WorldWideScience

Sample records for reaction pathway prevailing

  1. Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

    Directory of Open Access Journals (Sweden)

    Yiran Huang

    Full Text Available Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

  2. Combustion kinetics and reaction pathways

    Energy Technology Data Exchange (ETDEWEB)

    Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)

    1993-12-01

    This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

  3. Explorations into Chemical Reactions and Biochemical Pathways.

    Science.gov (United States)

    Gasteiger, Johann

    2016-12-01

    A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

    Science.gov (United States)

    Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

    2016-02-01

    Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.

  5. Kynurenine pathway metabolites and enzymes involved in redox reactions.

    Science.gov (United States)

    González Esquivel, D; Ramírez-Ortega, D; Pineda, B; Castro, N; Ríos, C; Pérez de la Cruz, V

    2017-01-01

    Oxido-reduction reactions are a fundamental part of the life due to support many vital biological processes as cellular respiration and glucose oxidation. In the redox reactions, one substance transfers one or more electrons to another substance. An important electron carrier is the coenzyme NAD + , which is involved in many metabolic pathways. De novo biosynthesis of NAD + is through the kynurenine pathway, the major route of tryptophan catabolism, which is sensitive to redox environment and produces metabolites with redox capacity, able to alter biological functions that are controlled by redox-responsive signaling pathways. Kynurenine pathway metabolites have been implicated in the physiology process and in the physiopathology of many diseases; processes that also share others factors as dysregulation of calcium homeostasis, mitochondrial dysfunction, oxidative stress, inflammation and cell death, which impact the redox environment. This review examines in detail the available evidence in which kynurenine pathway metabolites participate in redox reactions and their effect on cellular redox homeostasis, since the knowledge of the main factors and mechanisms that lead to cell death in many neurodegenative disorders and other pathologies, such as mitochondrial dysfunction, oxidative stress and kynurenines imbalance, will allow to develop therapies using them as targets. This article is part of the Special Issue entitled 'The Kynurenine Pathway in Health and Disease'. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Minimum Energy Pathways for Chemical Reactions

    Science.gov (United States)

    Walch, S. P.; Langhoff, S. R. (Technical Monitor)

    1995-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

  7. A multi-pathway model for photosynthetic reaction center

    International Nuclear Information System (INIS)

    Qin, M.; Shen, H. Z.; Yi, X. X.

    2016-01-01

    Charge separation occurs in a pair of tightly coupled chlorophylls at the heart of photosynthetic reaction centers of both plants and bacteria. Recently it has been shown that quantum coherence can, in principle, enhance the efficiency of a solar cell, working like a quantum heat engine. Here, we propose a biological quantum heat engine (BQHE) motivated by Photosystem II reaction center (PSII RC) to describe the charge separation. Our model mainly considers two charge-separation pathways which is more than that typically considered in the published literature. We explore how these cross-couplings increase the current and power of the charge separation and discuss the effects of multiple pathways in terms of current and power. The robustness of the BQHE against the charge recombination in natural PSII RC and dephasing induced by environments is also explored, and extension from two pathways to multiple pathways is made. These results suggest that noise-induced quantum coherence helps to suppress the influence of acceptor-to-donor charge recombination, and besides, nature-mimicking architectures with engineered multiple pathways for charge separations might be better for artificial solar energy devices considering the influence of environments.

  8. Identifying Reaction Pathways and their Environments

    DEFF Research Database (Denmark)

    Maronsson, Jon Bergmann

    Finding the mechanisms and estimating the rate of chemical reactions is an essential part of modern research of atomic scale systems. In this thesis, the application of well established methods for reaction rates and paths to important systems for hydrogen storage is considered before developing...... extensions to further identify the reaction environment for a more accurate rate. Complex borohydrides are materials of high hydrogen storage capacity and high thermodynamic stability (too high for hydrogen storage). In an effort to gain insight into the structural transitions of two such materials, Ca(BH4......-interstitial defects. In good agreement with the experiments, C3-type rotations activate at lower temperature than C2-type rotations. In order to investigate the environment of reaction pathways, a method for finding the ridge between first order saddle points on a multidimensional surface was developed...

  9. Serpentinization reaction pathways: implications for modeling approach

    Energy Technology Data Exchange (ETDEWEB)

    Janecky, D.R.

    1986-01-01

    Experimental seawater-peridotite reaction pathways to form serpentinites at 300/sup 0/C, 500 bars, can be accurately modeled using the EQ3/6 codes in conjunction with thermodynamic and kinetic data from the literature and unpublished compilations. These models provide both confirmation of experimental interpretations and more detailed insight into hydrothermal reaction processes within the oceanic crust. The accuracy of these models depends on careful evaluation of the aqueous speciation model, use of mineral compositions that closely reproduce compositions in the experiments, and definition of realistic reactive components in terms of composition, thermodynamic data, and reaction rates.

  10. Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

    Science.gov (United States)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

  11. Multistage reaction pathways in detonating high explosives

    International Nuclear Information System (INIS)

    Li, Ying; Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya

    2014-01-01

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N 2 and H 2 O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N 2 and H 2 O productions

  12. Multistage reaction pathways in detonating high explosives

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States); Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Kalia, Rajiv K.; Nakano, Aiichiro; Nomura, Ken-ichi; Vashishta, Priya [Collaboratory for Advanced Computing and Simulations, Department of Physics and Astronomy, Department of Computer Science, and Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-0242 (United States)

    2014-11-17

    Atomistic mechanisms underlying the reaction time and intermediate reaction products of detonating high explosives far from equilibrium have been elusive. This is because detonation is one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. Here, large spatiotemporal-scale reactive molecular dynamics simulations validated by quantum molecular dynamics simulations reveal a two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine crystal. Rapid production of N{sub 2} and H{sub 2}O within ∼10 ps is followed by delayed production of CO molecules beyond ns. We found that further decomposition towards the final products is inhibited by the formation of large metastable carbon- and oxygen-rich clusters with fractal geometry. In addition, we found distinct unimolecular and intermolecular reaction pathways, respectively, for the rapid N{sub 2} and H{sub 2}O productions.

  13. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  14. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy

  15. 12 CFR 747.603 - Prevailing party.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Prevailing party. 747.603 Section 747.603 Banks... in NCUA Board Adjudications § 747.603 Prevailing party. An eligible applicant may be a “prevailing... dismissed. In appropriate situations an applicant may also have prevailed if the outcome of the proceeding...

  16. Stepwise radical cation Diels-Alder reaction via multiple pathways.

    Science.gov (United States)

    Shimizu, Ryo; Okada, Yohei; Chiba, Kazuhiro

    2018-01-01

    Herein we disclose the radical cation Diels-Alder reaction of aryl vinyl ethers by electrocatalysis, which is triggered by an oxidative SET process. The reaction clearly proceeds in a stepwise fashion, which is a rare mechanism in this class. We also found that two distinctive pathways, including "direct" and "indirect", are possible to construct the Diels-Alder adduct.

