Science.gov

Sample records for chemical structure information

  1. Automated extraction of chemical structure information from digital raster images

    PubMed Central

    Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

    2009-01-01

    Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research

  2. Recent Strategies for Retrieving Chemical Structure Information on the Web.

    ERIC Educational Resources Information Center

    Lo, Mei Ling

    1997-01-01

    Various methods for retrieving chemical structure information on the World Wide Web are discussed. Although graphical plug-in programs provide more search capabilities, users first have to obtain a copy of the programs. Tripos's WebSketch and ACD Interactive Lab adopt a different approach; using JAVA applets, users create and display a structure…

  3. 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…

  4. 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...

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

    PubMed Central

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

    2013-01-01

    Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

  6. Use of selected toxicology information resources in assessing relationships between chemical structure and biological activity

    SciTech Connect

    Wassom, J.S.

    1985-09-01

    This paper addresses the subject of the use of the selected toxicology information resources in assessing relationships between chemical structure and specific end points. To assist the researcher in how to access the primary literature of genetic toxicology, teratogenesis, and carcinogenesis, three specific specialized information centers are discussed - Environmental Mutagen Information Center, Environmental Teratology Information Center, and Environmental Carcinogenesis Information Center. Also included are descriptions of information resources that contain evaluated (peer-reviewed) biological research results. The US Environmental Protection Agency Genetic Toxicology Program, the International Agency for Research on Cancer Monographs, and the Toxicology Data Bank are the best sources currently available to obtain peer-reviewed results for compounds tested for genotoxicity, carcinogenicity, and other toxicological end points. The value of published information lies in its use. It has become evident that most information cannot be accepted at face value for interpretation and analysis when subjected to stringent quality evaluation criteria. This deficit can be corrected by rigid editorship and the cognizance of authors. Increased interest in alternative methods to in vivo animal testing will be exemplified by use of short-term bioassays and in structure-activity relationship studies. With respect to this latter area, it must be remembered that mechanically (computer generated) derived data cannot substitute, at least at this stage, for data obtained from actual animal testing. The future of structure-activity relationship studies will rest only in their use as a predictive tool.

  7. Use of selected toxicology information resources in assessing relationships between chemical structure and biological activity.

    PubMed Central

    Wassom, J S

    1985-01-01

    This paper addresses the subject of the use of selected toxicology information resources in assessing relationships between chemical structure and specific biological end points. To assist the researcher in how to access the primary literature of genetic toxicology, teratogenesis, and carcinogenesis, three specific specialized information centers are discussed--Environmental Mutagen Information Center, Environmental Teratology Information Center, and Environmental Carcinogenesis Information Center. Also included are descriptions of information resources that contain evaluated (peer-reviewed) biological research results. The U.S. Environmental Protection Agency Genetic Toxicology Program, the International Agency for Research on Cancer Monographs, and the Toxicology Data Bank are the best sources currently available to obtain peer-reviewed results for compounds tested for genotoxicity, carcinogenicity, and other toxicological end points. The value of published information lies in its use. It has become evident that most information cannot be accepted at face value for interpretation and analysis when subjected to stringent quality evaluation criteria. This deficit can be corrected by rigid editorship and the cognizance of authors. Increased interest in alternative methods to in vivo animal testing will be exemplified by use of short-term bioassays and in structure-activity relationship studies. With respect to this latter area, it must be remembered that mechanically (computer generated) derived data cannot substitute, at least at this stage, for data obtained from actual animal testing. The future of structure-activity relationship studies will rest only in their use as a predictive tool. PMID:4065070

  8. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    PubMed

    Shen, Yang; Bax, Ad

    2015-01-01

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

  9. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

    PubMed

    Hattori, Masahiro; Okuno, Yasushi; Goto, Susumu; Kanehisa, Minoru

    2003-10-01

    Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes. PMID:14505407

  10. CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins

    PubMed Central

    Arun, P. V. Parvati Sai; Bakku, Ranjith Kumar; Subhashini, Mranu; Singh, Pankaj; Prabhu, N. Prakash; Suzuki, Iwane; Prakash, Jogadhenu S. S.

    2012-01-01

    CyanoPhyChe is a user friendly database that one can browse through for physico-chemical properties, structure and biochemical pathway information of cyanobacterial proteins. We downloaded all the protein sequences from the cyanobacterial genome database for calculating the physico-chemical properties, such as molecular weight, net charge of protein, isoelectric point, molar extinction coefficient, canonical variable for solubility, grand average hydropathy, aliphatic index, and number of charged residues. Based on the physico-chemical properties, we provide the polarity, structural stability and probability of a protein entering in to an inclusion body (PEPIB). We used the data generated on physico-chemical properties, structure and biochemical pathway information of all cyanobacterial proteins to construct CyanoPhyChe. The data can be used for optimizing methods of expression and characterization of cyanobacterial proteins. Moreover, the ‘Search’ and data export options provided will be useful for proteome analysis. Secondary structure was predicted for all the cyanobacterial proteins using PSIPRED tool and the data generated is made accessible to researchers working on cyanobacteria. In addition, external links are provided to biological databases such as PDB and KEGG for molecular structure and biochemical pathway information, respectively. External links are also provided to different cyanobacterial databases. CyanoPhyChe can be accessed from the following URL: http://bif.uohyd.ac.in/cpc. PMID:23185330

  11. Systematically evaluating read-across prediction and performance using a local validity approach characterized by chemical structure and bioactivity information.

    PubMed

    Shah, Imran; Liu, Jie; Judson, Richard S; Thomas, Russell S; Patlewicz, Grace

    2016-08-01

    Read-across is a popular data gap filling technique within category and analogue approaches for regulatory purposes. Acceptance of read-across remains an ongoing challenge with several efforts underway for identifying and addressing uncertainties. Here we demonstrate an algorithmic, automated approach to evaluate the utility of using in vitro bioactivity data ("bioactivity descriptors", from EPA's ToxCast program) in conjunction with chemical descriptor information to derive local validity domains (specific sets of nearest neighbors) to facilitate read-across for up to ten in vivo repeated dose toxicity study types. Over 3239 different chemical structure descriptors were generated for a set of 1778 chemicals and supplemented with the outcomes from 821 in vitro assays. The read-across prediction of toxicity for 600 chemicals with in vivo data was based on the similarity weighted endpoint outcomes of its nearest neighbors. The approach enabled a performance baseline for read-across predictions of specific study outcomes to be established. Bioactivity descriptors were often found to be more predictive of in vivo toxicity outcomes than chemical descriptors or a combination of both. This generalized read-across (GenRA) forms a first step in systemizing read-across predictions and serves as a useful component of a screening level hazard assessment for new untested chemicals. PMID:27174420

  12. Information Structure and Linguistic Structure.

    ERIC Educational Resources Information Center

    Zierer, Ernesto

    1972-01-01

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

  13. Chemical structure of interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.

    1985-01-01

    The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

  14. 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,…

  15. Toxic chemical release inventory information.

    PubMed

    Bronson, R J

    1991-01-01

    As part of a U.S. government effort to inform the public about toxic or hazardous chemicals released into the environment, the National Library of Medicine (NLM) and the Environmental Protection Agency (EPA) are jointly producing the TRI (Toxic Chemical Release Inventory) databanks which consist of two separate files, TRI87 and TRI88. Both files reside on NLM's TOX-NET system. The files contain geographic information about reporting facilities and land, air, and water release data for approximately 300 listed chemicals. PMID:10111718

  16. Multimedia environmental chemical partitioning from molecular information.

    PubMed

    Martínez, Izacar; Grifoll, Jordi; Giralt, Francesc; Rallo, Robert

    2010-12-15

    The prospect of assessing the environmental distribution of chemicals directly from their molecular information was analyzed. Multimedia chemical partitioning of 455 chemicals, expressed in dimensionless compartmental mass ratios, was predicted by SimpleBox 3, a Level III Fugacity model, together with the propagation of reported uncertainty for key physicochemical and transport properties, and degradation rates. Chemicals, some registered in priority lists, were selected according to the availability of experimental property data to minimize the influence of predicted information in model development. Chemicals were emitted in air or water in a fixed geographical scenario representing the Netherlands and characterized by five compartments (air, water, sediments, soil and vegetation). Quantitative structure-fate relationship (QSFR) models to predict mass ratios in different compartments were developed with support vector regression algorithms. A set of molecular descriptors, including the molecular weight and 38 counts of molecular constituents were adopted to characterize the chemical space. Out of the 455 chemicals, 375 were used for training and testing the QSFR models, while 80 were excluded from model development and were used as an external validation set. Training and test chemicals were selected and the domain of applicability (DOA) of the QSFRs established by means of self-organizing maps according to structural similarity. Best results were obtained with QSFR models developed for chemicals belonging to either the class [C] and [C; O], or the class with at least one heteroatom different than oxygen in the structure. These two class-specific models, with respectively 146 and 229 chemicals, showed a predictive squared coefficient of q(2) ≥ 0.90 both for air and water, which respectively dropped to q(2)≈ 0.70 and 0.40 for outlying chemicals. Prediction errors were of the same order of magnitude as the deviations associated to the uncertainty of the

  17. Chemical documents: machine understanding and automated information extraction.

    PubMed

    Townsend, Joe A; Adams, Sam E; Waudby, Christopher A; de Souza, Vanessa K; Goodman, Jonathan M; Murray-Rust, Peter

    2004-11-21

    Automatically extracting chemical information from documents is a challenging task, but an essential one for dealing with the vast quantity of data that is available. The task is least difficult for structured documents, such as chemistry department web pages or the output of computational chemistry programs, but requires increasingly sophisticated approaches for less structured documents, such as chemical papers. The identification of key units of information, such as chemical names, makes the extraction of useful information from unstructured documents possible. PMID:15534707

  18. 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…

  19. 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.

  20. The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement.

    PubMed

    Brylinski, Michal; Lee, Seung Yup; Zhou, Hongyi; Skolnick, Jeffrey

    2011-03-01

    Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring functions, the genome-wide application of many ligand docking/screening algorithms is limited by the quality of the binding sites in theoretical receptor models constructed by protein structure prediction. In this study, we describe a new template-based method for the local refinement of ligand-binding regions in protein models using remotely related templates identified by threading. We designed a Support Vector Regression (SVR) model that selects correct binding site geometries in a large ensemble of multiple receptor conformations. The SVR model employs several scoring functions that impose geometrical restraints on the Cα positions, account for the specific chemical environment within a binding site and optimize the interactions with putative ligands. The SVR score is well correlated with the RMSD from the native structure; in 47% (70%) of the cases, the Pearson's correlation coefficient is >0.5 (>0.3). When applied to weakly homologous models, the average heavy atom, local RMSD from the native structure of the top-ranked (best of top five) binding site geometries is 3.1Å (2.9Å) for roughly half of the targets; this represents a 0.1 (0.3)Å average improvement over the original predicted structure. Focusing on the subset of strongly conserved residues, the average heavy atom RMSD is 2.6Å (2.3Å). Furthermore, we estimate the upper bound of template-based binding site refinement using only weakly related proteins to be ∼2.6Å RMSD. This value also corresponds to the plasticity of the ligand-binding regions in distant homologues. The Binding Site Refinement (BSR

  1. Chemical Structure Handling by Computer.

    ERIC Educational Resources Information Center

    Paris, C. Gregory

    1997-01-01

    Organized from the viewpoint of information retrieval theory, this review addresses issues of chemical information representation, comparison and matching, and retrieval strategies. Additional topics include similarity and clustering, visualization, and molecular diversity. Trends in research and application are identified, and gaps in the…

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

    PubMed Central

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

    2015-01-01

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

  3. Gauge theory and chemical structure.

    PubMed

    Mattingly, James

    2003-05-01

    The possibility of chemical structure in the context of quantized matter is examined by way of Richard Bader's Atoms in Molecules. I critically examine his notion of "electronic charge density"-showing that he cannot really mean "density of charge"-and I argue that the appropriate concept is expectation value of charge. This still allows him to define chemical structure, but it makes problematic his appeals to the explanatory power of structure. This is because, as Rosenfeld and Bohr showed, the expectation value of charge cannot be taken as the electronic field experienced by other charges. I suggest that we can recover the efficacy of structure by thinking of chemistry as a gauge theory. Current consensus in the study of gauge theories indicates that gauge potentials represent a new type of property; while no member of the family of functions comprising the gauge potential is real, the potential itself is causally potent. I illustrate this in the case of electrodynamics, where the vector potential can causally influence charges in the absence of electric or magnetic fields. I show how chemical structure can be considered to be a gauge field. Following Bader, I take it to be a family of geometric configurations, no one of which is possessed by a given molecule. I claim that current research in gauge theory licenses the attribution of causal potency to this notion of structure, despite its lack of reality. I thus begin the process of freeing the explanatory resources of gauge theory from physics alone. PMID:12796102

  4. InChI - the worldwide chemical structure identifier standard

    PubMed Central

    2013-01-01

    Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the extensive use and dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community, the chemical information community, and major publishers and disseminators of chemical and related scientific offerings in manuscripts and databases. PMID:23343401

  5. 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.

  6. Identification of Chemical Toxicity Using Ontology Information of Chemicals

    PubMed Central

    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. PMID:26508991

  7. 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.

  8. 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

  9. [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. PMID:17139152

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

    PubMed

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

    2006-01-01

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

  11. Chemical Biological Emergency Management Information System

    Energy Science and Technology Software Center (ESTSC)

    2004-06-15

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

  12. 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.

  13. Chemical structure representations and applications in computational toxicity.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2012-01-01

    Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies. PMID:23007430

  14. 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...

  15. 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.

  16. The past and future of chemical information - A report of the Chemical Information Division Session of the 200th Meeting of the American Chemical Society

    NASA Astrophysics Data System (ADS)

    Tokizane, Soichi

    At the historical meeting of the ACS CINF Division, the 1990 Herman Skolnik Award was presented to Dr. Ernst Meyer, who at BASF in Germany had developed a computer storage and retrieval system of chemical structures in 1960s. His and his colleagues' speeches in the award symposium were about the history of the development of chemical structure information in Germany. In the symposium of the Markush structure system, a hottest topic in this field, CAS's MARPAT and Markush-DARC co-developed by Questel, INPI, and Derwent were discussed by many papers. Other topics of this meeting were discussed, too.

  17. Mining chemical information from open patents

    PubMed Central

    2011-01-01

    Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured. PMID:21999425

  18. 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)

  19. 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…

  20. Bayesian inference of protein structure from chemical shift data

    PubMed Central

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

    2015-01-01

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

  1. 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.…

  2. Challenges and Benefits of Chemical Information Service in Industry.

    ERIC Educational Resources Information Center

    Hansen, Mary E.; Curtis, Jan M.

    1997-01-01

    Discusses chemical information services offered in industrial chemical libraries, based on experiences at the 3M Library. Topics include qualifications of chemical information professionals; corporate culture; clients; services, including reference, current awareness, confidentiality, and end-user support; and information resources, including…

  3. Views on chemical safety information and influences on chemical disposal behaviour in the UK.

    PubMed

    Hinks, J; Bush, J; Andras, P; Garratt, J; Pigott, G; Kennedy, A; Pless-Mulloli, T

    2009-02-01

    This study examined how groups representing four tiers in the chemical supply chain (manufacturers, vendors, workers and consumers) understood safety information, and the factors that influenced disposal behaviour. Data from seven, semi-structured, focus groups was analysed both qualitatively (textual analysis) and quantitatively (network analysis). Such combined analytical methods enabled us to achieve both detailed insights into perceptions and behaviour and an objective understanding of the prevailing opinions that occurred within and between the focus group discussions. We found issues around awareness, trust, access and disposal behaviours differed between groups within the supply chain. Participants from the lower tiers perceived chemical safety information to be largely inaccessible. Labels were the main source of information on chemical risks for the middle and bottom tiers of the supply chain. Almost all of the participants were aware of the St Andrew's Cross and skull and crossbones symbols but few were familiar with the Volatile Organic Compound logo or the fish and tree symbol. Both the network and thematic analysis demonstrated that whilst frequent references to health risks associated with chemicals were made environmental risks were usually only articulated after prompting. It is clear that the issues surrounding public understanding of chemical safety labels are highly complex and this is compounded by inconsistencies in the cognitive profiles of chemical users. Substantially different cognitive profiles are likely to contribute towards communication difficulties between different tiers of the supply chain. Further research is needed to examine the most effective ways of communicating chemical hazards information to the public. The findings demonstrate a need to improve and simplify disposal guidance to members of the public, to raise public awareness of the graphic symbols in the CHIP 3.1, 2005 regulations and to improve access to disposal guidance

  4. 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.

  5. 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.

  6. 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.

  7. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steve D; McDowell, Rod 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 and 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. 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

  10. Chemical and structural characterization of carbon nanotube surfaces.

    PubMed

    Wepasnick, Kevin A; Smith, Billy A; Bitter, Julie L; Howard Fairbrother, D

    2010-02-01

    To utilize carbon nanotubes (CNTs) in various commercial and scientific applications, the graphene sheets that comprise CNT surfaces are often modified to tailor properties, such as dispersion. In this article, we provide a critical review of the techniques used to explore the chemical and structural characteristics of CNTs modified by covalent surface modification strategies that involve the direct incorporation of specific elements and inorganic or organic functional groups into the graphene sidewalls. Using examples from the literature, we discuss not only the popular techniques such as TEM, XPS, IR, and Raman spectroscopy but also more specialized techniques such as chemical derivatization, Boehm titrations, EELS, NEXAFS, TPD, and TGA. The chemical or structural information provided by each technique discussed, as well as their strengths and limitations. Particular emphasis is placed on XPS and the application of chemical derivatization in conjunction with XPS to quantify functional groups on CNT surfaces in situations where spectral deconvolution of XPS lineshapes is ambiguous. PMID:20052581

  11. 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.

  12. Information System for Environmental Chemicals: Training for End Users.

    ERIC Educational Resources Information Center

    Voigt, Kristina; And Others

    1991-01-01

    Discusses factors to consider in identifying and accessing appropriate data sources for environmental chemical information and describes three training programs for end-users: (1) a course on retrieval of information on dangerous substances; (2) a seminar on German offline databases on chemicals; and (3) a workshop on the Information System for…

  13. 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.

  14. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    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).

  15. 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).

  16. 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.

  17. 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...

  18. CIStudio: A Worldwide Web-Based, Interactive Chemical Information Course

    NASA Astrophysics Data System (ADS)

    Holmes, Colette O.; Warden, Joseph T.

    1996-04-01

    CIStudio (Chemical Information Studio) is a one-credit undergraduate Chemistry course at Rensselaer Polytechnic Institute. This article describes in detail the course which focuses on the integration of electronic and print sources, especially Internet-accessible reference and database services. CIStudio is delivered via the World Wide Web (WWW) and is the first Web-centric course in Chemical Information.

  19. 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…

  20. 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)

  1. INTEGRATED CHEMICAL INFORMATION TECHNOLOGIES APPLIED TO TOXICOLOGY

    EPA Science Inventory

    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. Model...

  2. 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

  3. Informational laws of genome structures.

    PubMed

    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

  4. 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.

  5. 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…

  6. 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.

  7. 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

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

    PubMed

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

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

  9. AN OVERVIEW OF WORLDWIDE CHEMICAL INFORMATION FACILITIES AND RESOURCES.

    ERIC Educational Resources Information Center

    National Science Foundation, Washington, DC.

    THIS DESCRIPTIVE OVERVIEW OF CHEMICAL INFORMATION TRANSFER ACTIVITIES AND SYSTEMS COVERS THE FULL RANGE OF INFORMATION SERVICES FROM TRADITIONAL PUBLICATION SERVICES THROUGH THE DEVELOPING COMPUTER-BASED SERVICES. THE REPORT IS CONCERNED WITH DOCUMENTATION RATHER THAN ORAL COMMUNICATION AND WITH RECOGNIZED INFORMATION SYSTEMS RATHER THAN INFORMAL…

  10. 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.

