…

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 77 FR 69824 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-21

    ... CBI (G) Part of adhesive (G) Castor oil, system. polymer with glycol and phthalic anhydride. P-13-0004... adduct. P-13-0007 10/3/2012 12/31/2012 DIC International (S) Polymer resin for (G) Acrylic acids, (USA... Chemical (G) Open-non dispersive (G) Polyurethane Company. use. polymer. P-13-0014 10/8/2012 1/5/2013...

  15. 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.

  16. 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.

  17. 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…

  18. 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.

  19. 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.

  20. 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).

  1. 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…

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. 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

  9. 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.

  10. 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.

  11. 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…

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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

  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. 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.

  16. 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

  17. 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…

  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. 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.

  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. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. Using Fisher Information Criteria for Chemical Sensor Selection via Convex Optimization Methods

    DTIC Science & Technology

    2016-11-16

    best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex optimization may be used to...parametrized to select the best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex op...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6180--16-9711 Using Fisher Information Criteria for Chemical Sensor Selection via Convex

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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 ...

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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…

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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...

  11. 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...

  12. 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

  13. 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.

  14. 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,…

  15. 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

  16. 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

  17. 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.

  18. 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.

  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. 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).

  1. 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.

  2. 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…

  3. 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)

  4. 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.

  5. 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...

  6. 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…

  7. 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…

  8. 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…

  9. 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

  10. Structure, Thermodynamics and Kinetics of Chemically Heterogeneous Interfaces

    NASA Astrophysics Data System (ADS)

    Palafox Hernandez, Jesus Pablo

    2011-12-01

    In this work we have used atomistic computer simulations to examine the structure, thermodynamics and transport properties, for two models of chemically heterogeneous interfaces: an ideal model (repulsive soft spheres against a potential wall), and a metal alloy interface (Cu-Pb). In both systems, interfacial prefreezing (crystal formation above the melting point of the fluid) was observed and this prefreezing was seen to promote heterogeneous nucleation, when the systems were cooled below the melting temperature. In our study of inverse-power repulsive soft spheres, we found that the soft-sphere fluid exhibited prefreezing at the wall surface. Similar behavior was previously observed in hard-sphere fluids at hard wall [17, 18, 20], however, to our knowledge, this the first time that prefreezing is reported for soft spheres. The prediction of prefreezing is based on the calculation of interfacial free energies wall-crystal (gammawc) and wall-fluid (gammawf) using a variant of the cleaving wall method. With the calculated, gammawc and gamma wf together with gammacf, previously computed [79], the tendency to prefreeze was quantified by the wetting angle formed between the metastable crystal phase on the wall and the soft-sphere fluid. We found that all the closest packing orientations [(111) FCC and (110) BCC] developed prefreezing (complete wetting). A detailed atomic-level characterization of the structure, energetics and transport properties of the planar Cu/Pb solid-liquid interface in equilibrium was performed at a several temperatures (625K and 750K) above the melting point of Pb and for two Cu crystal orientations [(111) and (100)]. Among the most relevant findings are that the Cu(100)/Pb interfaces presents surfaces alloying and the Cu(111)/Pb exhibits a prefreezing layer of Pb crystal. It was also observed that both interfaces have a nucleation barrier that prevents heterogeneous nucleation and that the mechanisms by which each structure promotes

  11. 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

  12. 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...

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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 ...

  6. 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)

  7. 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.

  8. 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.

  9. 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…

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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…

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    ERIC Educational Resources Information Center

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Thesaurus of terms for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A Thesaurus of approximately 700 subject terms used to describe the six problem areas in the mechanics of structural failure is presented. The initial criteria for the selection of terms are their significance and frequency of use in the literature describing the mechanics of structural failure. The purpose of the Thesaurus is to provide the Aerospace Safety Research and Data Institute a list of key works and identifiers that afford effective retrieval of information regarding failure modes and mechanisms for aerospace structures. The Thesaurus includes both a conventional listing of subject terms and a Key Words In Context (KWIC) listing.

  10. Crystal Structure and Chemical Composition of a Presolar Silicate from the Queen Elizabeth Range 99177 Meteorite

    NASA Technical Reports Server (NTRS)

    Nguyen, A. N.; Keller, L. P.; Rahman, Z.; Messenger, S.

    2013-01-01

    Mineral characterization of presolar silicate grains, the most abundant stardust phase, has provided valuable information about the formation conditions in circumstellar environments and in super-nova (SN) outflows. Spectroscopic observations of dust around evolved stars suggest a majority of amor-phous, Mg-rich olivine grains, but crystalline silicates, most of which are pyroxene, have also been observed [1]. The chemical compositions of hundreds of presolar silicates have been determined by Auger spectroscopy and reveal high Fe contents and nonstoichiometric compositions intermediate to olivine and pyroxene [2-6]. The unexpectedly high Fe contents can partly be attributed to secondary alteration on the meteorite parent bodies, as some grains have Fe isotopic anomalies from their parent stellar source [7]. Only about 35 presolar silicates have been studied for their mineral structures and chemical compositions by transmission electron microscopy (TEM). These grains display a wide range of compositions and structures, including crystalline forsterite, crystalline pyroxene, nanocrystalline grains, and a majority of amorphous nonstoichiometric grains. Most of these grains were identified in the primitive Acfer 094 meteorite. Presolar silicates from this meteorite show a wide range of Fe-contents, suggestive of secondary processing on the meteorite parent body. The CR chondrite QUE 99177 has not suffered as much alteration [8] and displays the highest presolar silicate abundance to date among carbonaceous chondrites [3, 6]. However, no mineralogical studies of presolar silicates from this meteorite have been performed. Here we examine the mineralogy of a presolar silicate from QUE 99177.

  11. Ranking chemical structures for drug discovery: a new machine learning approach.

    PubMed

    Agarwal, Shivani; Dugar, Deepak; Sengupta, Shiladitya

    2010-05-24

    With chemical libraries increasingly containing millions of compounds or more, there is a fast-growing need for computational methods that can rank or prioritize compounds for screening. Machine learning methods have shown considerable promise for this task; indeed, classification methods such as support vector machines (SVMs), together with their variants, have been used in virtual screening to distinguish active compounds from inactive ones, while regression methods such as partial least-squares (PLS) and support vector regression (SVR) have been used in quantitative structure-activity relationship (QSAR) analysis for predicting biological activities of compounds. Recently, a new class of machine learning methods - namely, ranking methods, which are designed to directly optimize ranking performance - have been developed for ranking tasks such as web search that arise in information retrieval (IR) and other applications. Here we report the application of these new ranking methods in machine learning to the task of ranking chemical structures. Our experiments show that the new ranking methods give better ranking performance than both classification based methods in virtual screening and regression methods in QSAR analysis. We also make some interesting connections between ranking performance measures used in cheminformatics and those used in IR studies.

  12. A hierarachical data structure representation for fusing multisensor information

    SciTech Connect

    Maren, A.J.; Pap, R.M.; Harston, C.T.

    1989-12-31

    A major problem with MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the data element, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Data-element fusion has problems with coregistration. Attempts to fuse information using the features of segmented data relies on a Presumed similarity between the segmentation characteristics of each data stream. Symbolic-level fusion requires too much advance processing (including object identification) to be useful. MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Data Structure (HDS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The HDS is an intermediate representation between the raw or smoothed data stream and symbolic interpretation of the data. it represents the structural organization of the data. Fused HDSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based region interpretation.

  13. A hierarachical data structure representation for fusing multisensor information

    SciTech Connect

    Maren, A.J. . Space Inst.); Pap, R.M.; Harston, C.T. )

    1989-01-01

    A major problem with MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the data element, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Data-element fusion has problems with coregistration. Attempts to fuse information using the features of segmented data relies on a Presumed similarity between the segmentation characteristics of each data stream. Symbolic-level fusion requires too much advance processing (including object identification) to be useful. MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Data Structure (HDS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The HDS is an intermediate representation between the raw or smoothed data stream and symbolic interpretation of the data. it represents the structural organization of the data. Fused HDSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based region interpretation.

  14. Prosodic Marking of Information Structure by Malaysian Speakers of English

    ERIC Educational Resources Information Center

    Gut, Ulrike; Pillai, Stefanie

    2014-01-01

    Various researchers have shown that second language (L2) speakers have difficulties with marking information structure in English prosodically: They deviate from native speakers not only in terms of pitch accent placement (Grosser, 1997; Gut, 2009; Ramírez Verdugo, 2002) and the type of pitch accent they produce (Wennerstrom, 1994, 1998) but also…

  15. Shared Information Structure: Evidence from Cross-Linguistic Priming

    ERIC Educational Resources Information Center

    Fleischer, Zuzanna; Pickering, Martin J.; McLean, Janet F.

    2012-01-01

    This study asked whether bilinguals construct a language-independent level of information structure for the sentences that they produce. It reports an experiment in which a Polish-English bilingual and a confederate of the experimenter took turns to describe pictures to each other and to find those pictures in an array. The confederate produced a…

  16. Review of "Conceptual Structures: Information Processing in Mind and Machine."

    ERIC Educational Resources Information Center

    Smoliar, Stephen W.

    This review of the book, "Conceptual Structures: Information Processing in Mind and Machine," by John F. Sowa, argues that anyone who plans to get involved with issues of knowledge representation should have at least a passing acquaintance with Sowa's conceptual graphs for a database interface. (Used to model the underlying semantics of…

  17. Impact of Information Technology Governance Structures on Strategic Alignment

    ERIC Educational Resources Information Center

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  18. From Informal Strategies to Structured Procedures: Mind the Gap!

    ERIC Educational Resources Information Center

    Anghileri, Julia; Beishuizen, Meindert; Van Putten, Kees

    2002-01-01

    Explores written calculation methods for division used by pupils in England (n=276) and the Netherlands (n=259). Analyses informal strategies and identifies progression towards more structured procedures that result from different teaching approaches. Comparison of methods used shows greater success in the Dutch approach which is based on…

  19. Prenuclear Accentuation in English: Phonetics, Phonology, Information Structure

    ERIC Educational Resources Information Center

    Bishop, Jason Brandon

    2013-01-01

    A primary function of prosody in many languages is to convey information structure--the "packaging" of a sentence's content into categories such as "focus", "given" and "topic". In English and other West Germanic languages it is widely assumed that focus is signaled prosodically by the location of a…

  20. Environmental toxicological fate prediction of diverse organic chemicals based on steady-state compartmental chemical mass ratio using quantitative structure-fate relationship (QSFR) models.

    PubMed

    Pramanik, Subrata; Roy, Kunal

    2013-07-01

    Four quantitative prediction models for steady-state compartmental chemical mass concentrations (Wn,g) were obtained from structural information, physiochemical properties, degradation rate and transport coefficients of 455 diverse organic chemicals using chemometric tools in a quantitative structure-fate relationship (QSFR) study. The mass ratio assessment of environmentally prevalent organic chemicals may be helpful to predict their toxicological fate in the ecosystems. Four sets of mass ratios [(1) log(Wair) from water emissions (water to air compartment), (2) log(Wair) from air emissions (within different zones of the air compartment), (3) log(Wwater) from water emissions (within different zones of the water compartment) and (4) log(Wwater) from air emissions (air to water compartment)] have been used. The developed models using genetic function approximation followed by multiple linear regression (GFA-MLR) and subsequent partial least squares (PLS) treatment identify only four descriptors for log(Wair) from water emission, six descriptors for log(Wair) from air emission, five descriptors for log(Wwater) from water emission and seven descriptors for log(Wwater) from air emission for predicting efficiently a large number of test set chemicals (ntest=182). The conclusive models suggest that descriptors such as partition coefficients (Kaw, Kow and Ksw), degradation parameters (Ksoil,Kwater and Kair), vapor pressure (Pv), diffusivity (Dwater), spatial descriptors (Jurs-WNSA-1, Jurs-WNSA-2, Jurs-WPSA-3, Jurs-FNSA-3 and Density), thermodynamic descriptors (MolRef and AlogP98), electrotopological state indices (S_dsN, S_ssNH and S_dsCH) are important for predicting the chemical mass ratios. The developed models may be applicable in toxicological fate prediction of diverse chemicals in the ecosystems.

  1. Lunar clinopyroxenes: Chemical composition, structural state, and texture

    USGS Publications Warehouse

    Ross, M.; Bence, A.E.; Dwornik, E.J.; Clark, J.R.; Papike, J.J.

    1970-01-01

    Single-crystal x-ray diffraction, microprobe, optical and electron optical examinations of clinopyroxenes from Apollo 11 lunar samples 10003, 10047, 10050, and 10084 show that generally the crystals are composed of (001) augite-pigeonite intergrowths in varying ratios. Transmission electron micrographs reveal abundant exsolution lamellae, many only 60 A?? thick. In addition to the phase inhomogeneities, primary chemical inhomogeneities are clearly demonstrated. There are reciprocal relationships between calcium and iron and between Ti4+ + 2Al and R2+ + 2Si. Our evidence suggests that a chemically inhomogeneous subcalcic C2/c augite was the only primary pyroxene from which pigeonite later exsolved.

  2. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

    PubMed Central

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

  3. Three-dimensional microwave imaging with incorporated prior structural information

    NASA Astrophysics Data System (ADS)

    Golnabi, Amir H.; Meaney, Paul M.; Epstein, Neil R.; Paulsen, Keith D.

    2012-03-01

    Microwave imaging for biomedical applications, especially for early detection of breast cancer and effective treatment monitoring, has attracted increasing interest in last several decades. This fact is due to the high contrast between the dielectric properties of the normal and malignant breast tissues at microwave frequencies. The available range of dielectric properties for different soft tissue can provide important functional information about tissue health. Nonetheless, one of the limiting weaknesses of microwave imaging is that unlike conventional modalities, such as X-ray CT or MRI, it inherently cannot provide high-resolution images. The conventional modalities can produce highly resolved anatomical information but often cannot provide the functional information required for diagnoses. Previously, we have developed a regularization strategy that can incorporate prior anatomical information from MR or other sources and use it in a way to refine the resolution of the microwave images, while also retaining the functional nature of the reconstructed property values. In the present work, we extend the use of prior structural information in microwave imaging from 2D to 3D. This extra dimension adds a significant layer of complexity to the entire image reconstruction procedure. In this paper, several challenges with respect to the 3D microwave imaging will be discussed and the results of a series of 3D simulation and phantom experiments with prior structural information will be studied.

  4. Information diversity in structure and dynamics of simulated neuronal networks.

    PubMed

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  5. Structural Simulations and Conservation Analysis -Historic Building Information Model (HBIM)

    NASA Astrophysics Data System (ADS)

    Dore, C.; Murphy, M.; McCarthy, S.; Brechin, F.; Casidy, C.; Dirix, E.

    2015-02-01

    In this paper the current findings to date of the Historic Building Information Model (HBIM) of the Four Courts in Dublin are presented. The Historic Building Information Model (HBIM) forms the basis for both structural and conservation analysis to measure the impact of war damage which still impacts on the building. The laser scan survey was carried out in the summer of 2014 of the internal and external structure. After registration and processing of the laser scan survey, the HBIM was created of the damaged section of the building and is presented as two separate workflows in this paper. The first is the model created from historic data, the second a procedural and segmented model developed from laser scan survey of the war damaged drum and dome. From both models structural damage and decay simulations will be developed for documentation and conservation analysis.

  6. Alternatives Assessment Frameworks: Research Needs for the Informed Substitution of Hazardous Chemicals

    PubMed Central

    Jacobs, Molly M.; Malloy, Timothy F.; Tickner, Joel A.; Edwards, Sally

    2015-01-01

    Background Given increasing pressures for hazardous chemical replacement, there is growing interest in alternatives assessment to avoid substituting a toxic chemical with another of equal or greater concern. Alternatives assessment is a process for identifying, comparing, and selecting safer alternatives to chemicals of concern (including those used in materials, processes, or technologies) on the basis of their hazards, performance, and economic viability. Objectives The purposes of this substantive review of alternatives assessment frameworks are to identify consistencies and differences in methods and to outline needs for research and collaboration to advance science policy practice. Methods This review compares methods used in six core components of these frameworks: hazard assessment, exposure characterization, life-cycle impacts, technical feasibility evaluation, economic feasibility assessment, and decision making. Alternatives assessment frameworks published from 1990 to 2014 were included. Results Twenty frameworks were reviewed. The frameworks were consistent in terms of general process steps, but some differences were identified in the end points addressed. Methodological gaps were identified in the exposure characterization, life-cycle assessment, and decision–analysis components. Methods for addressing data gaps remain an issue. Discussion Greater consistency in methods and evaluation metrics is needed but with sufficient flexibility to allow the process to be adapted to different decision contexts. Conclusion Although alternatives assessment is becoming an important science policy field, there is a need for increased cross-disciplinary collaboration to refine methodologies in support of the informed substitution and design of safer chemicals, materials, and products. Case studies can provide concrete lessons to improve alternatives assessment. Citation Jacobs MM, Malloy TF, Tickner JA, Edwards S. 2016. Alternatives assessment frameworks: research

  7. One drop chemical derivatization--DESI-MS analysis for metabolite structure identification.

    PubMed

    Lubin, Arnaud; Cabooter, Deirdre; Augustijns, Patrick; Cuyckens, Filip

    2015-07-01

    Structural elucidation of metabolites is an important part during the discovery and development process of new pharmaceutical drugs. Liquid Chromatography (LC) in combination with Mass Spectrometry (MS) is usually the technique of choice for structural identification but cannot always provide precise structural identification of the studied metabolite (e.g. site of hydroxylation and site of glucuronidation). In order to identify those metabolites, different approaches are used combined with MS data including nuclear magnetic resonance, hydrogen/deuterium exchange and chemical derivatization followed by LC-MS. Those techniques are often time-consuming and/or require extra sample pre-treatment. In this paper, a fast and easy to set up tool using desorption electrospray ionization-MS for metabolite identification is presented. In the developed method, analytes in solution are simply dried on a glass plate with printed Teflon spots and then a single drop of derivatization mixture is added. Once the spot is dried, the derivatized compound is analyzed. Six classic chemical derivatizations were adjusted to work as a one drop reaction and applied on a list of compounds with relevant functional groups. Subsequently, two successive reactions on a single spot of amoxicillin were tested and the methodology described was successfully applied on an in vitro incubated alprazolam metabolite. All reactions and analyses were performed within an hour and gave useful structural information by derivatizing functional groups, making the method a time-saving and efficient tool for metabolite identification if used in addition or in some cases as an alternative to common methods.