  17. Density Functional Theory Study of Competitive Reaction Pathways of Ti+ with Fluorinated Acetone in the Gas Phase

    International Nuclear Information System (INIS)

    Hong, Kiryong; Kim, Tae Kyu

    2012-01-01

    We investigate the doublet and quartet potential energy surfaces associated with the gas-phase reaction between Ti + and CF 3 COCH 3 for two plausible reaction pathways, TiF 2 + and TiO + formation pathways by using the density functional theory (DFT) method. The molecular structures of intermediates and transition states involved in these reaction pathways are optimized at the DFT level by using the PBE0 functional. All transition states are identified by using the intrinsic reaction coordinate (IRC) method, and the resulting reaction coordinates describe how Ti + activates CF 3 COCH 3 and produces TiF 2 + and TiO + as products. On the basis of presented results, we propose the most favorable reaction pathway in the reaction between Ti + and CF 3 COCH 3

  18. 12 CFR 263.102 - Prevailing party.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Prevailing party. 263.102 Section 263.102 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM RULES... Prevailing party. Only an eligible applicant that prevailed on the merits of an adversary proceeding may...

  19. 12 CFR 308.173 - Prevailing party.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Prevailing party. 308.173 Section 308.173 Banks....173 Prevailing party. (a) General rule. An eligible applicant who, following an adversary adjudication has gained victory on the merits in the proceeding is a “prevailing party”. An eligible applicant may...

  20. Financing Educational Facility Construction: Prevailing Wage Litigation.

    Science.gov (United States)

    Goldblatt, Steven M.; Wood, R. Craig

    This chapter presents an up-to-date analysis of prevailing state wage laws that affect educational facility construction or renovation and highlights relevant prevailing wage litigation in many states. Currently, 13 states have no prevailing wage laws for public works. The other 37 states and the District of Columbia do have prevailing wage laws…

  1. Permanganate oxidation of α-amino acids: kinetic correlations for the nonautocatalytic and autocatalytic reaction pathways.

    Science.gov (United States)

    Perez-Benito, Joaquin F

    2011-09-08

    The reactions of permanganate ion with seven α-amino acids in aqueous KH(2)PO(4)/K(2)HPO(4) buffers have been followed spectrophotometrically at two different wavelengths: 526 nm (decay of MnO(4)(-)) and 418 nm (formation of colloidal MnO(2)). All of the reactions studied were autocatalyzed by colloidal MnO(2), with the contribution of the autocatalytic reaction pathway decreasing in the order glycine > l-threonine > l-alanine > l-glutamic acid > l-leucine > l-isoleucine > l-valine. The rate constants corresponding to the nonautocatalytic and autocatalytic pathways were obtained by means of either a differential rate law or an integrated one, the latter requiring the use of an iterative method for its implementation. The activation parameters for the two pathways were determined and analyzed to obtain statistically significant correlations for the series of reactions studied. The activation enthalpy of the nonautocatalytic pathway showed a strong, positive dependence on the standard Gibbs energy for the dissociation of the protonated amino group of the α-amino acid. Linear enthalpy-entropy correlations were found for both pathways, leading to isokinetic temperatures of 370 ± 21 K (nonautocatalytic) and 364 ± 28 K (autocatalytic). Mechanisms in agreement with the experimental data are proposed for the two reaction pathways.

  2. RhoA/ROCK Signaling Pathway Mediates Shuanghuanglian Injection-Induced Pseudo-allergic Reactions.

    Science.gov (United States)

    Han, Jiayin; Zhao, Yong; Zhang, Yushi; Li, Chunying; Yi, Yan; Pan, Chen; Tian, Jingzhuo; Yang, Yifei; Cui, Hongyu; Wang, Lianmei; Liu, Suyan; Liu, Jing; Deng, Nuo; Liang, Aihua

    2018-01-01

    Background: Shuanghuanglian injection (SHLI) is a famous Chinese medicine used as an intravenous preparation for the treatment of acute respiratory tract infections. In the recent years, the immediate hypersensitivity reactions induced by SHLI have attracted broad attention. However, the mechanism involved in these reactions has not yet been elucidated. The present study aims to explore the characteristics of the immediate hypersensitivity reactions induced by SHLI and deciphers the role of the RhoA/ROCK signaling pathway in these reactions. Methods: SHLI-immunized mice or naive mice were intravenously injected (i.v.) with SHLI (600 mg/kg) once, and vascular leakage in the ears was evaluated. Passive cutaneous anaphylaxis test was conducted using sera collected from SHLI-immunized mice. Naive mice were administered (i.v.) with a single dose of 150, 300, or 600 mg/kg of SHLI, and vascular leakage, histamine release, and histopathological alterations in the ears, lungs, and intestines were tested. In vitro , human umbilical vein endothelial cell (HUVEC) monolayer was incubated with SHLI (0.05, 0.1, or 0.15 mg/mL), and the changes in endothelial permeability and cytoskeleton were observed. Western blot analysis was performed and ROCK inhibitor was employed to investigate the contribution of the RhoA/ROCK signaling pathway in SHLI-induced hypersensitivity reactions, both in HUVECs and in mice. Results: Our results indicate that SHLI was able to cause immediate dose-dependent vascular leakage, edema, and exudates in the ears, lungs, and intestines, and histamine release in mice. These were pseudo-allergic reactions, as SHLI-specific IgE was not elicited during sensitization. In addition, SHLI induced reorganization of actin cytoskeleton and disrupted the endothelial barrier. The administration of SHLI directly activated the RhoA/ROCK signaling pathway both in HUVECs and in the ears, lungs, and intestines of mice. Fasudil hydrochloride, a ROCK inhibitor, ameliorated the

  3. Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

    DEFF Research Database (Denmark)

    Jin, Biao; Rolle, Massimo

    2016-01-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework ...

  4. Epistaxis: Prevailing Factors and Treatment

    Directory of Open Access Journals (Sweden)

    Secchi, Myrian Marajó Dal

    2009-12-01

    Full Text Available Introduction: The epistaxis is one the most frequent otorhinolaryngologic emergencies in the medical practice. It is a benign affection, but the refractory cases require hospital admission. Objective: To evaluate prevailing factors in patients with epistaxis and treatment. Form of study: Retrospective study. Method: 60 patients with diagnosis of epistaxis were evaluated and they needed hospital admission between 2005 and 2006. Results: The main prevailing factors were: Systemic arterial hypertension 36% (n= 22, trauma 16% (n=10 and coagulopathy 5% (n=3. The treatment was the use of nasal splint: anterior 58% (n=35 and antero-posterior 27% (n=16, the electrocauterization of the identified bloody point 7% (n=4, endoscopic arterial bandage 8% (n=5 in severe epistaxis. For the patients with antero-posterior splint with recurrence of bleeding in the first 24 hours (five patients, after clinical stabilization, an arterial bandage was indicated by endoscopic means; four patients had systemic arterial hypertension and in one patient no prevailing factor was identified. Conclusion: The main associated prevailing factors were systemic arterial hypertension, trauma and coagulopathy. The treatment depends on the type, severity and cause of bleeding, initially the anterior and antero-posterior splint for bleeding control. The early endoscopic arterial bandage is indicated in patients with severe epistaxis and prevailing factors, and prolonged admission and morbidities associated with nasal splint should be avoided.