  11. Fast Optical Chemical and Structural Classification of RNA.

    PubMed

    Morla-Folch, Judit; Xie, Hai-nan; Alvarez-Puebla, Ramon A; Guerrini, Luca

    2016-02-23

    As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs. PMID:26831953

  12. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  13. 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.

  14. 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

  15. 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. PMID:20877495

  16. On-line information sources on chemical substances.

    PubMed

    Castriotta, M; Dracos, A

    1994-01-01

    Information technology has brought about changes in the work patterns of researchers and scientists. After some hints on the on-line facilities needed to be connected to the international host computers, an analysis is made of some of the main automated sources available to retrieve information on chemical substances. Special emphasis is given to textual-numeric data banks, first reviewing the main chemical dictionaries, like Registry and Chemline, and then focusing on those sources that offer immediate information in case of emergency. Among the Toxnet files, produced and managed within the US National Library of Medicine Toxicology Information Program, play a very important role in offering publicly available data on toxicology and on hazardous chemicals. Therefore, the Hazardous Substances Data Bank (HSDB) and the Registry of Toxic Effects of Chemical Substances (RTECS) are described for their relevance thereon. Other data banks produced in Europe, like the Environmental Chemicals Data Information Network (ECDIN) and the very specialized Major Hazard Incident Data Service (MHIDAS) are also briefly outlined. To integrate this overview on online information, the attention is then shifted on sources having the characteristic of reference databases: prestigious files covering the international scientific literature, as CA/Chemabs, Toxline/Toxlit, Embase, Medline are introduced. Implications of on-line technology in enhancing information access in the next future are discussed, pointing out the new tools created to meet the information needs of end-users. PMID:7762934

  17. Systems approach to chemical spill response information needs

    SciTech Connect

    Parnarouskis, M.C.; Flessner, M.F.; Potts, R.G.

    1980-01-01

    The Chemical Hazards Response Information System (CHRIS) has been specifically designed to meet the emergency needs of US Coast Guard field personnel, currently providing them with information on 900 hazardous chemicals, with methods of predicting hazards resulting from accidental discharges, and with procedures for selecting and implementing response to accident discharges. The major components of CHRIS and the computerized hazard assessment models within the Hazard Assessment Computer System are described in detail.

  18. 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

  19. Chemical Structure of Trichomonas vaginalis Surface Lipoglycan

    PubMed Central

    Ryan, Christopher M.; Mehlert, Angela; Richardson, Julia M.; Ferguson, Michael A. J.; Johnson, Patricia J.

    2011-01-01

    The extracellular parasite Trichomonas vaginalis contains a surface glycoconjugate that appears to mediate parasite-host cell interaction via binding to human galectin-1. This glycoconjugate also elicits cytokine production from human vaginal epithelial cells, implicating its role in modulation of host immune responses. We have analyzed the structure of this glycoconjugate, previously described to contain the sugars rhamnose (Rha), N-acetylglucosamine (GlcNAc), galactose (Gal), xylose (Xyl), N-acetylgalactosamine (GalNAc), and glucose (Glc), using gas chromatograph mass spectrometry (GC-MS), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF), electrospray MS/MS, and nuclear magnetic resonance (NMR), combined with chemical and enzymatic digestions. Our data reveal a complex structure, named T. vaginalis lipoglycan (TvLG), that differs markedly from Leishmania lipophosphoglycan and Entamoeba lipopeptidophosphoglycan and is devoid of phosphosaccharide repeats. TvLG is composed of an α1–3 linked polyrhamnose core, where Rha residues are substituted at the 2-position with either β-Xyl or chains of, on average, five N-acetyllactosamine (-3Galβ1–4GlcNAcβ1-) (LacNAc) units and occasionally lacto-N-biose (-3Galβ1-3GlcNAcβ1-) (LNB). These chains are themselves periodically substituted at the Gal residues with Xyl-Rha. These structural analyses led us to test the role of the poly-LacNAc/LNB chains in parasite binding to host cells. We found that reduction of poly-LacNAc/LNB chains decreased the ability of TvLG to compete parasite binding to host cells. In summary, our data provide a new model for the structure of TvLG, composed of a polyrhamnose backbone with branches of Xyl and poly-LacNAc/LNB. Furthermore, the poly-LacNAc side chains are shown to be involved in parasite-host cell interaction. PMID:21900246

  20. Chemical syntheses of inulin and levan structures.

    PubMed

    Oscarson, Stefan; Sehgelmeble, Fernando W

    2002-11-29

    A fructofuranosyl thiglycoside donor, ethyl 6-O-acetyl-3-O-benzyl-1,4-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-2-thio-beta-D-fructofuranoside (11), designed to yield stereospecifically beta-linkages and also to allow subsequent elongation in the 6- and/or 1-positions, was prepared and used in syntheses of levan and inulin structures. DMTST-promoted glycosylation between 11 (1.3 mol equiv) and methyl beta-D-fructofuranoside 6-OH and 1-OH acceptors (3 and 6) gave stereospecifically the protected methyl levanobioside 12 and inulinobioside 17 in excellent yields (80 and 86%), respectively. Protecting group manipulations on these afforded new disaccharide 6'-OH and 1'-OH acceptors (13 and 19), which were coupled again with donor 11 (1.0 mol equiv) to yield methyl levanotrioside 14 and inulinotrioside 20 in high yields, 65 and 67%, respectively. These were transformed into new acceptors and also fully deprotected to afford the methyl glycosides of levanotriose and inulinotriose, all structures that have earlier not been accessible by chemical synthesis. PMID:12444625

  1. 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...

  2. 78 FR 16698 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-18

    ... Information (CVI) for an additional 30 days for public comments. \\1\\ See 77 FR 74685. The 60-day Federal... statutory mandate at 72 FR 17688. Section 550 of the Homeland Security Appropriations Act of 2007 requires a... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability...

  3. 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…

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

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

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

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

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

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

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

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

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

  9. 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.

  10. Chemical and structural modifications of RNAi therapeutics.

    PubMed

    Ku, Sook Hee; Jo, Sung Duk; Lee, Yeon Kyung; Kim, Kwangmeyung; Kim, Sun Hwa

    2016-09-01

    Small interfering RNA (siRNA), a 21-23nt double-stranded RNA responsible for post-transcriptional gene silencing, has attracted great interests as promising genomic drugs, due to its strong ability to silence target genes in a sequence-specific manner. Despite high silencing efficiency and on-target specificity, the clinical translation of siRNA has been hindered by its inherent features: poor intracellular delivery, limited blood stability, unpredictable immune responses and unwanted off-targeting effects. To overcome these hindrances, researchers have made various advances to modify siRNA itself and to improve its delivery. In this review paper, first we briefly discuss the innate properties and delivery barriers of siRNA. Then, we describe recent progress in (1) chemically and structurally modified siRNAs to solve their intrinsic problems and (2) siRNA delivery formulations including siRNA conjugates, polymerized siRNA, and nucleic acid-based nanoparticles to improve in vivo delivery. PMID:26549145

  11. Conservation-dissipation structure of chemical reaction systems.

    PubMed

    Yong, Wen-An

    2012-12-01

    In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics. PMID:23368081

  12. 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

  13. 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

  14. Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

    PubMed Central

    Allali-Hassani, Abdellah; Pan, Patricia W; Dombrovski, Ludmila; Najmanovich, Rafael; Tempel, Wolfram; Dong, Aiping; Loppnau, Peter; Martin, Fernando; Thonton, Janet; Edwards, Aled M; Bochkarev, Alexey; Plotnikov, Alexander N; Vedadi, Masoud; Arrowsmith, Cheryl H

    2007-01-01

    The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique “chemical fingerprints” for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural “priming” of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone. PMID:17425406

  15. Structural and chemical profiling of the human cytosolic sulfotransferases.

    PubMed

    Allali-Hassani, Abdellah; Pan, Patricia W; Dombrovski, Ludmila; Najmanovich, Rafael; Tempel, Wolfram; Dong, Aiping; Loppnau, Peter; Martin, Fernando; Thornton, Janet; Thonton, Janet; Edwards, Aled M; Bochkarev, Alexey; Plotnikov, Alexander N; Vedadi, Masoud; Arrowsmith, Cheryl H

    2007-05-01

    The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique "chemical fingerprints" for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural "priming" of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone. PMID:17425406

  16. 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…

  17. 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.…

  18. 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…

  19. Enhanced Sensitivity of Micro Mechanical Chemical Sensors Through Structural Variation

    SciTech Connect

    Harris, J.C.

    2001-04-16

    Chemical detection devices are very effective; however, their bulkiness makes them undesirable for portable applications. The next generation of chemical detectors is microscopic mechanical devices capable of measuring trace amounts of chemical vapor within the environment. The chemicals do not react directly with the detector, instead intermolecular forces cause chemicals to adhere to the surface. This surface adhesion of the chemical creates surface stress on the detectors leading to measurable movement. Modifications to the structural design of these microstructures have resulted in signal enhancement to over seven hundred percent.

  20. Design of a computerized chemical information file in response to the initial inventory requirements of TSCA.

    PubMed

    Vogt, H C; Kerfoot, E J; Ford, G J

    1980-09-01

    A computerized file of chemical information, "CHEMFO", was developed at BASF Wyandotte Corporation to help comply with the initial reporting requirements of the Toxic Substances Control Act. This organization and approach allowed collecting the required information on all the manufactured and imported chemicals, editing and entry of the data, structuring of the computer file and interactive capabilities, and selecting the final program and subsequent printout. Besides using this system to meet the TSCA initial inventory reporting requirements, the file also has the capacity to be updated and revised as needed, which further expands its potential benefits. Some of the other information that can be derived from this system are: identification of chemical substances, quantities, and each site; tie-in to the medical/occupational health data bank; foundation for recording the industrial hygiene monitoring data; supplement for toxicology and environmental data base; and index for generating compilation of site specific material on health and environmental information. PMID:7457385

  1. Information and computer-aided system for structural materials

    NASA Astrophysics Data System (ADS)

    Nekrashevitch, Ju. G.; Nizametdinov, Sh. U.; Polkovnikov, A. V.; Rumjantzev, V. P.; Surina, O. N.; Kalinin, G. M.; Sidorenkov, A. V.; Strebkov, Ju. S.

    1992-09-01

    An information and computer-aided system for structural materials data has been developed to provide data for the fusion and fission reactor system design. It is designed for designers, industrial engineers, and material science specialists and provides a friendly interface in an interactive mode. The database for structural materials contains the master files: chemical composition, physical, mechanical, corrosion, technological properties, regulatory and technical documentation. The system is implemented on a PC/AT running the PS/2 operating system.

  2. Development of an Exchange Format for the European Environmental Chemical Data and Information Network (ECDIN).

    ERIC Educational Resources Information Center

    And Others; Proctor, David, J.

    1978-01-01

    Uses collection and storage of data in an environmental chemicals data bank to develop an exchange format of hierarchical tree structure between network partners. Rules identify and process the nodes in the tree in such a way that information is neither lost nor degraded upon transfer between network partners. (CWM)

  3. 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.

  4. 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…

  5. 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…

  6. 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.

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

    PubMed Central

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

    2011-01-01

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

  8. 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.

  9. Approaches to Chemical and Biochemical Information and Signal Processing

    NASA Astrophysics Data System (ADS)

    Privman, Vladimir

    2012-02-01

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

  10. Information of Structures in Galaxy Distribution

    NASA Astrophysics Data System (ADS)

    Fang, Fan

    2006-06-01

    We introduce an information-theoretic measure, the Rényi information, to describe the galaxy distribution in space. We discuss properties of the information measure and demonstrate its relationship with the probability distribution function and multifractal descriptions. Using the First Look Survey galaxy samples observed by the Infrared Array Camera on board the Spitzer Space Telescope, we present measurements of the Rényi information, as well as the counts-in-cells distribution and multifractal properties of galaxies in mid-infrared wavelengths. Guided by a multiplicative cascade simulation based on a binomial model, we verify our measurements and discuss the spatial selection effects on measuring information of the spatial structures. We derive structure scan functions at scales where selection effects are small for the Spitzer samples. We discuss the results and the potential of applying the Rényi information to the measurement of other spatial structures.

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Hay, Mark E.

    2009-01-01

    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.

  13. The Intersection of Structural and Chemical Biology - An Essential Synergy.

    PubMed

    Zuercher, William J; Elkins, Jonathan M; Knapp, Stefan

    2016-01-21

    The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas. PMID:26933743

  14. 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

  15. PREDICTING MODES OF TOXIC ACTION FROM CHEMICAL STRUCTURE: AN OVERVIEW

    EPA Science Inventory

    In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARS) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. asic and fun...

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

    PubMed Central

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

    2011-01-01

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

  17. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    NASA Astrophysics Data System (ADS)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  18. 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…

  19. 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.

  20. 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.

  1. 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. PMID:16729727

  2. A relationship between chemical structure and the critical temperature

    NASA Technical Reports Server (NTRS)

    Fedors, R. F.

    1982-01-01

    The present investigation is concerned with the effect of both molecular weight and chemical structure on the critical temperature. Using data from the comprehensive compilation of critical constants of Kudchadker et al. (1968), a simple relationship could be developed between the critical temperature and chemical structure. This relationship does not require experimental data such as the normal boiling point. It was found that the critical temperature (Tc) is given by an expression containing m and the sum of delta-i, where m is the total number of atoms in the molecule and delta-i is a number whose value is obtained from a table of additive atomic, group, and structural constants.

  3. 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.

  4. Forgotten topological index of chemical structure in drugs.

    PubMed

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

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs. PMID:27275112

  5. 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. PMID:11341576

  6. Structural information in the inverse problem

    NASA Astrophysics Data System (ADS)

    Karaoulis, M.; Larson, T. H.; Ahmed, I.; Revil, A.; Thomason, J.

    2013-12-01

    Data integration in geophysics provides additional information to elucidate subsurface structure and reduce non-uniqueness of inverted models. There are several strategies for incorporating data integration into numerical models. A traditional approach is to use this information as a-priori knowledge, as an initial model or layer boundary specified on the mesh before the inversion. Although in some cases this approach has proven effective, the information is not directly incorporated into the inverse problem and might be lost in the final model. Another strategy is through joint inversion, where data and models are inverted simultaneous. The data integration comes from the joint operator as structural similarity or petrophysical equations. There are some limitations with this approach. In particular, structural similarity doesn't take into account different sensitivity patterns which differ for different geophysical methods, e.g. in a crosswell configuration electrical resistivity tomography is sensitive close to the borehole region while seismic waves are sensitive towards the center part. Moreover different methods have differing resolution. Therefore, a single joint operator might not be effective in all cases. In this work we demonstrate the use of image-guided inversion, where structural information is taken directly from a high resolution geophysical image (e.g. ground penetrating radar or seismic reflection) or from a geological cross-section. This structural information is introduced into the inverse problem through a weighted smoothing matrix, where it correlates and favors formations related to a specific structural feature and not just uniformly across the entire model. Both sharp and smooth features can be imaged and the recovered models can have a more realistic distribution of values. As an example of the method we use migrated seismic reflection images to extract the structural information and resistivity imaging to recover the resistivity

  7. 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

  8. 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

  9. 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 Convention Provisions of the Export Administration Regulations AGENCY: Bureau of Industry and Security...) 482-4895, Lawrence.Hall@bis.doc.gov . SUPPLEMENTARY INFORMATION: I. Abstract The Chemical...

  10. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 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 Information regarding security risk for a chemical facility. (a) Information to determine security risk. In order...

  11. Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products.

    PubMed

    Hu, Dennis X; Withall, David M; Challis, Gregory L; Thomson, Regan J

    2016-07-27

    The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized. PMID:27314508

  12. 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.

  13. 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)

  14. Management Information Systems and Organizational Structure.

    ERIC Educational Resources Information Center

    Cox, Bruce B.

    1987-01-01

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

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

    PubMed Central

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

    2008-01-01

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

  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. The expert system for toxicity prediction of chemicals based on structure-activity relationship.

    PubMed Central

    Nakadate, M; Hayashi, M; Sofuni, T; Kamata, E; Aida, Y; Osada, T; Ishibe, T; Sakamura, Y; Ishidate, M

    1991-01-01

    The prediction systems of chemical toxicity has been developed by means of structure-activity relationship based on the computerized fact database (BL-DB). Numbers and ratio of elements, side chains, bonding, position, and microenvironment of side chains were used as structural factors of the chemical for the prediction. Such information was obtained from the BL-DB database by Wiswesser line-formula chemical notation. In the present study, the Salmonella/microsome assay was chosen as indicative of the target toxicity of chemicals. A set of chemicals specified with mutagenicity data was retrieved, and necessary information was extracted and transferred to the working file. Rules of the relations between characteristics of chemical structure and the assay result are extracted as parameters for rules by experts on the rearranged data set. These were analyzed statistically by the discriminant analysis and the prediction with the rules were evaluated by the elimination method. Eight kinds of rules to predict Salmonella/microsome assay were constructed, and currently results of the assay on aliphatic and heterocyclic compounds can be predicted as accurately as +90%. PMID:1820282

  18. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects.

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest

  19. 77Se Chemical Shift Tensor of L-selenocystine: Experimental NMR Measurements and Quantum Chemical Investigations of Structural Effects

    PubMed Central

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-01-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine’s specialized biological roles, it is of interest to examine their 77Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state 77Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information of selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on 77Se L-selenocystine’s chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10–20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of −180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. −90°, the energy costs to alter the dihedral angle in the range from −120° to −60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. 77Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272±30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3–9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results

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

    PubMed Central

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

    2012-01-01

    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 , 13C, and 15N backbone and 13Cβ 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. PMID:22665781

  1. 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.

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

    PubMed

    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

  3. 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

  4. 78 FR 28586 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-15

    ...The Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. In addition under TSCA, EPA is required to publish in the Federal......

  5. 77 FR 21769 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-11

    ... intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory... manufacture a new chemical that the Agency has received under TSCA section 5 during this time period....

  6. 77 FR 5100 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-01

    ... intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory... the NOC to manufacture a new chemical that the Agency has received under TSCA section 5 during...

  7. 77 FR 48976 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-15

    ... intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory... manufacture a new chemical that the Agency has received under TSCA section 5 during this time period....

  8. 77 FR 74473 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-14

    ...The Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. In addition under TSCA, EPA is required to publish in the Federal......

  9. 78 FR 35904 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-14

    ...The Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. In addition under TSCA, EPA is required to publish in the Federal......

  10. 77 FR 56639 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-13

    ...The Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. In addition under TSCA, EPA is required to publish in the Federal......

  11. 77 FR 61600 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-10

    ...The Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. In addition under TSCA, EPA is required to publish in the Federal......

  12. 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/. PMID:27081156

  13. 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)

  14. 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)

  15. 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.

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

    PubMed

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

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets. PMID:20413617

  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. Structural Information from Methyl Internal Rotation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Spangler, Lee H.

    1997-10-01

    The fundamental quantum mechanics, group theory, and spectroscopy of methyl torsional structure accompanying electronic transitions is presented. The origin of barriers to internal rotation and the interaction of the methyl with the pi system via hyperconjugation are discussed. Because of the relationship between the methyl barrier and the pi system, measurement of the CH3 properties provides structural information about the molecule. In para'-substituted p-methyl-t-stilbenes, barriers in the S1 state show a strong dependence on the substituent, substituent conformation, and involvement of the substituent in hydrogen bonding interaction. The methyl torsional barrier reflects these changes despite the distance of the substitution site, 10 atoms away.