  8. Predicting modes of toxic action from chemical structure

    EPA Science Inventory

    Like many of the papers in the ET&C top 100 list, the development of the fathead minnow database and the assignment of modes of action to the 617 chemicals therein was the result of a comprehensive research effort by a multidisciplinary team of researchers with expertise in quant...

  9. Chemical Emissions of Residential Materials and Products: Review of Available Information

    SciTech Connect

    Willem, Henry; Singer, Brett

    2010-09-15

    This report is prepared in the context of a larger program whose mission is to advance understanding of ventilation and indoor air quality in U.S. homes. A specific objective of this program is to develop the scientific basis ? through controlled experiments, monitoring and analysis ? for health risk-based ventilation standards. Appropriate and adequate ventilation is a basic element of a healthy home. Ventilation provides outdoor air and in the process removes indoor odors and contaminants including potentially unhealthful chemicals emitted by indoor materials, products and activities. Ventilation traditionally was assured to occur via infiltration of outdoor air through cracks and other leakage pathways in the residential building envelope. As building air tightness is improved for energy efficiency, infiltration can be reduced to inadequate levels. This has lead to the development of standards requiring mechanical ventilation. Though nominally intended to ensure acceptable indoor air quality, the standards are not explicitly tied to health risk or pollutant exposure targets. LBNL is currently designing analyses to assess the impact of varying ventilation standards on pollutant concentrations, health risks and energy use. These analyses require information on sources of chemical pollutant emissions, ideally including emission rates and the impact of ventilation on emissions. Some information can be obtained from recent studies that report measurements of various air contaminants and their concentrations in U.S. residences. Another way to obtain this information is the bottom-up approach of collecting and evaluating emissions data from construction and interior materials and common household products. This review contributes to the latter approach by summarizing available information on chemical emissions from new residential products and materials. We review information from the scientific literature and public sources to identify and discuss the databases that

  10. Structuring Chemical Space: Similarity-Based Characterization of the PubChem Database.

    PubMed

    Cincilla, Giovanni; Thormann, Michael; Pons, Miquel

    2010-01-12

    The ensemble of conceivable molecules is referred to as the Chemical Space. In this article we describe a hierarchical version of the Affinity Propagation (AP) clustering algorithm and apply it to analyze the LINGO-based similarity matrix of a 500 000-molecule subset of the PubChem database, which contains more than 19 million compounds. The combination of two highly efficient methods, namely the AP clustering algorithm and LINGO-based molecular similarity calculations, allows the unbiased analysis of large databases. Hierarchical clustering generates a numerical diagonalization of the similarity matrix. The target-independent, intrinsic structure of the database , derived without any previous information on the physical or biological properties of the compounds, maps together molecules experimentally shown to bind the same biological target or to have similar physical properties.

  11. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  12. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical `atomistic' molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  13. Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

    NASA Astrophysics Data System (ADS)

    Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

    2008-06-01

    A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

  14. On the complexity and the information content of cosmic structures

    NASA Astrophysics Data System (ADS)

    Vazza, F.

    2017-03-01

    The emergence of cosmic structure is commonly considered one of the most complex phenomena in nature. However, this complexity has never been defined nor measured in a quantitative and objective way. In this work, we propose a method to measure the information content of cosmic structure and to quantify the complexity that emerges from it, based on Information Theory. The emergence of complex evolutionary patterns is studied with a statistical symbolic analysis of the datastream produced by state-of-the-art cosmological simulations of forming galaxy clusters. This powerful approach allows us to measure how many bits of information is necessary to predict the evolution of energy fields in a statistical way, and it offers a simple way to quantify when, where and how the cosmic gas behaves in complex ways. The most complex behaviours are found in the peripheral regions of galaxy clusters, where supersonic flows drive shocks and large energy fluctuations over a few tens of million years. Describing the evolution of magnetic energy requires at least twice as large amount of bits as required for the other energy fields. When radiative cooling and feedback from galaxy formation are considered, the cosmic gas is overall found to double its degree of complexity. In the future, Cosmic Information Theory can significantly increase our understanding of the emergence of cosmic structure as it represents an innovative framework to design and analyse complex simulations of the Universe in a simple, yet powerful way.

  15. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids.

  16. Ensuring Adequate Health and Safety Information for Decision Makers during Large-Scale Chemical Releases

    NASA Astrophysics Data System (ADS)

    Petropoulos, Z.; Clavin, C.; Zuckerman, B.

    2015-12-01

    The 2014 4-Methylcyclohexanemethanol (MCHM) spill in the Elk River of West Virginia highlighted existing gaps in emergency planning for, and response to, large-scale chemical releases in the United States. The Emergency Planning and Community Right-to-Know Act requires that facilities with hazardous substances provide Material Safety Data Sheets (MSDSs), which contain health and safety information on the hazardous substances. The MSDS produced by Eastman Chemical Company, the manufacturer of MCHM, listed "no data available" for various human toxicity subcategories, such as reproductive toxicity and carcinogenicity. As a result of incomplete toxicity data, the public and media received conflicting messages on the safety of the contaminated water from government officials, industry, and the public health community. Two days after the governor lifted the ban on water use, the health department partially retracted the ban by warning pregnant women to continue avoiding the contaminated water, which the Centers for Disease Control and Prevention deemed safe three weeks later. The response in West Virginia represents a failure in risk communication and calls to question if government officials have sufficient information to support evidence-based decisions during future incidents. Research capabilities, like the National Science Foundation RAPID funding, can provide a solution to some of the data gaps, such as information on environmental fate in the case of the MCHM spill. In order to inform policy discussions on this issue, a methodology for assessing the outcomes of RAPID and similar National Institutes of Health grants in the context of emergency response is employed to examine the efficacy of research-based capabilities in enhancing public health decision making capacity. The results of this assessment highlight potential roles rapid scientific research can fill in ensuring adequate health and safety data is readily available for decision makers during large

  17. A hierarchical structure approach to MultiSensor Information Fusion

    SciTech Connect

    Maren, A.J. . Space Inst.); Pap, R.M.; Harston, C.T. )

    1989-01-01

    A major problem with image-based MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the pixel, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Pixel-level fusion has problems with coregistration of the images or data. Attempts to fuse information using the features of segmented images or data relies an a presumed similarity between the segmentation characteristics of each image or data stream. Symbolic-level fusion requires too much advance processing to be useful, as we have seen in automatic target recognition tasks. Image-based MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Scene Structure (HSS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The MSS is intermediate between a pixel-based representation and a scene interpretation representation, and represents the perceptual organization of an image. Fused HSSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based,region interpretation.

  18. A hierarchical structure approach to MultiSensor Information Fusion

    SciTech Connect

    Maren, A.J.; Pap, R.M.; Harston, C.T.

    1989-12-31

    A major problem with image-based MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the pixel, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Pixel-level fusion has problems with coregistration of the images or data. Attempts to fuse information using the features of segmented images or data relies an a presumed similarity between the segmentation characteristics of each image or data stream. Symbolic-level fusion requires too much advance processing to be useful, as we have seen in automatic target recognition tasks. Image-based MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Scene Structure (HSS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The MSS is intermediate between a pixel-based representation and a scene interpretation representation, and represents the perceptual organization of an image. Fused HSSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based,region interpretation.

  19. Stereospecific assignment of 1H resonances through chemical shift calculation and their use in structure determination by NMR

    NASA Astrophysics Data System (ADS)

    Harvey, Timothy S.; van Gunsteren, Wilfred F.; Ikura, Mitsuhiko

    1995-04-01

    Understanding of the factors which influence proton chemical shifts in nuclear magnetic resonance (NMR) spectra of proteins has advanced steadily as the number of proteins, for which assignments in conjunction with high resolution structures have been obtained, has increased. Progress has been made in both the calculation of chemical shifts from given coordinates, both empirically for 1H (Williamson & Asakura J. Magn. Reson. (1991) 94, 557) and using ab initio approaches for calculation of 13C (De Dios et al. Science (1993) 260, 1491). Concomitantly Wishart et al. (J. Mol. Biol. (1992) 222, 311), using statistical methods have clarified the relationship between Hα chemical shift and regular secondary structure in proteins to a high degree of accuracy. We recently demonstrated the significant amount of structural information present in the Hα chemical shift through the use of chemical shift restrained molecular dynamics simulations (Harvey & van Gunsteren Techniques in Protein Chemistry IV (1993) 615, Academic Press). Here we apply a similar methodology to the stereospecific assignment of methylene and methyl proton resonances in proteins. Stereospecific assignment of such 1H resonances dramatically increases the degree of precision of ensembles of structures derived from NMR data. However, this is often a cumbersome process, requiring detailed analysis of large amounts of data. Furthermore, experimental considerations such as poor signal-to-noise ratios, spectral overlap and spin diffusion combine to make this process somewhat unreliable. We present calculations of the chemical shifts for the known structures of bovine pancreatic trypsin inhibitor (Mw 6.5 kDa) and the α-amylase inhibitor tendamistat (Mw 8 kDa), for which stereospecific assignments and high resolution structures from both NMR and crystallographic studies are available. The methods described are also applied to the ensemble of structures obtained for protein S (Mw 19 kDa) for both structure

  20. Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control

    PubMed Central

    Frank, Philipp; Schreiter, Joerg; Haefner, Sebastian; Paschew, Georgi; Voigt, Andreas; Richter, Andreas

    2016-01-01

    Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature. PMID:27571209

  1. Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

    PubMed

    Vila, Jorge A; Scheraga, Harold A

    2009-10-20

    Two major techniques have been used to determine the three-dimensional structures of proteins: X-ray diffraction and NMR spectroscopy. In particular, the validation of NMR-derived protein structures is one of the most challenging problems in NMR spectroscopy. Therefore, researchers have proposed a plethora of methods to determine the accuracy and reliability of protein structures. Despite these proposals, there is a growing need for more sophisticated, physics-based structure validation methods. This approach will enable us to (a) characterize the "quality" of the NMR-derived ensemble as a whole by a single parameter, (b) unambiguously identify flaws in the sequence at a residue level, and (c) provide precise information, such as sets of backbone and side-chain torsional angles, that we can use to detect local flaws. Rather than reviewing all of the existing validation methods, this Account describes the contributions of our research group toward a solution of the long-standing problem of both global and local structure validation of NMR-derived protein structures. We emphasize a recently introduced physics-based methodology that makes use of observed and computed (13)C(alpha) chemical shifts (at the density functional theory (DFT) level of theory) for an accurate validation of protein structures in solution and in crystals. By assessing the ability of computed (13)C(alpha) chemical shifts to reproduce observed (13)C(alpha) chemical shifts of a single structure or ensemble of structures in solution and in crystals, we accomplish a global validation by using the conformationally averaged root-mean-square deviation, ca-rmsd, as a scoring function. In addition, the method enables us to provide local validation by identifying a set of individual amino acid conformations for which the computed and observed (13)C(alpha) chemical shifts do not agree within a certain error range and may represent a nonreliable fold of the protein model. Although it is computationally

  2. Approaches to Establishing the Chemical Structure of Extraterrestrial Organic Solids

    NASA Technical Reports Server (NTRS)

    Cody, G. D.; Alexander, C. M. OD.; Wirick, Susan

    2003-01-01

    The majority of extraterrestrial organic matter in carbonaceous chondrites resides in a chemically complex, insoluble and perhaps macromolecular phase. We have been applying a series of independent solid state NMR experiments that are designed to provide a self consistent chemical characterization of this complex material. To date we have thoroughly analyzed 8 organic residues from different meteorites, including a CR2 (EET92042), CIl(Orgueil), CM2 (Murchison), Tagish Lake, CM2 (AlH83100), CM2 (Cold Bokkefeld), CM2 (Mighei), CM3 (Y86720). In fig 1. (1)H to (13)C cross polarization NMR spectra of four of these are shown. Note that there exists an enormous range in chemistry exhibited in organic solid [evident by the breadth of the spectral features both in the aliphatic region (sp(sup 3)) and the aromatic region (sp(sup 2))]. There is also considerable differences in the carbon chemistry across the meteorite groups.

  3. Effects of chemical treatments on hemp fibre structure

    NASA Astrophysics Data System (ADS)

    Kabir, M. M.; Wang, H.; Lau, K. T.; Cardona, F.

    2013-07-01

    In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

  4. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    SciTech Connect

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  5. Investigation of Chemical Durability Mechanisms and Structure of Fluoride Glasses.

    DTIC Science & Technology

    1988-03-01

    coatings on fluoride glasses , it is possible to state the following conclusions: ()Coatings are necessary for both bulk and fiber optics to avoid major...interest for fiber optics applications.’ The chemicalSp . b g rdurability behavior of fluoride glasses not containing zirconium will be reported in later... fiber optics glass containing the base ZBL composition with where X = ppm in solution. V = solution volume (mL), S = additives of Al, Li, and Pb (Fig. 2

  6. Kinetics with chemical reactions and nonequilibrium structures in open systems

    NASA Astrophysics Data System (ADS)

    Aristov, Vladimir; Frolova, Anna; Zabelok, Sergei

    2013-10-01

    Simulations of flows on the basis of kinetic equations for mixtures with chemical reactions are performed. The Nonuniform Relaxation Problems (NRP) are formulated and solved. The Unified Flow Solver (UFS) is used for 1D and 2D NRP. The nonequilibrium kinetics can provide results outside the traditional theory of macroscopic phenomena based on the Navier-Stokes equations. Nonequilibrium flows with different properties in relaxation zones are described.

  7. Chemical Safety Information, Site Security and Fuels Regulatory Relief Act: Public Distribution of Off-Site Consequence Analysis Information Fact Sheet

    EPA Pesticide Factsheets

    Based on assessments of increased risk of terrorist/criminal activity, EPA and DOJ have issued a rule that allows public access to OCA information in ways that are designed to minimize likelihood of chemical accidents and public harm.

  8. Utilizing the Structure and Content Information for XML Document Clustering

    NASA Astrophysics Data System (ADS)

    Tran, Tien; Kutty, Sangeetha; Nayak, Richi

    This paper reports on the experiments and results of a clustering approach used in the INEX 2008 document mining challenge. The clustering approach utilizes both the structure and content information of the Wikipedia XML document collection. A latent semantic kernel (LSK) is used to measure the semantic similarity between XML documents based on their content features. The construction of a latent semantic kernel involves the computing of singular vector decomposition (SVD). On a large feature space matrix, the computation of SVD is very expensive in terms of time and memory requirements. Thus in this clustering approach, the dimension of the document space of a term-document matrix is reduced before performing SVD. The document space reduction is based on the common structural information of the Wikipedia XML document collection. The proposed clustering approach has shown to be effective on the Wikipedia collection in the INEX 2008 document mining challenge.

  9. Eco-evolutionary dynamics, coding structure and the information threshold

    PubMed Central

    2010-01-01

    Background The amount of information that can be maintained in an evolutionary system of replicators is limited by genome length, the number of errors during replication (mutation rate) and various external factors that influence the selection pressure. To date, this phenomenon, known as the information threshold, has been studied (both genotypically and phenotypically) in a constant environment and with respect to maintenance (as opposed to accumulation) of information. Here we take a broader perspective on this problem by studying the accumulation of information in an ecosystem, given an evolvable coding structure. Moreover, our setup allows for individual based as well as ecosystem based solutions. That is, all functions can be performed by individual replicators, or complementing functions can be performed by different replicators. In this setup, where both the ecosystem and the individual genomes can evolve their structure, we study how populations cope with high mutation rates and accordingly how the information threshold might be alleviated. Results We observe that the first response to increased mutation rates is a change in coding structure. At moderate mutation rates evolution leads to longer genomes with a higher diversity than at high mutation rates. Thus, counter-intuitively, at higher mutation rates diversity is reduced and the efficacy of the evolutionary process is decreased. Therefore, moderate mutation rates allow for more degrees of freedom in exploring genotype space during the evolutionary trajectory, facilitating the emergence of solutions. When an individual based solution cannot be attained due to high mutation rates, spatial structuring of the ecosystem can accommodate the evolution of ecosystem based solutions. Conclusions We conclude that the evolutionary freedom (eg. the number of genotypes that can be reached by evolution) is increasingly restricted by higher mutation rates. In the case of such severe mutation rates that an individual

  10. Encoding techniques for complex information structures in connectionist systems

    NASA Technical Reports Server (NTRS)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  11. Instruction in information structuring improves Bayesian judgment in intelligence analysts

    PubMed Central

    Mandel, David R.

    2015-01-01

    An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information) for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts' probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem). Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target's membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments. PMID:25904882

  12. Instruction in information structuring improves Bayesian judgment in intelligence analysts.

    PubMed

    Mandel, David R

    2015-01-01

    An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information) for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts' probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem). Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target's membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments.

  13. Precession technique and electron diffractometry as new tools for crystal structure analysis and chemical bonding determination.