  5. A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text

    Science.gov (United States)

    Miwa, Makoto; Ohta, Tomoko; Rak, Rafal; Rowley, Andrew; Kell, Douglas B.; Pyysalo, Sampo; Ananiadou, Sophia

    2013-01-01

    Motivation: To create, verify and maintain pathway models, curators must discover and assess knowledge distributed over the vast body of biological literature. Methods supporting these tasks must understand both the pathway model representations and the natural language in the literature. These methods should identify and order documents by relevance to any given pathway reaction. No existing system has addressed all aspects of this challenge. Method: We present novel methods for associating pathway model reactions with relevant publications. Our approach extracts the reactions directly from the models and then turns them into queries for three text mining-based MEDLINE literature search systems. These queries are executed, and the resulting documents are combined and ranked according to their relevance to the reactions of interest. We manually annotate document-reaction pairs with the relevance of the document to the reaction and use this annotation to study several ranking methods, using various heuristic and machine-learning approaches. Results: Our evaluation shows that the annotated document-reaction pairs can be used to create a rule-based document ranking system, and that machine learning can be used to rank documents by their relevance to pathway reactions. We find that a Support Vector Machine-based system outperforms several baselines and matches the performance of the rule-based system. The success of the query extraction and ranking methods are used to update our existing pathway search system, PathText. Availability: An online demonstration of PathText 2 and the annotated corpus are available for research purposes at http://www.nactem.ac.uk/pathtext2/. Contact: makoto.miwa@manchester.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813008

  6. On the deduction of chemical reaction pathways from measurements of time series of concentrations.

    Science.gov (United States)

    Samoilov, Michael; Arkin, Adam; Ross, John

    2001-03-01

    We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.

  7. Competing retention pathways of uranium upon reaction with Fe(II)

    Science.gov (United States)

    Massey, Michael S.; Lezama-Pacheco, Juan S.; Jones, Morris E.; Ilton, Eugene S.; Cerrato, José M.; Bargar, John R.; Fendorf, Scott

    2014-10-01

    Biogeochemical retention processes, including adsorption, reductive precipitation, and incorporation into host minerals, are important in contaminant transport, remediation, and geologic deposition of uranium. Recent work has shown that U can become incorporated into iron (hydr)oxide minerals, with a key pathway arising from Fe(II)-induced transformation of ferrihydrite, (Fe(OH)3·nH2O) to goethite (α-FeO(OH)); this is a possible U retention mechanism in soils and sediments. Several key questions, however, remain unanswered regarding U incorporation into iron (hydr)oxides and this pathway's contribution to U retention, including: (i) the competitiveness of U incorporation versus reduction to U(IV) and subsequent precipitation of UO2; (ii) the oxidation state of incorporated U; (iii) the effects of uranyl aqueous speciation on U incorporation; and, (iv) the mechanism of U incorporation. Here we use a series of batch reactions conducted at pH ∼7, [U(VI)] from 1 to 170 μM, [Fe(II)] from 0 to 3 mM, and [Ca] at 0 or 4 mM coupled with spectroscopic examination of reaction products of Fe(II)-induced ferrihydrite transformation to address these outstanding questions. Uranium retention pathways were identified and quantified using extended X-ray absorption fine structure (EXAFS) spectroscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. Analysis of EXAFS spectra showed that 14-89% of total U was incorporated into goethite, upon reaction with Fe(II) and ferrihydrite. Uranium incorporation was a particularly dominant retention pathway at U concentrations ⩽50 μM when either uranyl-carbonato or calcium-uranyl-carbonato complexes were dominant, accounting for 64-89% of total U. With increasing U(VI) and Fe(II) concentrations, U(VI) reduction to U(IV) became more prevalent, but U incorporation remained a functioning retention pathway. These findings highlight the potential importance of U(V) incorporation within iron

  8. Reactivity of Single-Walled Carbon Nanotubes in the Diels-Alder Cycloaddition Reaction: Distortion-Interaction Analysis along the Reaction Pathway.

    Science.gov (United States)

    Li, Yingzi; Osuna, Sílvia; Garcia-Borràs, Marc; Qi, Xiaotian; Liu, Song; Houk, Kendall N; Lan, Yu

    2016-08-26

    Diels-Alder cycloaddition is one of the most powerful tools for the functionalization of single-walled carbon nanotubes (SWCNTs). Density functional theory at the B3-LYP level of theory has been used to investigate the reactivity of different-diameter SWCNTs (4-9,5) in Diels-Alder reactions with 1,3-butadiene; the reactivity was found to decrease with increasing SWCNT diameter. Distortion/interaction analysis along the whole reaction pathway was found to be a better way to explore the reactivity of this type of reaction. The difference in interaction energy along the reaction pathway is larger than that of the corresponding distortion energy. However, the distortion energy plots for these reactions show the same trend. Therefore, the formation of the transition state can be determined from the interaction energy. A lower interaction energy leads to an earlier transition state, which indicates a lower activation energy. The computational results also indicate that the original distortion of the SWCNTs leads to an increase in the reactivity of the SWCNTs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. 29 CFR 505.3 - Prevailing minimum compensation.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Prevailing minimum compensation. 505.3 Section 505.3 Labor... HUMANITIES § 505.3 Prevailing minimum compensation. (a)(1) In the absence of an alternative determination...)(2) of this section, the prevailing minimum compensation required to be paid under the Act to the...

  10. 26 CFR 301.7430-5 - Prevailing party.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Prevailing party. 301.7430-5 Section 301.7430-5... Prevailing party. (a) In general. For purposes of an award of reasonable administrative costs under section... prevailing party only if— (1) The position of the Internal Revenue Service was not substantially justified...

  11. Exploring the Reaction Pathways of Bioglycerol Hydrodeoxygenation to Propene over Molybdena-Based Catalysts.

    Science.gov (United States)

    Zacharopoulou, Vasiliki; Vasiliadou, Efterpi S; Lemonidou, Angeliki A

    2018-01-10

    The one-step reaction of glycerol with hydrogen to form propene selectively is a particularly challenging catalytic pathway that has not yet been explored thoroughly. Molybdena-based catalysts are active and selective to C-O bond scission; propene is the only product in the gas phase under the standard reaction conditions, and further hydrogenation to propane is impeded. Within this context, this work focuses on the exploration of the reaction pathways and the investigation of various parameters that affect the catalytic performance, such as the role of hydrogen on the product distribution and the effect of the catalyst pretreatment step. Under a hydrogen atmosphere, propene is produced primarily via 2-propenol, whereas under an inert atmosphere propanal and glycerol dissociation products are formed mainly. The reaction most likely proceeds through a reverse Mars-van Krevelen mechanism as partially reduced Mo species drive the reaction to the formation of the desired product. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Reaction pathways for catalytic gas-phase oxidation of glycerol over mixed metal oxides

    Energy Technology Data Exchange (ETDEWEB)

    Suprun, W.; Glaeser, R.; Papp, H. [Leipzig Univ. (Germany). Inst. of Chemical Technology

    2011-07-01

    Glycerol as a main by-product from bio-diesel manufacture is a cheap raw material with large potential for chemical or biochemical transformations to value-added C3-chemicals. One possible way of glycerol utilization involves its catalytic oxidation to acrylic acid as an alternative to petrochemical routes. However, this catalytic conversion exhibits various problems such as harsh reaction conditions, severe catalyst coking and large amounts of undesired by-products. In this study, the reaction pathways for gas-phase conversion of glycerol over transition metal oxides (Mo, V und W) supported on TiO{sub 2} and SiO{sub 2} were investigated by two methods: (i) steady state experiments of glycerol oxidation and possible reactions intermediates, i.e., acrolein, 3-hydroxy propionaldehyde and acetaldehyde, and (ii) temperature-programmed surface reaction (TPSR) studies of glycerol conversion in the presence and in the absence of gas-phase oxygen. It is shown that the supported W-, V and Mo-oxides possess an ability to catalyze the oxidation of glycerol to acrylic acid. These investigations allowed us to gain a deeper insight into the reaction mechanism. Thus, based on the obtained results, three possible reactions pathways for the selective oxidation of glycerol to acrylic acid on the transition metal-containing catalysts are proposed. The major pathways in presence of molecular oxygen are a fast successive destructive oxidation of glycerol to CO{sub x} and the dehydration of glycerol to acrolein which is a rate-limiting step. (orig.)