  19. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces. PMID:26444084

  20. 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…

  1. 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

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

    Code of Federal Regulations, 2014 CFR

    2014-01-01

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

  3. 77 FR 45600 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-01

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  4. 76 FR 43327 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-20

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  5. 76 FR 57734 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-16

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  6. 77 FR 48514 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-14

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  7. 76 FR 69723 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-09

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  8. 77 FR 10512 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-22

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  9. 76 FR 76963 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-09

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  10. 76 FR 58498 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-21

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  11. 76 FR 36109 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Chemical Substances Inventory (TSCA Inventory)) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under TSCA sections 5(d)(2) and 5(d)(3), EPA is required......

  12. 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

  13. Enhancing retinal images by extracting structural information

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

  14. 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…

  15. 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.

  16. Chemical and structural features influencing the biological activity of curcumin.

    PubMed

    Priyadarsini, K Indira

    2013-01-01

    Curcumin, a polyphenolic natural product, exhibits therapeutic activity against a number of diseases, attributed mainly to its chemical structure and unique physical, chemical, and biological properties. It is a diferuloyl methane molecule [1,7-bis (4-hydroxy-3- methoxyphenyl)-1,6-heptadiene-3,5-dione)] containing two ferulic acid residues joined by a methylene bridge. It has three important functionalities: an aromatic o-methoxy phenolic group, α, β-unsaturated β-diketo moiety and a seven carbon linker. Extensive research in the last two decades has provided evidence for the role of these different functional groups in its crucial biological activities. A few highlights of chemical structural features associated with the biological activity of curcumin are: The o-methoxyphenol group and methylenic hydrogen are responsible for the antioxidant activity of curcumin, and curcumin donates an electron/ hydrogen atom to reactive oxygen species. Curcumin interacts with a number of biomolecules through non-covalent and covalent binding. The hydrogen bonding and hydrophobicity of curcumin, arising from the aromatic and tautomeric structures along with the flexibility of the linker group are responsible for the non-covalent interactions. The α, β-unsaturated β-diketone moiety covalently interacts with protein thiols, through Michael reaction. The β-diketo group forms chelates with transition metals, there by reducing the metal induced toxicity and some of the metal complexes exhibit improved antioxidant activity as enzyme mimics. New analogues with improved activity are being developed with modifications on specific functional groups of curcumin. The physico-chemical and structural features associated with some of the biological activities of curcumin and important analogues are summarized in this article. PMID:23116315

  17. 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.

  18. 75 FR 57770 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-22

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  19. 75 FR 60444 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  20. 75 FR 39520 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-09

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  1. 75 FR 11414 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-10

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  2. 75 FR 11403 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-10

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  3. 75 FR 32754 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ...Section 5 of the Toxic Substances Control Act (TSCA) requires any person who intends to manufacture (defined by statute to include import) a new chemical (i.e., a chemical not on the TSCA Inventory) to notify EPA and comply with the statutory provisions pertaining to the manufacture of new chemicals. Under sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of......

  4. 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.

  5. An informationally structured room for robotic assistance.

    PubMed

    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

  6. Structural information from methyl internal rotation spectroscopy.

    PubMed

    Spangler, L H

    1997-01-01

    The fundamental quantum mechanics, group theory, and spectroscopy of methyl torsional structure accompanying electronic transitions is presented. The origin of barriers to internal rotation and the interaction of the methyl with the pi system via hyperconjugation are discussed. Because of the relationship between the methyl barrier and the pi system, measurement of the CH3 properties provides structural information about the molecule. In para'-substituted p-methyl-t-stilbenes, barriers in the S1 state show a strong dependence on the substituent, substituent conformation, and involvement of the substituent in hydrogen bonding interaction. The methyl torsional barrier reflects these changes despite the distance of the substitution site, 10 atoms away. PMID:15012450

  7. 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.

  8. 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…

  9. 78 FR 11871 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-20

    ... and silica complex P-13-0151 12/6/2012 3/5/2013 CBI (G) Chemical (G) Vegetable intermediate. oil based... with [(2- water-based ink Aminoalkyl)amin vehicle. o]alkylsulfonic acid monosodium salt. alkyldiol... ether- blocked P-13-0164 12/10/2012 3/9/2013 CBI (G) Chemical (G) intermediate. Benzotriazole...

  10. 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.

  11. Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

    PubMed

    Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

    2016-08-01

    The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach. PMID:27312313

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

  13. 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…

  14. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    NASA Astrophysics Data System (ADS)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

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

    PubMed

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

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  16. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

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

  17. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 6 Domestic Security 1 2011-01-01 2011-01-01 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...

  18. 75 FR 68370 - Agency Information Collection Activities: Office of Infrastructure Protection; Chemical Security...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-05

    .... DHS previously published this ICR in the Federal Register on August 27, 2010 at 75 FR 52768, for a 60... in the chemical industry sector. Information is automatically collected in a computer database as... training is designed for the general chemical facility employee. U.S. chemical industry direct...

  19. 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…

  20. Chemical structure and immunobiological activity of Porphyromonas gingivalis lipid A.

    PubMed

    Ogawa, Tomohiko; Asai, Yasuyuki; Makimura, Yutaka; Tamai, Riyoko

    2007-01-01

    In 1933, Boivin et al. extracted an endotoxin from Salmonella typhimurium for the first time, after which a variety of chemical and biological studies on endotoxins have been performed. In 1952, the structural and functional properties of endotoxic lipopolysaccharide (LPS), extracted by a hot phenol and water method devised by Westphal et al., were reported, which led to a number of studies of Gram-negative bacteria in regards to the host defense mechanism. Since 1960, the unique chemical structure and biological activity of Bacteroides species LPS have received a great deal of attention, and there is a long history of such studies. In addition, among oral bacterial strains that have received attention as causative periodontopathic bacteria, many have been classified as Bacteroides species. In particular, a number of researchers have investigated whether LPS of Porphyromonas gingivalis (formerly Bacteroides gingivalis), a black-pigmented oral anaerobic rod, is a virulent factor of the bacterium. The active center of the LPS of these Bacteroides species, the lipid A molecule, is known to be an active participant in endotoxic activation, though its other biological activities are weak, due to its unique chemical structure and action as an antagonist of LPS. On the other hand, many reports have noted that the LPS of those species activate cells in C3H/HeJ mice, which generally do not respond to LPS. We were the first to reveal the chemical structure of P. gingivalis lipid A and, together with other researchers, reported that P. gingivalis LPS and its lipid A have activities toward C3H/HeJ mice. Since that time, because of the popularity of Toll-like receptor (TLR) studies, a great deal of evidence has been reported indicating that P. gingivalis LPS and its lipid A are ligands that act on TLR2. In order to solve such problems as heterogeneity and contamination of the biologically active components of P. gingivalis lipid A, we produced a chemical synthesis counterpart

  1. Aromatic rings in chemical and biological recognition: energetics and structures.

    PubMed

    Salonen, Laura M; Ellermann, Manuel; Diederich, François

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

  2. 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...

  3. EXPANDING CHEMICAL-TOXICITY INFORMATION RESOURCES IN SUPPORT OF PREDICTIVE TOXICOLOGY.

    EPA Science Inventory

    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.

  4. 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. PMID:22035594

  5. Spectroscopic elucidation of chemical structure of plasma-polymerized pyridine

    SciTech Connect

    Hozumi, K.; Kitamura, K.; Hashimoto, H.; Hamaoka, T.; Fujisawa, H.; Ishizawa, T.

    1983-05-01

    Chemical structure of the plasma-polymerized pyridine film produced on a glass reactor wall by means of the plasma technique in which the pyridine vapor was electronically excited by high-frequency power under a reduced pressure was elucidated. The polymer was highly hydrophilic and was soluble to some of the polar organic solvents so that nitrogen-containing polar functional groups were predicted to participate in the chemical structure of the polymer molecules. /sup 1/H-NMR, /sup 13/CNMR, and IR spectroscopies, high-resolution mass spectral data, and number-average molecular weight determination with some aid of microelemental analysis revealed the presence of various functional groups such as imine, nitrile, amine, pyridine ring, its N-oxide, and even amide. The oxygen atoms involved in the last two groups were supposedly introduced by contact with ambient air after the plasma process. The hydrophilic nature of the polymer which was essential for preparing reverse osmosis membrane was therefore due to the overall hydration effect of these polar functional groups.

  6. 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. PMID:16100780

  7. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  8. 77 FR 22780 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-17

    ...) Polyester resin (G) Alkyl carboxylic acid, solution. oxiranyl alkyl ester, polymer with cycloalkyl...) Polyester type dispersive use). polyurethane resin. P-12-0249 03/22/2012 06/19/2012 CBI (G) Chemical (G.../2012 02/17/2012 (G) Polyester resin. P-10-0531 03/01/2012 02/17/2012 (G) Unsaturated polyester resin....

  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. 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 explained. (SW)

  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. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    NASA Astrophysics Data System (ADS)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

  13. 77 FR 69824 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-21

    ... required by TSCA section 5 to provide EPA with a PMN, before initiating the activity. Section 5(h)(1) of............ (S) Fragrance (S) 2- ingredient. octenenitrile,3,5,7- trimethyl-. P-13-0013 10/5/2012 1/2/2013 Dow Chemical (G) Open-non dispersive (G) Polyurethane Company. use. polymer. P-13-0014 10/8/2012 1/5/2013...

  14. 76 FR 35886 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... leather. P-11-0368 5/11/2011 8/8/2011 CBI (G) Lamination adhesive.... (G) IPDI modified polyester resin. P.../21/2011 (G) Polyester type polyurethane resin. P-11-0164 5/9/2011 5/5/2011 (G) 2-propenoic acid, 2.../ importer Use Chemical date date P-11-0341 4/25/2011 7/23/2011 CBI (S) One resin component for (G)...

  15. 77 FR 40033 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-06

    ...-12-0338 05/03/2012 07/31/2012 3M Company...... (S) Matrix resin (G) Modified epoxy for carbon resin.... polyisocyanate. P-12-0355 05/16/2012 08/13/2012 CBI (G) Chemical (G) Aromatic intermediate. polyester. P-12-0356.../26/2012 (G) Mdi modified polyester with 1,4 butanediol, iso-pr alcohol-blocked. P-12-0163...

  16. 75 FR 71688 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-24

    ...Under sections 5(d)(2) and 5(d)(3) of the Toxic Substances Control Act (TSCA), EPA is required to publish in the Federal Register a notice of receipt of a premanufacture notice (PMN) or an application for a test marketing exemption (TME), and to publish in the Federal Register periodic status reports on the new chemicals under review and the receipt of notices of commencement (NOC) to begin......

  17. 75 FR 32751 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ...) Aromatic dispersive(polyureth isocyanate ane resin) prepolymer P-10-0226 02/12/10 05/12/10 CBI (G... varnish polyester imide for motors, generators, transformers P-10-0232 02/17/10 05/17/10 Kemira Chemicals...-decyl- consumer use products; dispersive use P-10-0236 02/18/10 05/18/10 Coim USA Inc. (S) Resin used...

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

    PubMed

    Hauschild, Veronique D; Watson, Annetta

    2013-01-01

    Although not widely known, a robust set of peer-reviewed public health and occupational exposure levels presently exist for key chemical warfare agents (CWAs) and certain acutely toxic industrial chemicals (TICs) identified as terrorist attack threats. Familiarity with these CWA and TIC exposure levels and their historic applications has facilitated emergency management decision-making by public and environmental health decision-makers. Specifically, multiple air, soil, and water exposure levels for CWAs and TICs summarized here have been extensively peer-reviewed and published; many have been recognized and are in use by federal and state health agencies as criteria for hazard zone prediction and assessment, occupational safety, and "how clean is clean enough" decisions. The key, however, is to know which criteria are most appropriate for specific decisions. While public safety is critical, high levels of concern often associated with perceived or actual proximity to extremely toxic chemical agents could result in overly cautious decisions that generate excessive delays, expenditure of scarce resources, and technological difficulties. Rapid selection of the most appropriate chemical exposure criteria is recommended to avoid such problems and expedite all phases of chemical incident response and recovery. PMID:24340456

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

    MedlinePlus

    ... Occupational Diseases High Risk Jobs Non-Occupational Activities Industries Job Tasks Processes Symptoms/Findings Customer Service: tehip@teh.nlm.nih.gov Specialized Information Services U.S.National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894 ...

  20. 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.

  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. Conversion of lignocellulosic biomass to nanocellulose: structure and chemical process.

    PubMed

    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

  3. 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

  4. Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine.

    PubMed

    Li, Hongbao; Li, Leilei; Jiang, Jun; Lin, Zijing; Luo, Yi

    2015-10-14

    The energy differences between canonical and zwitterionic isomers of arginylglycine (ArgGly) at the CCSD/aug-cc-pVDZ level are too small (less than 1 kcal mol(-1)) to determine the dominant form in the gas phase from the energetic point of view. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of neutral ArgGly. Noticeable spectral differences were found which enable the unambiguous identification of different neutral groups. We thus demonstrate X-ray spectroscopy as a powerful technique to study the conformation dependent chemical and electronic properties of neutral ArgGly. PMID:26266331

  5. 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. PMID:27023229

  6. 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

  7. May Auger electron spectroscopy provide surface structural information?

    NASA Astrophysics Data System (ADS)

    Alonso, M.; Soria, F.

    1986-12-01

    Quantitative analysis of Auger electron spectroscopy peak energies, lineshapes and heights allows to determine the chemical composition of the surface layer, and in binary (111) semiconductors even the composition of the outermost surface bilayer, if the composition of a standard surface is known. Surface structural information can also be obtained by the interaction of these surfaces with some gases used as markers, when the gas absorption proceeds by an over/underlayer mechanism, as it happens in the initial stages of the interaction of oxygen with differently prepared GaAs(111) surfaces. Thus, we have been able to confirm the structure of the (111) 2 × 2 Ga surface, and to determine the oxygen absorption sites and occupation sequence, by comparison of the experimental intensities with calculations which model the surface structure and absorption sites. This formalism has also been applied to ( overline1overline1overline1) 1 × 1 facetted surfaces, where very different absorption behaviour is seen for surfaces prepared at different ion energies, but annealed at the same temperature.

  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. Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

    SciTech Connect

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

    2012-08-07

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

  10. Temporal and Statistical Information in Causal Structure Learning

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  11. 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...

  12. System-level responses of lake ecosystems to chemical stresses using exergy and structural exergy as ecological indicators.

    PubMed

    Xu, Fu-Liu; Dawson, R W; Tao, Shu; Li, Ben-Gang; Cao, Jun

    2002-01-01

    This paper presents the system-level responses of experimental lake ecosystems to three chemical stresses (acidification, copper and pesticide contamination) using exergy and structural exergy as ecological indicators. The results indicate that the doses or toxicity of the three chemical stressors contributed to changes in both exergy and structural exergy. Remarkable changes in exergy and structural exergy occurred under acidic conditions and in the presence of Dursban, 24D-DMA, permethrin, bifenthrin, Carbaryl, TCP, PCP, trichlorethylene, benzene, and high doses of Cu, oil, and hexazinone. This seemed to indicate that the subject ecosystems were seriously contaminated by these chemical stressors. For low doses of Cu, oil, atrazine, HCBP, and hexazinone, exergy and structural exergy were either unchanged or only slightly changed, suggesting that the lake ecosystems were not significantly impacted by these chemical stressors. Discussion of the relationships between ecosystem-level changes and structural and functional changes in stressed lake ecosystems indicates that the above-mentioned ecosystem-level changes were in accordance with the changes in structure and function. The observed changes in exergy and structural exergy were also consistent with Odum's predictions of shortened food chains, reduced resource use efficiency, poor stability, low information, and high entropy in stressed aquatic ecosystems. The findings lead the authors to conclude that it is feasible for exergy and structural exergy to serve as ecological indicators when characterizing the system-level responses of experimental lake ecosystems to chemical stress. These results for experimental lake ecosystems would be extrapolated to actual lakes. PMID:11827273

  13. The U.S. EPA Geographic Information System for mapping environmental releases of Toxic Chemical Release Inventory (TRI) chemicals.

    PubMed

    Stockwell, J R; Sorensen, J W; Eckert, J W; Carreras, E M

    1993-04-01

    This study characterizes the environmental releases of toxic chemicals of the Toxic Chemical Release Inventory (TRI) in the southeastern United States by using the U.S. Environmental Protection Agency (EPA) Geographic Information System (GIS) to map them. These maps show that the largest quantities of TRI releases in the Southeast are usually near densely populated areas. This GIS mapping approach takes the first steps in defining those areas in the region which may be potential exposure zones and which could be strategic targets for future risk screening efforts in this geographic area. PMID:8502789

  14. Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols.

    PubMed

    Liu, Zhengchun; Liu, Yi; Kim, Eunkyoung; Bentley, William E; Payne, Gregory F

    2016-07-19

    The acquisition of chemical information is a critical need for medical diagnostics, food/environmental monitoring, and national security. Here, we report an electrochemical information processing approach that integrates (i) complex electrical inputs/outputs, (ii) mediators to transduce the electrical I/O into redox signals that can actively probe the chemical environment, and (iii) a redox capacitor that manipulates signals for information extraction. We demonstrate the capabilities of this chemical information processing strategy using biothiols because of the emerging importance of these molecules in medicine and because their distinct chemical properties allow evaluation of hypothesis-driven information probing. We show that input sequences can be tailored to probe for chemical information both qualitatively (step inputs probe for thiol-specific signatures) and quantitatively. Specifically, we observed picomolar limits of detection and linear responses to concentrations over 5 orders of magnitude (1 pM-0.1 μM). This approach allows the capabilities of signal processing to be extended for rapid, robust, and on-site analysis of chemical information. PMID:27385047

  15. 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 ...

  16. One-pot hydrazide-based native chemical ligation for efficient chemical synthesis and structure determination of toxin Mambalgin-1.

    PubMed

    Pan, Man; He, Yao; Wen, Ming; Wu, Fangming; Sun, Demeng; Li, Sijian; Zhang, Longhua; Li, Yiming; Tian, Changlin

    2014-06-01

    An efficient one-pot chemical synthesis of snake venom toxin Mambalgin-1 was achieved using an azide-switch strategy combined with hydrazide-based native chemical ligation. Synthetic Mambalgin-1 exhibited a well-defined structure after sequential folding in vitro. NMR spectroscopy revealed a three-finger toxin family structure, and the synthetic toxin inhibited human acid-sensing ion channel 1a. PMID:24619065

  17. 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...

  18. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

    PubMed Central

    Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

    2010-01-01

    Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its intrinsic cell-based nature, can hardly provide insights into the molecular targets for screened compounds. On the other hand, the abundant information of the compound–target associations in PubChem can offer extensive experimental evidence of molecular targets for tested compounds. Therefore, by taking advantages of the data from both public repositories, one may investigate the correlations between the bioactivity profiles of small molecules from the NCI-60 dataset (cellular level) and their patterns of interactions with relevant protein targets from PubChem (molecular level) simultaneously. Results: We investigated a set of 37 small molecules by providing links among their bioactivity profiles, protein targets and chemical structures. Hierarchical clustering of compounds was carried out based on their bioactivity profiles. We found that compounds were clustered into groups with similar mode of actions, which strongly correlated with chemical structures. Furthermore, we observed that compounds similar in bioactivity profiles also shared similar patterns of interactions with relevant protein targets, especially when chemical structures were related. The current work presents a new strategy for combining and data mining the NCI-60 dataset and PubChem. This analysis shows that bioactivity profile comparison can provide insights into the mode of actions at the molecular level, thus will facilitate the knowledge-based discovery of novel compounds with desired pharmacological properties. Availability: The bioactivity profiling data and the target annotation information are publicly available in the PubChem BioAssay database (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/). Contact: ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20947527

  19. Transfer of the EPA/NIH Chemical Information System (CIS) to Private Management.

    ERIC Educational Resources Information Center

    Kadec, Sarah T.; Jover, Antonio

    This paper discusses the programmatic concerns, the evaluation, and the ultimate decisions which led to the transfer of CIS (Chemical Information System) to the private sector. CIS is a complex, integrated system of some 20 chemical databases and data analysis programs which provide access to physical, toxicological, environmental effects, and…

  20. 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.