    PubMed

    Avilov, A; Kuligin, K; Nicolopoulos, S; Nickolskiy, M; Boulahya, K; Portillo, J; Lepeshov, G; Sobolev, B; Collette, J P; Martin, N; Robins, A C; Fischione, P

    2007-01-01

    We have developed a new fast electron diffractometer working with high dynamic range and linearity for crystal structure determinations. Electron diffraction (ED) patterns can be scanned serially in front of a Faraday cage detector; the total measurement time for several hundred ED reflections can be tens of seconds having high statistical accuracy for all measured intensities (1-2%). This new tool can be installed to any type of TEM without any column modification and is linked to a specially developed electron beam precession "Spinning Star" system. Precession of the electron beam (Vincent-Midgley technique) reduces dynamical effects allowing also use of accurate intensities for crystal structure analysis. We describe the technical characteristics of this new tool together with the first experimental results. Accurate measurement of electron diffraction intensities by electron diffractometer opens new possibilities not only for revealing unknown structures, but also for electrostatic potential determination and chemical bonding investigation. As an example, we present detailed atomic bonding information of CaF(2) as revealed for the first time by precise electron diffractometry.

  14. Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

    PubMed

    Menestrina, G; Belmonte, G; Parisi, V; Morante, S

    1992-09-01

    Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

  15. Allocation of chemical and structural defenses in the sponge Melophlus sarasinorum

    PubMed Central

    Rohde, Sven; Schupp, Peter J.

    2011-01-01

    Sponges have evolved a variety of chemical and structural defense mechanisms to avoid predation. While chemical defense is well established in sponges, studies on structural defense are rare and with ambiguous results. We used field and laboratory experiments to investigate predation patterns and the anti-predatory defense mechanisms of the sponge Melophlus sarasinorum, a common inhabitant of Indo-pacific coral reefs. Specifically, we aimed to investigate whether M. sarasinorum is chemically or structurally defended against predation and if the defenses are expressed differently in the ectosomal and choanosomal tissue of the sponge. Chemical defense was measured as feeding deterrence, structural defense as feeding deterrence and toughness. Our results demonstrated that chemical defense is evenly distributed throughout the sponge and works in conjunction with a structurally defended ectosome to further reduce predation levels. The choanosome of the sponge contained higher protein levels, but revealed no structural defense. We conclude that the equal distribution of chemical defenses throughout M. sarasinorum is in accordance with Optimal Defense Theory (ODT) in regards to fish predation, while structural defense supports ODT by being restricted to the surface layer which experiences the highest predation risks from mesograzers. PMID:21461028

  16. STRUCTURE AND FEEDBACK IN 30 DORADUS. II. STRUCTURE AND CHEMICAL ABUNDANCES

    SciTech Connect

    Pellegrini, E. W.; Baldwin, J. A.; Ferland, G. J.

    2011-09-01

    We use our new optical-imaging and spectrophotometric survey of key diagnostic emission lines in 30 Doradus, together with CLOUDY photoionization models, to study the physical conditions and ionization mechanisms along over 4000 individual lines of sight at points spread across the face of the extended nebula, out to a projected radius 75 pc from R136 at the center of the ionizing cluster NGC 2070. We focus on the physical conditions, geometry, and importance of radiation pressure on a point-by-point basis, with the aim of setting observational constraints on important feedback processes. We find that the dynamics and large-scale structure of 30 Dor are set by a confined system of X-ray bubbles in rough pressure equilibrium with each other and with the confining molecular gas. Although the warm (10,000 K) gas is photoionized by the massive young stars in NGC 2070, the radiation pressure does not currently play a major role in shaping the overall structure. The completeness of our survey also allows us to create a composite spectrum of 30 Doradus, simulating the observable spectrum of a spatially unresolved, distant giant extragalactic H II region. We find that the highly simplified models used in the 'strong line' abundance technique do in fact reproduce our observed line strengths and deduced chemical abundances, in spite of the more than one order of magnitude range in the ionization parameter and density of the actual gas in 30 Dor.

  17. Computer Translation of Systematic Chemical Nomenclature to Structural Formulas--Steroids

    ERIC Educational Resources Information Center

    Stillwell, R. N.

    1973-01-01

    A program (FORMULA) is described which translates the systematic chemical names of steroids to structural formulas which, with a suitable graphic output device could be used for direct typesetting. (10 references) (Author)

  18. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  19. Register of experts for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Stuhrke, W. F.

    1975-01-01

    This register is comprised of a list of approximately 300 experts from approximately 90 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure: (1) life prediction for structural materials, (2) fracture toughness testing, (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. The criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. Each author included is listed by organizational affiliation, address, and principal field of expertise. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The register includes two indexes; an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  20. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  1. Fiber ring laser interrogated zeolite-coated singlemode-multimode-singlemode structure for trace chemical detection.

    PubMed

    Lan, X; Huang, J; Han, Q; Wei, T; Gao, Z; Jiang, H; Dong, J; Xiao, H

    2012-06-01

    Zeolite thin films were synthesized on the claddingless multimode portion of a singlemode-multimode-singlemode (SMS) fiber structure to construct a chemical vapor sensor. The zeolite-coated SMS structure was inserted into a fiber ring amplifier to produce a laser line. Combining the strong molecular adsorption capability of the nanoporous zeolite and the high signal-to-noise ratio of the fiber laser, the device was demonstrated for chemical vapor sensing with a low detection limit.

  2. Some basic data structures and algorithms for chemical generic programming.

    PubMed

    Zhang, Wei; Hou, Tingjun; Qiao, Xuebin; Xu, Xiaojie

    2004-01-01

    Here, we report a template library used for molecular operation, the Molecular Handling Template Library (MHTL). The library includes some generic data structures and generic algorithms, and the two parts are associated with each other by two concepts: Properties and Molecule. The concept Properties describes the interface to access objects' properties, and the concept Molecule describes the minimum requirement for a molecular class. Data structures include seven models of Properties, each using a different method to access properties, and two models of molecular classes. Algorithms include molecular file manipulation subroutines, SMARTS language interpreter and matcher functions, and molecular OpenGL rendering functions.

  3. Chemical Structures and Bioactivities of Sulfated Polysaccharides from Marine Algae

    PubMed Central

    Jiao, Guangling; Yu, Guangli; Zhang, Junzeng; Ewart, H. Stephen

    2011-01-01

    Sulfated polysaccharides and their lower molecular weight oligosaccharide derivatives from marine macroalgae have been shown to possess a variety of biological activities. The present paper will review the recent progress in research on the structural chemistry and the bioactivities of these marine algal biomaterials. In particular, it will provide an update on the structural chemistry of the major sulfated polysaccharides synthesized by seaweeds including the galactans (e.g., agarans and carrageenans), ulvans, and fucans. It will then review the recent findings on the anticoagulant/antithrombotic, antiviral, immuno-inflammatory, antilipidemic and antioxidant activities of sulfated polysaccharides and their potential for therapeutic application. PMID:21566795

  4. Seeing is believing: information content and behavioural response to visual and chemical cues

    PubMed Central

    Gonzálvez, Francisco G.; Rodríguez-Gironés, Miguel A.

    2013-01-01

    Predator avoidance and foraging often pose conflicting demands. Animals can decrease mortality risk searching for predators, but searching decreases foraging time and hence intake. We used this principle to investigate how prey should use information to detect, assess and respond to predation risk from an optimal foraging perspective. A mathematical model showed that solitary bees should increase flower examination time in response to predator cues and that the rate of false alarms should be negatively correlated with the relative value of the flower explored. The predatory ant, Oecophylla smaragdina, and the harmless ant, Polyrhachis dives, differ in the profile of volatiles they emit and in their visual appearance. As predicted, the solitary bee Nomia strigata spent more time examining virgin flowers in presence of predator cues than in their absence. Furthermore, the proportion of flowers rejected decreased from morning to noon, as the relative value of virgin flowers increased. In addition, bees responded differently to visual and chemical cues. While chemical cues induced bees to search around flowers, bees detecting visual cues hovered in front of them. These strategies may allow prey to identify the nature of visual cues and to locate the source of chemical cues. PMID:23698013

  5. Seeing is believing: information content and behavioural response to visual and chemical cues.

    PubMed

    Gonzálvez, Francisco G; Rodríguez-Gironés, Miguel A

    2013-07-22

    Predator avoidance and foraging often pose conflicting demands. Animals can decrease mortality risk searching for predators, but searching decreases foraging time and hence intake. We used this principle to investigate how prey should use information to detect, assess and respond to predation risk from an optimal foraging perspective. A mathematical model showed that solitary bees should increase flower examination time in response to predator cues and that the rate of false alarms should be negatively correlated with the relative value of the flower explored. The predatory ant, Oecophylla smaragdina, and the harmless ant, Polyrhachis dives, differ in the profile of volatiles they emit and in their visual appearance. As predicted, the solitary bee Nomia strigata spent more time examining virgin flowers in presence of predator cues than in their absence. Furthermore, the proportion of flowers rejected decreased from morning to noon, as the relative value of virgin flowers increased. In addition, bees responded differently to visual and chemical cues. While chemical cues induced bees to search around flowers, bees detecting visual cues hovered in front of them. These strategies may allow prey to identify the nature of visual cues and to locate the source of chemical cues.

  6. Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

    PubMed

    Gao, Yu-Fei; Chen, Lei; Cai, Yu-Dong; Feng, Kai-Yan; Huang, Tao; Jiang, Yang

    2012-01-01

    Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.

  7. Unraveling the 13C NMR chemical shifts in single-walled carbon nanotubes: dependence on diameter and electronic structure.

    PubMed

    Engtrakul, Chaiwat; Irurzun, Veronica M; Gjersing, Erica L; Holt, Josh M; Larsen, Brian A; Resasco, Daniel E; Blackburn, Jeffrey L

    2012-03-14

    The atomic specificity afforded by nuclear magnetic resonance (NMR) spectroscopy could enable detailed mechanistic information about single-walled carbon nanotube (SWCNT) functionalization as well as the noncovalent molecular interactions that dictate ground-state charge transfer and separation by electronic structure and diameter. However, to date, the polydispersity present in as-synthesized SWCNT populations has obscured the dependence of the SWCNT (13)C chemical shift on intrinsic parameters such as diameter and electronic structure, meaning that no information is gleaned for specific SWCNTs with unique chiral indices. In this article, we utilize a combination of (13)C labeling and density gradient ultracentrifugation (DGU) to produce an array of (13)C-labeled SWCNT populations with varying diameter, electronic structure, and chiral angle. We find that the SWCNT isotropic (13)C chemical shift decreases systematically with increasing diameter for semiconducting SWCNTs, in agreement with recent theoretical predictions that have heretofore gone unaddressed. Furthermore, we find that the (13)C chemical shifts for small diameter metallic and semiconducting SWCNTs differ significantly, and that the full-width of the isotropic peak for metallic SWCNTs is much larger than that of semiconducting nanotubes, irrespective of diameter.

  8. The chemical and hydrologic structure of Poas volcano, Costa Rica

    USGS Publications Warehouse

    Rowe, G.L.; Brantley, S.L.; Fernandez, J.F.; Borgia, A.

    1995-01-01

    Comparison of the chemical characteristics of spring and river water draining the flanks of Poas Volcano, Costa Rica indicates that acid chloride sulfate springs of the northwestern flank of the volcano are derived by leakage and mixing of acid brines formed in the summit hydrothermal system with dilute flank groundwater. Acid chloride sulfate waters of the Rio Agrio drainage basin on the northwestern flank are the only waters on Poas that are affected by leakage of acid brines from the summit hydrothermal system. Acid sulfate waters found on the northwestern flank are produced by the interaction of surface and shallow groundwater with dry and wet acid deposition of SO2 and H2SO4 aerosols, respectively. The acid deposition is caused by a plume of acid gases that is released by a shallow magma body located beneath the active crater of Poas. -from Authors

  9. Chemical structure of the deep atmosphere of Jupiter

    NASA Technical Reports Server (NTRS)

    Barshay, S. S.; Lewis, J. S.

    1978-01-01

    Equilibrium abundances calculated for a system of over 500 compounds of 27 selected elements along a nominal Jupiter adiabat are reported. Several species predicted to be of negligible abundance in the visible upper troposphere if chemical equilibrium is exactly attained are found to be potential tracers of rapid vertical motions. Vertical mixing of certain species, especially CO, PH3, AsH3, GeS, and GeH4, may provide detectable quantities of these species near the visible cloudtops due to quenching and incomplete equilibration of the rapidly rising, rapidly cooling gas. Observational prospects for detecting such tracers of deep circulation are discussed in the light of the spectroscopic detection of CO in the 5-micron window on Jupiter and the confirmation of PH3 on both Jupiter and Saturn.

  10. Reconstructing Information in Large-Scale Structure via Logarithmic Mapping

    NASA Astrophysics Data System (ADS)

    Szapudi, Istvan

    We propose to develop a new method to extract information from large-scale structure data combining two-point statistics and non-linear transformations; before, this information was available only with substantially more complex higher-order statistical methods. Initially, most of the cosmological information in large-scale structure lies in two-point statistics. With non- linear evolution, some of that useful information leaks into higher-order statistics. The PI and group has shown in a series of theoretical investigations how that leakage occurs, and explained the Fisher information plateau at smaller scales. This plateau means that even as more modes are added to the measurement of the power spectrum, the total cumulative information (loosely speaking the inverse errorbar) is not increasing. Recently we have shown in Neyrinck et al. (2009, 2010) that a logarithmic (and a related Gaussianization or Box-Cox) transformation on the non-linear Dark Matter or galaxy field reconstructs a surprisingly large fraction of this missing Fisher information of the initial conditions. This was predicted by the earlier wave mechanical formulation of gravitational dynamics by Szapudi & Kaiser (2003). The present proposal is focused on working out the theoretical underpinning of the method to a point that it can be used in practice to analyze data. In particular, one needs to deal with the usual real-life issues of galaxy surveys, such as complex geometry, discrete sam- pling (Poisson or sub-Poisson noise), bias (linear, or non-linear, deterministic, or stochastic), redshift distortions, pro jection effects for 2D samples, and the effects of photometric redshift errors. We will develop methods for weak lensing and Sunyaev-Zeldovich power spectra as well, the latter specifically targetting Planck. In addition, we plan to investigate the question of residual higher- order information after the non-linear mapping, and possible applications for cosmology. Our aim will be to work out

  11. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  12. Are the Chemical Structures in your QSAR Correct?

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are used to predict many different endpoints, utilize hundreds and even thousands of different parameters (or descriptors), and are created using a variety of approaches. The one thing they all have in common is the assumptio...

  13. Chemical structure and biological activity of the diazepines

    PubMed Central

    Danneberg, P.; Weber, K. H.

    1983-01-01

    1 Since the introduction of chlordiazepoxide and diazepam many diazepines have been developed. Use of these drugs is increasing and considerable knowledge has accumulated about their mechanisms of action. 2 The structural and pharmacological properties of these drugs are surveyed briefly. PMID:6140944

  14. Chemical Structure and Accidental Explosion Risk in the Research Laboratory

    ERIC Educational Resources Information Center

    Churchill, David G.

    2006-01-01

    Tips that laboratory researchers and beginning graduate students can use to safeguard against explosion hazard with emphasis on clear illustrations of molecular structure are discussed. Those working with hazardous materials must proceed cautiously and may want to consider alternative and synthetic routes.

  15. Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity

    PubMed Central

    Anderson, Janet S.; Hernández, Griselda; LeMaster, David M.

    2012-01-01

    Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. PMID:23182463

  16. Prediction of retention in hydrophilic interaction liquid chromatography using solute molecular descriptors based on chemical structures.

    PubMed

    Taraji, Maryam; Haddad, Paul R; Amos, Ruth I J; Talebi, Mohammad; Szucs, Roman; Dolan, John W; Pohl, Christopher A

    2017-02-24

    Quantitative structure-retention relationship (QSRR) models are developed to predict the retention times of analytes on five hydrophilic interaction liquid chromatography (HILIC) stationary phases (bare silica, amine, amide, diol and zwitterionic), with a view to selecting the most suitable stationary phase(s) for the separation of these analytes. The study was conducted using six β-adrenergic agonists as target analytes. Molecular descriptors were calculated based only on chemical structures optimized using density functional theory. A genetic algorithm (GA) was then used to select the most relevant molecular descriptors and these were used to build a retention model for each stationary phase using partial least squares (PLS) regression. This model was then used to predict the retention of the test set of target analytes. This process created an optimized descriptor set which enhanced the reliability of the developed QSRR models. Finally, the QSRR models developed in the work were utilized to provide some insight into the separation mechanisms operating in the HILIC mode. Three performance criteria - mean absolute error (MAE), root mean square error of prediction scaled to retention time (RMSEP), and the number of selected descriptors, were used to evaluate the developed models when applied to an external test set of six β-adrenergic agonists and showed highly predictive abilities. MAE values ranged from 13 to 25s on four of the stationary phases, with a somewhat higher error (50s) being observed for the zwitterionic phase. RMSEP values of 4.88-11.12% were recorded. Validation was performed through Y-randomization and chemical domain applicability, from which it was evident that the developed optimized GA-PLS models were robust. The high levels of accuracy, reliability and applicability of the models were to a large extent due to the optimization of the GA descriptor set and the presence of relevant structural and geometric molecular descriptors, together with

  17. Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

    NASA Astrophysics Data System (ADS)

    Manojkumar, P. A.; Chirayath, V. A.; Balamurugan, A. K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A. K.; Raj, Baldev

    2016-09-01

    Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  18. Temperature effects on chemical structure and motion in coal. Final report

    SciTech Connect

    Maciel, G.E.