  13. Pathways of the Maillard reaction under physiological conditions.

    Science.gov (United States)

    Henning, Christian; Glomb, Marcus A

    2016-08-01

    Initially investigated as a color formation process in thermally treated foods, nowadays, the relevance of the Maillard reaction in vivo is generally accepted. Many chronic and age-related diseases such as diabetes, uremia, atherosclerosis, cataractogenesis and Alzheimer's disease are associated with Maillard derived advanced glycation endproducts (AGEs) and α-dicarbonyl compounds as their most important precursors in terms of reactivity and abundance. However, the situation in vivo is very challenging, because Maillard chemistry is paralleled by enzymatic reactions which can lead to both, increases and decreases in certain AGEs. In addition, mechanistic findings established under the harsh conditions of food processing might not be valid under physiological conditions. The present review critically discusses the relevant α-dicarbonyl compounds as central intermediates of AGE formation in vivo with a special focus on fragmentation pathways leading to formation of amide-AGEs.

  14. Reaction pathways of the dissociation of methylal: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Frey, H -M; Beaud, P; Gerber, T; Mischler, B; Radi, P P; Tzannis, A -P [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    Schemata for modelling combustion processes do not yet include reaction rates for oxygenated fuels like methylal (DMM) which is considered as an additive or replacement for diesel due to its low sooting propensity. Density functional theory (DFT) studies of the possible reaction pathways for different dissociation steps of methylal are presented. Cleavage of a hydrogen bond to the methoxy group or the central carbon atom were simulated at the BLYP/6-311++G{sup **} level of theory. The results are compared to the experiment when dissociating and/or ionising DMM with femtosecond pulses. (author) 1 fig., 1 tab., 1 ref.

  15. Position-specific isotope modeling of organic micropollutants transformation through different reaction pathways

    International Nuclear Information System (INIS)

    Jin, Biao; Rolle, Massimo

    2016-01-01

    The degradation of organic micropollutants occurs via different reaction pathways. Compound specific isotope analysis is a valuable tool to identify such degradation pathways in different environmental systems. We propose a mechanism-based modeling approach that provides a quantitative framework to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. To demonstrate specific features of the modeling approach, we simulated the degradation of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model accurately reproduces the multi-element isotope data observed in previous experimental studies. Furthermore, it precisely captures the dual element isotope trends characteristic of different reaction pathways as well as their range of variation consistent with observed bulk isotope fractionation. It was also possible to directly validate the model capability to predict the evolution of position-specific isotope ratios with available experimental data. Therefore, the approach is useful both for a mechanism-based evaluation of experimental results and as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. - Highlights: • Mechanism-based, position-specific isotope modeling of micropollutants degradation. • Simultaneous description of concentration and primary and secondary isotope effects. • Key features of the model are demonstrated with three illustrative examples. • Model as a tool to explore reaction mechanisms and to design experiments. - We propose a modeling approach incorporating mechanistic information and

  16. Reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma

    Science.gov (United States)

    Zhao, Yuefeng; Wang, Chao; Li, Li; Wang, Lijuan; Pan, Jie

    2018-03-01

    In this work, a two-dimensional fluid model is built up to numerically investigate the reaction pathways of producing and losing particles in atmospheric pressure methane nanosecond pulsed needle-plane discharge plasma. The calculation results indicate that the electron collisions with CH4 are the key pathways to produce the neutral particles CH2 and CH as well as the charged particles e and CH3+. CH3, H2, H, C2H2, and C2H4 primarily result from the reactions between the neutral particles and CH4. The charge transfer reactions are the significant pathways to produce CH4+, C2H2+, and C2H4+. As to the neutral species CH and H and the charged species CH3+, the reactions between themselves and CH4 contribute to substantial losses of these particles. The ways responsible for losing CH3, H2, C2H2, and C2H4 are CH3 + H → CH4, H2 + CH → CH2 + H, CH4+ + C2H2 → C2H2+ + CH4, and CH4+ + C2H4 → C2H4+ + CH4, respectively. Both electrons and C2H4+ are consumed by the dissociative electron-ion recombination reactions. The essential reaction pathways of losing CH4+ and C2H2+ are the charge transfer reactions.

  17. Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

    Science.gov (United States)

    Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

    1994-01-01

    Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

  18. 29 CFR 525.10 - Prevailing wage rates.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 3 2010-07-01 2010-07-01 false Prevailing wage rates. 525.10 Section 525.10 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR DIVISION, DEPARTMENT OF LABOR REGULATIONS EMPLOYMENT OF WORKERS WITH DISABILITIES UNDER SPECIAL CERTIFICATES § 525.10 Prevailing wage rates. (a) A...

  19. Federal Prevailing Rate Advisory Committee (FPRAC) Annual Reports

    Data.gov (United States)

    Office of Personnel Management — Annual reports of the Federal Prevailing Rate Advisory Committee (FPRAC), which studies the prevailing (market) rate system for wages and other matters pertinent to...

  20. 29 CFR 4.51 - Prevailing in the locality determinations.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 1 2010-07-01 2010-07-01 true Prevailing in the locality determinations. 4.51 Section 4.51... Procedures § 4.51 Prevailing in the locality determinations. (a) Information considered. The minimum monetary... benefits contained in collective bargaining agreements where they have been determined to prevail in a...

  1. Kinetic and reaction pathways of methanol oxidation on platinum

    International Nuclear Information System (INIS)

    McCabe, R.W.; McCready, D.F.

    1986-01-01

    Methanol oxidation kinetics were measured on Pt wires in a flow reactor at pressures between 30 and 130 Pa. The kinetics were measured as a function of oxygen-to-methanol equivalence ratio phi and wire temperature. In methanol-lean feeds (phi 2 CO, CO 2 , and H 2 O were the only products; in methanol-rich feeds (phi > 1), CO, H 2 , H 2 CO, CO 2 , and H 2 O were observed. Experiments with 18 O 2 showed that the principal methanol oxidation pathway does not involve C-O bond dissociation. However, the 18 O 2 experiments, together with other features of the methanol oxidation data, also provided evidence for a minor oxidation pathway (accounting for less than 1% of the product CO 2 ) which proceeds through a carbon intermediate. A mathematical model is presented which describes the principal CH 3 OH oxidation pathway as a series reaction involving adsorbed H 2 CO and CO intermediates. Consistent with experimental results, the model predicts that inhibition by adsorbed CO should be weaker for CH 3 OH and H 2 CO oxidation than for CO oxidation. 34 references, 10 figures, 2 tables

  2. Hydrogen oxidation mechanisms on Ni/yttria stabilized zirconia anodes: Separation of reaction pathways by geometry variation of pattern electrodes

    Science.gov (United States)

    Doppler, M. C.; Fleig, J.; Bram, M.; Opitz, A. K.