  1. 75 FR 63827 - Integrated Risk Information System (IRIS); Request for Chemical Substance Nominations for 2011...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-18

    ...EPA's IRIS is a human health assessment program that evaluates quantitative and qualitative risk information on effects that may result from exposure to specific chemical substances found in the environment. EPA is soliciting public nominations for chemical substances for its 2011 agenda. EPA invites the public to submit nominations for substances to be considered for an assessment or......

  2. Electronic structure and chemical bonding in PuO2

    NASA Astrophysics Data System (ADS)

    Teterin, Yu. A.; Maslakov, K. I.; Teterin, A. Yu.; Ivanov, K. E.; Ryzhkov, M. V.; Petrov, V. G.; Enina, D. A.; Kalmykov, St. N.

    2013-06-01

    Quantitative analysis of the x-ray photoelectron spectra structure in the binding energy (BE) range of 0 eV-˜35 eV for plutonium dioxide (PuO2) valence electrons was done. The BEs and structure of the core electronic shells (35 eV-1250 eV BE), as well as the relativistic discrete variation calculation results for the finite fragments of the PuO2 lattice and the data of other authors, were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the outer (0 eV-˜15 eV) and the inner (˜15 eV-˜35 eV) valence molecular orbitals (OVMO and IVMO, respectively). The filled Pu 5f electronic states were shown to form in the PuO2 valence band. The Pu 6p electrons participate in the formation of both the IVMO and the OVMO (bands). The filled Pu 6p3/2 and the O 2s electronic shells were found to take maximum part in the IVMO formation. The MO composition and the sequence order in the BE range of 0 eV-˜35 eV in PuO2 were established. The experimental and theoretical data allowed a quantitative MO scheme for PuO2, which is fundamental for understanding both the chemical bond nature in plutonium dioxide and the interpretation of other x-ray spectra of PuO2.

  3. Elucidating the chemical structure of native 1-deoxysphingosine.

    PubMed

    Steiner, Regula; Saied, Essa M; Othman, Alaa; Arenz, Christoph; Maccarone, Alan T; Poad, Berwyck L J; Blanksby, Stephen J; von Eckardstein, Arnold; Hornemann, Thorsten

    2016-07-01

    The 1-deoxysphingolipids (1-deoxySLs) are formed by an alternate substrate usage of the enzyme, serine-palmitoyltransferase, and are devoid of the C1-OH-group present in canonical sphingolipids. Pathologically elevated 1-deoxySL levels are associated with the rare inherited neuropathy, HSAN1, and diabetes type 2 and might contribute to β cell failure and the diabetic sensory neuropathy. In analogy to canonical sphingolipids, it was assumed that 1-deoxySLs also bear a (4E) double bond, which is normally introduced by sphingolipid delta(4)-desaturase 1. This, however, was never confirmed. We therefore supplemented HEK293 cells with isotope-labeled D3-1-deoxysphinganine and compared the downstream formed D3-1-deoxysphingosine (1-deoxySO) to a commercial synthetic SPH m18:1(4E)(3OH) standard. Both compounds showed the same m/z, but differed in their RPLC retention time and atmospheric pressure chemical ionization in-source fragmentation, suggesting that the two compounds are structural isomers. Using dimethyl disulfide derivatization followed by MS(2) as well as differential-mobility spectrometry combined with ozone-induced dissociation MS, we identified the carbon-carbon double bond in native 1-deoxySO to be located at the (Δ14) position. Comparing the chromatographic behavior of native 1-deoxySO to chemically synthesized SPH m18:1(14Z) and (14E) stereoisomers assigned the native compound to be SPH m18:1(14Z). This indicates that 1-deoxySLs are metabolized differently than canonical sphingolipids. PMID:27165858

  4. Ideologically Structured Information Exchange among Environmental Groups

    ERIC Educational Resources Information Center

    Lhotka, Laura; Bailey, Conner; Dubois, Mark

    2008-01-01

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

  5. 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

  6. 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...

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

    PubMed Central

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

    2009-01-01

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

  8. SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES.

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  9. 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...

  10. 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…

  11. Perspective: On the relevance of slower-than-femtosecond time scales in chemical structural-dynamics studies

    PubMed Central

    Coppens, Philip

    2015-01-01

    A number of examples illustrate structural-dynamics studies of picosecond and slower photo-induced processes. They include molecular rearrangements and excitations. The information that can be obtained from such studies is discussed. The results are complementary to the information obtained from femtosecond studies. The point is made that all pertinent time scales should be covered to obtain comprehensive insight in dynamic processes of chemical and biological importance. PMID:26798788

  12. 77 FR 74685 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ...The Department of Homeland Security (DHS), National Protection and Programs Directorate (NPPD), Office of Infrastructure Protection (IP), Infrastructure Security Compliance Division (ISCD) will submit the following Information Collection Request to the Office of Management and Budget (OMB) for review and clearance in accordance with the Paperwork Reduction Act of 1995 (Pub. L. 104-13, 44......

  13. 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.

  14. 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…

  15. CMB topography and electrical conductivity as additional constraints for the lowermost mantle thermo-chemical structure

    NASA Astrophysics Data System (ADS)

    Deschamps, F.; Yin, Y.; Tackley, P. J.

    2013-12-01

    A variety of seismic observations, including tomographic models, indicate that the lowermost mantle is strongly heterogeneous. Seismic observations further support a thermo-chemical origin for the large scale heterogeneities. In particular, the large low-shear wave velocity provinces (LLSVP) observed by global tomographic images are better explained by a combination of thermal and chemical anomalies. Despite the accuracy of seismic information, uncertainties and trade-off still prevent the determination of a detailed lower mantle thermo-chemical structure. For instance, the nature of chemical heterogeneities and the exact role played by the post-perovskite phase transition are still debated. Additional constraints are needed to discriminate between the possible models of structure and dynamics of the lower mantle. Here, we consider two potential additional constraints, the electrical conductivity and the dynamic topography at the core-mantle boundary (CMB). Unlike density and seismic velocities, electrical conductivity increases with temperature. In addition, it strongly varies with the iron and silicate content. Using appropriate mineral physics data, we calculated a 3D distribution of electrical conductivity in lower mantle from the thermo-chemical structure inferred by probabilistic tomography, which maps iron and silicate excess in the LLSVP. In the lowermost mantle, we observe a belt of high conductivity, with maximum values around 20 S/m located in the LLSVP. Such a belt may trigger electric currents in the lowermost mantle and induce magnetic field variations with period of one year or more. It may thus be seen by global models of electrical conductivity. Unfortunately, such models do not sample yet regions deeper than 2000 km. A second, independent constraint we explored is the dynamic topography at the CMB. We used stagYY to calculate the dynamic topography associated with several models of thermo-chemical convection, and observe strong differences

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

    ERIC Educational Resources Information Center

    Callaghan, A.; And Others

    Part II of the Students' Chemical Information Project (SCIP), designed to spread the use of computer-based information services among research scientists and technologists, contains details of the project operations, statistics, results of questionnaires and research reports from liaison scientists (See LI 002 562 for Part I). Chapter I: Operation…

  17. Quantitative Survey and Structural Classification of Hydraulic Fracturing Chemicals Reported in Unconventional Gas Production.

    PubMed

    Elsner, Martin; Hoelzer, Kathrin

    2016-04-01

    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. PMID:26902161

  18. The chemical structure of the Main-Belt

    NASA Astrophysics Data System (ADS)

    Carry, Benoit; DeMeo, Francesca

    2015-08-01

    The asteroid main belt between Mars and Jupiter holds evidences from the early Solar System history. The original chemical stratification of the accretion disk has been scrambled by planetary migrations, resulting in a radial mixing of compositions. Since the 1970s, spectral surveys have characterized the surface compositions of the largest members first, then of smaller bodies, slowly tapering into the size-frequency distribution. These surveys led to major discoveries, including the succession of dominating taxonomic classes along heliocentric distances, stained by the presence of interlopers in this over-arching structure. In the 2000s, these results have sustained the emergence of the current paradigm of Solar System formation: the Nice model, in which planets migrated from their formation locations to their current orbits.Since then, all-sky surveys in the visible and mid-infrared, the Sloan Digital Sky Survey and NASA WISE mission, have observed tens of thousands of asteroids, allowing characterization of their surface composition and estimation of their diameter. Simultaneously, our knowledge on asteroid density greatly improved: the sample of density determinations presented a tenfold increase. Such a rich dataset opened the possibility to scrutinize asteroid compositions to smaller sizes and to study the distribution of material in the main belt by mass, rather than by numbers. The picture resulting from these data go back over the previous view, and the few interlopers seem to be rule. The large scale structure seen on the largest bodies holds, but mixing increases at smaller sizes. This detailed picture supports the main results from recent dynamical models of planetary migration and radial mixing of smaller bodies, albeit several observed structures remain yet to be explained: numerous primitive D-type in the inner belt, apparently missing mantle counterpart (A-types) to the crustal and iron core-like (V- and M-types) material.Observational evidences

  19. Informational biopolymer structure in early living forms.

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  20. 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

  1. 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. PMID:25934803

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

    PubMed Central

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

    2015-01-01

    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. PMID:25934803

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

    ERIC Educational Resources Information Center

    Hsu, Yu-Yin

    2013-01-01

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

  4. 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. PMID:19623488

  5. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

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

  6. Informal Reading Inventories & Text Type/Structure.

    ERIC Educational Resources Information Center

    Gillis, M. K.; Olson, Mary W.

    Experienced teachers enrolled in two graduate reading classes examined seven informal reading inventories (IRIs)--three at the elementary level and four at the secondary level--to (1) discover what text types (narrative or expository) they used at each level to measure student comprehension skills and determine instructional levels and (2)…

  7. DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

    PubMed

    Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

    2014-07-15

    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 (1)H (400 MHz; CDCl3) and (13)C (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. PMID:24662754

  8. Summary information of human health hazard assessment of existing chemical substances (I).

    PubMed

    Matsumoto, Mariko; Kobayashi, Katsumi; Takahashi, Mika; Hirata-Koizumi, Mutsuko; Ono, Atsushi; Hirose, Akihiko

    2015-01-01

    Under the Chemical Substances Control Law (CSCL) in Japan, initial hazard information tor existing chemical substances has been collected by the Ministry of Health, Labour and Welfare, Japan (MHLW) to assess potential initial risks to human health. We have reviewed all collected toxicity information pertaining to acute toxicity, repeated dose toxicity, genotoxicity, and/or reproductive/developmental toxicity and performed hazard assessments. Approximately 150 substances are currently undergoing review and assessment. For clarification and evaluation of each toxicity study, we have created a dossier (a collection of study data containing a detailed summary of the methods, results, and conclusions of each study) in English using the International Uniform Chemical Information Database (IUCLID) version 5. The IUCLID dossier format is widely used and has been accepted as one of the most beneficial formats for providing summarized chemical substance toxicity assessments. In this report, as a contribution to our ongoing hazard assessment activity, we present summary hazard information related to the potential human health effects of the following 5 chemical substances: 4-chlorobenzoyl chloride (CAS: 122-01-0); benzenesulfonic acid, 4-hydroxy-, tin (2+) salt (CAS: 70974- 33-3); chlorocyclohexane (CAS: 542-18-7); 1,3-cyclohexanedimethanamine (CAS: 2579-20-6); and 1,3,5-triazine-2,4,6 (1H,3H,5H) -trithione (CAS: 638-16-4). The IUCLID dossiers created for these 5 chemical substances will be made available via the Japan Existing Chemical Data Base (JECDB) at . Additional human health hazard information on existing chemical substances will be provided using the same methodology and website when it is available. PMID:26821470

  9. 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…

  10. 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

  11. Phase structure rewrite systems in information retrieval

    NASA Technical Reports Server (NTRS)

    Klingbiel, P. H.

    1985-01-01

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

  12. 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.

  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. Thermodynamical and Informational Structure of Superstatistics

    NASA Astrophysics Data System (ADS)

    Yamano, T.

    A generating function in statistical mechanics (i.e., the Laplace transform of a density of states) suggests that the superstatistics proposed by Beck and Cohen can be viewed as a counterpart of the canonical partition function since inverse temperature β and energy E appear symmetrically in the Gibbsian factor. Some formal properties of the superstatistics are presented in connection with thermodynamic relations and information aspects.

  15. 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

  16. 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

    2016-01-01

    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. 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.

  18. Probing the water on chemically heterogeneous surface: interfacial-structural analysis for surface charge distribution

    NASA Astrophysics Data System (ADS)

    Shin, Sucheol; Willard, Adam

    We introduce the novel method for predicting the charge distribution of chemically heterogeneous surface, but reconstructed from the perspective of the interfacial water molecules. Our approach is to analyze the response of water to a disordered surface and infer from that response the heterogeneous distribution of surface charge. We accomplish this using a framework that is based on a probabilistic description of water's interfacial molecular structure and maximum likelihood estimation. This framework allows to deduce the apparent charge that is most congruently represented by the set of water configurations over the particular region of a surface. We demonstrate that the estimated charge distribution is consistent to the actual distribution for a static model substrate and hence that our method can be applied to investigate a dynamic fluctuating substrate such as the surface of a hydrated protein. This novel technique provides the useful information that can reflect the influence of fluctuations in the structure of biomolecule.

  19. Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set.

    PubMed

    Klimenko, Kyrylo; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2016-08-22

    Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set, providing an association of antiviral compounds to seven broadly defined antiviral activity classes. Generative topographic mapping (GTM) subjected to evolutionary tuning was then used to produce maps of the antiviral chemical space, providing an optimal separation of compound families associated with the different antiviral classes. The ability to pinpoint the specific spots occupied (responsibility patterns) on a map by various classes of antiviral compounds opened the way for a GTM-supported search for privileged structural motifs, typical for each antiviral class. The privileged locations of antiviral classes were analyzed in order to highlight underlying privileged common structural motifs. Unlike in classical medicinal chemistry, where privileged structures are, almost always, predefined scaffolds, privileged structural motif detection based on GTM responsibility patterns has the decisive advantage of being able to automatically capture the nature ("resolution detail"-scaffold, detailed substructure, pharmacophore pattern, etc.) of the relevant structural motifs. Responsibility patterns were found to represent underlying structural motifs of various natures-from very fuzzy (groups of various "interchangeable" similar scaffolds), to the classical scenario in medicinal chemistry (underlying motif actually being the scaffold), to very precisely defined motifs (specifically substituted scaffolds). PMID:27410486

  20. 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.

  1. 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 ...

  2. 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)

  3. Review of the Literature on Determinants of Chemical Hazard Information Recall among Workers and Consumers.

    PubMed

    Sathar, Farzana; Dalvie, Mohamed Aqiel; Rother, Hanna-Andrea

    2016-01-01

    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

  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. Information-preserving structures: A general framework for quantum zero-error information

    SciTech Connect

    Blume-Kohout, Robin; Ng, Hui Khoon; Poulin, David; Viola, Lorenza

    2010-12-15

    Quantum systems carry information. Quantum theory supports at least two distinct kinds of information (classical and quantum), and a variety of different ways to encode and preserve information in physical systems. A system's ability to carry information is constrained and defined by the noise in its dynamics. This paper introduces an operational framework, using information-preserving structures, to classify all the kinds of information that can be perfectly (i.e., with zero error) preserved by quantum dynamics. We prove that every perfectly preserved code has the same structure as a matrix algebra, and that preserved information can always be corrected. We also classify distinct operational criteria for preservation (e.g., 'noiseless','unitarily correctible', etc.) and introduce two natural criteria for measurement-stabilized and unconditionally preserved codes. Finally, for several of these operational criteria, we present efficient (polynomial in the state-space dimension) algorithms to find all of a channel's information-preserving structures.

  6. 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.

  7. The modular structure of informational sequences.

    PubMed

    Schmitt, A O; Ebeling, W; Herzel, H

    1996-01-01

    It is shown that DNA sequences can be decomposed into smaller units much the same as texts can be decomposed into syllables, words, or groups of words. Those smaller units (modules) are extracted from DNA sequences according to statistical criteria. Tests with sequences of known modular structure (two novels and a FORTRAN source code) were performed. The rate to which DNA sequences can be decomposed into modules (modularity) turns out to be a very sensitive measure to distinguish DNA sequences from random sequences. PMID:8924645

  8. 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

  9. STRUCTURE-ACTIVITY RELATIONSHIPS FOR SCREENING ORGANIC CHEMICALS FOR POTENTIAL ECOTOXICITY EFFECTS

    EPA Science Inventory

    The paper presents structure-activity relationships (QSAR) for estimating the bioconcentration factor and acute toxicity of some classes of industrial chemicals using only the n-octanol/water partition coefficient (Log P) which is derived from chemical structure. The bioconcentra...

  10. 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…

  11. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    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. PMID:25451822

  12. 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. PMID:24710340

  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. PMID:19433131

  14. 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.

  15. 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.

  16. The chemical, physical and structural properties of estuarine ice in Great Bay, New Hampshire

    USGS Publications Warehouse

    Meese, D.A.; Gow, A.J.; Mayewski, P.A.; Ficklin, W.; Loder, T.C.

    1987-01-01

    The purpose of this study was to provide general information on the chemical, physical and structural properties of estuarine ice and show how it compares with sea ice found at higher latitudes in order to determine whether the ice in Great Bay can be used as an analog in the study of arctic sea ice. Ice cores and water samples were collected during the 1983-1984 winter season at Adams Point in Great Bay, New Hampshire. Concentrations of chloride, nitrogen (as nitrate and nitrite), bromide, phosphate, sulfate and silicate were determined for samples chosen on the basis of identifiable stratigraphic layers (i.e. bubble size and shape, sediment layers, etc.). Similarities between ice formation in Great Bay and those in the arctic regions include the nature of the freezing process and the ice types produced. In addition, the distribution and concentration of chemical constituents were found to be similar to those observed in arctic sea ice. Factors affecting the chemistry of the ice in Great Bay include rainfall during the freezing season, the presence of sediment layers in the ice cores, the nature of incorporation of brine into the crystal structure of the ice and the drainage of brine. ?? 1987.

  17. 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.

  18. Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

    NASA Astrophysics Data System (ADS)

    Lebiedz, Dirk; Brandt-Pollmann, Ulrich

    2004-09-01

    Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

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

    PubMed

    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

  20. 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

  1. 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...

  2. 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…

  3. Incorporating Chemical Information Instruction and Environmental Science into the First-Year Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Landolt, R. G.

    2006-01-01

    The chemical information instruction and environmental science which is incorporated into a first-year organic chemistry laboratory is presented. The students are charged with devised search strategies, conducting online searches and limiting the project scope to ocean systems. The laboratory serves to provide for search strategy development…

  4. Four-Year Summary, Educational and Commercial Utilization of a Chemical Information Center. Part I.

    ERIC Educational Resources Information Center

    Schipma, Peter B., Ed.

    The major objective of the Illinois Institute of Technology (IIT) Computer Search Center (CSC) is to educate and link industry, academia, and government institutions to chemical and other scientific information systems and sources. The CSC is in full operation providing services to users from a variety of machine-readable data bases with minimal…

  5. 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. PMID:26913193

  6. 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...