    1996-09-30

    The objective of this project was to apply recently developed, state-of-the-art nuclear magnetic resonance (NMR) techniques to examine in situ changes in the chemical structure and molecular/macromolecular motion in coal as the temperature is increased above room temperature. Although alterations in the chemical structure of coal have been studied previously by {sup 13}C NMR, using quenched samples, the goal of this project was to examine these chemical structural changes, and changes in molecular/macromolecular mobility that may precede or accompany the chemical changes, at elevated temperatures, using modern {sup 13}C and {sup 1}H NMR techniques, especially {sup 1}H dipolar-dephasing techniques and related experiments pioneered in the laboratory for examining pyridine-saturated coals. This project consisted of the following four primary segments and related efforts on matters relevant to the first four tasks. (1) {sup 1}H NMR characterization of coal structure and mobility as a function of temperature variation over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (2) {sup 1}H NMR characterization of coal structure, mobility and conversion as a function of temperature variation over a temperature range (240--500 C) for which chemical transformations of coal are known to occur. (3) {sup 13}C NMR investigation of coal structure/mobility as a function of temperature over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (4) {sup 13}C NMR investigation of coal structure, dynamics and conversion as a function of temperature variation over a range (240--500 C) for which chemical transformations of coal are known to occur. (5) Related matters relevant to the first four tasks: (a) {sup 1}H CRAMPS NMR characterization of oil shales and their kerogen concentrates; and (b) improved quantitation in {sup 13}C MAS characterization of coals.

  19. Atmospheric chemical and thermal structure evolution after one Titan year

    NASA Astrophysics Data System (ADS)

    Coustenis, Athena; Bampasidis, Georgios; Achterberg, Richard; Lavvas, Panayiotis; Vinatier, Sandrine; Nixon, Conor; Jennings, Donald; Teanby, Nicolas; Flasar, F. Michael; Carlson, Ronald; Orton, Glenn; Romani, Paul; Guandique, Ever

    2013-04-01

    Our radiative transfer code (ARTT) was applied to Cassini Composite Infrared Spectrometer (CIRS) data taken during Titan flybys from 2004-2010 and to the 1980 Voyager 1 flyby values inferred from the re-analysis of the Infrared Radiometer Spectrometer (IRIS) spectra [1], as well as to the intervening ground- and space- based observations (such as with ISO, [2]), providing us with a new view of the stratospheric evolution over a Titanian year (V1 encounter Ls=9° was reached in mid-2010). CIRS nadir and limb spectral [3,4] show variations in temperature and chemical composition in the stratosphere during the Cassini mission, before and after the Northern Spring Equinox (NSE). We find indication for a weakening of the temperature gradient with warming of the stratosphere and cooling of the lower mesosphere. In addition, we infer precise concentrations for the trace gases and their main isotopologues and find that the chemical composition in Titan's stratosphere varied significantly with latitude during the 6 terrestrial years investigated here, with increased mixing ratios towards the northern latitudes. In particular, we find a maximum enhancement of several gases observed at northern latitudes up to 50°N around mid-2009, at the time of the NSE. We find that this raise is followed by a rapid decrease in chemical inventory in 2010 probably due to changes in the cross vortex mixing or northward migration of the vortex boundary [5,6,7] consistent with the weakening thermal gradient. The finding also ties into the location of the maximum temperature gradient, which appears to be moving northward over the winter/spring season. The return of today's abundances close to the Voyager values (at the same season) is an indication that, as for the Earth, the solar radiation dominates over the other energy sources even at 10AU [8]. Nevertheless, the differences observed for some complex hydrocarbons in the North pole indicate that the other processes could be at play as well

  20. Environmental chemicals and breast cancer risk--a structural chemistry perspective.

    PubMed

    Weyandt, Jamie; Ellsworth, Rachel E; Hooke, Jeffrey A; Shriver, Craig D; Ellsworth, Darrell L

    2008-01-01

    In modern industrialized societies, people are exposed to thousands of naturally occurring and synthetic chemicals throughout their lifetime. Although certain occupational chemicals are known to be carcinogenic in humans, it has been difficult to definitively determine the adverse health effects of many environmental pollutants due to their tremendous chemical diversity and absence of a consistent structural motif. Many environmental chemicals are metabolized in the body to reactive intermediates that readily react with DNA to form modified bases known as adducts, while other compounds mimic the biological function of estrogen. Because environmental chemicals tend to accumulate in human tissues and have carcinogenic and/or estrogenic properties, there is heightened interest in determining whether environmental chemicals increase risk for endocrine-related cancers, including breast cancer. Breast cancer is the most common cancer in women worldwide, but established risk factors account for a relatively small proportion of cases and causative factors remain ambiguous and poorly defined. In this review, we outline the structural chemistry of environmental contaminants, describe mechanisms of carcinogenesis and molecular pathways through which these chemicals may exert detrimental health effects, review current knowledge of relationships between chemicals and breast cancer risk, and highlight future directions for research on environmental contributions to breast cancer. Improved understanding of the relationship between environmental chemicals and breast cancer will help to educate the general public about real and perceived dangers of these pollutants in our environment and has the potential to reduce individual risk by changing corporate practices and improving public health policies.

  1. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable

    NASA Astrophysics Data System (ADS)

    Werheit, Helmut

    2016-10-01

    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  2. Deriving Structural Information from Experimentally Measured Data on Biomolecules.

    PubMed

    van Gunsteren, Wilfred F; Allison, Jane R; Daura, Xavier; Dolenc, Jožica; Hansen, Niels; Mark, Alan E; Oostenbrink, Chris; Rusu, Victor H; Smith, Lorna J

    2016-12-23

    During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q(exp) of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q(exp) , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Q(exp) , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.

  3. Structural features of endocrine active chemicals--A comparison of in vivo and in vitro data.

    PubMed

    Lewin, Geertje; Escher, Sylvia E; van der Burg, Bart; Simetska, Nelly; Mangelsdorf, Inge

    2015-08-01

    Studies on reproductive toxicity need high numbers of test animals. Therefore, we investigated whether chemical structural features (SF) in combination with in vitro data on specific adverse outcome pathways (AOPs) may be used for predicting reproductive toxicity of untested chemicals. Using the OECD Toolbox and expert judgment, we identified 89 structure groups for 275 chemicals for which the results of prenatal developmental toxicity or multigeneration studies were present in the Fraunhofer database on Fertility and Developmental Toxicity in experimental animals (FeDTex) database. Likewise, we evaluated 220 chemicals which had been tested in reporter gene assays on endocrine ((anti)estrogenic and (anti)androgenic) properties in the CALUX(®) test battery. There was a large spread of effect levels for substances within the chemical structure groups for both, in vivo and in vitro results. The groups of highest concern (diphenyl derivatives, planar conjugated systems with fused rings, phenols and organophosphates) correlated quite well, however, between the in vivo and in vitro data on estrogenic activity. For the 56 chemicals represented in both databases, lowest effect doses in vivo correlated well with the estrogenic activity in vitro. These results suggest that a panel of assays covering relevant AOPs and data on metabolism and toxicokinetics may allow prediction of relative reproductive or development toxicity potency within the identified chemical structure groups.

  4. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

  5. Structural elucidation of organic contaminants by chemical ionisation mass spectrometry

    NASA Astrophysics Data System (ADS)

    Moldovan, Zaharie

    2009-08-01

    The PI-CI mass spectra formation for a new family of aromatic amines, with general formula: R1-Ph-NH-Ph-R2 is discussed in correlation with the R1 and R2 structure. The compounds where isolated from some environmental samples by GC/MS technique. The characteristic ions are produced by rearrangement processes involving olefin and alkane neutral molecule elimination from [M+H]+ and sole olefin molecule elimination from [M+ C2H5]+.

  6. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-05

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+).

  7. Current Challenges in Development of a Database of Three-Dimensional Chemical Structures

    PubMed Central

    Maeda, Miki H.

    2015-01-01

    We are developing a database named 3DMET, a three-dimensional structure database of natural metabolites. There are two major impediments to the creation of 3D chemical structures from a set of planar structure drawings: the limited accuracy of computer programs and insufficient human resources for manual curation. We have tested some 2D–3D converters to convert 2D structure files from external databases. These automatic conversion processes yielded an excessive number of improper conversions. To ascertain the quality of the conversions, we compared IUPAC Chemical Identifier and canonical SMILES notations before and after conversion. Structures whose notations correspond to each other were regarded as a correct conversion in our present work. We found that chiral inversion is the most serious factor during the improper conversion. In the current stage of our database construction, published books or articles have been resources for additions to our database. Chemicals are usually drawn as pictures on the paper. To save human resources, an optical structure reader was introduced. The program was quite useful but some particular errors were observed during our operation. We hope our trials for producing correct 3D structures will help other developers of chemical programs and curators of chemical databases. PMID:26075200

  8. Magnetic and Structural Properties of Chemically Synthesized Ni and

    NASA Astrophysics Data System (ADS)

    Bonder, Michael; Leslie-Pelecky, Diandra L.; Zhang, X. Q.; Rieke, R. D.

    1996-03-01

    The reduction of nickel salts using a technique developed by Rieke and co-workers produces highly chemically reactive particles with enhanced magnetic properties due to their nanoscale size. As-synthesized particles are 2-5 nm in diameter and range from superparamagnetic to ferromagnetic, depending on synthesis details. Grain sizes from 5 nm to 1000 nm have been produced by subsequent vacuum annealing. The maximum coercivities and remanence ratios are obtained during the first half-hour to hour of annealing. Coercivities in these systems may be up to ten times the value of bulk nickel, with remanence ratios approaching 0.5. Transmission electron microscopy shows that the nickel grains are square and sometimes embedded in a lithium halide matrix. Under appropriate synthesis and annealing conditions, the as-synthesized particles can be transformed into the metastable Ni_3C phase, which has important implications in catalysis. Comparison with Stoner-Wohlfarth and Holz-Scherrer predictions of the magnetic properties will be made.

  9. Nano structured carbon nitrides prepared by chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Karuppannan, Ramesh; Prashantha, M.

    2010-08-01

    Nanostructured carbon nitride films were prepared by pyrolysis assisted chemical vapour deposition(CVD). A two zone furnace with a temperature profile having a uniform temperature over a length of 20 cm length has been designed and developed. The precursor Azabenzimidazole was taken in a quartz tube and evaporated at 400 0C. The dense vapours enter the pyrolysis zone kept at a desired temperature and deposit on the quartz substrates. The FTIR spectrum of the prepared samples shows peaks at 1272 cm-1 (C.N stretching) and 1600 cm-1 (C=N) confirms the bonding of nitrogen with carbon. Raman D and G peaks, are observed at 1360 cm-1 and 1576 cm-1 respectively. XPS core level spectra of C 1s and N 1s show the formation of π bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is ~100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

  10. Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Characterization of chemical structure.

    PubMed

    Wang, Junlong; Yang, Wen; Wang, Jiancheng; Wang, Xia; Wu, Fang; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2015-11-20

    The biological activities of sulfated polysaccharides are related to the substitution positions of functional groups. In this study, regioselective sulfation of Artemisia sphaerocephala polysaccharides (SRSASP) was prepared by using triphenylchloromethane (TrCl) as protecting precursor. FT-IR spectra and X-ray photoelectron spectroscopy (XPS) showed that SO(3-) group (S(6+), high binding energy of 168.7eV) was widely present in sulfated polysaccharides. (13)C NMR spectroscopy showed that C-2 and C-3 substitution was occurred but not fully sulfation. Meanwhile, C-6 substituted signals near 65ppm were not observed. The degree of substitution varied from 0.44 to 0.63 in SRSASP which could be attributed to the low reactivity at secondary hydroxyl. Monosaccharide composition result showed a decrease in the ratio of mannose/glucose, indicating the change of chemical composition in sulfated polysaccharides. In size-exclusion chromatograph analysis, a decrease in molecular weight and broadening of molecular weight distribution of sulfated polysaccharides was also observed. It could be attributed to the hydrolysis of polysaccharide in the sulfated reaction.

  11. An Informationally Structured Room for Robotic Assistance †

    PubMed Central

    Tsuji, Tokuo; Mozos, Oscar Martinez; Chae, Hyunuk; Pyo, Yoonseok; Kusaka, Kazuya; Hasegawa, Tsutomu; Morooka, Ken'ichi; Kurazume, Ryo

    2015-01-01

    The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot. PMID:25912347

  12. Structural, optical and charge generation properties of chalcostibite and tetrahedrite copper antimony sulfide thin films prepared from metal xanthates† †Electronic supplementary information (ESI) available: Chemical structures of the used metal xanthates, additional XRD, SEM-EDX and UV-vis data. See DOI: 10.1039/c5ta05777a Click here for additional data file.

    PubMed Central

    MacLachlan, Andrew J.; Brown, Michael D.

    2015-01-01

    Herein, we report on a solution based approach for the preparation of thin films of copper antimony sulfide, an emerging absorber material for third generation solar cells. In this work, copper and antimony xanthates are used as precursor materials for the formation of two different copper antimony sulfide phases: chalcostibite (CuSbS2) and tetrahedrite (Cu12Sb4S13). Both phases were thoroughly investigated regarding their structural and optical properties. Moreover, thin films of chalcostibite and tetrahedrite were prepared on mesoporous TiO2 layers and photoinduced charge transfer in these metal sulfide/TiO2 heterojunctions was studied via transient absorption spectroscopy. Photoinduced charge transfer was detected in both the chalcostibite as well as the tetrahedrite sample, which is an essential property in view of applying these materials as light-harvesting agents in semiconductor sensitized solar cells. PMID:27019713

  13. Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

    NASA Astrophysics Data System (ADS)

    Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2014-01-01

    The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

  14. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    PubMed

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

  15. The chemical structure of Gloeocapsomorpha prisca microfossils: implications for their origin

    NASA Astrophysics Data System (ADS)

    Blokker, Peter; van Bergen, Pim; Pancost, Rich; Collinson, Margaret E.; de Leeuw, Jan W.; Sinninghe Damste, Jaap S.

    2001-03-01

    Two Estonian Kukersites (Ordovician) and two samples from the Guttenberg Member (Ordovician) of the Decorah formation (North America) containing botryoidal aggregates of Gloeocapsomorpha prisca were investigated by RuO 4 chemical degradation, FTIR, and flash pyrolysis-GC/MS to obtain information about the polymeric structure of these microfossils. The products formed upon oxidation by RuO 4 were analysed by GC/MS and revealed the presence of a wide range of carboxyl and/or carbonyl moiety containing compounds with carbon skeletons ranging from C 5 to C 20. The Estonian Kukersites reveal the presence of a characteristic set of mono-, di-, and tricarboxylic acids. These compounds suggest that the Estonian Kukersites are composed of a polymer consisting of mainly C 21 and C 23n-alkenyl resorcinol building blocks. Similarly, although the tricarboxylic acids are not present, the RuO 4 degradation product mixtures of the Guttenberg Member samples, suggest a poly( n-alkyl resorcinol) structure. The higher thermal maturity is most likely responsible for the different chemistry and morphology of the G. prisca microfossils in these samples. Because compounds like n-alkenyl resorcinols are known to polymerise under oxygenated conditions even in an aqueous environment, it is not per se necessary that these microfossils are composed of a selectively preserved biopolymeric cell wall. It is also possible that G. prisca microfossils are composed of a cell wall or sheath component that polymerised during senescence or diagenesis of the organism.

  16. Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

    PubMed

    Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

    2011-06-02

    Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS.

  17. Structure and Chemical Durability of Lead Crystal Glass.

    PubMed

    Angeli, Frédéric; Jollivet, Patrick; Charpentier, Thibault; Fournier, Maxime; Gin, Stéphane

    2016-11-01

    Silicate glasses containing lead, also called lead crystal glasses, are commonly used as food product containers, in particular for alcoholic beverages. Lead's health hazards require major attention, which can first be investigated through the understanding of Pb release mechanisms in solution. The behavior of a commercial crystal glass containing 10.6 mol % of PbO (28.3 wt %) was studied in a reference solution of 4% acetic acid at 22, 40, and 70 °C at early and advanced stages of reaction. High-resolution solid-state (17)O and (29)Si NMR was used to probe the local structure of the pristine and, for the first time, of the altered lead crystal glass. Inserted into the vitreous structure between the network formers as Si-O-Pb bonds, Pb does not form Pb-O-Pb clusters which are expected to be more easily leached. A part of K is located near Pb, forming mixed Si-O-(Pb,K) near the nonbridging oxygens. Pb is always released into the solution following a diffusion-controlled dissolution over various periods of time, at a rate between 1 and 2 orders of magnitude lower than the alkalis (K and Na). The preferential release of alkalis is followed by an in situ repolymerization of the silicate network. Pb is only depleted in the outermost part of the alteration layer. In the remaining part, it stays mainly surrounded by Si in a stable structural configuration similar to that of the pristine glass. A simple model is proposed to estimate the Pb concentration as a function of glass surface, solution volume, temperature, and contact time.

  18. Register of experts for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A list of approximately 150 experts from approximately 60 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure is presented. Each author included is listed by organizational affiliation, address and principal field of expertise. The initial criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The Register includes two indexes: an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  19. Chemical Physics Courses.

    ERIC Educational Resources Information Center

    Lee, J.; Munn, R. W.

    1978-01-01

    This is a guide to the chemical physics major. The scope of chemical physics is presented, along with the general features of course contents and possible course structures. This information was derived from a survey of British universities and colleges offering undergraduate degree courses in chemical physics. (BB)

  20. Electronic structure modulation of graphene edges by chemical functionalization

    NASA Astrophysics Data System (ADS)

    Taira, Remi; Yamanaka, Ayaka; Okada, Susumu

    2016-11-01

    Using the density functional theory with the effective screening medium method, we study the electronic properties of graphene nanoribbons with zigzag edges that are terminated by hydrogen and ketone, hydroxyl, carbonyl, and carboxyl functional groups. Our calculations showed that the work function and electronic structures of the edges of the nanoribbons are sensitive to the functional groups attached to the edges. The nearly free electron state emerges in the vacuum region outside the hydroxylated edges and crosses the Fermi level, indicating the possibility of negative electron affinity at the edges.