    2018-03-01

    Nickel/yttria stabilized zirconia (YSZ) electrodes are affecting the overall performance of solid oxide fuel cells (SOFCs) in general and strongly contribute to the cell resistance in case of novel metal supported SOFCs in particular. The electrochemical fuel conversion mechanisms in these electrodes are, however, still only partly understood. In this study, micro-structured Ni thin film electrodes on YSZ with 15 different geometries are utilized to investigate reaction pathways for the hydrogen electro-oxidation at Ni/YSZ anodes. From electrodes with constant area but varying triple phase boundary (TPB) length a contribution to the electro-catalytic activity is found that does not depend on the TPB length. This additional activity could clearly be attributed to a yet unknown reaction pathway scaling with the electrode area. It is shown that this area related pathway has significantly different electrochemical behavior compared to the TPB pathway regarding its thermal activation, sulfur poisoning behavior, and H2/H2O partial pressure dependence. Moreover, possible reaction mechanisms of this reaction pathway are discussed, identifying either a pathway based on hydrogen diffusion through Ni with water release at the TPB or a path with oxygen diffusion through Ni to be a very likely explanation for the experimental results.

  3. Reaction-transport simulations of non-oxidative methane conversion with continuous hydrogen removal: Homogeneous-heterogeneous methane reaction pathways

    International Nuclear Information System (INIS)

    Li, Lin; Borry, Richard W.; Iglesia, Enrique

    2000-01-01

    Detailed kinetic-transport models were used to explore thermodynamic and kinetic barriers in the non-oxidative conversion of CH4 via homogeneous and homogeneous-heterogeneous pathways and the effects of continuous hydrogen removal and of catalytic sites on attainable yields of useful C2-C10 products. The homogeneous kinetic model combines separately developed models for low-conversion pyrolysis and for chain growth to form large aromatics and carbon. The H2 formed in the reaction decreases CH4 pyrolysis rates and equilibrium conversions and it favors the formation of lighter products. The removal of H2 along tubular reactors with permeable walls increases reaction rates and equilibrium CH4 conversions. C2-C10 yields reach values greater than 90 percent at intermediate values of dimensionless transport rates (delta=1-10), defined as the ratio hydrogen transport and methane conversion rates. Homogeneous reactions require impractical residence times, even with H2 removal, because of slow initiation and chain transfer rates. The introduction of heterogeneous chain initiation pathways using surface sites that form methyl radicals eliminates the induction period without influencing the homogeneous product distribution. Methane conversion, however, occurs predominately in the chain transfer regime, within which individual transfer steps and the formation of C2 intermediates become limited by thermodynamic constraints. Catalytic sites alone cannot overcome these constraints. Catalytic membrane reactors with continuous H2 removal remove these thermodynamic obstacles and decrease the required residence time. Reaction rates become limited by homogeneous reactions of C2 products to form C6+ aromatics. Higher delta values lead to subsequent conversion of the desired C2-C10 products to larger polynuclear aromatics. We conclude that catalytic methane pyrolysis at the low temperatures required for restricted chain growth and the elimination of thermodynamics constraints via

  4. Gas-Phase Reaction Pathways and Rate Coefficients for the Dichlorosilane-Hydrogen and Trichlorosilane-Hydrogen Systems

    Science.gov (United States)

    Dateo, Christopher E.; Walch, Stephen P.

    2002-01-01

    As part of NASA Ames Research Center's Integrated Process Team on Device/Process Modeling and Nanotechnology our goal is to create/contribute to a gas-phase chemical database for use in modeling microelectronics devices. In particular, we use ab initio methods to determine chemical reaction pathways and to evaluate reaction rate coefficients. Our initial studies concern reactions involved in the dichlorosilane-hydrogen (SiCl2H2--H2) and trichlorosilane-hydrogen (SiCl2H-H2) systems. Reactant, saddle point (transition state), and product geometries and their vibrational harmonic frequencies are determined using the complete-active-space self-consistent-field (CASSCF) electronic structure method with the correlation consistent polarized valence double-zeta basis set (cc-pVDZ). Reaction pathways are constructed by following the imaginary frequency mode of the saddle point to both the reactant and product. Accurate energetics are determined using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations (CCSD(T)) extrapolated to the complete basis set limit. Using the data from the electronic structure calculations, reaction rate coefficients are obtained using conventional and variational transition state and RRKM theories.

  5. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

    KAUST Repository

    Kuwahara, Hiroyuki; Alazmi, Meshari; Cui, Xuefeng; Gao, Xin

    2016-01-01

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

  6. MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind

    KAUST Repository

    Kuwahara, Hiroyuki

    2016-04-29

    To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.

  7. The PREVAIL Study

    DEFF Research Database (Denmark)

    Evans, Christopher P; Higano, Celestia S; Keane, Thomas

    2016-01-01

    BACKGROUND: Enzalutamide, an oral androgen receptor inhibitor, significantly improved overall survival (OS) and radiographic progression-free survival (rPFS) versus placebo in the PREVAIL trial of men with chemotherapy-naïve metastatic castration-resistant prostate cancer. OBJECTIVE: To assess...... in men with chemotherapy-naïve metastatic castration-resistant prostate cancer, with or without visceral disease, low- or high-volume bone disease, or lymph node only disease. PATIENT SUMMARY: Patients with metastatic castration-resistant prostate cancer-including those with or without visceral disease...

  8. The role of grain boundaries and transient porosity increase as fluid pathways for reaction front propagation

    Science.gov (United States)

    Jonas, Laura; John, Timm; Geisler, Thorsten; Putnis, Andrew

    2013-04-01

    The pseudomorphic replacement of Carrara marble by calcium phosphates was studied as a model system to examine the influence of different fluid pathways for reaction front propagation induced by fluid-rock interaction. In this model system, the grain boundaries present in the rock and the transient porosity structures developing throughout the replacement reaction enable the reaction front to progress further into the rock as well as to the center of each single grain until complete transformation. Hydrothermal treatment of the marble using phosphate bearing solutions at temperature levels of 150° C and 200° C for different durations lead to the formation of two product phases which were identified as hydroxyapatite [Ca5(PO4)3OH] as well as β-tricalcium phosphate [β-Ca3(PO4)2] (β-TCP). The formation of β-TCP was probably favored by the presence of ~0.6wt.% of Mg in the parent phase. Completely transformed single grains show a distinctive zoning, both in composition and texture. Whereas areas next to the grain boundary consist of nearly pure hydroxyapatite and show a coarse porosity, areas close to the center of the single grains show a high amount of β-TCP and a very fine porous microstructure. If F was added as an additional solution component, the formation of β-TCP was avoided and up to 3wt.% of F were incorporated into the product apatite. The use of the isotope 18O as a chronometer for the replacement reaction makes it possible to reconstruct the chronological development of the calcium phosphate reaction front. Raman analysis revealed that the incorporation of 18O in the PO4 tetrahedron of hydroxyapatite results in the development of distinct profiles in the calcium phosphate reaction front perpendicular to the grain boundaries of the marble. Through the use of the 18O chronometer, it is possible to estimate and compare the time effectiveness of the different fluid pathways in this model system. The results show that the grain boundaries serve as a

  9. Reaction pathways of model compounds of biomass-derived oxygenates on Fe/Ni bimetallic surfaces

    Science.gov (United States)

    Yu, Weiting; Chen, Jingguang G.

    2015-10-01

    Controlling the activity and selectivity of converting biomass-derivatives to fuels and valuable chemicals is critical for the utilization of biomass feedstocks. There are primarily three classes of non-food competing biomass, cellulose, hemicellulose and lignin. In the current work, glycolaldehyde, furfural and acetaldehyde are studied as model compounds of the three classes of biomass-derivatives. Monometallic Ni(111) and monolayer (ML) Fe/Ni(111) bimetallic surfaces are studied for the reaction pathways of the three biomass surrogates. The ML Fe/Ni(111) surface is identified as an efficient surface for the conversion of biomass-derivatives from the combined results of density functional theory (DFT) calculations and temperature programmed desorption (TPD) experiments. A correlation is also established between the optimized adsorption geometry and experimental reaction pathways. These results should provide helpful insights in catalyst design for the upgrading and conversion of biomass.