  7. 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,…

  8. Information on Quantifiers and Argument Structure in English Learner's Dictionaries.

    ERIC Educational Resources Information Center

    Lee, Thomas Hun-tak

    1993-01-01

    Lexicographers have been arguing for the inclusion of abstract and complex grammatical information in dictionaries. This paper examines the extent to which information about quantifiers and the argument structure of verbs is encoded in English learner's dictionaries. The Oxford Advanced Learner's Dictionary (1989), the Longman Dictionary of…

  9. 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. PMID:26349641

  10. 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

  11. 75 FR 68809 - Agency Information Collection Activities: Importation Bond Structure

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-09

    ... information collection was previously published in the Federal Register (75 FR 50772) on August 17, 2010... Structure AGENCY: U.S. Customs and Border Protection, Department of Homeland Security. ACTION: 30-day notice... review and approval in accordance with the Paperwork Reduction Act: Importation Bond Structure. This is...

  12. Information Structure and the Licensing of English Subjects

    ERIC Educational Resources Information Center

    Mack, Jennifer Elaine

    2010-01-01

    Most approaches to argument realization in English are grounded in lexical semantic structure. While it is widely acknowledged that there is an intimate relationship between information structure and grammatical relations such as "subject," there have been few attempts to formalize this observation. This dissertation proposes an "interface model…

  13. Structural information content of networks: graph entropy based on local vertex functionals.

    PubMed

    Dehmer, Matthias; Emmert-Streib, Frank

    2008-04-01

    In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties. PMID:18243802

  14. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    PubMed

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Chemical composition and temperature structure of Titan's stratosphere

    NASA Astrophysics Data System (ADS)

    Coustenis, A.; Bampasidis, G.; Achterberg, R.; Lavvas, P.; Vinatier, S.; Nixon, C.; Jennings, D.; Teanby, N.; Flasar, F. M.; Orton, G.; Romani, P.; Carlson, R.; Guandique, E. A.

    2013-09-01

    We have explored the thermal and chemical composition of Titan's atmosphere by combining Cassini CIRS recordings and the related ground - and space - based observations. The fulfillment of one Titanian year of space observations provides us for the first time with the opportunity to evaluate the relative role of different physical processes in the long term evolution of this complex environment. 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 varies significantly with latitude during the 6 years investigated here, with increased mixing ratios towards the northern latitudes. In particular, we monitor and quantify the amplitu de of 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 a weakening north polar vortex with reduced lateral mixing across the vortex boundary. By comparing the Cassini/CIRS results from both the limb and the nadir observations with past V1 (1980) and ISO (1997)inferences we find indication for seasonal variations.

  1. 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. PMID:27172125

  2. De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds

    PubMed Central

    Shen, Yang; Bryan, Philip N; He, Yanan; Orban, John; Baker, David; Bax, Ad

    2010-01-01

    Proteins with high-sequence identity but very different folds present a special challenge to sequence-based protein structure prediction methods. In particular, a 56-residue three-helical bundle protein (GA95) and an α/β-fold protein (GB95), which share 95% sequence identity, were targets in the CASP-8 structure prediction contest. With only 12 out of 300 submitted server-CASP8 models for GA95 exhibiting the correct fold, this protein proved particularly challenging despite its small size. Here, we demonstrate that the information contained in NMR chemical shifts can readily be exploited by the CS-Rosetta structure prediction program and yields adequate convergence, even when input chemical shifts are limited to just amide 1HN and 15N or 1HN and 1Hα values. PMID:19998407

  3. Using the Viking biology experimental results to obtain chemical information about Martian regolith

    NASA Technical Reports Server (NTRS)

    Plumb, Robert C.

    1992-01-01

    Although initially formulated as biology experiments, most of the results produced by the Viking Labeled Release (LR), Gas Exchange (GEX), and Pyrolytic Release (PR) experiments have been reproduced by chemical means. The experiments do not need more study as 'biological' phenomena, but they do deserve much more careful consideration from a chemical viewpoint. They are the only 'wet-chemical' experiments that scientists have performed on another planet, but they have not found very general use as sources of scientific information. There is a large set of potentially useful chemical observations, e.g., the three resolvable and precisely measured kinetic components of the release of C-14-labeled gases, the thermal sensitivity and magnitudes of the oxidation reaction(s) of the LR experiments, the kinetics and magnitude of the O2 and CO2 release of the GEX experiments, the thermal sensitivity of the GEX results, the differences between the thermal sensitivity of the GEX and the thermal sensitivity of the LR responses, and the kinetics and magnitudes of the LR successive injection reabsorption effect. It should be possible to test many chemical aspects of hypothetical martian phenomena in experiments using the biology experimental configurations and derive much valuable information by comparisons with the Viking observations.

  4. Complementary molecular information changes our perception of food web structure

    PubMed Central

    Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

    2014-01-01

    How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

  5. 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.

  6. 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.

  7. Chemical feasibility of lithium as a matrix for structural composites

    NASA Technical Reports Server (NTRS)

    Swann, R. T.; Esterling, D. M.

    1984-01-01

    The chemical compatibility of lithium with tows of carbon and aramid fibers and silicon carbide and boron monofilaments was investigated by encapsulating the fibers in liquid lithium and also by sintering. The lithium did not readily wet the various fibers. In particular, very little lithium infiltration into the carbon and aramid tows was achieved and the strength of the tows was seriously degraded. The strength of the boron and silicon carbide monofilaments, however, was not affected by the liquid lithium. Therefore lithium is not feasible as a matrix for carbon and aramid fibers, but a composite containing boron or silicon carbide fibers in a lithium matrix may be feasible for specialized applications.

  8. Protein secondary structure classification revisited: processing DSSP information with PSSC.

    PubMed

    Zacharias, Jan; Knapp, Ernst-Walter

    2014-07-28

    A first step toward three-dimensional protein structure description is the characterization of secondary structure. The most widely used program for secondary structure assignment remains DSSP, introduced in 1983, with currently more than 400 citations per year. DSSP output is in a one-letter representation, where much of the information on DSSP's internal description is lost. Recently it became evident that DSSP overlooks most π-helical structures, which are more prevalent and important than anticipated before. We introduce an alternative concept, representing the internal structure characterization of DSSP as an eight-character string that is human-interpretable and easy to parse by software. We demonstrate how our protein secondary structure characterization (PSSC) code allows for inspection of complicated structural features. It recognizes ten times more π-helical residues than does the standard DSSP. The plausibility of introduced changes in interpreting DSSP information is demonstrated by better clustering of secondary structures in (φ, ψ) dihedral angle space. With a sliding sequence window (SSW), helical assignments with PSSC remain invariant compared with an assignment based on the complete structure. In contrast, assignment with DSSP can be changed by residues in the neighborhood that are in fact not interacting with the residue under consideration. We demonstrate how one can easily define new secondary structure classification schemes with PSSC and perform the classifications. Our approach works without changing the DSSP source code and allows for more detailed protein characterization. PMID:24866861

  9. Linking structure and function: Information processing in the brain

    SciTech Connect

    Gremillion, M.A.V.

    1990-01-01

    Traditionally, theories of function in neuroscience have emerged from physiology. Physiologists have suggested a number of means by which information in the brain can be processed, yet the principles underlying the generation of these phenomena are not well understood. A complex systems approach would be to examine the overall structure and function of the system and to attempt to establish a common framework for information processing interactions. This paper will use the structure-function relationship as a basis for exploring units of information processing. It will examine the brain as a whole, first providing the non-specialists with an short overview of the structure and some of the functions or outputs of the brain. It then very briefly reviews three of the prominent theoretical concepts that have emerged in the last few decades: receptive fields, feature extraction, and parallel processing. Next, it addresses the question of information processing and outlines the structures which have traditionally been proposed to be the basic unit of information processing. An alternative unit on which information processing in the brain might be based is then proposed, and data outlined to support it. Finally, the implications of this different mode of processing are discussed, both for the brain and for other complex systems. 40 refs., 4 figs., 2 tabs.

  10. 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.

  11. Chemical cross-linkers for protein structure studies by mass spectrometry.

    PubMed

    Paramelle, David; Miralles, Guillaume; Subra, Gilles; Martinez, Jean

    2013-02-01

    The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies. PMID:23255214

  12. Molecular structure, spectroscopic assignments and other quantum chemical calculations of anticancer drugs - A review.

    PubMed

    Ghasemi, A S; Deilam, M; Sharifi-Rad, J; Ashrafi, F; Hoseini-Alfatemi, S M

    2015-01-01

    In many texts, both theoretical and experimental studies on molecular structure and spectroscopic assignments of anticancer medicines have been reported. Molecular geometry parameters have been experimentally obtained by x-ray structure determination method and optimized using computational chemistry method like density functional theory. In this review, we consider calculations based on density function theory at B3LYP/6-31G (d,p) and B3LYP/6-311++G (d,p) levels of theory. Based on optimized geometric parameters of the molecules, molecular structures (length of bonds, bond angles and torsion angles) and vibrational assignments have been obtained. Molecular stability and bond strength have been investigated by applying natural bond orbital (NBO) analysis. Other molecular properties such as mulliken population analysis, thermodynamic properties and polarizabitities of these drugs have been reported. Calculated energies of HOMO and LUMO show that charge transfer occurs in the molecular. Information about the size, shape, charge density distribution and site of molecular chemical reactivity has been obtained by mapping electron density isosurface of electrostatic and compared with experiment data. PMID:26638891

  13. 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

  14. Insight into the informational-structure behavior of the Diels-Alder reaction of cyclopentadiene and maleic anhydride.

    PubMed

    Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Kohout, Miroslav; Angulo, Juan Carlos; Dobado, José A; Dehesa, Jesús S; LópezRosa, Sheila; Soriano-Correa, Catalina

    2014-08-01

    The course of the Diels-Alder reactions of cyclopentadiene and maleic anhydride were studied. Two reaction paths were modelled: endo- and exo-selective paths. All structures within the transient region were characterized and analyzed by means of geometrical descriptors, physicochemical parameters and information-theoretical measures in order to observe the linkage between chemical behavior and the carriage of information. We have shown that the information-theoretical characterization of the chemical course of the reaction is in complete agreement with its phenomenological behavior in passing from reactants to products. In addition, we were able to detect the main differences between the two reaction mechanisms. This type of informational analysis serves to provide tools to help understand the chemical reactivity of the two simplest Diels-Alder reactions, which permits the establishment of a connection between the quantum changes that molecular systems exert along reaction coordinates and standard physicochemical phenomenology. In the present study, we have shown that every reaction stage has a family of subsequent structures that are characterized not solely by their phenomenological behavior but also by informational properties of their electronic density distribution (localizability, order, uniformity). Moreover, we were able to describe the main differences between endo-adduct and exo-adduct pathways. With the advent of new experimental techniques, it is in principle possible to observe the structural changes in the transient regions of chemical reactions. Indeed, through this work we have provided the theoretical concepts needed to unveil the concurrent processes associated with chemical reactions. PMID:25086767

  15. 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...

  16. STRUCTURE-TOXICITY RELATIONSHIPS FOR INDUSTRIAL CHEMICALS CAUSING TYPE(II) NARCOSIS SYNDROME

    EPA Science Inventory

    Several structure-activity relationships have been published for estimating the lethality of nonpolar nonelectrolytes to fish. The vast majority of non-reactive industrial chemicals produce toxicity symptoms consistent with narcosis. However, researchers have found that many chem...

  17. 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

  18. 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. PMID:15446814

  19. 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. PMID:26356911

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

    USGS Publications Warehouse

    Rowe, G.L., Jr.; 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

  1. Recognition and repair of chemically heterogeneous structures at DNA ends.

    PubMed

    Andres, Sara N; Schellenberg, Matthew J; Wallace, Bret D; Tumbale, Percy; Williams, R Scott

    2015-01-01

    Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not "clean." Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini. PMID:25111769

  2. Recognition and repair of chemically heterogeneous structures at DNA ends

    PubMed Central

    Andres, Sara N.; Schellenberg, Matthew J.; Wallace, Bret D.; Tumbale, Percy; Williams, R. Scott

    2014-01-01

    Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not “clean”. Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini. PMID:25111769

  3. Quantum chemical modeling of UV Spectra of Polyurethane Structural Fragments

    NASA Astrophysics Data System (ADS)

    Ksenofontov, M. A.; Umreiko, D. S.; Shundalau, M. B.

    2012-07-01

    Results of TDDFT calculations of characteristics for excited singlet states of mono- and diisocyanates and carbamates containing from one to three phenyl groups are presented. The influence of the structural composition of the isocyanate/carbamate on the formation of its UV absorption spectrum was analyzed.

  4. 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...

  5. 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.

  6. 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.

  7. 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,…

  8. Toxic chemical report, first annual: a summary of information contained in the toxic chemical report forms for calendar year 1987. Final report

    SciTech Connect

    Carlson, R.L.; Lampe, J.A.; Goodner, J.F.

    1989-02-01

    This report summarizes the information contained in the Toxic Chemical Release Inventory Reporting Forms (Form R) for calendar year 1987 as submitted to the Illinois Environmental Protection Agency. The information includes all routine and non-routine releases of toxic chemicals in Illinois to the air, water, and land, as well as transfers of wastes to offsite treatment storage and disposal facilities. Title III, Section 313 of the Superfund Amendments and Reauthorization Act of 1986 (SARA) requires Form Rs to be filed by certain companies that release any of the listed toxic chemicals to the environment.

  9. 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

    2016-05-01

    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+). PMID:26852210

  10. 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.

  11. Knowledge Structures, Social Information Processing, and Children's Aggressive Behavior

    PubMed Central

    Burks, Virginia Salzer; Laird, Robert D.; Dodge, Kenneth A.; Pettit, Gregory S.; Bates, John E.

    2009-01-01

    Although a multitude of factors may be involved in the development of children's violent behavior, the actual aggressive act is preceded by a decision-making process that serves as the proximal control mechanism. The primary goal of this longitudinal study was to understand the nature of this proximal control mechanism involved in children's aggressive acts by focusing on two aspects of social cognitions: social information processing and stored knowledge (i.e., internal knowledge structures that are the latent memories of past events). It was hypothesized that: (1) children with hostile knowledge structures will display more biased patterns of aggressive social information processing than children whose knowledge structures are less hostile and negative; (2) children who display hostile knowledge structures will behave in chronically aggressive ways; and (3) the development of hostile knowledge structures and hostile patterns of social information processing contribute to the stability of aggressive behavior and thus partially mediate the relation between early and later aggressive behavior. 585 boys and girls (19% African-American) were followed from kindergarten through eighth grade. Results from this investigation support the hypotheses and are discussed in terms of the significance of the inclusion of knowledge structures in our theories of the mental processes involved in children's violent behaviour. PMID:20011226

  12. 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.

  13. Brazilian kefir: structure, microbial communities and chemical composition

    PubMed Central

    Magalhães, Karina Teixeira; de Melo Pereira, Gilberto Vinícius; Campos, Cássia Roberta; Dragone, Giuliano; Schwan, Rosane Freitas

    2011-01-01

    Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml. PMID:24031681

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

    PubMed Central

    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. PMID:27493549

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

    PubMed

    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

  16. 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

  17. Establishing relationships between the geometric structure and chemical reactivity of alloy catalysts based on their measured electronic structure.

    SciTech Connect

    Schweitzer, N.; Xin, H.; Nikolla, E.; Miller, J. T.; Linic, S.; Chemical Sciences and Engineering Division; Univ. of Michigan

    2010-01-01

    While it is fairly straightforward to predict the relative chemical reactivity of pure metals, obtaining similar structure-performance relationships for alloys is more challenging. In this contribution we present experimental analysis supported with quantum chemical DFT calculations which allowed us to propose a simple, physically transparent model to predict the impact of alloying on the local electronic structure of different sites in alloys and on the local chemical reactivity. The model was developed through studies of a number of Pt alloys. The central feature of the model is that hybridization of d-orbitals in alloys does not lead to significant charge transfer between the constituent elements in the alloy, and therefore the width of the local density of d-states projected on a site, which is easily calculated from tabulated parameters, is an excellent descriptor of the chemical reactivity of the site.

  18. 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.

  19. Chemical structure of a sporinite from a lignite: Comparison with a synthetic sporinite transformed from sporopollenin

    SciTech Connect

    Hayatsu, R.; Botto, R.E.; Mc Beth, R.L.; Scott, R.G.; Winans, R.E.

    1987-04-01

    The maceral sporinite is thought to be derived from spores and pollen. Both sporinite and sporopollenin, the insoluble cell wall residue after chemical treatment, are considered to have a highly polymerized, cross-linked aliphatic structure with some aromatics. Many investigators have endeavored to characterize the physical and chemical nature of sporinites and sporopollenin; however, their chemical structures have not been well defined. Furthermore, little is known about how sporopollenin transforms to sporinites during the early stage of coalification. The aim of the present study is to compare chemical structures of an immature sporinite and its precursor, sporopollenin. In a parallel experiment, the transformation of sporopollenin into a synthetic sporinite has been carried out in the laboratory using thermal catalytic reactions under conditions of simulated catagenetic maturation.

  20. Chemical structure of a sporinite from a lignite: Comparison with a synthetic sporinite transformed from sporopollenin

    SciTech Connect

    Hayatsu, R.; Botto, R.E.; McBeth, R.L.; Scott, R.G.; Winans, R.E.

    1987-01-01

    The maceral sporinite is thought to be derived from spores and pollen. Both sporinite and sporopollenin, the insoluble cell wall residue after chemical treatment, are considered to have a highly polymerized, cross-linked aliphatic structure with some aromatics. Many investigators have endeavored to characterize the physical and chemical nature of sporinites and sporopollenin; however, their chemical structures have not been well defined. Furthermore, little is known about how sporopollenin transforms to sporinites during the early stage of coalification. Aim of the present study is to compare chemical structures of an immature sporinite and its precursor, sporopollenin. In a parallel experiment, the transformation of sporopollenin into a synthetic sporinite has been carried out in the laboratory using thermal catalytic reactions under conditions of simulated catagenetic maturation.

  1. 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.

  2. 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

    2011-06-01

    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. PMID:26295414

  3. 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. PMID:26822930

  4. 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.

  5. Predicting total clearance in humans from chemical structure.

    PubMed

    Yu, Melvin J

    2010-07-26

    A conceptually simple, fully in silico model to predict total clearance of new compounds in humans is described. Based on the premise that similar molecules will exhibit similar pharmacokinetic properties, we used a k-nearest-neighbors (kNN) technique to predict total clearance by comparison with known reference agents. Molecular similarity was defined using readily calculated one- and two-dimensional molecular descriptors, and the reference set was obtained by combining the Obach and Berellini sets of human pharmacokinetic data. Neutral molecules and drugs whose biological activity is associated with a metal center were removed from the combined set. The remaining 462 compounds were partitioned into a training and external test set of 370 and 92 compounds, respectively. For acids, bases, zwitterions, and quaternary ammonium/pyridinium ions, average prediction accuracy was within two-fold of observed for the external test set (n = 92). Using a collection of 20 drugs from the literature with > or =3 preclinical animal species allometric scaling data, accuracy of the in silico kNN model was not as good as the rule of exponents, but better than simple allometry (SA), and approached that of combination multiexponential allometry (ME) as defined by the number of predictions with < or =50% error. For a collection of 18 drugs with two species (rat-dog) data, the kNN model outperformed both SA and combination ME using the same performance standard. Since the model is fully in silico and, therefore, capable of generating total clearance predictions in the absence of any experimental data, it can be used to help guide early drug discovery research efforts, such as virtual compound library screening, and analogue prioritization prior to chemical synthesis and biological evaluation. Model validation was accomplished using the external test set, three- and five-fold cross-validation and two different y-randomization techniques (y-shuffling and random number pseudodescriptors

  6. Structural and fluid-chemical properties of fault zones

    SciTech Connect

    Bruhn, R.L. . Dept. of Geology and Geophysics)

    1992-01-01

    Fault fluids are mostly NaCl-CO[sub 2]-H[sub 2]O mixtures that originate by metamorphism, escape of connate water from wall rock, circulation of meteoric water, and perhaps contain components derived form igneous and subcrustal sources. Rupturing extends downward into metamorphic terrains undergoing greenschist and amphibolite facies metamorphism, where mineral alteration triggered by fluid pressure transients may extend several hundred meters to perhaps several kilometers into the wall rock. Fluid flowing into regions of lower temperature and/or pressure causes retrograde metamorphic alteration of fault and wall rock, and cementation of fractures. Fault permeability is heterogeneous because irregular, discontinuous lenses of cataclastic and gouge are encased in a heterogeneous damage layer characterized by intense fracturing and hydrothermal alteration. Permeability is also controlled by the geometry of corrugated slip surfaces which create anisotropic flow channels with greatest permeability parallel to long-axes of corrugations. Mineral assemblages and fluid inclusions provide evidence for fluid pressure cycling. Fluid pressure drops when permeability is enhanced by rupturing and subsequently increases as fractures deform, heal and become cemented with alteration minerals. Rates of hydrothermal alteration are comparable to, and sometimes faster, than those of mechanically induced permeability reduction. Effects of fluid chemistry on fault mechanics are not as well understood as fluid pressure effects. Frictional properties of fault surfaces are changed by chemical corrosion, cementation, and pressure solution. Strengthening by fluid pressure drop during dilatant fracturing may be partially offset by a decrease in fluid bulk modulus triggered by effervescence of CO[sub 2].