  1. Quantitative structure-activity relationship analysis of acute toxicity of diverse chemicals to Daphnia magna with whole molecule descriptors.

    PubMed

    Moosus, M; Maran, U

    2011-10-01

    Quantitative structure-activity relationship analysis and estimation of toxicological effects at lower-mid trophic levels provide first aid means to understand the toxicity of chemicals. Daphnia magna serves as a good starting point for such toxicity studies and is also recognized for regulatory use in estimating the risk of chemicals. The ECOTOX database was queried and analysed for available data and a homogenous subset of 253 compounds for the endpoint LC50 48 h was established. A four-parameter quantitative structure-activity relationship was derived (coefficient of determination, r (2) = 0.740) for half of the compounds and internally validated (leave-one-out cross-validated coefficient of determination, [Formula: see text] = 0.714; leave-many-out coefficient of determination, [Formula: see text] = 0.738). External validation was carried out with the remaining half of the compounds (coefficient of determination for external validation, [Formula: see text] = 0.634). Two of the descriptors in the model (log P, average bonding information content) capture the structural characteristics describing penetration through bio-membranes. Another two descriptors (energy of highest occupied molecular orbital, weighted partial negative surface area) capture the electronic structural characteristics describing the interaction between the chemical and its hypothetic target in the cell. The applicability domain was subsequently analysed and discussed.

  2. Titan's winter polar vortex structure revealed by chemical tracers

    NASA Astrophysics Data System (ADS)

    Teanby, N. A.; de Kok, R.; Irwin, P. G. J.; Osprey, S.; Vinatier, S.; Gierasch, P. J.; Read, P. L.; Flasar, F. M.; Conrath, B. J.; Achterberg, R. K.; Bézard, B.; Nixon, C. A.; Calcutt, S. B.

    2008-12-01

    The winter polar vortex on Saturn's largest moon Titan has profound effects on atmospheric circulation and chemistry and for the current northern midwinter season is the major dynamical feature of Titan's stratosphere and mesosphere. We use 2 years of observations from Cassini's composite infrared spectrometer to determine cross sections of five independent chemical tracers (HCN, HC3N, C2H2, C3H4, and C4H2), which are then used to probe dynamical processes occurring within the vortex. Our results provide compelling evidence that the vortex acts as a strong mixing barrier in the stratosphere and mesosphere, effectively separating a tracer-enriched air mass in the north from air at lower latitudes. In the mesosphere, above the level of the vortex jet, a tracer-depleted zone extends away from the north pole toward the equator and enrichment is confined to high northern latitudes. However, below this level, mixing processes cause tongues of gas to extend away from the polar region toward the equator. These features are not reproduced by current general circulation models and suggest that a residual polar circulation is present and that waves and instabilities form a more important part of Titan's atmospheric dynamics than previously thought. We also observe an unexpected enrichment of C4H2 in the northern stratosphere, which suggests photochemical polymerization of C2H2. Our observations provide stringent new constraints for dynamical and photochemical models and identify key polar processes for the first time. Some of the processes we see have analogues in Earth's polar vortex, while others are unique to Titan.

  3. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures.

    PubMed

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Castranova, Vincent; Porter, Dale W; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2015-12-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential.

  4. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures

    PubMed Central

    Castranova, Vincent; Porter, Dale W.; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2016-01-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential. PMID:26783369

  5. ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

    PubMed Central

    2012-01-01

    The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly

  6. Tenth anniversary of CAS ONLINE service : What CAS services should be in the new era of chemical information

    NASA Astrophysics Data System (ADS)

    Kostakos, Charles N.

    Chemical Abstracts Service celebrated 10th anniversary of CAS online information service in 1990. A speech given on the occasion reviewed history of the CAS ONLINE, in relation to its most important benefits for scientists and engineers. The development of STN international, the network through which CAS ONLINE is accessible around the world, was also discussed in the speech. The CAS ONLINE now contains a wide variety of files relating to chemical field including CA file, Registry file. CA previews,. CASREACT, CIN. MARPAT, etc for supplying chemical information worldwide.

  7. Sample Collection Information Document for Chemical & Radiochemical Analytes – Companion to Selected Analytical Methods for Environmental Remediation and Recovery (SAM) 2012

    EPA Pesticide Factsheets

    Sample Collection Information Document is intended to provide sampling information to be used during site assessment, remediation and clearance activities following a chemical or radiological contamination incident.

  8. Cosmological parameters from large scale structure - geometric versus shape information

    SciTech Connect

    Hamann, Jan; Hannestad, Steen; Lesgourgues, Julien; Rampf, Cornelius; Wong, Yvonne Y.Y. E-mail: sth@phys.au.dk E-mail: rampf@physik.rwth-aachen.de

    2010-07-01

    The matter power spectrum as derived from large scale structure (LSS) surveys contains two important and distinct pieces of information: an overall smooth shape and the imprint of baryon acoustic oscillations (BAO). We investigate the separate impact of these two types of information on cosmological parameter estimation for current data, and show that for the simplest cosmological models, the broad-band shape information currently contained in the SDSS DR7 halo power spectrum (HPS) is by far superseded by geometric information derived from the baryonic features. An immediate corollary is that contrary to popular beliefs, the upper limit on the neutrino mass m{sub ν} presently derived from LSS combined with cosmic microwave background (CMB) data does not in fact arise from the possible small-scale power suppression due to neutrino free-streaming, if we limit the model framework to minimal ΛCDM+m{sub ν}. However, in more complicated models, such as those extended with extra light degrees of freedom and a dark energy equation of state parameter w differing from -1, shape information becomes crucial for the resolution of parameter degeneracies. This conclusion will remain true even when data from the Planck spacecraft are combined with SDSS DR7 data. In the course of our analysis, we update both the BAO likelihood function by including an exact numerical calculation of the time of decoupling, as well as the HPS likelihood, by introducing a new dewiggling procedure that generalises the previous approach to models with an arbitrary sound horizon at decoupling. These changes allow a consistent application of the BAO and HPS data sets to a much wider class of models, including the ones considered in this work. All the cases considered here are compatible with the conservative 95%-bounds Σm{sub ν} < 1.16eV, N{sub eff} = 4.8±2.0.

  9. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  10. The relationship between the toxicity and structure of nitroaromatic chemicals

    SciTech Connect

    Bailey, M.C.; Spanggord, R.J.

    1981-10-01

    The acute toxicities of nitrotoluene, dinitrotoluene, trinitrotoluene, aminonitrotoluene, aminodinitrotoluene, and dinitrobenzene isomers were evaluated in fathead minnows. For the nitroaromatics, toxicity appeared to be related to the number and orientation of nitro groups; compounds with nitro groups positioned ortho or para to each other were appreciably more toxic than isomers having the nitro groups in the meta orientation. In contrast, the toxicities of the aminonitrotoluenes and aminodinitrotoluenes were not related in any obvious way to their structures. Two mechanisms may account for the differences in toxicity between the nitroaromatic isomers: nucleophilic displacement of a nitro group and reduction of a nitro group. The available data indicate that reduction of a nitro group is the more likely pathway.

  11. Materials ``alchemy'': Shape-preserving chemical transformation of micro-to-macroscopic 3-D structures

    NASA Astrophysics Data System (ADS)

    Sandhage, Kenneth H.

    2010-06-01

    The scalable fabrication of nano-structured materials with complex morphologies and tailorable chemistries remains a significant challenge. One strategy for such synthesis consists of the generation of a solid structure with a desired morphology (a “preform”), followed by reactive conversion of the preform into a new chemistry. Several gas/solid and liquid/solid reaction processes that are capable of such chemical conversion into new micro-to-nano-structured materials, while preserving the macroscopic-to-microscopic preform morphologies, are described in this overview. Such shape-preserving chemical transformation of one material into another could be considered a modern type of materials “alchemy.”

  12. Informing the Human Plasma Protein Binding of Environmental Chemicals by Machine Learning in the Pharmaceutical Space: Applicability Domain and Limits of Predictability.

    PubMed

    Ingle, Brandall L; Veber, Brandon C; Nichols, John W; Tornero-Velez, Rogelio

    2016-11-28

    The free fraction of a xenobiotic in plasma (Fub) is an important determinant of chemical adsorption, distribution, metabolism, elimination, and toxicity, yet experimental plasma protein binding data are scarce for environmentally relevant chemicals. The presented work explores the merit of utilizing available pharmaceutical data to predict Fub for environmentally relevant chemicals via machine learning techniques. Quantitative structure-activity relationship (QSAR) models were constructed with k nearest neighbors (kNN), support vector machines (SVM), and random forest (RF) machine learning algorithms from a training set of 1045 pharmaceuticals. The models were then evaluated with independent test sets of pharmaceuticals (200 compounds) and environmentally relevant ToxCast chemicals (406 total, in two groups of 238 and 168 compounds). The selection of a minimal feature set of 10-15 2D molecular descriptors allowed for both informative feature interpretation and practical applicability domain assessment via a bounded box of descriptor ranges and principal component analysis. The diverse pharmaceutical and environmental chemical sets exhibit similarities in terms of chemical space (99-82% overlap), as well as comparable bias and variance in constructed learning curves. All the models exhibit significant predictability with mean absolute errors (MAE) in the range of 0.10-0.18Fub. The models performed best for highly bound chemicals (MAE 0.07-0.12), neutrals (MAE 0.11-0.14), and acids (MAE 0.14-0.17). A consensus model had the highest accuracy across both pharmaceuticals (MAE 0.151-0.155) and environmentally relevant chemicals (MAE 0.110-0.131). The inclusion of the majority of the ToxCast test sets within the AD of the consensus model, coupled with high prediction accuracy for these chemicals, indicates the model provides a QSAR for Fub that is broadly applicable to both pharmaceuticals and environmentally relevant chemicals.

  13. Structural, chemical, and isotopic microanalytical investigations of graphite from supernovae

    NASA Astrophysics Data System (ADS)

    Croat, T. Kevin; Bernatowicz, Thomas; Amari, Sachiko; Messenger, Scott; Stadermann, Frank J.

    2003-12-01

    value of 0.122. Significant variations about the mean V/Ti ratio were also seen among TiCs in the same graphite, likely indicating chemical equilibration with the surrounding gas over a range of temperatures. In general, the diversity in internal TiC properties suggests that TiCs formed first and had substantially diverse histories before incorporation into the graphite, implying some degree of turbulent mixing in the SN outflows. In most graphites, there is a decrease in the number density of TiCs as a function of increasing radial dis- tance, caused by either preferential depletion of TiCs from the gas or an acceleration of graphite growth with decreasing ambient temperature. In several graphites, TiCs showed a trend of larger V/Ti ratios with increasing distance from the graphite center, an indication of progressive equilibration with the surrounding gas before they were sequestered in the graphites. In all but one graphite, no trend was seen in the TiC size vs. distance from the graphite center, implying that appreciable TiC growth had effectively stopped before the graphites formed, or else that graphite growth was rapid compared to TiC growth. Taken together, the chemical variations among internal grains as well as the presence of partially amorphous rims and epitaxial Fe phases on some TiCs clearly indicate that the phase condensation sequence was TiC, followed by the iron phases (only found in some graphites) and finally graphite. Since graphite typically condenses at a higher temperature than iron at low pressures (<10 -3 bars) in a gas with C > O and otherwise solar composition, the observed condensation sequence implies a relative iron enrichment in the gas or greater supersaturation of graphite relative to iron. The TEM observations allow inferences to be made about the physical conditions in the gas from which the grains condensed. Given the TiC sizes and abundances, the gas was evidently quite dusty. From the observed TiC size range of ˜20 nm to ˜500 nm

  14. The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

    NASA Technical Reports Server (NTRS)

    Wolf, David R.

    2004-01-01

    The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

  15. Computer prediction of possible toxic action from chemical structure; the DEREK system.

    PubMed

    Sanderson, D M; Earnshaw, C G

    1991-07-01

    1. The development of DEREK, a computer-based expert system (derived from the LHASA chemical synthesis design program) for the qualitative prediction of possible toxic action of compounds on the basis of their chemical structure is described. 2. The system is able to perceive chemical sub-structures within molecules and relate these to a rulebase linking the sub-structures with likely types of toxicity. 3. Structures can be drawn in directly at a computer graphics terminal or retrieved automatically from a suitable in-house database. 4. The system is intended to aid the selection of compounds based on toxicological considerations, or separately to indicate specific toxicological properties to be tested for early in the evaluation of a compound, so saving time, money and some laboratory animals and resources.

  16. Effect of mechanical activation on structure changes and reactivity in further chemical modification of lignin.

    PubMed

    Zhao, Xiaohong; Zhang, Yanjuan; Hu, Huayu; Huang, Zuqiang; Yang, Mei; Chen, Dong; Huang, Kai; Huang, Aimin; Qin, Xingzhen; Feng, Zhenfei

    2016-10-01

    Lignin was treated by mechanical activation (MA) in a customized stirring ball mill, and the structure and reactivity in further esterification were studied. The chemical structure and morphology of MA-treated lignin and the esterified products were analyzed by chemical analysis combined with UV/vis spectrometer, FTIR,NMR, SEM and particle size analyzer. The results showed that MA contributed to the increase of aliphatic hydroxyl, phenolic hydroxyl, carbonyl and carboxyl groups but the decrease of methoxyl groups. Moreover, MA led to the decrease of particle size and the increase of specific surface area and roughness of surface in lignin. The reactivity of lignin was enhanced significantly for the increase of hydroxyl content and the improvement of mass transfer in chemical reaction caused by the changes of molecular structure and morphological structure. The process of MA is green and simple, and is an effective method for enhancing the reactivity of lignin.

  17. Chemical structures of hydrazine-treated graphene oxide and generation of aromatic nitrogen doping.

    PubMed

    Park, Sungjin; Hu, Yichen; Hwang, Jin Ok; Lee, Eui-Sup; Casabianca, Leah B; Cai, Weiwei; Potts, Jeffrey R; Ha, Hyung-Wook; Chen, Shanshan; Oh, Junghoon; Kim, Sang Ouk; Kim, Yong-Hyun; Ishii, Yoshitaka; Ruoff, Rodney S

    2012-01-24

    Chemically modified graphene platelets, produced via graphene oxide, show great promise in a variety of applications due to their electrical, thermal, barrier and mechanical properties. Understanding the chemical structures of chemically modified graphene platelets will aid in the understanding of their physical properties and facilitate development of chemically modified graphene platelet chemistry. Here we use (13)C and (15)N solid-state nuclear magnetic resonance spectroscopy and X-ray photoelectron spectroscopy to study the chemical structure of (15)N-labelled hydrazine-treated (13)C-labelled graphite oxide and unlabelled hydrazine-treated graphene oxide, respectively. These experiments suggest that hydrazine treatment of graphene oxide causes insertion of an aromatic N(2) moiety in a five-membered ring at the platelet edges and also restores graphitic networks on the basal planes. Furthermore, density-functional theory calculations support the formation of such N(2) structures at the edges and help to elucidate the influence of the aromatic N(2) moieties on the electronic structure of chemically modified graphene platelets.

  18. Bridging the pressure gap: Can we get local quantitative structural information at 'near-ambient' pressures?

    NASA Astrophysics Data System (ADS)

    Woodruff, D. P.

    2016-10-01

    In recent years there have been an increasing number of investigations aimed at 'bridging the pressure gap' between UHV surface science experiments on well-characterised single crystal surfaces and the much higher (ambient and above) pressures relevant to practical catalyst applications. By applying existing photon-in/photon-out methods and developing instrumentation to allow photoelectron emission to be measured in higher-pressure sample environments, it has proved possible to obtain surface compositions and spectroscopic fingerprinting of chemical and molecular states of adsorbed species at pressures up to a few millibars. None of these methods, however, provide quantitative structural information on the local adsorption sites of isolated atomic and molecular adsorbate species under these higher-pressure reaction conditions. Methods for gaining this information are reviewed and evaluated.

  19. Raman investigation of magma mingling experiments as a tool for tracking the chemical and structural evolution of melt.

    NASA Astrophysics Data System (ADS)

    Di Genova, D.; Morgavi, D.; Hess, K. U.; Pritchard, C. J.; Borovkov, N.; Perugini, D.; Larson, P. B.; Dingwell, D. B.

    2014-12-01

    Magma mixing is a petrologic phenomenon, for which extensive evidence has been documented in rocks young and old, from intrusive and effusive igneous environments. Although magma mixing between mafic and silicic magmas is regarded as a major differentiation process, documentation of the mechanisms acting in melt interaction, both in its physical and chemical aspects, is still incomplete. We present the first Raman spectroscopic investigation of the products of magma-mixing experiments performed using natural basaltic and rhyolitic melts from the Yellowstone Norris-Mammoth Corridor. The mixing process is driven by a recently-developed apparatus that generates chaotic streamlines in the melts, mimicking the development of magma mixing in nature. The chemical variation of major elements is studied in detail by electron microprobe (EMPA) on mixed filaments of 1000 μm diameter. Raman and microprobe measurements have been performed every 10 μm this allow us to investigate the evolution of silicate structure, from the rhyolitic to the basaltic composition. Deconvoluted Raman spectra collected from the mixed experiment yield information about network-forming structural units (Qn species, where n indicates the number of bridging oxygen). By combining Raman spectra and chemical analyses we show, for the first time, how the percent of Qn species evolve with chemical composition in these natural silicate melts. Moreover, our results show how the ratio of network modifiers respect to network former cations, dramatically affects the Raman spectra of the rhyolitic end-member.