  10. 48 CFR 22.1002-2 - Wage determinations based on prevailing rates.

    Science.gov (United States)

    2010-10-01

    ... on prevailing rates. 22.1002-2 Section 22.1002-2 Federal Acquisition Regulations System FEDERAL... Contract Act of 1965, as Amended 22.1002-2 Wage determinations based on prevailing rates. Contractors... Department of Labor to prevail in the locality or, in the absence of a wage determination, the minimum wage...

  11. Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates

    DEFF Research Database (Denmark)

    Nielsen, Jens Bredal

    1997-01-01

    Metabolic control analysis is a powerful technique for the evaluation of flux control within biochemical pathways. Its foundation is the elasticity coefficients and the flux control coefficients (FCCs). On the basis of a thermokinetic description of reaction rates it is here shown...... that the elasticity coefficients can be calculated directly from the pool levels of metabolites at steady state. The only requirement is that one thermodynamic parameter be known, namely the reaction affinity at the intercept of the tangent in the inflection point of the curve of reaction rate against reaction...... of the thermokinetic description of reaction rates to include the influence of effecters. Here the reaction rate is written as a linear function of the logarithm of the metabolite concentrations. With this type of rate function it is shown that the approach of Delgado and Liao [Biochem. J. (1992) 282, 919-927] can...

  12. Kinetics of the glucose/glycine Maillard reaction pathways: influences of pH and reactant initial concentrations

    NARCIS (Netherlands)

    Martins, S.I.F.S.; Boekel, van M.A.J.S.

    2005-01-01

    A previously proposed kinetic model for the glucose/glycine Maillard reaction pathways has been validated by changing the initial pH (4.8, 5.5, 6.0, 6.8 and 7.5) of the reaction and reactant initial concentrations (1:2 and 2:1 molar ratios were compared to the 1:1 ratio). The model consists of 10

  13. 75 FR 34182 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2010-06-16

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the June 17, 2010, public [email protected] ; or FAX: (202) 606-4264. Sheldon Friedman, Chairman, Federal Prevailing Rate...

  14. Degradation of ibuprofen by hydrodynamic cavitation: Reaction pathways and effect of operational parameters.

    Science.gov (United States)

    Musmarra, Dino; Prisciandaro, Marina; Capocelli, Mauro; Karatza, Despina; Iovino, Pasquale; Canzano, Silvana; Lancia, Amedeo

    2016-03-01

    Ibuprofen (IBP) is an anti-inflammatory drug whose residues can be found worldwide in natural water bodies resulting in harmful effects to aquatic species even at low concentrations. This paper deals with the degradation of IBP in water by hydrodynamic cavitation in a convergent-divergent nozzle. Over 60% of ibuprofen was degraded in 60 min with an electrical energy per order (EEO) of 10.77 kWh m(-3) at an initial concentration of 200 μg L(-1) and a relative inlet pressure pin=0.35 MPa. Five intermediates generated from different hydroxylation reactions were identified; the potential mechanisms of degradation were sketched and discussed. The reaction pathways recognized are in line with the relevant literature, both experimental and theoretical. By varying the pressure upstream the constriction, different degradation rates were observed. This effect was discussed according to a numerical simulation of the hydroxyl radical production identifying a clear correspondence between the maximum kinetic constant kOH and the maximum calculated OH production. Furthermore, in the investigated experimental conditions, the pH parameter was found not to affect the extent of degradation; this peculiar feature agrees with a recently published kinetic insight and has been explained in the light of the intermediates of the different reaction pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Prevailing Torque Locking Feature in Threaded Fasteners Using Anaerobic Adhesive

    Science.gov (United States)

    Hernandez, Alan; Hess, Daniel P.

    2016-01-01

    This paper presents results from tests to assess the use of anaerobic adhesive for providing a prevailing torque locking feature in threaded fasteners. Test procedures are developed and tests are performed on three fastener materials, four anaerobic adhesives, and both unseated assembly conditions. Five to ten samples are tested for each combination. Tests for initial use, reuse without additional adhesive, and reuse with additional adhesive are performed for all samples. A 48-hour cure time was used for all initial use and reuse tests. Test data are presented as removal torque versus removal angle with the specification required prevailing torque range added for performance assessment. Percent specification pass rates for the all combinations of fastener material, adhesive, and assembly condition are tabulated and reveal use of anaerobic adhesive as a prevailing torque locking feature is viable. Although not every possible fastener material and anaerobic adhesive combination provides prevailing torque values within specification, any combination can be assessed using the test procedures presented. Reuse without additional anaerobic adhesive generally provides some prevailing torque, and in some cases within specification. Reuse with additional adhesive often provides comparable removal torque data as in initial use.

  16. 76 FR 12769 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2011-03-08

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the March 17, 2011, public meeting..., Chairman, Federal Prevailing Rate Advisory Committee. [FR Doc. 2011-5266 Filed 3-7-11; 8:45 am] BILLING...

  17. 78 FR 20359 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2013-04-04

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the April 18, 2013, public meeting... Officer, Federal Prevailing Rate Advisory Committee. [FR Doc. 2013-07875 Filed 4-3-13; 8:45 am] BILLING...

  18. 76 FR 70512 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2011-11-14

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the November 17, 2011, public meeting..., Chairman, Federal Prevailing Rate Advisory Committee. [FR Doc. 2011-29274 Filed 11-10-11; 8:45 am] BILLING...

  19. Dynamics of anion-molecule reactions at low energy

    International Nuclear Information System (INIS)

    Mikosch, J.

    2007-11-01

    Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S N 2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S N 2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S N 2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S N 2 mechanism involving CH 3 -rotation. (orig.)

  20. Dynamics of anion-molecule reactions at low energy

    Energy Technology Data Exchange (ETDEWEB)

    Mikosch, J.

    2007-11-15

    Anion-molecule reactions must find their way through deeply bound entrance and exit channel complexes separated by a central barrier. This results in low reaction rates and rich dynamics since direct pathways compete with the formation of transient intermediates. In this thesis we examine the probability of proton transfer to a small anion and transient lifetimes of a thermoneutral bimolecular nucleophilic substitution (S{sub N}2) reaction at well defined variable temperature down to 8 Kelvin in a multipole trap. The observed strong inverse temperature dependence is attributed to the deficit of available quantum states in the entrance channel at decreasing temperature. Furthermore we investigate scattering dynamics of S{sub N}2 reactions at defined relative energy between 0.4 and 10 eV by crossed beam slice imaging. A weakly exothermic reaction with high central barrier proceeds via an indirect, complex-mediated mechanism at low relative energies featuring high internal product excitation in excellent quantitative agreement with a statistical model. In contrast, direct backward scattering prevails for higher energies with product velocities close to the kinematical cutoff. For a strongly exothermic reaction, competing S{sub N}2-, dihalide- and proton transfer-channels are explored which proceed by complex mediation for low energy and various rebound-, grazing- and collision induced bond rupture-mechanisms at higher energy. From our data and a collaboration with theory we identify a new indirect roundabout S{sub N}2 mechanism involving CH{sub 3}-rotation. (orig.)