  7. Surface chemical functionalized single-walled carbon nanotube with anchored phenol structures: Physical and chemical characterization

    NASA Astrophysics Data System (ADS)

    Bae, Jong Hyun; Shanmugharaj, A. M.; Noh, Woo Hyun; Choi, Won Seok; Ryu, Sung Hun

    2007-02-01

    Surface functionalization of single-walled carbon nanotube was carried out by introducing ylides groups containing anchored phenol structures. The functionalized nanotube is characterized using elemental analysis, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, thermogravimetric analysis, Raman spectroscopy and zeta potential measurements. Elemental and FT-IR analysis reveal the successful functionalization of azomethine ylides. Raman spectroscopic studies corroborates that the surface functionalization does not affect the basic crystal domain size of the nanotubes. Functionalized carbon nanotubes exhibit higher zeta potential values showing its higher dispersant ability in water and acetone solvent in comparison to pure carbon nanotube.

  8. 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

  9. 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…

  10. Renyi complexities and information planes: Atomic structure in conjugated spaces

    NASA Astrophysics Data System (ADS)

    Antolín, J.; López-Rosa, S.; Angulo, J. C.

    2009-05-01

    Generalized Renyi complexity measures are defined and numerically analyzed for atomic one-particle densities in both conjugated spaces. These complexities provide, as particular cases, the previously known statistical and Fisher-Shannon complexities. The generalized complexities provide information on the atomic shell structure and shell-filling patterns, allowing to appropriately weight different regions of the electronic cloud.

  11. 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…

  12. 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 a…

  13. 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…

  14. 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…

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. Organohelium compounds: structures, stabilities and chemical bonding analyses.

    PubMed

    Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

    2014-02-24

    This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology. PMID:24488791

  20. 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

  1. 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

  2. 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

  3. 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

  4. Molecular-structure-based models of chemical inventories using neural networks.

    PubMed

    Wernet, Gregor; Hellweg, Stefanie; Fischer, Ulrich; Papadokonstantakis, Stavros; Hungerbühler, Konrad

    2008-09-01

    Chemical synthesis is a complex and diverse procedure, and production data are often scarce or incomplete. A detailed inventory analysis of all mass and energy flows necessary for the production of chemicals is often costly and time-intensive. Therefore only few chemical inventories exist, even though they are essential for process optimization and the environmental assessment of many products. This paper introduces a newtype of model to provide estimates for inventory data and environmental impacts of chemical production based on the molecular structure of a chemical and without a priori knowledge of the production process. These molecular-structure-based models offer inventory data for users in process design and optimization, screening life cycle assessment (LCA), and supply chain management. They can be applied even if the producer is unknown or the production process is not documented. We assessed the capabilities of linear regression and neural network models for this purpose. All models were generated with a data set of inventory data on 103 chemicals. Different input sets were chosen as ways to transform the chemical structure into a numerical vector of descriptors and the effectiveness of the different input sets was analyzed. The results show that a correctly developed neural network model can perform on an acceptable level for many purposes. The models can assist process developers to improve energy efficiency in all design stages and aid in LCA and supply chain management by filling data gaps. PMID:18800554

  5. 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.”

  6. Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea.

    PubMed

    Ridder, Lars; van der Hooft, Justin J J; Verhoeven, Stefan; de Vos, Ric C H; Bino, Raoul J; Vervoort, Jacques

    2013-06-18

    Liquid chromatography coupled with multistage accurate mass spectrometry (LC-MS(n)) can generate comprehensive spectral information of metabolites in crude extracts. To support structural characterization of the many metabolites present in such complex samples, we present a novel method ( http://www.emetabolomics.org/magma ) to automatically process and annotate the LC-MS(n) data sets on the basis of candidate molecules from chemical databases, such as PubChem or the Human Metabolite Database. Multistage MS(n) spectral data is automatically annotated with hierarchical trees of in silico generated substructures of candidate molecules to explain the observed fragment ions and alternative candidates are ranked on the basis of the calculated matching score. We tested this method on an untargeted LC-MS(n) (n ≤ 3) data set of a green tea extract, generated on an LC-LTQ/Orbitrap hybrid MS system. For the 623 spectral trees obtained in a single LC-MS(n) run, a total of 116,240 candidate molecules with monoisotopic masses matching within 5 ppm mass accuracy were retrieved from the PubChem database, ranging from 4 to 1327 candidates per molecular ion. The matching scores were used to rank the candidate molecules for each LC-MS(n) component. The median and third quartile fractional ranks for 85 previously identified tea compounds were 3.5 and 7.5, respectively. The substructure annotations and rankings provided detailed structural information of the detected components, beyond annotation with elemental formula only. Twenty-four additional components were putatively identified by expert interpretation of the automatically annotated data set, illustrating the potential to support systematic and untargeted metabolite identification. PMID:23662787

  7. 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. PMID:27344951

  8. 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)

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

    PubMed

    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

  10. 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

  11. Advanced exact structure searching in large databases of chemical compounds.

    PubMed

    Trepalin, Sergey V; Skorenko, Andrey V; Balakin, Konstantin V; Nasonov, Anatoly F; Lang, Stanley A; Ivashchenko, Andrey A; Savchuk, Nikolay P

    2003-01-01

    Efficient recognition of tautomeric compound forms in large corporate or commercially available compound databases is a difficult and labor intensive task. Our data indicate that up to 0.5% of commercially available compound collections for bioscreening contain tautomers. Though in the large registry databases, such as Beilstein and CAS, the tautomers are found in an automated fashion using high-performance computational technologies, their real-time recognition in the nonregistry corporate databases, as a rule, remains problematic. We have developed an effective algorithm for tautomer searching based on the proprietary chemoinformatics platform. This algorithm reduces the compound to a canonical structure. This feature enables rapid, automated computer searching of most of the known tautomeric transformations that occur in databases of organic compounds. Another useful extension of this methodology is related to the ability to effectively search for different forms of compounds that contain ionic and semipolar bonds. The computations are performed in the Windows environment on a standard personal computer, a very useful feature. The practical application of the proposed methodology is illustrated by several examples of successful recovery of tautomers and different forms of ionic compounds from real commercially available nonregistry databases. PMID:12767143

  12. 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. PMID:15930646

  13. 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

    2015-01-01

    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. PMID:26703557

  14. 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.

  15. 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.

  16. 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.

  17. MPOD: A Material Property Open Database linked to structural information

    NASA Astrophysics Data System (ADS)

    Pepponi, Giancarlo; Gražulis, Saulius; Chateigner, Daniel

    2012-08-01

    Inspired by the Crystallography Open Database (COD), the Material Properties Open Database (MPOD) was given birth. MPOD aims at collecting and making publicly available at no charge tensorial properties (including scalar properties) of phases and linking such properties to structural information of the COD when available. MPOD files are written with the STAR file syntax, used and developed for the Crystallographic Information Files. A dictionary containing new definitions has been written according to the Dictionary Definition Language 1, although some tricks were adopted to allow for multiple entries still avoiding ambiguousness. The initial set includes mechanical properties, elastic stiffness and compliance, internal friction; electrical properties, resistivity, dielectric permittivity and stiffness, thermodynamic properties, heat capacity, thermal conductivity, diffusivity and expansion; electromechanical properties, piezoelectricity, electrostriction, electromechanical coupling; optical properties; piezooptic and photoelastic properties; superconducting properties, critical fields, penetration and coherence lengths. Properties are reported in MPOD files where the original published paper containing the data is cited and structural and experimental information is also given. One MPOD file contains information relative to only one publication and one phase. The files and the information contained therein can also be consulted on-line at http://www.materialproperties.org.

  18. 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

  19. Synthesis of cobalt oxides thin films fractal structures by laser chemical vapor deposition.

    PubMed

    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

  20. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 CH3 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.

  2. 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.

  3. 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.

  4. Visualizing chemical structure-subcellular localization relationships using fluorescent small molecules as probes of cellular transport

    PubMed Central

    2013-01-01

    Background To study the chemical determinants of small molecule transport inside cells, it is crucial to visualize relationships between the chemical structure of small molecules and their associated subcellular distribution patterns. For this purpose, we experimented with cells incubated with a synthetic combinatorial library of fluorescent, membrane-permeant small molecule chemical agents. With an automated high content screening instrument, the intracellular distribution patterns of these chemical agents were microscopically captured in image data sets, and analyzed off-line with machine vision and cheminformatics algorithms. Nevertheless, it remained challenging to interpret correlations linking the structure and properties of chemical agents to their subcellular localization patterns in large numbers of cells, captured across large number of images. Results To address this challenge, we constructed a Multidimensional Online Virtual Image Display (MOVID) visualization platform using off-the-shelf hardware and software components. For analysis, the image data set acquired from cells incubated with a combinatorial library of fluorescent molecular probes was sorted based on quantitative relationships between the chemical structures, physicochemical properties or predicted subcellular distribution patterns. MOVID enabled visual inspection of the sorted, multidimensional image arrays: Using a multipanel desktop liquid crystal display (LCD) and an avatar as a graphical user interface, the resolution of the images was automatically adjusted to the avatar’s distance, allowing the viewer to rapidly navigate through high resolution image arrays, zooming in and out of the images to inspect and annotate individual cells exhibiting interesting staining patterns. In this manner, MOVID facilitated visualization and interpretation of quantitative structure-localization relationship studies. MOVID also facilitated direct, intuitive exploration of the relationship between the

  5. Designing Chemically and Structurally Stable Cathode Hosts for Lithium Ion Cells

    NASA Astrophysics Data System (ADS)

    Manthiram, A.

    2002-12-01

    With an objective to fully understand the factors that control the practically utilizable capacity and cyclability of lithium ion battery cathodes, the chemical and structural stabilities of the layered Li1-xCoO2, Li1-xNi0.85Co0.15O2, and cation-substituted Li1-xMnO2 are investigated systematically. The investigation is carried out by chemically extracting lithium with an oxidizing agent followed by characterizing the products by both X-ray diffraction and wet chemical redox titrations. The Li1-xCoO2 system is found to experience chemical instability at deep lithium extraction with (1-x) < 0.5, which could play a role in limiting its practical capacity. The Li1-xNi0.85Co0.15O2 system, on the other hand, is found to experience structural instability at T > 50 °C due to a migration of nickel ions to the lithium plane; such a migration occurs at ambient temperature in the case of Li1-xMnO2. The understanding gained from the investigation is used to develop chemically and structurally more stable cathode hosts by surface/chemical modifications and cationic substitutions.

  6. Evolutionary Optimization of Network Structures using Informative Genotype Tag

    NASA Astrophysics Data System (ADS)

    Ando, Shin; Iba, Hitoshi

    Evolutionary computation has been applied to numerous design tasks, including design of electric circuits, neural networks, and genetic circuits. Though it is a very effective solution for optimizing network structures, genetic algorithm faces many difficulties, often referred to as the permutation problems, when both topologies and the weights of the network are the target of optimization. We propose a new crossover method used in conjunction with a genotype with information tags. The information tags allow GA to recognize and preserve the common structure of parent chromosomes during genetic crossover. The method is implemented along with subpopulating strategies to make the parallel evolution of network topology and weights feasible and efficient. The proposed method is evaluated on a few typical and practical problems, and shows improvement from conventional methodologies and genotypes.

  7. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-01-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule. PMID:26178193

  8. 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

  9. A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

    PubMed

    Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

    2016-01-01

    When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity. PMID:27311473

  10. 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

  11. Information-driven structural modelling of protein-protein interactions.

    PubMed

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes. PMID:25330973

  12. Structured information exchange on infectious diseases for prisoners.

    PubMed

    Flühmann, Paul; Wassmer, Max; Schwendimann, René

    2012-07-01

    Infectious diseases such as HIV/AIDS, hepatitis C, and sexually transmitted diseases are more prevalent in prisoners than in the general population. In Western European prisons, inmates have HIV infection rates 25 times higher and hepatitis C infection rates 40 times higher than their national averages. To inform prisoners about the dangers of these diseases, a structured information exchange was developed. In a pre-/post- design with repeated measurement, 21 male prisoners' knowledge of infectious diseases was analyzed. A significant improvement of knowledge (p < .0001) was observed. One striking finding was that knowledge of hepatitis C was clearly lower than that of HIV and that prisoners enrolled in drug substitution programs were significantly better informed about hepatitis C than the other participating prisoners. PMID:22569902

  13. 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.

  14. 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. PMID:25820469

  15. Structure and local chemical properties of boron-terminated tetravacancies in hexagonal boron nitride.

    PubMed

    Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H G; Liu, Zheng; Suenaga, Kazutomo

    2015-02-20

    Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride. We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sample regions. We correlate our experimental data with calculations which help explain our observations. PMID:25763963

  16. 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.

  17. The IAEA system and experience as a model for Information Management under the Chemical Weapons Convention

    SciTech Connect

    Bieber, A.M. Jr.; Kempf, C.R.

    1992-01-01

    Similarities in the verification aims of the monitoring regimes of the future Organization for the Prohibition of chemical Weapons (OPCW) and of the International Atomic Energy Agency (IAEA), make their general data requirements similar: data are needed for planning inspections, for evaluating inspections, and for preparation of reports on compliance with the relevant treaty In this paper we discuss the legal, procedural and administrative structure behind the data system associated with IAEA safeguards, and, after comparing this to the CWC regime, suggest possible improvements for consideration during the development of national implementation programs and of the declaration and inspection data management system for the OPCW.

  18. The IAEA system and experience as a model for Information Management under the Chemical Weapons Convention

    SciTech Connect

    Bieber, A.M. Jr.; Kempf, C.R.

    1992-09-01

    Similarities in the verification aims of the monitoring regimes of the future Organization for the Prohibition of chemical Weapons (OPCW) and of the International Atomic Energy Agency (IAEA), make their general data requirements similar: data are needed for planning inspections, for evaluating inspections, and for preparation of reports on compliance with the relevant treaty In this paper we discuss the legal, procedural and administrative structure behind the data system associated with IAEA safeguards, and, after comparing this to the CWC regime, suggest possible improvements for consideration during the development of national implementation programs and of the declaration and inspection data management system for the OPCW.

  19. RBO Aleph: leveraging novel information sources for protein structure prediction

    PubMed Central

    Mabrouk, Mahmoud; Putz, Ines; Werner, Tim; Schneider, Michael; Neeb, Moritz; Bartels, Philipp; Brock, Oliver

    2015-01-01

    RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue–residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/. PMID:25897112

  20. RBO Aleph: leveraging novel information sources for protein structure prediction.

    PubMed

    Mabrouk, Mahmoud; Putz, Ines; Werner, Tim; Schneider, Michael; Neeb, Moritz; Bartels, Philipp; Brock, Oliver

    2015-07-01

    RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue-residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/. PMID:25897112

  1. 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.

  2. 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.

  3. Use of toxicokinetics to support chemical evaluation: Informing high dose selection and study interpretation.

    PubMed

    Creton, Stuart; Saghir, Shakil A; Bartels, Michael J; Billington, Richard; Bus, James S; Davies, Will; Dent, Matthew P; Hawksworth, Gabrielle M; Parry, Simon; Travis, Kim Z

    2012-03-01

    Toxicokinetic (TK) information can substantially enhance the value of the data generated from toxicity testing, and is an integral part of pharmaceutical safety assessment. It is less widely used in the chemical, agrochemical and consumer products industries, but recognition of its value is growing, as reflected by increased reference to the use of TK information in new and draft OECD test guidelines. To help promote increased consideration of the important role TK can play in chemical risk assessment, we have gathered practical examples from the peer-reviewed literature, as well as in-house industry data, that highlight opportunities for the use of TK in the selection of dose levels. Use of TK can help to ensure studies are designed to be of most relevance to assessing potential risk in humans, and avoid the use of excessively high doses that could result in unnecessary suffering in experimental animals. Greater emphasis on the potential contribution of TK in guiding study design and interpretation should be incorporated in regulatory data requirements and associated guidance. PMID:22198561

  4. Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5.

    PubMed Central

    Auer, C M; Nabholz, J V; Baetcke, K P

    1990-01-01

    Section 5 of the Toxic Substances Control Act (TSCA) requires that manufacturers and importers of new chemicals must submit a Premanufacture Notification (PMN) to the U.S. Environmental Protection Agency 90 days before they intend to commence manufacture or import. Certain information such as chemical identity, uses, etc., must be included in the notification. The submission of test data on the new substance, however, is not required, although any available health and environmental information must be provided. Nonetheless, over half of all PMNs submitted to the agency do not contain any test data; because PMN chemicals are new, no test data is generally available in the scientific literature. Given this situation, EPA has had to develop techniques for hazard assessment that can be used in the presence of limited test data. EPA's approach has been termed "structure-activity relationships" (SAR) and involves three major components: the first is critical evaluation and interpretation of available toxicity data on the chemical; the second component involves evaluation of test data available on analogous substances and/or potential metabolites; and the third component involves the use of mathematical expressions for biological activity known as "quantitative structure-activity relationships" (QSARs). At present, the use of QSARs is limited to estimating physical chemical properties, environmental toxicity, and bioconcentration factors. An important overarching element in EPA's approach is the experience and judgment of scientific assessors in interpreting and integrating the available data and information. Examples are provided that illustrate EPA's approach to hazard assessment for PMN chemicals. PMID:2269224

  5. 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.

  6. Nanoscale chemical and structural study of Co-based FEBID structures by STEM-EELS and HRTEM

    PubMed Central

    2011-01-01

    Nanolithography techniques in a scanning electron microscope/focused ion beam are very attractive tools for a number of synthetic processes, including the fabrication of ferromagnetic nano-objects, with potential applications in magnetic storage or magnetic sensing. One of the most versatile techniques is the focused electron beam induced deposition, an efficient method for the production of magnetic structures highly resolved at the nanometric scale. In this work, this method has been applied to the controlled growth of magnetic nanostructures using Co2(CO)8. The chemical and structural properties of these deposits have been studied by electron energy loss spectroscopy and high-resolution transmission electron microscopy at the nanometric scale. The obtained results allow us to correlate the chemical and structural properties with the functionality of these magnetic nanostructures. PMID:22085532

  7. Formation of copper porous structures under near-equilibrium chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Kornyushchenko, A. S.; Natalich, V. V.; Perekrestov, V. I.