  20. Extended Functional Groups (EFG): An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds.

    PubMed

    Salmina, Elena S; Haider, Norbert; Tetko, Igor V

    2015-12-23

    The article describes a classification system termed "extended functional groups" (EFG), which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts) of the On-line CHEmical database and Modeling (OCHEM) environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models.

  1. Using phylogenetic information and chemical properties to predict species tolerances to pesticides.

    PubMed

    Guénard, Guillaume; Carsten von der Ohe, Peter; Carlisle Walker, Steven; Lek, Sovan; Legendre, Pierre

    2014-08-22

    Direct estimation of species' tolerance to pesticides and other toxic organic substances is a combinatorial problem, because of the large number of species-substance pairs. We propose a statistical modelling approach to predict tolerances associated with untested species-substance pairs, by using models fitted to tested pairs. This approach is based on the phylogeny of species and physico-chemical descriptors of pesticides, with both kinds of information combined in a bilinear model. This bilinear modelling approach predicts tolerance in untested species-compound pairs based on the facts that closely related species often respond similarly to toxic compounds and that chemically similar compounds often have similar toxic effects. The three tolerance models (median lethal concentration after 96 h) used up to 25 aquatic animal species and up to nine pesticides (organochlorines, organophosphates and carbamates). Phylogeny was estimated using DNA sequences, while the pesticides were described by their mode of toxic action and their octanol-water partition coefficients. The models explained 77-84% of the among-species variation in tolerance (log10 LC50). In cross-validation, 84-87% of the predicted tolerances for individual species were within a factor of 10 of the observed values. The approach can also be used to model other species response to multivariate stress factors.

  2. Social learning of predators in the dark: understanding the role of visual, chemical and mechanical information

    PubMed Central

    Manassa, R. P.; McCormick, M. I.; Chivers, D. P.; Ferrari, M. C. O.

    2013-01-01

    The ability of prey to observe and learn to recognize potential predators from the behaviour of nearby individuals can dramatically increase survival and, not surprisingly, is widespread across animal taxa. A range of sensory modalities are available for this learning, with visual and chemical cues being well-established modes of transmission in aquatic systems. The use of other sensory cues in mediating social learning in fishes, including mechano-sensory cues, remains unexplored. Here, we examine the role of different sensory cues in social learning of predator recognition, using juvenile damselfish (Amphiprion percula). Specifically, we show that a predator-naive observer can socially learn to recognize a novel predator when paired with a predator-experienced conspecific in total darkness. Furthermore, this study demonstrates that when threatened, individuals release chemical cues (known as disturbance cues) into the water. These cues induce an anti-predator response in nearby individuals; however, they do not facilitate learnt recognition of the predator. As such, another sensory modality, probably mechano-sensory in origin, is responsible for information transfer in the dark. This study highlights the diversity of sensory cues used by coral reef fishes in a social learning context. PMID:23804616

  3. Using phylogenetic information and chemical properties to predict species tolerances to pesticides

    PubMed Central

    Guénard, Guillaume; Carsten von der Ohe, Peter; Carlisle Walker, Steven; Lek, Sovan; Legendre, Pierre

    2014-01-01

    Direct estimation of species' tolerance to pesticides and other toxic organic substances is a combinatorial problem, because of the large number of species–substance pairs. We propose a statistical modelling approach to predict tolerances associated with untested species–substance pairs, by using models fitted to tested pairs. This approach is based on the phylogeny of species and physico-chemical descriptors of pesticides, with both kinds of information combined in a bilinear model. This bilinear modelling approach predicts tolerance in untested species–compound pairs based on the facts that closely related species often respond similarly to toxic compounds and that chemically similar compounds often have similar toxic effects. The three tolerance models (median lethal concentration after 96 h) used up to 25 aquatic animal species and up to nine pesticides (organochlorines, organophosphates and carbamates). Phylogeny was estimated using DNA sequences, while the pesticides were described by their mode of toxic action and their octanol–water partition coefficients. The models explained 77–84% of the among-species variation in tolerance (log10 LC50). In cross-validation, 84–87% of the predicted tolerances for individual species were within a factor of 10 of the observed values. The approach can also be used to model other species response to multivariate stress factors. PMID:25009056

  4. Social learning of predators in the dark: understanding the role of visual, chemical and mechanical information.

    PubMed

    Manassa, R P; McCormick, M I; Chivers, D P; Ferrari, M C O

    2013-08-22

    The ability of prey to observe and learn to recognize potential predators from the behaviour of nearby individuals can dramatically increase survival and, not surprisingly, is widespread across animal taxa. A range of sensory modalities are available for this learning, with visual and chemical cues being well-established modes of transmission in aquatic systems. The use of other sensory cues in mediating social learning in fishes, including mechano-sensory cues, remains unexplored. Here, we examine the role of different sensory cues in social learning of predator recognition, using juvenile damselfish (Amphiprion percula). Specifically, we show that a predator-naive observer can socially learn to recognize a novel predator when paired with a predator-experienced conspecific in total darkness. Furthermore, this study demonstrates that when threatened, individuals release chemical cues (known as disturbance cues) into the water. These cues induce an anti-predator response in nearby individuals; however, they do not facilitate learnt recognition of the predator. As such, another sensory modality, probably mechano-sensory in origin, is responsible for information transfer in the dark. This study highlights the diversity of sensory cues used by coral reef fishes in a social learning context.

  5. Setting the most robust effluent level under severe uncertainty: application of information-gap decision theory to chemical management.

    PubMed

    Yokomizo, Hiroyuki; Naito, Wataru; Tanaka, Yoshinari; Kamo, Masashi

    2013-11-01

    Decisions in ecological risk management for chemical substances must be made based on incomplete information due to uncertainties. To protect the ecosystems from the adverse effect of chemicals, a precautionary approach is often taken. The precautionary approach, which is based on conservative assumptions about the risks of chemical substances, can be applied selecting management models and data. This approach can lead to an adequate margin of safety for ecosystems by reducing exposure to harmful substances, either by reducing the use of target chemicals or putting in place strict water quality criteria. However, the reduction of chemical use or effluent concentrations typically entails a financial burden. The cost effectiveness of the precautionary approach may be small. Hence, we need to develop a formulaic methodology in chemical risk management that can sufficiently protect ecosystems in a cost-effective way, even when we do not have sufficient information for chemical management. Information-gap decision theory can provide the formulaic methodology. Information-gap decision theory determines which action is the most robust to uncertainty by guaranteeing an acceptable outcome under the largest degree of uncertainty without requiring information about the extent of parameter uncertainty at the outset. In this paper, we illustrate the application of information-gap decision theory to derive a framework for setting effluent limits of pollutants for point sources under uncertainty. Our application incorporates a cost for reduction in pollutant emission and a cost to wildlife species affected by the pollutant. Our framework enables us to settle upon actions to deal with severe uncertainty in ecological risk management of chemicals.

  6. Supersaturated lysozyme solution structure studied by chemical cross-linking.

    PubMed

    Hall, Clayton L; Clemens, John R; Brown, Amanda M; Wilson, Lori J

    2005-06-01

    Glutaraldehyde cross-linking followed by separation has been used to detect aggregates of chicken egg-white lysozyme (CEWL) in supersaturated solutions. In solutions of varying NaCl content, the number of aggregates was found to be related to the ionic strength of the solution. Separation by SDS-PAGE showed that percentage of dimer in solution ranged from 25.3% for no NaCl to 27.1% at 15% NaCl, and the aggregates larger than dimer increased from 1.9% for no NaCl to 36.8% at 15% NaCl. Conversely, the percentage of monomers decreased from 72.8% without NaCl to 36.1% at 15% NaCl. Molecular weights by capillary electrophoresis (SDS-CE) were found to be multiples of the monomer molecular weights, with the exception of trimer, which indicates a very compact structure. Native separation was accomplished using size-exclusion chromatography (SEC) and gave a lower monomer concentration and higher aggregate concentration than SDS-CE, which is a denaturing separation method. Most noticeably, trimers were absent in the SEC separation. The number of aggregates did not change with increased time between addition of NaCl and addition of cross-linking agent when separated by gel electrophoresis (SDS-PAGE). The results suggest that high ionic strength CEWL solutions are highly aggregated and that denaturing separation methods disrupt cross-linked products.

  7. Educational and Commercial Utilization of a Chemical Information Center. Biannual Summary, June 25, 1968 to June 25, 1970.

    ERIC Educational Resources Information Center

    Schwartz, Eugene S.; And Others

    The design, implementation and operation of the Computer Search Center of IIT Research Institute, an information center to educate and link industry and academic institutions to chemical and other scientific information systems, is described. Format conversion, profile input, search and output programs developed over a two-year period are detailed…

  8. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

    PubMed

    Christensen, Anders S; Linnet, Troels E; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3)J(NC')) spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  9. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    PubMed Central

    Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

  10. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    NASA Astrophysics Data System (ADS)

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-10-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  11. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease.

    PubMed

    Beck, Michael W; Derrick, Jeffrey S; Kerr, Richard A; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D; Kim, Kwang S; Lee, Joo-Yong; Ruotolo, Brandon T; Lim, Mi Hee

    2016-10-13

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  12. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    SciTech Connect

    Sakai, Osamu Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-15

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH{sub 3} in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

  13. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    PubMed Central

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-01-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal–Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs. PMID:27734843

  14. Molecule database framework: a framework for creating database applications with chemical structure search capability

    PubMed Central

    2013-01-01

    Background Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Results Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes: • Support for multi-component compounds (mixtures) • Import and export of SD-files • Optional security (authorization) For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures). Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. Conclusions By using a simple web application it was

  15. Mashed potatoes enriched with soy protein isolate and inulin: chemical, rheological and structural basis.

    PubMed

    Alvarez, M D; Olivares, M D; Blanch, M; Canet, W

    2013-10-01

    Soy protein isolate is typical vegetable protein with health-enhancing activities. Inulin, a prebiotic no digestible carbohydrate, has functional properties. A mashed potato serving of 200 g with added soy protein isolate and/or inulin concentrations of 15-60 g/kg provides from 3 to 12 g of soy protein isolate and/or inulin, respectively. Currently, no information is available about the possible texture-modifying effect of this non-ionizable polar carbohydrate in different soy-based food systems. In this study, the effect of the addition of soy protein isolate and inulin blends at different soy protein isolate: inulin ratios on the degree of inulin polymerization and the rheological and structural properties of fresh mashed and frozen/thawed mashed potatoes were evaluated. The inulin chemical structure remained intact throughout the various treatments, and soy protein isolate did not affect inulin composition being a protein compatible with this fructan. Small-strain rheology showed that both ingredients behaved like soft fillers. In the frozen/thawed mashed potatoes samples, addition of 30 : 30 and 15 : 60 blend ratios significantly increased elasticity (G' value) compared with 0 : 0 control, consequently reducing the freeze/thaw stability conferred by the cryoprotectants. Inulin crystallites caused a significant strengthening effect on soy protein isolate gel. Micrographs revealed that soy protein isolate supports the inulin structure by building up a second fine-stranded network. Thereby, possibility of using soy protein isolate and inulin in combination with mashed potatoes to provide a highly nutritious and healthy product is promising.

  16. Synthesis of Cobalt Oxides Thin Films Fractal Structures by Laser Chemical Vapor Deposition

    PubMed Central

    Haniam, P.; Kunsombat, C.; Chiangga, S.; Songsasen, A.

    2014-01-01

    Thin films of cobalt oxides (CoO and Co3O4) fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures. PMID:24672354

  17. Structure-activity comparison of hydrazine to other Nasotoxic chemicals. Final report, August-October 1991

    SciTech Connect

    Godin, C.S.; Wall, H.G.

    1992-08-01

    The biotransformation of 19 chemicals that have caused nasal epithelial toxicity in-long-term carcinogenesis experiments in laboratory rodents was compared with the biotransformation of hydrazine, in order to determine if these chemicals share common metabolic pathways. Ten of the 19 chemicals were tumorigenic; four were epoxides or epoxide-formers; three were metabolized to reactive aldehydes; and one was metabolized to a lactone ring. The two remaining chemicals, p-cresidene and 2,6-xylidene, possess an amino group that can undergo biotransformation to reactive metabolites in a way similar to hydrazine, but there is no evidence to support this hypothesis. Therefore, none of the 19 chemicals are metabolized in a way similar to hydrazine.... Structure-activity, Hydrazine, Nasotoxicity, Carcinogenicity.

  18. Spatial data in geographic information system format on agricultural chemical use, land use, cropping practices in the United States

    USGS Publications Warehouse

    Battaglin, W.A.; Goolsby, D.A.

    1995-01-01

    The spatial data in geographic information system format described in this report consist of estimates for all counties in the conterminous United States of the annual use of 96 herbicides in 1989; annual sales of nitrogen fertilizer, in tons, for 1985-91; and agricultural expenses, land use, chemical use, livestock holdings, and cropping practices in 1987. The source information, originally in tabular form, is summarized as digital polygon attribute data in the 18 geographic information system spatial data layers (coverages) provided. The information in these coverages can be used in estimating regional agricultural-chemical use or agricultural practices and in producing visual displays and mapping relative rates of agricultural-chemical use or agricultural practices across broad regions of the United States.

  19. Chemical Carcinogenesis Research Information System (CCRIS) data bank, 1981-June 1986 (1988 version). Data file

    SciTech Connect

    Cameron, T.P.; Stump, J.M.; Schofield, L.

    1986-01-01

    CCRIS is a scientifically evaluated and fully referenced data bank, developed and maintained by the National Cancer Institute (NCI), containing carcinogenicity, tumor promotion, and mutagenicity test results. Data are derived from the scanning of primary journals, current-awareness tools, and a special core set of sources, including a wide range of NCI reports. Test results have been reviewed by experts in carcinogenesis. CCRIS File Structure: CCRIS data fields are arranged in two broad subject categories plus a category for administrative information: Administrative Information, Substance Identification/Use, Carcinogenicity/Tumor Promotion/Mutagenicity Studies. The three data fields within category 2 and the information contained therein are: Carcinogenicity Studies: Species; Strain/Sex; Route; Dose; Tumor site/Type of lesion; Results; Reference. Tumor Promotion Studies; Species; Strain/Sex; Promoter Route; Target Tissue/Type of Lesion, Promoter Doses, Carcinogen Route; Carcinogen Doses; Reference. Mutagenicity studies: Test System; Strain/Indicator; Metabolic Activation; Method; Dose range; Reference. A new file dictionary has been enclosed that is a result of minor changes to the file structure. All other documentation on file at the NTIS is still applicable.

  20. Influence of Transducer Structure on Mechanical and Chemical Effects of 20 kHz Sonication

    NASA Astrophysics Data System (ADS)

    Tran, Khuyen Viet Bao; Asakura, Yoshiyuki; Koda, Shinobu

    2012-07-01

    In this work, we examined the influence of transducer structure on the mechanical and chemical effects of 20 kHz sonication, where the dissipated power measured by calorimetry was kept constant (5 W). The mechanical effects were evaluated from the degradation rate of poly(ethylene oxide) in aqueous solution, and the chemical effects were measured with potassium iodide solution. The mechanical effects for a bath-type apparatus with the transducers fixed at a node with a diameter of 50 mm are nearly equal to those for a horn-type apparatus. The former transducer showed the strongest chemical effects among the transducers investigated here.

  1. Influence of the chemical structure of functional monomers on their adhesive performance.

    PubMed

    Van Landuyt, K L; Yoshida, Y; Hirata, I; Snauwaert, J; De Munck, J; Okazaki, M; Suzuki, K; Lambrechts, P; Van Meerbeek, B

    2008-08-01

    Functional monomers in adhesive systems can improve bonding by enhancing wetting and demineralization, and by chemical bonding to calcium. This study tested the hypothesis that small changes in the chemical structure of functional monomers may improve their bonding effectiveness. Three experimental phosphonate monomers (HAEPA, EAEPA, and MAEPA), with slightly different chemical structures, and 10-MDP (control) were evaluated. Adhesive performance was determined in terms of microtensile bond strength of 4 cements that differed only for the functional monomer. Based on the Adhesion-Decalcification concept, the chemical bonding potential was assessed by atomic absorption spectrophotometry of the dissolution rate of the calcium salt of the functional monomers. High bond strength of the adhesive cement corresponded to low dissolution rate of the calcium salt of the respective functional monomer. The latter is according to the Adhesion-Decalcification concept, suggestive of a high chemical bonding capacity. We conclude that the adhesive performance of an adhesive material depends on the chemical structure of the functional monomer.

  2. First report on development of quantitative interspecies structure-carcinogenicity relationship models and exploring discriminatory features for rodent carcinogenicity of diverse organic chemicals using OECD guidelines.

    PubMed

    Kar, Supratik; Roy, Kunal

    2012-04-01

    Different regulatory agencies in food and drug administration and environmental protection worldwide are employing quantitative structure-activity relationship (QSAR) models to fill the data gaps related with properties of chemicals affecting the environment and human health. Carcinogenicity is a toxicity endpoint of major concern in recent times. Interspecies toxicity correlations may provide a tool for estimating sensitivity towards toxic chemical exposure with known levels of uncertainty for a diversity of wildlife species. In this background, we have developed quantitative interspecies structure-carcinogenicity correlation models for rat and mouse [rodent species according to the Organization for Economic Cooperation and Development (OECD) guidelines] based on the carcinogenic potential of 166 organic chemicals with wide diversity of molecular structures, spanning a large number of chemical classes and biological mechanisms. All the developed models have been assessed according to the OECD principles for the validation of QSAR models. Consensus predictions for carcinogenicity of the individual compounds are presented here for any one species when the data for the other species are available. Informative illustrations of the contributing structural fragments of chemicals which are responsible for specific carcinogenicity endpoints are identified by the developed models. The models have also been used to predict mouse carcinogenicities of 247 organic chemicals (for which rat carcinogenicities are present) and rat carcinogenicities of 150 chemicals (for which mouse carcinogenicities are present). Discriminatory features for rat and mouse carcinogenicity values have also been explored.