  1. Reaction of H2 with O2 in Excited Electronic States: Reaction Pathways and Rate Constants.

    Science.gov (United States)

    Pelevkin, Alexey V; Loukhovitski, Boris I; Sharipov, Alexander S

    2017-12-21

    Comprehensive quantum chemical analysis with the use of the multireference state-averaged complete active space self-consistent field approach was carried out to study the reactions of H 2 with O 2 in a 1 Δ g , b 1 Σ g + , c 1 Σ u - , and A' 3 Δ u electronically excited states. The energetically favorable reaction pathways and possible intersystem crossings have been revealed. The energy barriers were refined employing the extended multiconfiguration quasi-degenerate second-order perturbation theory. It has been shown that the interaction of O 2 (a 1 Δ g ) and O 2 (A' 3 Δ u ) with H 2 occurs through the H-abstraction process with relatively low activation barriers that resulted in the formation of the HO 2 molecule in A″ and A' electronic states, respectively. Meanwhile, molecular oxygen in singlet sigma states (b 1 Σ g + and c 1 Σ u - ) was proved to be nonreactive with respect to the molecular hydrogen. Appropriate rate constants for revealed reaction and quenching channels have been estimated using variational transition-state theory including corrections for the tunneling effect, possible nonadiabatic transitions, and anharmonicity of vibrations for transition states and reactants. It was demonstrated that the calculated reaction rate constant for the H 2 + O 2 (a 1 Δ g ) process is in reasonable agreement with known experimental data. The Arrhenius approximations for these processes have been proposed for the temperature range T = 300-3000 K.

  2. Laccase-catalyzed removal of the antimicrobials chlorophene and dichlorophen from water: Reaction kinetics, pathway and toxicity evaluation.

    Science.gov (United States)

    Shi, Huanhuan; Peng, Jianbiao; Li, Jianhua; Mao, Liang; Wang, Zunyao; Gao, Shixiang

    2016-11-05

    As active agents in cleaning and disinfecting products, antimicrobials have been widely spread in the environment and have drawn extensive attention as potential threats to the ecological system and human health. In this study, the laccase-catalyzed removal of two emerging antimicrobials, chlorophene (CP) and dichlorophen (DCP), was investigated under simulated environmental conditions. Intrinsic reaction kinetics showed that the removal of CP and DCP followed second-order reaction kinetics, first-order with respect to both the enzyme and the substrate concentration. It was also found that fulvic acid could suppress the transformation of CP and DCP by reversing the oxidation reactions through its action as a scavenger of the free radical intermediates produced from reactions between laccase and the substrates. Several reaction products were identified by a quadrupole time-of-flight mass spectrometer, and detailed reaction pathways were proposed. For both CP and DCP, direct polymerization was the principal pathway, and the coupling patterns were further corroborated based on molecular modeling. The nucleophilic substitution of chlorine by the hydroxyl group was observed, and further oxidation products capable of coupling with each other were also found. Additionally, toxicity evaluation tests using Scenedesmus obliquus confirmed that the toxicity of CP and DCP was effectively eliminated during the reaction processes. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. 78 FR 41962 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2013-07-12

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the July 18, 2013, public meeting... Prevailing Rate Advisory Committee. [FR Doc. 2013-16763 Filed 7-11-13; 8:45 am] BILLING CODE 6325-49-P ...

  4. 77 FR 28640 - Federal Prevailing Rate Advisory Committee; Cancellation of Upcoming Meeting

    Science.gov (United States)

    2012-05-15

    ... OFFICE OF PERSONNEL MANAGEMENT Federal Prevailing Rate Advisory Committee; Cancellation of... Prevailing Rate Advisory Committee is issuing this notice to cancel the May 24, 2012, public meeting..., Federal Prevailing Rate Advisory Committee. [FR Doc. 2012-11728 Filed 5-14-12; 8:45 am] BILLING CODE 6325...

  5. A mechanistic study on the reaction pathways leading to benzene and naphthalene in cellulose vapor phase cracking

    International Nuclear Information System (INIS)

    Norinaga, Koyo; Yang, Huamei; Tanaka, Ryota; Appari, Srinivas; Iwanaga, Keita; Takashima, Yuka; Kudo, Shinji; Shoji, Tetsuya; Hayashi, Jun-ichiro

    2014-01-01

    The reaction pathways leading to aromatic hydrocarbons such as benzene and naphthalene in gas-phase reactions of multi-component mixtures derived from cellulose fast pyrolysis were studied both experimentally and numerically. A two-stage tubular reactor was used for evaluating the reaction kinetics of secondary vapor phase cracking of the nascent pyrolysates at temperature ranging from 400 to 900 °C, residence time from 0.2 to 4.3 s, and at 241 kPa. The products of alkyne and diene were identified from the primary pyrolysis of cellulose even at low temperature range 500–600 °C. These products include acetylene, propyne, propadiene, vinylacetylene, and cyclopentadiene. Experiments were also numerically validated by a detailed chemical kinetic model consisting of more than 8000 elementary step-like reactions with over 500 chemical species. Acceptable capabilities of the kinetic model in predicting concentration profiles of the products enabled us to assess reaction pathways leading to benzene and naphthalene via the alkyne and diene from primary pyrolysates of cellulose. C 3 alkyne and diene are primary precursors of benzene at 650 °C, while combination of ethylene and vinylacetylene produces benzene dominantly at 850 °C. Cyclopentadiene is a prominent precursor of naphthalene. Combination of acetylene with propyne or allyl radical leads to the formation of cyclopentadiene. Furan and acrolein are likely important alkyne precursors in cellulose pyrolysis at low temperature, whereas dehydrogenations of olefins are major route to alkyne at high temperatures. - Highlights: • Analytical pyrolysis experiments provided data for kinetic modeling. • Detailed chemical kinetic model was used and evaluated. • Alkyne and diene were important intermediates for aromatic hydrocarbon formation. • Reaction pathways leading to aromatic hydrocarbons were proposed

  6. Study of the optimal reaction conditions for assay of the mouse alternative complement pathway

    NARCIS (Netherlands)

    Dijk, H. van; Rademaker, P.M.; Klerx, J.P.A.M.; Willers, J.M.M.

    1985-01-01

    The optimal reaction conditions for hemolytic assay of alternative complement pathway activity in mouse serum were investigated. A microtiter system was used, in which a number of 7.5×106 rabbit erythrocytes per test well appeared to be optimal. Rabbit erythrocytes were superior as target cells over

  7. PREVAIL: IBM's e-beam technology for next generation lithography

    Science.gov (United States)

    Pfeiffer, Hans C.

    2000-07-01

    PREVAIL - Projection Reduction Exposure with Variable Axis Immersion Lenses represents the high throughput e-beam projection approach to NGL which IBM is pursuing in cooperation with Nikon Corporation as alliance partner. This paper discusses the challenges and accomplishments of the PREVAIL project. The supreme challenge facing all e-beam lithography approaches has been and still is throughput. Since the throughput of e-beam projection systems is severely limited by the available optical field size, the key to success is the ability to overcome this limitation. The PREVAIL technique overcomes field-limiting off-axis aberrations through the use of variable axis lenses, which electronically shift the optical axis simultaneously with the deflected beam so that the beam effectively remains on axis. The resist images obtained with the Proof-of-Concept (POC) system demonstrate that PREVAIL effectively eliminates off- axis aberrations affecting both resolution and placement accuracy of pixels. As part of the POC system a high emittance gun has been developed to provide uniform illumination of the patterned subfield and to fill the large numerical aperture projection optics designed to significantly reduce beam blur caused by Coulomb interaction.