    2016-05-01

    The mechanism of copper structure formation under near-equilibrium conditions in a chemically-active medium-condensate system has been investigated. The desired conditions have been implemented using CVD system. Copper chloride CuCl2 was used as a source material, and mixture of hydrogen with nitrogen served as a working gas. The influence of the evaporation temperature, condensation temperature and state of the growth surface on the porous structures formation has been investigated. It has been established, that the structure formation mechanism is determined by layer-by-layer or normal crystal growth, nucleation and growth of whiskers, and also by partial intergrowth of structural elements.

  8. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays. PMID:27285961

  9. 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

  10. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    PubMed

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  11. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure.

    PubMed

    Liu, Jie; Mansouri, Kamel; Judson, Richard S; Martin, Matthew T; Hong, Huixiao; Chen, Minjun; Xu, Xiaowei; Thomas, Russell S; Shah, Imran

    2015-04-20

    The U.S. Tox21 and EPA ToxCast program screen 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, then used supervised machine learning to predict in vivo hepatotoxic effects. A set of 677 chemicals was represented by 711 in vitro bioactivity descriptors (from ToxCast assays), 4,376 chemical structure descriptors (from QikProp, OpenBabel, PaDEL, and PubChem), and three hepatotoxicity categories (from animal studies). Hepatotoxicants were defined by rat liver histopathology observed after chronic chemical testing and grouped into hypertrophy (161), injury (101) and proliferative lesions (99). Classifiers were built using six machine learning algorithms: linear discriminant analysis (LDA), Naïve Bayes (NB), support vector machines (SVM), classification and regression trees (CART), k-nearest neighbors (KNN), and an ensemble of these classifiers (ENSMB). Classifiers of hepatotoxicity were built using chemical structure descriptors, ToxCast bioactivity descriptors, and hybrid descriptors. Predictive performance was evaluated using 10-fold cross-validation testing and in-loop, filter-based, feature subset selection. Hybrid classifiers had the best balanced accuracy for predicting hypertrophy (0.84 ± 0.08), injury (0.80 ± 0.09), and proliferative lesions (0.80 ± 0.10). Though chemical and bioactivity classifiers had a similar balanced accuracy, the former were more sensitive, and the latter were more specific. CART, ENSMB, and SVM classifiers performed the best, and nuclear receptor activation and mitochondrial functions were frequently found in highly predictive classifiers of hepatotoxicity. ToxCast and ToxRefDB provide the largest and richest publicly available data sets for mining linkages between the in vitro bioactivity of environmental chemicals and their adverse histopathological outcomes

  12. Etching anisotropy mechanisms lead to morphology-controlled silicon nanoporous structures by metal assisted chemical etching.

    PubMed

    Jiang, Bing; Li, Meicheng; Liang, Yu; Bai, Yang; Song, Dandan; Li, Yingfeng; Luo, Jian

    2016-02-01

    The etching anisotropy induced by the morphology and rotation of silver particles controls the morphology of silicon nanoporous structures, through various underlying complex etching mechanisms. The level of etching anisotropy can be modulated by controlling the morphology of the silver catalyst to obtain silicon nanoporous structures with straight pores, cone-shaped pores and pyramid-shaped pores. In addition, the structures with helical pores are obtained by taking advantage of the special anisotropic etching, which is induced by the rotation and revolution of silver particles during the etching process. An investigation of the etching anisotropy during metal assisted chemical etching will promote a deep understanding of the chemical etching mechanism of silicon, and provide a feasible approach to fabricate Si nanoporous structures with special morphologies. PMID:26785718

  13. Structure-informed insights for NLR functioning in plant immunity.

    PubMed

    Sukarta, Octavina C A; Slootweg, Erik J; Goverse, Aska

    2016-08-01

    To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning. PMID:27208725

  14. Bioluminescence tomography with structural and functional a priori information

    NASA Astrophysics Data System (ADS)

    Yan, Han; Unlu, Mehmet B.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-02-01

    Multispectral bioluminescence tomography (BLT) is one of the seemingly promising approaches to recover 3D tomographic images of bioluminescence source distribution in vivo. In bioluminescence tomography, internal light source, such as luciferase is activated within a volume and multiple wavelength emission data from the internal bioluminescence sources is acquired for reconstruction. The underline non-uniqueness problem associated with non-spectrally resolved intensity-based bioluminescence tomography was demonstrated by Dehghani et al. and it also shown that using a spectrally resolved technique, an accurate solution for the source distribution can be calculated from the measured data if both functional and anatomical a priori information are at hand. Thus it is of great desire to develop an imaging system that is capable of simultaneously acquiring both the optical and structural a priori information as well as acquiring the bioluminescence data. In this paper we present our first combined optical tomography and CT system which constitutes with a cool CCD camera ( perkin elmer "cold blue"), laser launching units and Xray CT( Dxray proto-type). It is capable of acquiring non contact diffuse optical tomography (DOT) data which is used for functional a priori; X-ray CT images which yields the structure information; and BLT images. Physical phantom experiments are designed to verify the system accuracy, repeatability and resolution. These studies shows the feasibility of such imaging system and its potential.

  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. 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.

  17. Identifying the structural requirements for chromosomal aberration by incorporating molecular flexibility and metabolic activation of chemicals.

    PubMed

    Mekenyan, Ovanes; Todorov, Milen; Serafimova, Rossitsa; Stoeva, Stoyanka; Aptula, Aynur; Finking, Robert; Jacob, Elard

    2007-12-01

    Modeling the potential of chemicals to induce chromosomal damage has been hampered by the diversity of mechanisms which condition this biological effect. The direct binding of a chemical to DNA is one of the underlying mechanisms that is also responsible for bacterial mutagenicity. Disturbance of DNA synthesis due to inhibition of topoisomerases and interaction of chemicals with nuclear proteins associated with DNA (e.g., histone proteins) were identified as additional mechanisms leading to chromosomal aberrations (CA). A comparative analysis of in vitro genotoxic data for a large number of chemicals revealed that more than 80% of chemicals that elicit bacterial mutagenicity (as indicated by the Ames test) also induce CA; alternatively, only 60% of chemicals that induce CA have been found to be active in the Ames test. In agreement with this relationship, a battery of models is developed for modeling CA. It combines the Ames model for bacterial mutagenicity, which has already been derived and integrated into the Optimized Approach Based on Structural Indices Set (OASIS) tissue metabolic simulator (TIMES) platform, and a newly derived model accounting for additional mechanisms leading to CA. Both models are based on the classical concept of reactive alerts. Some of the specified alerts interact directly with DNA or nuclear proteins, whereas others are applied in a combination of two- or three-dimensional quantitative structure-activity relationship models assessing the degree of activation of the alerts from the rest of the molecules. The use of each of the alerts has been justified by a mechanistic interpretation of the interaction. In combination with a rat liver S9 metabolism simulator, the model explained the CA induced by metabolically activated chemicals that do not elicit activity in the parent form. The model can be applied in two ways: with and without metabolic activation of chemicals. PMID:18052113

  18. Electrical conductivity as a constraint on lower mantle thermo-chemical structure

    NASA Astrophysics Data System (ADS)

    Deschamps, Frédéric; Khan, Amir

    2016-09-01

    Electrical conductivity of the Earth's mantle depends on both temperature and compositional parameters. Radial and lateral variations in conductivity are thus potentially a powerful means to investigate its thermo-chemical structure. Here, we use available electrical conductivity data for the major lower mantle minerals, bridgmanite and ferropericlase, to calculate 3D maps of lower mantle electrical conductivity for two possible models: a purely thermal model, and a thermo-chemical model. Both models derive from probabilistic seismic tomography, and the thermo-chemical model includes, in addition to temperature anomalies, variations in volume fraction of bridgmanite and iron content. The electrical conductivity maps predicted by these two models are clearly different. Compared to the purely thermal model, the thermo-chemical model leads to higher electrical conductivity, by about a factor 2.5, and stronger lateral anomalies. In the lowermost mantle (2000-2891 km) the thermo-chemical model results in a belt of high conductivity around the equator, whose maximum value reaches ∼120% of the laterally-averaged value and is located in the low shear-wave velocity provinces imaged in tomographic models. Based on our electrical conductivity maps, we computed electromagnetic response functions (C-responses) and found, again, strong differences between the C-responses for purely thermal and thermo-chemical models. At periods of 1 year and longer, C-responses based on thermal and thermo-chemical models are easily distinguishable. Furthermore, C-responses for thermo-chemical model vary geographically. Our results therefore show that long-period (1 year and more) variations of the magnetic field may provide key insights on the nature and structure of the deep mantle.

  19. 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.

  20. Effect of chemical structure on film-forming properties of seed oils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The film thickness of seven seed oils and two petroleum-based oils of varying chemical structures, was investigated by the method of optical interferometry under pure rolling conditions, and various combinations of entrainment speed (u), load, and temperature. The measured film thickness (h measured...

  1. Use of 13Cα Chemical-Shifts in Protein Structure Determination

    PubMed Central

    Vila, Jorge A.; Ripoll, Daniel R.; Scheraga, Harold A.

    2008-01-01

    A physics-based method, aimed at determining protein structures by using NOE-derived distances together with observed and computed 13C chemical shifts, is proposed. The approach makes use of 13Cα chemical shifts, computed at the density functional level of theory, to obtain torsional constraints for all backbone and side-chain torsional angles without making a priori use of the occupancy of any region of the Ramachandran map by the amino acid residues. The torsional constraints are not fixed but are changed dynamically in each step of the procedure, following an iterative self-consistent approach intended to identify a set of conformations for which the computed 13Cα chemical shifts match the experimental ones. A test is carried out on a 76-amino acid all-α-helical protein, namely the B. Subtilis acyl carrier protein. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than an existing NMR-derived structure model of this protein, in terms of both the agreement between predicted and observed 13Cα chemical shifts and some stereochemical quality indicators, and of similar accuracy as one of the protein models solved at a high level of resolution. The results provide evidence that this methodology can be used not only for structure determination but also for additional protein structure refinement of NMR-derived models deposited in the Protein Data Bank. PMID:17516673

  2. The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

    ERIC Educational Resources Information Center

    Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

    2009-01-01

    In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a…

  3. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    PubMed Central

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  4. 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…

  5. 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,…

  6. Microwave imaging of the breast with incorporated structural information

    NASA Astrophysics Data System (ADS)

    Golnabi, Amir H.; Meaney, Paul M.; Geimer, Shireen D.; Paulsen, Keith D.

    2010-03-01

    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 ranging from high megahertz to low gigahertz. The available range of dielectric properties for different soft tissue can provide considerable functional information about tissue health. Nonetheless, one of the limiting weaknesses of microwave imaging is, unlike that for conventional modalities such as X-ray CT or MRI, it cannot inherently provide high-resolution images. The conventional modalities can produce highly resolved anatomical information but often cannot provide the functional information required for diagnoses. We have developed a soft prior regularization strategy that can incorporate the prior anatomical information from X-ray CT, MR or other sources, and use it in a way to exploit the resolution of these images while also retaining the functional nature of the microwave images. The anatomical information is first used to create an imaging zone mesh, which segments separate internal substructures, and an associated weighting matrix that numerically groups the values of closely related nodes within the mesh. This information is subsequently used as a regularizing term for the Gauss-Newton reconstruction algorithm. This approach exploits existing technology in a systematic way without making potentially biased assumptions about the properties of visible structures. In this paper we continue our initial investigation on this matter with a series of breast-shaped simulation and phantom experiments.

  7. 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

  8. Predicate argument structure frames for modeling information in operative notes.

    PubMed

    Wang, Yan; Pakhomov, Serguei; Melton, Genevieve B

    2013-01-01

    The rich information about surgical procedures contained in operative notes is a valuable data source for improving the clinical evidence base and clinical research. In this study, we propose a set of Predicate Argument Structure (PAS) frames for surgical action verbs to assist in the creation of an information extraction (IE) system to automatically extract details about the techniques, equipment, and operative steps from operative notes. We created PropBank style PAS frames for the 30 top surgical action verbs based on examination of randomly selected sample sentences from 3,000 Laparoscopic Cholecystectomy notes. To assess completeness of the PAS frames to represent usage of same action verbs, we evaluated the PAS frames created on sample sentences from operative notes of 6 other gastrointestinal surgical procedures. Our results showed that the PAS frames created with one type of surgery can successfully denote the usage of the same verbs in operative notes of broader surgical categories. PMID:23920664

  9. 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

  10. Structural segmentation for multimedia content-based information retrieval

    NASA Astrophysics Data System (ADS)

    Carli, Marco; Degli Esposti, Alberto; Micarelli, Alessandro; Neri, Alessandro

    2001-12-01

    In this contribution we propose a novel semantic-based architecture to manage multimedia data. We propose an innovatory approach, introducing an abstraction level to study the relationships among the low level attributes, as color, motion, in a systematic way, before the visual image content estimation. Aim of this analysis is to unify the descriptors information and to gather them into structures that we call over-regions, which represent particular configurations of the objects to be recognized. This step will allow for the higher abstraction level effective object-based or event-based image recognition. The case-based reasoning paradigm is used in our approach for the high level analysis.

  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.

    1999-05-14

    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

  12. 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

  13. 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.

  14. Method to find community structures based on information centrality

    NASA Astrophysics Data System (ADS)

    Fortunato, Santo; Latora, Vito; Marchiori, Massimo

    2004-11-01

    Community structures are an important feature of many social, biological, and technological networks. Here we study a variation on the method for detecting such communities proposed by Girvan and Newman and based on the idea of using centrality measures to define the community boundaries [M. Girvan and M. E. J. Newman, Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002)]. We develop an algorithm of hierarchical clustering that consists in finding and removing iteratively the edge with the highest information centrality. We test the algorithm on computer generated and real-world networks whose community structure is already known or has been studied by means of other methods. We show that our algorithm, although it runs to completion in a time O(n4) , is very effective especially when the communities are very mixed and hardly detectable by the other methods.

  15. 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…

  16. 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.

  17. 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.

  18. 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. PMID:26826354

  19. Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

    PubMed Central

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

    2014-01-01

    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 LiNi0.4Mn0.4Co0.18Ti0.02O2 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. PMID:25027190

  20. A Script for Automated 3-Dimentional Structure Generation and Conformer Search from 2- Dimentional Chemical Drawing

    PubMed Central

    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. PMID:24391363

  1. Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

    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 LiNi0.4Mn0.4Co0.18Ti0.02O2 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.

  2. 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

    2014-01-01

    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. PMID:25027190

  3. 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. PMID:24391363

  4. 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.

  5. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

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

    DOE PAGESBeta

    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

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

    PubMed

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-01-01

    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. PMID:27215369

  8. Electronic structure and chemical bonding of amorphous chromium carbide thin films

    NASA Astrophysics Data System (ADS)

    Magnuson, Martin; Andersson, Matilda; Lu, Jun; Hultman, Lars; Jansson, Ulf

    2012-06-01

    The microstructure, electronic structure and chemical bonding of chromium carbide thin films with different carbon contents have been investigated with high-resolution transmission electron microscopy, electron energy loss spectroscopy and soft x-ray absorption-emission spectroscopies. Most of the films can be described as amorphous nanocomposites with non-crystalline CrCx in an amorphous carbon matrix. At high carbon contents, graphene-like structures are formed in the amorphous carbon matrix. At 47 at.% carbon content, randomly oriented nanocrystallites are formed creating a complex microstructure of three components. The soft x-ray absorption-emission study shows additional peak structures exhibiting non-octahedral coordination and bonding.

  9. Wet-chemical synthesis and applications of non-layer structured two-dimensional nanomaterials

    PubMed Central

    Tan, Chaoliang; Zhang, Hua

    2015-01-01

    Non-layer structured nanomaterials with single- or few-layer thickness have two-dimensional sheet-like structures and possess intriguing properties. Recent years have seen major advances in development of a host of non-layer structured ultrathin two-dimensional nanomaterials such as noble metals, metal oxides and metal chalcogenides. The wet-chemical synthesis has emerged as the most promising route towards high-yield and mass production of such nanomaterials. These nanomaterials are now finding increasing applications in a wide range of areas including catalysis, energy production and storage, sensor and nanotherapy, to name but a few. PMID:26303763

  10. Studying the explanatory capacity of artificial neural networks for understanding environmental chemical quantitative structure-activity relationship models.

    PubMed

    Yang, Lei; Wang, Peng; Jiang, Yilin; Chen, Jian

    2005-01-01

    Although artificial neural networks (ANNs) have been shown to exhibit superior predictive power in the study of quantitative structure-activity relationships (QSARs), they have also been labeled a "black box" because they provide little explanatory insight into the relative influence of the independent variables in the predictive process so that little information on how and why compounds work can be obtained. Here, we have turned our interests to their explanatory capacities; therefore, a method was proposed for assessing the relative importance of variables indicating molecular structure, on the basis of axon connection weights and partial derivatives of the ANN output with respect to its input, which can identify variables that significantly contribute to network predictions, and providing a variable selection method for ANNs. We show that, by extending this approach to ANNs, the "black box" mechanics of ANNs can be greatly illuminated, thereby making it very useful in understanding environmental chemical QSAR models. PMID:16309287

  11. Structure and chemical composition of the dentin-enamel junction analyzed by Confocal Raman Microscopy

    NASA Astrophysics Data System (ADS)

    Desoutter, A.; Salehi, H.; Slimani, A.; Marquet, P.; Jacquot, B.; Tassery, H.; Cuisinier, F. J. G.

    2014-02-01

    The structure and chemical composition of the human dentin-enamel junction (DEJ) was studied using confocal Raman microscopy - a chemical imaging technique. Slices of non-fixed, sound teeth were prepared with an Isomet diamond saw and scanned with Witec Alpha300R system. The combination of different characteristics peaks of phosphate, carbonate and organic matrix (respectively 960, 1072 and 1545 cm-1), generates images representing the chemical composition of the DEJ area. Images are also calculated using peak ratios enabling precise determination of the chemical composition across the DEJ. Then, with two characterized peaks, different pictures are calculated to show the ratio of two components. The images of the spatial distribution of mineral phosphate (960cm-1) to organic matrix (1545 cm-1) ratios, mineral carbonates (1072cm-1) to mineral phosphate ratios; and mineral carbonates to organic matrix ratios were reconstructed. Cross sectional and calculated graphic profile show the variations of the different chemical component ratios through the enamel and the dentin. Phosphate to organic ratio shows an accumulation of organic material under the enamel surface. The cross sectional profile of these pictures shows a high phosphate content compared to enamel in the vicinity of the DEJ. The Confocal Raman imaging technique can be used to further provide full chemical imaging of tooth, particularly of the whole DEJ and to study enamel and dentin decay.

  12. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

    PubMed Central

    2014-01-01

    Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

  13. Chemical structure of vanadium-based contact formation on n-AlN

    SciTech Connect

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  14. Chemical structures of constituents from the whole plant of Bacopa monniera.