  3. An Overview of Worldwide Chemical Information Facilities and Resources; "A Precis." Prepared...for the Joint Study on the Communication of Scientific Information and on the Feasibility of a Worldwide Science Information System.

    ERIC Educational Resources Information Center

    International Council of Scientific Unions, Paris (France).

    The first section of this precis summarizes the general nature of the present chemical information systems of the world. The discussion is presented in four parts: (1) the primary literature, (2) secondary sources and services, (3) libraries and information centers and (4) other elements categorized as informal communications. The second section…

  4. Using structure to inform carbohydrate binding module function.

    PubMed

    Abbott, D Wade; van Bueren, Alicia Lammerts

    2014-10-01

    Generally, non-catalytic carbohydrate binding module (CBM) specificity has been shown to parallel the catalytic activity of the carbohydrate active enzyme (CAZyme) module it is appended to. With the rapid expansion in metagenomic sequence space for the potential discovery of new CBMs in addition to the recent emergence of several new CBM families that display diverse binding profiles and novel functions, elucidating the function of these protein modules has become a much more challenging task. This review summarizes several approaches that have been reported for using primary structure to inform CBM specificity and streamlining their biophysical characterization. In addition we discuss general trends in binding site architecture and several newly identified functions for CBMs. Streams of investigation that will facilitate the development and refinement of sequence-based prediction tools are suggested.

  5. Microfabricated self-resonant structure as a passive wireless chemical sensor

    NASA Astrophysics Data System (ADS)

    Zhang, Sheng; Pasupathy, Praveenkumar; Neikirk, Dean P.

    2011-06-01

    This paper describes ongoing work to develop a low cost, passive wireless chemical sensor using a microfabricated inductor with interdigitated capacitors (IDC). A self-resonant-structure (SRS) is designed by incorporating IDC electrodes in the inter-winding space of the inductor. The distributed IDC capacitance is affected by dielectric constant and conductivity of its environment or material under test (MUT). This serves as a capacitive transducer changing the resonant frequency of the SRS. The SRS is interrogated using a non-contact inductively coupled reader coil. The shift in resonance frequency of the SRS is used to detect material properties of the environment/MUT. The dielectric constant (ɛ) and conductivity (σ) can be used to provide information about the surrounding environment. The ɛ and the σ are determined by fitting and extraction from circuit models of the IDC. Relationship between sensor layout and coupling factor between sensor and reader is investigated. Optimizations of the coupling factor based on this relationship are discussed. IDC design trade-offs between the sensor's sensitivity and coupling factor are investigated. The sensor's response to variety of liquid MUTs with a wide range of dielectric constant and conductivity is presented.

  6. Structural-chemical modeling of transition of coals to the plastic state

    SciTech Connect

    A.M. Gyul'maliev; S.G. Gagarin

    2007-02-15

    The structural-chemical simulation of the formation of plastic state during the thermal treatment (pyrolysis, coking) of coals is based on allowance for intermolecular interactions in the organic matter. The feasibility of transition of coals to the plastic state is determined by the ratio between the onset plastic state (softening) and runaway degradation temperatures, values that depend on the petrographic composition and the degree of metamorphism of coals and the distribution of structural and chemical characteristics of organic matter. 33 refs., 8 figs., 2 tabs.

  7. Relationship between chemical structure and the occupational asthma hazard of low molecular weight organic compounds

    PubMed Central

    Jarvis, J; Seed, M; Elton, R; Sawyer, L; Agius, R

    2005-01-01

    Aims: To investigate quantitatively, relationships between chemical structure and reported occupational asthma hazard for low molecular weight (LMW) organic compounds; to develop and validate a model linking asthma hazard with chemical substructure; and to generate mechanistic hypotheses that might explain the relationships. Methods: A learning dataset used 78 LMW chemical asthmagens reported in the literature before 1995, and 301 control compounds with recognised occupational exposures and hazards other than respiratory sensitisation. The chemical structures of the asthmagens and control compounds were characterised by the presence of chemical substructure fragments. Odds ratios were calculated for these fragments to determine which were associated with a likelihood of being reported as an occupational asthmagen. Logistic regression modelling was used to identify the independent contribution of these substructures. A post-1995 set of 21 asthmagens and 77 controls were selected to externally validate the model. Results: Nitrogen or oxygen containing functional groups such as isocyanate, amine, acid anhydride, and carbonyl were associated with an occupational asthma hazard, particularly when the functional group was present twice or more in the same molecule. A logistic regression model using only statistically significant independent variables for occupational asthma hazard correctly assigned 90% of the model development set. The external validation showed a sensitivity of 86% and specificity of 99%. Conclusions: Although a wide variety of chemical structures are associated with occupational asthma, bifunctional reactivity is strongly associated with occupational asthma hazard across a range of chemical substructures. This suggests that chemical cross-linking is an important molecular mechanism leading to the development of occupational asthma. The logistic regression model is freely available on the internet and may offer a useful but inexpensive adjunct to the

  8. Quantifying the value of information for uncertainty reduction in chemical EOR modeling

    NASA Astrophysics Data System (ADS)

    Leray, Sarah; Yeates, Christopher; Douarche, Frédéric; Roggero, Frédéric

    2016-04-01

    Reservoir modeling is a powerful tool to assess the technical and economic feasibility of chemical Enhanced Oil Recovery methods such as the joint injection of surfactant and polymer. Laboratory recovery experiments are usually undertaken on cores to understand recovery mechanisms and to estimate properties, that will be further used to build large scale models. To capture the different processes involved in chemical EOR, models are described by a large number of parameters which are basically only partially constrained by recovery experiments and additional characterizations, mainly because of cost and time restrictions or limited representativeness. Among the most uncertain properties, features the surfactant adsorption which cannot be straightforwardly derived from bulk or simplified dynamic measurements (e.g. single phase dynamic adsorption experiments). It is unfortunately critical for the economics of the process. Identifying the most informative observations (e.g. saturation scans, pressure differential, surfactant production, oil recovery) is of primary interest to compensate deficiency of some characterizations and improve models robustness and their predictive capability. Building a consistent set of recovery experiments that will allow to seize recovery mechanisms is critical as well. To address these inverse methodology issues, we create a synthetic numerical model with a well-defined set of parameter values, considered to be our reference case. This choice of model is based on a similar real data set and a broad literature review. It consists of a water-wet sandstone subject to typical surfactant-polymer injections. We first study the effect of a salinity gradient injected after a surfactant-polymer slug, as it is known to significantly improve oil recovery. We show that reaching optimal conditions of salinity gradient is a fragile balance between surfactant desorption and interfacial tension increase. This high dependence on surfactant adsorption

  9. Chemical separation of primordial Li+ during structure formation caused by nanogauss magnetic field

    NASA Astrophysics Data System (ADS)

    Kusakabe, Motohiko; Kawasaki, Masahiro

    2015-01-01

    During the structure formation, charged and neutral chemical species may have separated from each other at the gravitational contraction in primordial magnetic field (PMF). A gradient in the PMF in a direction perpendicular to the field direction leads to the Lorentz force on the charged species. Resultantly, an ambipolar diffusion occurs, and charged species can move differently from neutral species, which collapses gravitationally during the structure formation. We assume a gravitational contraction of neutral matter in a spherically symmetric structure, and calculate fluid motions of charged and neutral species. It is shown that the charged fluid, i.e. proton, electron, and 7Li+, can significantly decouple from the neutral fluid depending on the field amplitude. The charged species can, therefore, escape from the gravitational collapse. We take the structure mass, the epoch of the gravitational collapse, and the comoving Lorenz force as parameters. We then identify a parameter region for an effective chemical separation. This type of chemical separation can reduce the abundance ratio of Li/H in early structures because of inefficient contraction of 7Li+ ion. Therefore, it may explain Li abundances of Galactic metal-poor stars which are smaller than the prediction in standard big bang nucleosynthesis model. Amplitudes of the PMFs are controlled by a magnetohydrodynamic turbulence. The upper limit on the field amplitude derived from the turbulence effect is close to the value required for the chemical separation.

  10. Chemicals of military deployments: revisiting Gulf War Syndrome in light of new information.

    PubMed

    Brimfield, A A

    2012-01-01

    Despite the amount of hard work that has gone into elucidating a toxicological basis for Gulf War Illness, we do not appear to have reached a mechanistic understanding. Investigation of long-term low-level exposure as a basis does not seem to have provided an answer. Nor does the deployment-related toxic soup idea, where exposure to a mixture of toxic chemicals not usually encountered in the same physical vicinity, seems to have explained the symptoms developed by Gulf War Veterans. The idea that an overabundance of CNS acetylcholine leftover from excessive cholinesterase inhibition is at the basis of this syndrome is intellectually appealing and offers a level of neurochemical complexity that may be just beyond the reach of our technical understanding. But no one has yet assembled a coherent mechanism from it either. It seems reasonable that chemical warfare agents were involved. They were not included in early work because it was felt that the toxicant plumes produced during the destruction of stockpiled Iraqi chemical weapons had not been large enough to cause an exposure of US forces and those of our allies. That misconception was disproven, and it is now accepted that people could very well have been exposed to low levels of massive quantities of sarin, cyclosarin, and sulfur mustard. It also seems reasonable that excess acetylcholine or neurological consequences of its presence that we do not fully understand were involved. The combination of nerve agents and the insecticidal anticholinesterases plus the pyridostigmine bromide given prophylactically were probably sufficient to cause the problem. However, the most notable thing is the result of recent work on the toxic mechanism of sulfur mustard showing that it can inhibit the microsomal electron transport chain as a result of sulfonium ion reduction to carbon free radicals by NADPH-cytochrome P450 reductase. This information was not available during the work on Gulf War Illness. So this provides an

  11. Chemical input and I-V output: stepwise chemical information processing in dye-sensitized solar cells.

    PubMed

    Satoh, Norifusa; Han, Liyuan

    2012-12-14

    As a complex system, a dye-sensitized solar cell (DSC) exhibits emergent photovoltaics not obvious from the properties of the individual components. The chemical input of 4-tert-butylpyridine (TBP) into DSC improves the open circuit voltage (V(oc)) and reduces the short circuit current (I(sc)) in I-V output through multiple interactions with the components, yet it has been difficult to distinguish the multiple interactions and correlate the interactions with the influences on I-V output due to the complexity of the system. To deal with the multiple interactions, we have adapted a conceptual framework and methodology from coordination chemistry. First, we titrated the photovoltaic interface and electrolyte with TBP to identify the stepwise chemical interaction processes. An isopotential point observed in I-V output indicates that most of the inputted chemicals interact with the electrolyte. Cyclic voltammetric titration of the electrolyte demonstrates asymmetric redox peaks and two different isopotential points, indicating that the two-step coordination-decoordination process inhibits the reduction current of the electrolyte. Second, we set an interaction model bridging the hierarchical gaps between the multiple interactions and the I-V output to address the influences on outputs from the amount of the inputs. From the viewpoint of the interaction model and interactions observed, we are able to comprehend the processes of the complex system and suggest a direction to improve V(oc) without sacrificing I(sc) in DSCs. We conclude that the conceptual framework and methodology adapted from coordination chemistry is beneficial to enhance the emergent outputs of complex systems.

  12. SARANEA: a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets.

    PubMed

    Lounkine, Eugen; Wawer, Mathias; Wassermann, Anne Mai; Bajorath, Jürgen

    2010-01-01

    We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data structure for visualization. The program enables the systematic detection of activity and selectivity cliffs and corresponding key compounds across multiple targets. Advanced SAR analysis functions implemented in SARANEA include, among others, layered chemical neighborhood graphs, cliff indices, selectivity trees, editing functions for molecular networks and pathways, bioactivity summaries of key compounds, and markers for bioactive compounds having potential side effects. We report the application of SARANEA to identify SAR and SSR determinants in different sets of serine protease inhibitors. It is found that key compounds can influence SARs and SSRs in rather different ways. Such compounds and their SAR/SSR characteristics can be systematically identified and explored using SARANEA. The program and source code are made freely available under the GNU General Public License.

  13. Qualitative and quantitative structure-activity relationship modelling for predicting blood-brain barrier permeability of structurally diverse chemicals.

    PubMed

    Gupta, S; Basant, N; Singh, K P

    2015-01-01

    In this study, structure-activity relationship (SAR) models have been established for qualitative and quantitative prediction of the blood-brain barrier (BBB) permeability of chemicals. The structural diversity of the chemicals and nonlinear structure in the data were tested. The predictive and generalization ability of the developed SAR models were tested through internal and external validation procedures. In complete data, the QSAR models rendered ternary classification accuracy of >98.15%, while the quantitative SAR models yielded correlation (r(2)) of >0.926 between the measured and the predicted BBB permeability values with the mean squared error (MSE) <0.045. The proposed models were also applied to an external new in vitro data and yielded classification accuracy of >82.7% and r(2) > 0.905 (MSE < 0.019). The sensitivity analysis revealed that topological polar surface area (TPSA) has the highest effect in qualitative and quantitative models for predicting the BBB permeability of chemicals. Moreover, these models showed predictive performance superior to those reported earlier in the literature. This demonstrates the appropriateness of the developed SAR models to reliably predict the BBB permeability of new chemicals, which can be used for initial screening of the molecules in the drug development process.

  14. Chemical structure and physical properties of radiation-induced crosslinking of polytetrafluoroethylene

    NASA Astrophysics Data System (ADS)

    Oshima, Akihiro; Ikeda, Shigetoshi; Katoh, Etsuko; Tabata, Yoneho

    2001-07-01

    The chemical structure and physical properties of polytetrafluoroethylene (PTFE) that has been crosslinked by radiation have been studied by various methods. It has been found that a Y-type crosslinking structure and a Y-type structure incorporating a double bond (modified Y-type) is formed in PTFE by radiation-crosslinking in the molten state. In addition, various types of double bond structures, excluding the crosslinking site, have been identified. The crosslinked PTFE has a good light transparency due to the loss of crystallites, whilst it retains the excellent properties of electrical insulation and heat resistance. The coefficient of abrasion and the permanent creep are also greatly improved by crosslinking.

  15. Chemical and structural analysis of the bone-implant interface by TOF-SIMS, SEM, FIB and TEM: Experimental study in animal

    NASA Astrophysics Data System (ADS)

    Palmquist, Anders; Emanuelsson, Lena; Sjövall, Peter

    2012-06-01

    Although bone-anchored implants are widely used in reconstructive medicine, the mechanism of osseointegration is still not fully understood. Novel analytical tools are needed to further understand this process, where both the chemical and structural aspects of the bone-implant interface are important. The aim of this study was to evaluate the advantages of combining time-of-flight secondary ion mass spectroscopy (TOF-SIMS) with optical (LM), scanning (SEM) and transmission electron microscopy (TEM) techniques for studying the bone-implant interface of bone-anchored implants. Laser-modified titanium implants with surrounded bone retrieved after 8 weeks healing in rabbit were dehydrated and resin embedded. Three types of sample preparation were studied to evaluate the information gained by combining TOF-SIMS, SEM, FIB and TEM. The results show that imaging TOF-SIMS can provide detailed chemical information, which in combination with structural information from microscopy methods provide a more complete characterization of anatomical structures at the bone-implant interface. By investigating various sample preparation techniques, it is shown that grinded cross section samples can be used for chemical imaging using TOF-SIMS, if careful consideration of potential preparation artifacts is taken into account. TOF-SIMS analysis of FIB-prepared bone/implant cross section samples show distinct areas corresponding to bone tissue and implant with a sharp interface, although without chemical information about the organic components.

  16. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    PubMed

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  17. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

    PubMed Central

    Staley, Christopher; Gould, Trevor J.; Wang, Ping; Phillips, Jane; Cotner, James B.; Sadowsky, Michael J.

    2014-01-01

    Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of 14 bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046) between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River. PMID:25339945

  18. Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure

    PubMed Central

    Ytreberg, F Marty; Borcherds, Wade; Wu, Hongwei; Daughdrill, Gary W

    2015-01-01

    A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

  19. Syntax Encodes Information Structure: Evidence from On-Line Reading Comprehension

    ERIC Educational Resources Information Center

    Brown, Meredith; Savova, Virginia; Gibson, Edward

    2012-01-01

    Although sentences are thought to be generally easier to process when given information precedes new information, closer examination reveals that these preferences only manifest within some syntactic structures. Here, we examine the consequences of the relative ordering of given and new information ("information structure") for the on-line…

  20. Graphene oxide thin films: influence of chemical structure and deposition methodology.

    PubMed

    Hidalgo, R S; López-Díaz, D; Velázquez, M Mercedes

    2015-03-10

    We synthesized graphene oxide sheets of different functionalization by oxidation of two different starting materials, graphite and GANF nanofibers, followed by purification based on alkaline washing. The chemical structure of graphene oxide materials was determined by X-ray photoelectron spectroscopy (XPS), and the nanoplatelets were characterized by ζ potential and dynamic light scattering (DLS) measurements. The XPS results indicated that the chemical structure depends on the starting material. Two different deposition methodologies, Langmuir-Blodgett (LB) and Langmuir-Schaefer (LS), were employed to build the graphene oxide thin films. The film morphology was analyzed by scanning electron microscopy (SEM). The SEM images allow us to conclude that the LB methodology provides the highest coverage. This coverage is almost independent of the chemical composition of sheets. Conversely, the coverage obtained by the LS methodology increases with the percentage of C-O groups attached to sheets. Surface-pressure isotherms of these materials were interpreted according to the Volmer model.

  1. Electronic Structure of Pi Systems: Part III--Applications in Spectroscopy and Chemical Reactivity.

    ERIC Educational Resources Information Center

    Fox, Marye Anne; Matsen, F. A.

    1985-01-01

    Shows that electronic structure diagrams make more accurate predictions of spectral properties and chemical reactivity for simple pi systems than do either Huckel molecular orbital or valence bond theory alone. Topics addressed include absorption and photoelectron spectra, spin density distribution in radicals, and several problems regarding…

  2. Test results of chemical reactivity test (CRT) analysis of structural materials and explosives

    SciTech Connect

    Back, P.S.; Barnhart, B.V.; Walters, R.R.; Haws, L.D.; Collins, L.W.

    1980-03-21

    The chemical reactivity test, CRT, is a procedure used to screen the compatibility of component structure materials with explosives. This report contains the results of CRT materials evaluations conducted at Mound Facility. Data about materials combinations are catalogued both under the name of the explosive and the nonexplosive.

  3. Correlation between chemical structure and rodent repellency of benzoic acid derivatives

    USGS Publications Warehouse

    Fearn, J.E.; DeWitt, J.B.

    1965-01-01

    Sixty-five benzoic acid derivatives were either prepared or obtained from commercial concerns, tested for rat repellency, and their indices of repellency computed. The data from these tests were considered analytically for any correlation between chemical structure and rat repellency. The results suggest a qualitative relationship which is useful in deciding probability of repellency in other compounds.

  4. Using Concept Mapping to Uncover Students' Knowledge Structures of Chemical Bonding Concepts

    ERIC Educational Resources Information Center

    Burrows, Nikita L.; Mooring, Suazette Reid

    2015-01-01

    General chemistry is the first undergraduate course in which students further develop their understanding of fundamental chemical concepts. Many of these fundamental topics highlight the numerous conceptual interconnections present in chemistry. However, many students possess incoherent knowledge structures regarding these topics. Therefore,…

  5. Assessment of quantitative structure-activity relationship of toxicity prediction models for Korean chemical substance control legislation

    PubMed Central

    Kim, Kwang-Yon; Shin, Seong Eun; No, Kyoung Tai

    2015-01-01

    Objectives For successful adoption of legislation controlling registration and assessment of chemical substances, it is important to obtain sufficient toxicological experimental evidence and other related information. It is also essential to obtain a sufficient number of predicted risk and toxicity results. Particularly, methods used in predicting toxicities of chemical substances during acquisition of required data, ultimately become an economic method for future dealings with new substances. Although the need for such methods is gradually increasing, the-required information about reliability and applicability range has not been systematically provided. Methods There are various representative environmental and human toxicity models based on quantitative structure-activity relationships (QSAR). Here, we secured the 10 representative QSAR-based prediction models and its information that can make predictions about substances that are expected to be regulated. We used models that predict and confirm usability of the information expected to be collected and submitted according to the legislation. After collecting and evaluating each predictive model and relevant data, we prepared methods quantifying the scientific validity and reliability, which are essential conditions for using predictive models. Results We calculated predicted values for the models. Furthermore, we deduced and compared adequacies of the models using the Alternative non-testing method assessed for Registration, Evaluation, Authorization, and Restriction of Chemicals Substances scoring system, and deduced the applicability domains for each model. Additionally, we calculated and compared inclusion rates of substances expected to be regulated, to confirm the applicability. Conclusions We evaluated and compared the data, adequacy, and applicability of our selected QSAR-based toxicity prediction models, and included them in a database. Based on this data, we aimed to construct a system that can be used

  6. Toward Accessing Spatial Structure from Building Information Models

    NASA Astrophysics Data System (ADS)

    Schultz, C.; Bhatt, M.

    2011-08-01

    Data about building designs and layouts is becoming increasingly more readily available. In the near future, service personal (such as maintenance staff or emergency rescue workers) arriving at a building site will have immediate real-time access to enormous amounts of data relating to structural properties, utilities, materials, temperature, and so on. The critical problem for users is the taxing and error prone task of interpreting such a large body of facts in order to extract salient information. This is necessary for comprehending a situation and deciding on a plan of action, and is a particularly serious issue in time-critical and safety-critical activities such as firefighting. Current unifying building models such as the Industry Foundation Classes (IFC), while being comprehensive, do not directly provide data structures that focus on spatial reasoning and spatial modalities that are required for high-level analytical tasks. The aim of the research presented in this paper is to provide computational tools for higher level querying and reasoning that shift the cognitive burden of dealing with enormous amounts of data away from the user. The user can then spend more energy and time in planning and decision making in order to accomplish the tasks at hand. We present an overview of our framework that provides users with an enhanced model of "built-up space". In order to test our approach using realistic design data (in terms of both scale and the nature of the building models) we describe how our system interfaces with IFC, and we conduct timing experiments to determine the practicality of our approach. We discuss general computational approaches for deriving higher-level spatial modalities by focusing on the example of route graphs. Finally, we present a firefighting scenario with alternative route graphs to motivate the application of our framework.

  7. Upper thoracic postsynaptic dorsal column neurons conduct cardiac mechanoreceptive information, but not cardiac chemical nociception in rats.

    PubMed

    Goodman-Keiser, Melanie D; Qin, Chao; Thompson, Ann M; Foreman, Robert D

    2010-12-17

    Postsynaptic dorsal column (PSDC) neurons transmit noxious visceral information from the lower thoracic and lumbosacral spinal cord. Cuneothalamic neurons in the PSDC pathway and upper thoracic (T(3)-T(4)) spinal neurons ascending through the ventrolateral funiculus (VLF) have been shown to transmit nociceptive cardiac information. Therefore, we hypothesized that upper thoracic PSDC neurons transmit noxious cardiac information. Neuronal responses to intrapericardially injected mechanical (1.0 ml saline) and noxious chemical (0.2 ml algogenic chemicals) stimuli were recorded from antidromically activated PSDC and VLF neurons in the T(3)-T(4) spinal cord of anesthetized Sprague-Dawley rats. Of the PSDC neurons, 43% responded to mechanical stimulation, but only one responded to noxious chemical stimuli. Fifty-eight percent of VLF neurons responded to mechanical stimulation and all responded to noxious chemical stimulation. Fluoro-Ruby (FR)-labeled PSDC neurons in the T(3)-T(4) spinal cord of Sprague-Dawley rats were processed for c-fos immunohistochemistry following intrapericardial stimulation with mechanical, chemical, or control stimuli. Sections were viewed under epifluorescence and light microscopy to detect FR-labeled neurons containing a c-fos immunoreactive (IR) nucleus. An average of 6 PSDC neurons per rat was found in the T(3) and T(4) spinal segments. The average number of c-fos-IR neurons per segment varied by type of stimulus: 12 (control), 67 (chemical) and 85 (mechanical) for T(3) and 8 (control), 37 (chemical) and 62 (mechanical) for T(4). None of the 200 PSDC neurons examined expressed c-fos-IR regardless of stimulus. Together, these results suggest that thoracic PSDC neurons transmit mechanical cardiac information, but they play a minimal role in cardiac nociception.

  8. The Informational Text Structure Survey (ITS[superscript 2]): An Exploration of Primary Grade Teachers' Sensitivity to Text Structure in Young Children's Informational Texts

    ERIC Educational Resources Information Center

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

    2016-01-01

    There has been no research reported about if or how well primary grade teachers can identify information text structures in children's authentic informational texts. The ability to do so accurately and reliably is a prerequisite for teachers to be able to teach students how to recognize and use text structures to assist them in comprehending…

  9. Revealing biological information using data structuring and automated learning.

    PubMed

    Mohorianu, Irina; Moulton, Vincent

    2010-11-01

    The intermediary steps between a biological hypothesis, concretized in the input data, and meaningful results, validated using biological experiments, commonly employ bioinformatics tools. Starting with storage of the data and ending with a statistical analysis of the significance of the results, every step in a bioinformatics analysis has been intensively studied and the resulting methods and models patented. This review summarizes the bioinformatics patents that have been developed mainly for the study of genes, and points out the universal applicability of bioinformatics methods to other related studies such as RNA interference. More specifically, we overview the steps undertaken in the majority of bioinformatics analyses, highlighting, for each, various approaches that have been developed to reveal details from different perspectives. First we consider data warehousing, the first task that has to be performed efficiently, optimizing the structure of the database, in order to facilitate both the subsequent steps and the retrieval of information. Next, we review data mining, which occupies the central part of most bioinformatics analyses, presenting patents concerning differential expression, unsupervised and supervised learning. Last, we discuss how networks of interactions of genes or other players in the cell may be created, which help draw biological conclusions and have been described in several patents.

  10. Development of a Fundamental Understanding of Chemical Bonding and Electronic Structure in Spinel Compounds

    SciTech Connect

    Sickafus, K.E.; Wills, J.M.; Chen, S.-P.; Terry, J.H., Jr.; Hartmann, T.; Sheldon, R.I.

    1999-05-14

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos national Laboratory (LANL). Hundreds of ceramic compounds possess the spinel crystal structure and exhibit a remarkable variety of properties, ranging from compounds that are electrical insulators to compounds that are superconducting, or from compounds with ferri- and antiferromagnetic behavior to materials with colossal magnetoresistive characteristics. The unique crystal structure of spinel compounds is in many ways responsible for the widely varying physical properties of spinels. The objective of this project is to investigate the nature of chemical bonding, point defects, and electronic structure in compounds with the spinel crystal structure. Our goal is to understand and predict the stability of the spinel structure as a function of chemical composition, stoichiometry, and cation disorder. The consequences of cation disorder in spinel materials can be profound . The ferromagnetic characteristics of magnesioferrite, for instance, are entirely attributable to disorder on the cation sublattices. Our studies provide insight into the mechanisms of point defect formation and cation disorder and their effects on the electronic band structure and crystal structure of spinel-structure materials. our ultimate objective is to develop a more substantive knowledge of the spinel crystal structure and to promote new and novel uses for spinel compounds. The technical approach to achieve our goals is to combine first-principles calculations with experimental measurements. The structural and electronic properties of spinel samples were experimentally determined primarily with X-ray and neutron scattering, optical and X-ray absorption, and electron energy-loss spectroscopy. Total energy electronic structure calculations were performed to determine structural stability, band structure, density of states, and electron distribution. We also used shell

  11. Development of a Fundamental Understanding of Chemical Bonding and Electronic Structure in Spinel Compounds

    SciTech Connect

    Sickafus, K.E.; Wills, J.M.; Chen, S.-P.; Terry, J.H., Jr.; Hartmann, T.; Sheldon, R.I.

    1999-06-03

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Hundreds of ceramic compounds possess the spinel crystal structure and exhibit a remarkable variety of properties, ranging from compounds that are electrical insulators to compounds that are superconducting, or from compounds with ferri- and antiferromagnetic behavior to materials with colossal magnetoresistive characteristics. The unique crystal structure of spinel compounds is in many ways responsible for the widely varying physical properties of spinels. The objective of this project is to investigate the nature of chemical bonding, point defects, and electronic structure in compounds with the spinel crystal structure. Our goal is to understand and predict the stability of the spinel structure as a function of chemical composition, stoichiometry, and cation disorder. The consequences of cation disorder in spinel materials can be profound . The ferromagnetic characteristics of magnesioferrite, for instance, are entirely attributable to disorder on the cation sublattices. Our studies provide insight into the mechanisms of point defect formation and cation disorder and their effects on the electronic band structure and crystal structure of spinel-structure materials. Our ultimate objective is to develop a more substantive knowledge of the spinel crystal structure and to promote new and novel uses for spinel compounds. The technical approach to achieve our goals is to combine first-principles calculations with experimental measurements. The structural and electronic properties of spinel samples were experimentally determined primarily with X-ray and neutron scattering, optical and X-ray absorption, and electron energy-loss spectroscopy. Total energy electronic structure calculations were performed to determine structural stability, band structure, density of states, and electron distribution. We also used shell

  12. Effects of lignin structure on hydrodeoxygenation reactivity of pine wood lignin to valuable chemicals

    DOE PAGES

    Wang, Hongliang; Ben, Haoxi; Southeast Univ., Nanjing; ...

    2017-01-05

    Hydrodeoxygenation (HDO) of two dilute acid flow through pretreated softwood lignin samples, including residual lignin in pretreated solid residues (ReL) and recovered insoluble lignin in pretreated liquid (RISL), with apparent different physical and chemical structures, was comprehensively studied. A combination of catalysts (HY zeolite and Ru/Al2O3) was employed to investigate the effects of lignin structures, especially condensed structures, on the HDO upgrading process. Results indicated that the condensed structure and short side chains in lignin hindered its HDO conversion under different reaction conditions, including catalyst loading and composition, hydrogen pressure, and reaction time. In addition to lignin structure, HY zeolitemore » was found crucial for lignin depolymerization, while Ru/Al2O3 and relatively high hydrogen pressure (4 MPa) were necessary for upgrading unstable oxy-compounds to cyclohexanes at high selectivity (>95 wt %). Since the lignin structure essentially affects its reactivity during HDO conversion, the yield and selectivity of HDO products can be predicted by detailed characterization of the lignin structure. Furthermore, the insights gained from this study in the fundamental reaction mechanisms based on the lignin structure will facilitate upgrading of lignin to high-value products for applications in the production of both fuels and chemicals.« less

  13. Exploring 3D structural influences of aliphatic and aromatic chemicals on α-cyclodextrin binding.

    PubMed

    Linden, Lukas; Goss, Kai-Uwe; Endo, Satoshi

    2016-04-15

    Binding of solutes to macromolecules is often influenced by steric effects caused by the 3D structures of both binding partners. In this study, the 1:1 α-cyclodextrin (αCD) binding constants (Ka1) for 70 organic chemicals were determined to explore the solute-structural effects on the αCD binding. Ka1 was measured using a three-part partitioning system with either a headspace or a passive sampler serving as the reference phase. The Ka1 values ranged from 1.08 to 4.97 log units. The results show that longer linear aliphatic chemicals form more stable complexes than shorter ones, and that the position of the functional group has a strong influence on Ka1, even stronger than the type of the functional group. Comparison of linear and variously branched aliphatic chemicals indicates that having a sterically unhindered alkyl chain is favorable for binding. These results suggest that only one alkyl chain can enter the binding cavity. Relatively small aromatic chemicals such as 1,3-dichlorobenzene bind to αCD well, while larger ones like tetrachlorobenzene and 3-ring aromatic chemicals show only a weak interaction with αCD, which can be explained by cavity exclusion. The findings of this study help interpret cyclodextrin binding data and facilitate the understanding of binding processes to macromolecules.

  14. Physico-Chemical Structural and Electrical Studies of Cu-Zn Ferrites Synthesized by Novel Chemical Route

    NASA Astrophysics Data System (ADS)

    Lohar, K. S.; Patange, S. M.; Mane, D. R.; Shirsath, Sagar E.; Shinde, N. D.; Kulkarni, Nilesh

    The physico-chemical, structural and electrical properties of zinc substituted copper ferrites having the general formula Cu1-xZnxFe2O4 (x=0.0 to x=0.8) have been studied as a function of zinc ion concentration. The sample was prepared by co-precipitation method from corresponding metal sulphates. X-ray diffraction patterns were used to confirm the structure of synthesized samples. The calculated and theoretical values of average lattice constant, tetrahedral bond, tetrahedral edge and unshared octahedral edge were found to increase, while the shared octahedral edge and octahedral bond decrease as the Zn ion concentration increases. The dielectric constant (ε‧) and dielectric loss tangent (tan δ) were measured at a constant frequency 1 kHz as a function of temperature. The dielectric constant and loss tangent were found to increase with rise in temperature. The conduction mechanism in these ferrites is discussed on the basis of electron exchange between Fe2+ and Fe3+ ions. The temperature dependent dc resistivity was carried out in the temperature range 300 to 800 K. The plots of log ρ versus 103/T are linear showing two regions, corresponding to ferrimagnetic and paramagnetic regions.

  15. Chemical synthesis and structure elucidation of bovine {kappa}-casein (1-44)

    SciTech Connect

    Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F. . E-mail: p.alewood@imb.uq.edu.au

    2006-02-24

    The caseins ({alpha}{sub s1}, {alpha}{sub s2}, {beta}, and {kappa}) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine {kappa}-casein, the protein which maintains the micellar structure of the caseins. {kappa}-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro{sup 8} to Arg{sup 34}. This is First report which demonstrates extensive secondary structure within the casein class of proteins.

  16. Chemical and structural stability of lithium-ion battery electrode materials under electron beam.

    PubMed

    Lin, Feng; Markus, Isaac M; Doeff, Marca M; Xin, Huolin L

    2014-07-16

    The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi(0.4)Mn(0.4)Co(0.18)Ti(0.02)O2 particles, repeated electron beam irradiation induced a phase transition from an layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.

  17. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    PubMed

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.

  18. Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

    DOE PAGES

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

  19. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    PubMed

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.

  20. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin.

    PubMed

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-05-23

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their toxic side effects and increasing number of resistant pathogens set limits on their use. This review focuses on recent advances concerning quinolones and fluoroquinolones, we will be summarising chemical structure, mode of action, pharmacokinetic properties and toxicity. We will be describing fluoroquinolones introduced in clinical trials, namely avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and non-fluorinated nemonoxacin. These agents have been proved to have enhanced antibacterial effect even against ciprofloxacin resistant pathogens, and found to be well tolerated in both oral and parenteral administrations. These features are going to make them potential antimicrobial agents in the future.