    PubMed

    Ohta, Tomoe; Nakamura, Seikou; Nakashima, Souichi; Oda, Yoshimi; Matsumoto, Takahiro; Fukaya, Masashi; Yano, Mamiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2016-07-01

    Two new dammarane-type triterpene oligoglycosides, bacomosaponins A and B, and three new phenylethanoid glycosides, bacomosides A, B1, and B2, were isolated from the whole plant of Bacopa monniera Wettst. The chemical structures of the new constituents were characterized on the basis of chemical and physicochemical evidence. In the present study, bacomosaponins A and B with acyl groups were obtained from the whole plant of B. monniera. This is the first report of acylated dammarane-type triterpene oligoglycosides isolated from B. monniera. In addition, dammarane-type triterpene saponins significantly inhibited the aggregation of 42-mer amyloid β-protein. PMID:27010932

  15. A structured approach to occupational hygiene in the design and operation of fine chemical plant.

    PubMed

    Money, C D

    1992-12-01

    In order to ensure appropriate occupational hygiene controls can be incorporated in the design and operation of fine chemical plant, a structured scheme has been developed based upon the intrinsic hazard of the materials in use. The scheme provides guidelines for managing the inherent risks to health presented by the operation of such plant, including basic recommendations on the selection and operation of selected plant equipment. Although the scheme has focused on a carcinogenic ranking system for aromatic amines and nitro compounds, with suitable modifications its underlying philosophy and principles should be capable of application to any toxicological scheme for ranking the relative hazard of chemical substances. PMID:1471813

  16. Herschel/HIFI Observations of Extra-Ordinary Sources: The physical and chemical structure of the Orion Bar

    NASA Astrophysics Data System (ADS)

    Nagy, Zsofia; Ossenkopf, Volker; van der Tak, Floris; Choi, Yunhee; Bergin, Edwin; Gerin, Maryvonne; Joblin, Christine; Röllig, Markus; Simon, Robert; Stutzki, Jürgen

    2015-08-01

    Young massive stars have a strong impact on their environment, including feedback due to their Far Ultraviolet (FUV) radiation. The penetration of FUV radiation into the interstellar medium affects the physical and chemical structure of high-mass star forming regions. Photon-Dominated Regions (PDRs) are interfaces between fully ionized and cold molecular material. Spectral line observations at sub-mm and far-infrared wavelengths provide information on the physics and chemistry of PDRs, and therefore help us to understand the impact of young massive stars on their surrounding interstellar medium.One of the best targets to probe PDR structure and chemistry is the Orion Bar, located at a distance of about 415 pc, with a nearly edge-on geometry. We have carried out an unbiased spectral line survey with Herschel/HIFI in the 480-1250 GHz and 1410-1910 GHz frequency range. We have identified lines from about 30 molecules, including the reactive ions CH+, SH+, CF+, and OH+ (Nagy et al., 2013; Van der Tak and Nagy et al., 2013), the high-J ladder of CO isotopes, and grain chemistry tracers such as H2CO.We interpret the molecular line emission observed in the HIFI range using detailed non-LTE and PDR models in order to probe the structure and chemistry of the Orion Bar. We present an overview of the HIFI line survey observations and their interpretation using radiative transfer and chemical models.

  17. 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.

  18. Use of chemical-mechanical polishing for fabricating photonic bandgap structures

    DOEpatents

    Fleming, James G.; Lin, Shawn-Yu; Hetherington, Dale L.; Smith, Bradley K.

    1999-01-01

    A method is disclosed for fabricating a two- or three-dimensional photonic bandgap structure (also termed a photonic crystal, photonic lattice, or photonic dielectric structure). The method uses microelectronic integrated circuit (IC) processes to fabricate the photonic bandgap structure directly upon a silicon substrate. One or more layers of arrayed elements used to form the structure are deposited and patterned, with chemical-mechanical polishing being used to planarize each layer for uniformity and a precise vertical tolerancing of the layer. The use of chemical-mechanical planarization allows the photonic bandgap structure to be formed over a large area with a layer uniformity of about two-percent. Air-gap photonic bandgap structures can also be formed by removing a spacer material separating the arrayed elements by selective etching. The method is useful for fabricating photonic bandgap structures including Fabry-Perot resonators and optical filters for use at wavelengths in the range of about 0.2-20 .mu.m.

  19. Ab initio studies of equations of state and chemical reactions of reactive structural materials

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava

    The motivations for the research issues addressed in this thesis are based on the needs of the aerospace structural analysis and the design community. The specific focus is related to the characterization and shock induced chemical reactions of multi-functional structural-energetic materials that are also known as the reactive structural materials and their reaction capabilities. Usually motivation for selection of aerospace structural materials is to realize required strength characteristics and favorable strength to weight ratios. The term strength implies resistance to loads experienced during the service life of the structure, including resistance to fatigue loads, corrosion and other extreme conditions. Thus, basically the structural materials are single function materials that resist loads experienced during the service life of the structure. However, it is desirable to select materials that are capable of offering more than one basic function of strength. Very often, the second function is the capability to provide functions of sensing and actuation. In this thesis, the second function is different. The second function is the energetic characteristics. Thus, the choice of dual functions of the material are the structural characteristics and energetic characteristics. These materials are also known by other names such as the reactive material structures or dual functional structural energetic materials. Specifically the selected reactive materials include mixtures of selected metals and metal oxides that are also known as thermite mixtures, reacting intermetallic combinations and oxidizing materials. There are several techniques that are available to synthesize these structural energetic materials or reactive material structures and new synthesis techniques constitute an open research area. The focus of this thesis, however, is the characterization of chemical reactions of reactive material structures that involve two or more solids (or condensed matter). The

  20. SMILES (SIMPLIFIED MOLECULAR IDENTIFICATION AND LINE ENTRY SYSTEM): A LINE NOTATION AND COMPUTERIZED INTERPRETER FOR CHEMICAL STRUCTURES

    EPA Science Inventory

    A line notation syntax and software interpreter for specifying chemical structures on small and large computers is presented. The Simplified Molecular Identification and Line Entry System, SMILES, contains the advantages of line notations for specifying structures but avoids the ...

  1. Remote monitoring of instrumented structures using the Internet information superhighway

    NASA Astrophysics Data System (ADS)

    Fuhr, Peter L.; Huston, Dryver R.; Ambrose, Timothy P.

    1994-09-01

    The requirements of sensor monitoring associated with instrumented civil structures poses potential logistical constraints on manpower, training, and costs. The need for frequent or even continuous data monitoring places potentially severe constraints on overall system performance given real-world factors such as available manpower, geographic separation of the instrumented structures, and data archiving as well as the training and cost issues. While the pool of available low wage, moderate skill workers available to the authors is sizable (undergraduate engineering students), the level of performance of such workers is quite variable leading to data acquisition integrity and continuity issues - matters that are not acceptable in the practical field implementation of such developed systems. In the case of acquiring data from the numerous sensors within the civil structures which the authors have instrumented (e.g., a multistory building, roadway/railway bridges, and a hydroelectric dam), we have found that many of these concerns may be alleviated through the use of an automated data acquisition system which archives the acquired information in an electronic location remotely accessible through the Internet global computer network. It is therefore a possible for the data monitoring to be performed at a remote location with the only requirements for data acquisition being Internet accessibility. A description of the developed scheme is presented as well as guiding philosophies.

  2. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure

    PubMed Central

    Hollister, Kyle A.; Conner, Elizabeth S.; Zhang, Xinxing; Spell, Mark; Bernard, Gary M.; Patel, Pratik; de Carvalho, Ana Carolina G.V.; Butcher, Rebecca A.; Ragains, Justin R.

    2015-01-01

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This panel includes a number of natural ascarosides that were detected in crude pheromone extract, but as yet have no assigned function, as well as many unnatural ascaroside derivatives. Most of these ascarosides, some of which have significant structural similarity to the natural dauer pheromone components, have very little dauer-inducing activity. Our results provide a primer to ascaroside structure-activity relationships and suggest that slight modifications to ascaroside structure dramatically influence binding to the relevant G protein-coupled receptors that control dauer formation. PMID:23920482

  3. Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone.

    PubMed

    Arjunan, V; Devi, L; Subbalakshmi, R; Rani, T; Mohan, S

    2014-09-15

    The stable geometry of 2-hydroxy-4-methoxyacetophenone is optimised by DFT/B3LYP method with 6-311++G(∗∗) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry have been determined. The effects of substituents (hydroxyl, methoxy and acetyl groups) on the benzene ring vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of 2-hydroxy-4-methoxyacetophenone have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and assignments made are compared with the experimental values. The energies of important MO's, the total electron density and electrostatic potential of the compound are determined. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities are calculated. PMID:24792193

  4. Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Devi, L.; Subbalakshmi, R.; Rani, T.; Mohan, S.

    2014-09-01

    The stable geometry of 2-hydroxy-4-methoxyacetophenone is optimised by DFT/B3LYP method with 6-311++G∗∗ and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry have been determined. The effects of substituents (hydroxyl, methoxy and acetyl groups) on the benzene ring vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of 2-hydroxy-4-methoxyacetophenone have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and assignments made are compared with the experimental values. The energies of important MO’s, the total electron density and electrostatic potential of the compound are determined. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities are calculated.

  5. Development of new materials and structures based on managed physical-chemical factors of local interaction

    NASA Astrophysics Data System (ADS)

    Urakov, A. L.

    2016-04-01

    The paper states that assigning certain physical and chemical characteristics to pills and medical drugs solutions can substitute for the development of new drugs (which is essentially equivalent to the creation of new medicines). It is established that the purposeful change of physical and chemical characteristics of the standard ("old") materials (in other words, the known substances) is fundamental for the production of solid and liquid medicines, which allows us to get "new" structures and materials. The paper shows that assigning new physical and chemical properties to "old" materials and their further usage for the production of tablets and solutions from the "old" and well-known medicines can turn even very "old" medicine into very "novel" (moreover, even very fashionable) one with unprecedented (fantastic) pharmacological activity and new mechanisms of action.

  6. Chemical structure of wood charcoal by infrared spectroscopy and multivariate analysis.

    PubMed

    Labbé, Nicole; Harper, David; Rials, Timothy; Elder, Thomas

    2006-05-17

    In this work, the effect of temperature on charcoal structure and chemical composition is investigated for four tree species. Wood charcoal carbonized at various temperatures is analyzed by mid infrared spectroscopy coupled with multivariate analysis and by thermogravimetric analysis to characterize the chemical composition during the carbonization process. The multivariate models of charcoal were able to distinguish between species and wood thermal treatments, revealing that the characteristics of the wood charcoal depend not only on the wood species, but also on the carbonization temperature. This work demonstrates the potential of mid infrared spectroscopy in the whiskey industry, from the identification and classification of the wood species for the mellowing process to the chemical characterization of the barrels after the toasting and charring process. PMID:19127715

  7. Automated detection of structural alerts (chemical fragments) in (eco)toxicology

    PubMed Central

    Lepailleur, Alban; Poezevara, Guillaume; Bureau, Ronan

    2013-01-01

    This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (eco)toxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data. PMID:24688706

  8. 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.

  9. A novel predictor for protein structural class based on integrated information of the secondary structure sequence.

    PubMed

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang; Liu, Shuxia

    2014-08-01

    The structural class has become one of the most important features for characterizing the overall folding type of a protein and played important roles in many aspects of protein research. At present, it is still a challenging problem to accurately predict protein structural class for low-similarity sequences. In this study, an 18-dimensional integrated feature vector is proposed by fusing the information about content and position of the predicted secondary structure elements. The consistently high accuracies of jackknife and 10-fold cross-validation tests on different low-similarity benchmark datasets show that the proposed method is reliable and stable. Comparison of our results with other methods demonstrates that our method is an effective computational tool for protein structural class prediction, especially for low-similarity sequences. PMID:24859536

  10. The bulk and interfacial electronic and chemical structure of amorphous hydrogenated boron carbide

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

    The chemical and electronic structure, as related to the surface, interface and bulk of amorphous hydrogenated boron carbide (a-BxC:H y), is of interest in neutron detection and microelectronics. This dissertation investigates the chemical and electronic structure of semiconducting thin-film a-BxC:Hy grown by plasma enhanced chemical vapor deposition (PECVD) of ortho-carborane (1,2-C2B10H12). Experimental methods used include: x-ray and ultraviolet photoelectron spectroscopies (XPS/UPS) and x-ray absorption/emission spectroscopies (XAS/XES). These methods were used to investigate the chemical species, bonding and hybridizations, and band gaps of a-BxC:Hy prepared or treated under varying conditions. Additionally, a detailed examination of the formation of Schottky barriers was implemented. Throughout this dissertation the chemical structure was studied. One study was to understand various growth conditions. The effects of the PECVD growth parameters were evaluated by comparing changes in atomic percentages (at.%'s) between thin-films from various substrate temperatures. Additionally, detailed studies of the photoelectron core level under two different growth conditions were undertaken to evaluate the effects of pre-/post- argon ion etching (Ar+) for the following: the chemical structural change for both an as grown (AG) and in-situ thermal treatment (500°C), and post Ar+ etch of samples thermally treated ranging from as grown to 850°C. The as grown and in-situ treated samples were used in conjunction to determine the formation of the Schottky barrier. The electronic structure was determined by the changes within the valence band of the thermally treated samples and formation of Schottky barrier. Thermally treated samples (as grown to 850°C) were further evaluated with respect to their occupied and unoccupied electronic states. The atomic percentage gave a stoichiometry range for a-B xC:Hy (given as x=1.5 to 3.0 with y= decreases with thermal treatment and Oz: z

  11. Chemical diversity among populations of Mikania micrantha: geographic mosaic structure and herbivory.

    PubMed

    Bravo-Monzón, Angel Eliezer; Ríos-Vásquez, Eunice; Delgado-Lamas, Guillermo; Espinosa-García, Francisco J

    2014-01-01

    Populations of the same species vary in their secondary metabolite content. This variation has been attributed to biotic and abiotic environmental conditions as well as to historical factors. Some studies have focused on the geographic variation of chemical diversity in plant populations, but whether this structure conforms to a central-marginal model or a mosaic pattern remains unclear. Furthermore, assessing the chemical diversity of invasive plants in their native distribution facilitates the understanding of their relationships with natural enemies. We examined the geographic variation of chemical diversity in Mexican populations of the bittervine weed Mikania micrantha and its relationship to herbivore damage. The foliar volatile terpenoid blend was analyzed in 165 individuals of 14 populations in the Pacific and Gulf of Mexico tropical watersheds. A cluster analysis grouped individuals with similar terpenoid blends into 56 compositional types. Chemical diversity was measured using the number of compounds and their concentration within the blends for individuals, and the number and frequency of compositional types for populations. A stepwise multiple regression analysis performed with geographic, climatic, and chemical diversity variables explained herbivore damage. However, population-level chemical diversity was the only variable found to be significant (β = -0.79, P = 0.042) in the model (R(2) = 0.89). A Mantel test using Euclidean distances did not indicate any separation by geographic origin; however, four barriers were identified using Monmonier's algorithm. We conclude that variation in population-level chemical diversity follows a mosaic pattern in which geographic factors (i.e., natural barriers) have some effect and that variation is also associated with the local intensity of herbivore attack. PMID:23942983

  12. Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research

    PubMed Central

    Fourches, Denis; Muratov, Eugene; Tropsha, Alexander

    2010-01-01

    Molecular modelers and cheminformaticians typically analyze experimental data generated by other scientists. Consequently, when it comes to data accuracy, cheminformaticians are always at the mercy of data providers who may inadvertently publish (partially) erroneous data. Thus, dataset curation is crucial for any cheminformatics analysis such as similarity searching, clustering, QSAR modeling, virtual screening, etc., especially nowadays when the availability of chemical datasets in public domain has skyrocketed in recent years. Despite the obvious importance of this preliminary step in the computational analysis of any dataset, there appears to be no commonly accepted guidance or set of procedures for chemical data curation. The main objective of this paper is to emphasize the need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation. Herein, we discuss several simple but important steps for cleaning chemical records in a database including the removal of a fraction of the data that cannot be appropriately handled by conventional cheminformatics techniques. Such steps include the removal of inorganic and organometallic compounds, counterions, salts and mixtures; structure validation; ring aromatization; normalization of specific chemotypes; curation of tautomeric forms; and the deletion of duplicates. To emphasize the importance of data curation as a mandatory step in data analysis, we discuss several case studies where chemical curation of the original “raw” database enabled the successful modeling study (specifically, QSAR analysis) or resulted in a significant improvement of model's prediction accuracy. We also demonstrate that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds. We believe that good practices for curation of chemical records outlined in this paper will be of value to all

  13. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  14. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study.

    PubMed

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules. PMID:24013676

  15. 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…

  16. Studies on Brassica carinata seed. 2. Carbohydrate molecular structure in relation to carbohydrate chemical profile, energy values, and biodegradation characteristics.

    PubMed

    Xin, Hangshu; Falk, Kevin C; Yu, Peiqiang

    2013-10-23

    The objectives of this study were to investigate (1) the carbohydrate chemical profile, (2) the energy values, (3) the rumen neutral detergent fiber (NDF) degradation kinetics, (4) the carbohydrate-related functional group structural features using a Fourier transform infrared (FTIR) spectroscopic technique with attenuated total reflectance (ATR), and (5) the correlations between carbohydrate intrinsic structural features and nutritional profiles in three strains of Brassica carinata in yellow and brown seed coats, with comparison to canola seed as a reference. The results showed that yellow B. carinata strains 111000EM and AAC A100 were lower for contents of neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and carbohydrate (CHO) and higher for contents of total digestible nutrients (TDN), energy values, and effective degradable NDF (EDNDF) than brown-seeded 110915EM. In comparison, brown canola seed (Brassica napus L.) had more fiber content and less EDNDF. Also, carinata strains showed significantly different IR intensities in structural carbohydrate (SCHO), cellulosic compounds (CELC), and total CHO profiles. These structural variations might be one of the possible reasons for various fiber profile and biodegradation characteristics for ruminants in oilseeds. However, multivariate analyses within carbohydrate regions indicated there were still some structural relationships among the four oilseed samples. Moreover, the correlation study showed that the changes of CELC and CHO peak intensities were highly related with some changes in CHO chemical profile, energy values, and in situ NDF degradation kinetics in B. carinata and canola seeds. Further study with a large sample size is still necessary to figure out whether CHO molecular spectral information could be used to predict nutrient values and biological behavior in oilseeds. PMID:24059242

  17. Structural Evolution of SiC Films During Plasma-Assisted Chemical Vapour Deposition

    NASA Astrophysics Data System (ADS)

    Ding, Siye; Yan, Guanchao; Zhu, Xiaodong; Zhou, Haiyang

    2009-04-01

    Evolution of chemical bonding configurations for the films deposited from hexamethyldisiloxane (HMDSO) diluted with H2 during plasma assisted chemical vapour deposition is investigated. In the experiment a small amount of CH4 was added to adjust the plasma environment and modify the structure of the deposited films. The measurements of Raman spectroscopy and X-ray diffraction (XRD) revealed the production of 6H-SiC embedded in the amorphous matrix without the input of CH4. As CH4 was introduced into the deposition reaction, the transition of 6H-SiC to cubic SiC in the films took place, and also the film surfaces changed from a structure of ellipsoids to cauliflower-like shapes. With a further increase of CH4 in the flow ratio, the obtained films varied from Si-C bonding dominant to a sp2/sp3 carbon-rich composition.

  18. Chemical bonding and electronic structures at magnesium/copper phthalocyanine interfaces

    NASA Astrophysics Data System (ADS)

    Tang, J. X.; Lee, C. S.; Lee, S. T.

    2006-03-01

    Chemistry, electronic structure and electrical behavior at the interfaces between copper phthalocyanine (CuPc) and Mg with a reverse formation sequence were investigated using X-ray photoemission spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS), and current-voltage ( I- V) measurements. A chemical reaction occurs between CuPc and Mg irrespective of the deposition sequence. Despite having different reaction zone thicknesses, both the CuPc-on-Mg and the Mg-on-CuPc interfaces exhibit chemistry-induced gap states and identical carrier injection barriers, which are confirmed by the symmetric electrical behavior obtained from I- V characteristics of devices with a structure of Mg/CuPc/Mg. These findings contrast with those expected from physisorptive noble metal-CuPc interfaces and suggest that strong local chemical bonding is a primary factor determining molecular level alignment at reactive metal-CuPc interfaces.

  19. Three-dimensionality of space in the structure of the periodic table of chemical elements

    SciTech Connect

    Veremeichik, T. F.

    2006-07-15

    The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed.

  20. Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

    NASA Astrophysics Data System (ADS)

    Bai, Rekha; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K.

    2016-05-01

    Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.