  8. 29 CFR 2704.202 - Contents of application-where the applicant has prevailed.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 9 2010-07-01 2010-07-01 false Contents of application-where the applicant has prevailed... Information Required From Applicants § 2704.202 Contents of application—where the applicant has prevailed. (a) An application for an award under § 2704.105(a) shall show that the applicant has prevailed in a...

  9. Position-specific isotope modeling of organic micropollutants transformations through different reaction pathways

    Science.gov (United States)

    Jin, Biao; Rolle, Massimo

    2016-04-01

    Organic compounds are produced in vast quantities for industrial and agricultural use, as well as for human and animal healthcare [1]. These chemicals and their metabolites are frequently detected at trace levels in fresh water environments where they undergo degradation via different reaction pathways. Compound specific stable isotope analysis (CSIA) is a valuable tool to identify such degradation pathways in different environmental systems. Recent advances in analytical techniques have promoted the fast development and implementation of multi-element CSIA. However, quantitative frameworks to evaluate multi-element stable isotope data and incorporating mechanistic information on the degradation processes [2,3] are still lacking. In this study we propose a mechanism-based modeling approach to simultaneously evaluate concentration as well as bulk and position-specific multi-element isotope evolution during the transformation of organic micropollutants. The model explicitly simulates position-specific isotopologues for those atoms that experience isotope effects and, thereby, provides a mechanistic description of isotope fractionation occurring at different molecular positions. We validate the proposed approach with the concentration and multi-element isotope data of three selected organic micropollutants: dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model precisely captures the dual element isotope trends characteristic of different reaction pathways and their range of variation consistent with observed multi-element (C, N) bulk isotope fractionation. The proposed approach can also be used as a tool to explore transformation pathways in scenarios for which position-specific isotope data are not yet available. [1] Schwarzenbach, R.P., Egli, T., Hofstetter, T.B., von Gunten, U., Wehrli, B., 2010. Global Water Pollution and Human Health. Annu. Rev. Environ. Resour. doi:10.1146/annurev-environ-100809-125342. [2] Jin, B., Haderlein, S.B., Rolle, M

  10. Methane coupling reaction in an oxy-steam stream through an OH radical pathway by using supported alkali metal catalysts

    KAUST Repository

    Liang, Yin

    2014-03-24

    A universal reaction mechanism involved in the oxidative coupling of methane (OCM) is demonstrated under oxy-steam conditions using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from a H 2O-O2 reaction followed by C-H activation in CH 4 with an OH radical. Thus, the presence of water enhances both the CH4 conversion rate and the C2 selectivity. This OH radical pathway that is selective for the OCM was observed for the catalyst without Mn, which suggests clearly that Mn is not the essential component in a selective OCM catalyst. The experiments with different catalyst compositions revealed that the OH.-mediated pathway proceeded in the presence of catalysts with different alkali metals (Na, K) and different oxo anions (W, Mo). This difference in catalytic activity for OH radical generation accounts for the different OCM selectivities. As a result, a high C2 yield is achievable by using Na2WO4/SiO2, which catalyzes the OH.-mediated pathway selectively. Make it methane: A universal reaction mechanism involved in the oxidative coupling of methane is demonstrated under oxy-stream conditions by using alkali-metal-based catalysts. Rigorous kinetic measurements indicated a reaction mechanism that is consistent with OH radical formation from an H2O-O2 reaction, followed by C-H activation in CH4 with an OH radical. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Conferring specificity in redox pathways by enzymatic thiol/disulfide exchange reactions.

    Science.gov (United States)

    Netto, Luis Eduardo S; de Oliveira, Marcos Antonio; Tairum, Carlos A; da Silva Neto, José Freire

    2016-01-01

    Thiol-disulfide exchange reactions are highly reversible, displaying nucleophilic substitutions mechanism (S(N)2 type). For aliphatic, low molecular thiols, these reactions are slow, but can attain million times faster rates in enzymatic processes. Thioredoxin (Trx) proteins were the first enzymes described to accelerate thiol-disulfide exchange reactions and their high reactivity is related to the high nucleophilicity of the attacking thiol. Substrate specificity in Trx is achieved by several factors, including polar, hydrophobic, and topological interactions through a groove in the active site. Glutaredoxin (Grx) enzymes also contain the Trx fold, but they do not share amino acid sequence similarity with Trx. A conserved glutathione binding site is a typical feature of Grx that can reduce substrates by two mechanisms (mono and dithiol). The high reactivity of Grx enzymes is related to the very acid pK(a) values of reactive Cys that plays roles as good leaving groups. Therefore, although distinct oxidoreductases catalyze similar thiol–disulfide exchange reactions, their enzymatic mechanisms vary. PDI and DsbA are two other oxidoreductases, but they are involved in disulfide bond formation, instead of disulfide reduction, which is related to the oxidative environment where they are found. PDI enzymes and DsbC are endowed with disulfide isomerase activity, which is related with their tetra-domain architecture. As illustrative description of specificity in thiol-disulfide exchange, redox aspects of transcription activation in bacteria, yeast, and mammals are presented in an evolutionary perspective. Therefore, thiol-disulfide exchange reactions play important roles in conferring specificity to pathways, a required feature for signaling.

  12. Heterogeneous reaction of particulate chlorpyrifos with NO3 radicals: Products, pathways, and kinetics

    Science.gov (United States)

    Li, Nana; Zhang, Peng; Yang, Bo; Shu, Jinian; Wang, Youfeng; Sun, Wanqi

    2014-08-01

    Chlorpyrifos is a typical chlorinated organophosphorus pesticide. The heterogeneous reaction of chlorpyrifos particles with NO3 radicals was investigated using a vacuum ultraviolet photoionization aerosol time-of-flight mass spectrometer (VUV-ATOFMS) and a real-time atmospheric gas analysis mass spectrometer. Chlorpyrifos oxon, 3,5,6-trichloro-2-pyridinol, O,O-diethyl O-hydrogen phosphorothioate, O,O-diethyl ester thiophosphoric acid, diethyl hydrogen phosphate and a phosphinyl disulfide compound were identified as the main degradation products. The heterogeneous reaction pathways were proposed and their kinetic processes were investigated via a mixed-phase relative rate method. The observed effective rate constant is 3.4 ± 0.2 × 10-12 cm3 molecule-1 s-1.

  13. Catalytic Hydrotreatment of Fast Pyrolysis Oil : Model Studies on Reaction Pathways for the Carbohydrate Fraction

    NARCIS (Netherlands)

    Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

    2009-01-01

    Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions

  14. Roles of different initial Maillard intermediates and pathways in meat flavor formation for cysteine-xylose-glycine model reaction systems.

    Science.gov (United States)

    Hou, Li; Xie, Jianchun; Zhao, Jian; Zhao, Mengyao; Fan, Mengdie; Xiao, Qunfei; Liang, Jingjing; Chen, Feng

    2017-10-01

    To explore initial Maillard reaction pathways and mechanisms for maximal formation of meaty flavors in heated cysteine-xylose-glycine systems, model reactions with synthesized initial Maillard intermediates, Gly-Amadori, TTCA (2-threityl-thiazolidine-4-carboxylic acids) and Cys-Amadori, were investigated. Relative relativities were characterized by spectrophotometrically monitoring the development of colorless degradation intermediates and browning reaction products. Aroma compounds formed were determined by solid-phase microextraction combined with GC-MS and GC-olfactometry. Gly-Amadori showed the fastest reaction followed by Cys-Amadori then TTCA. Free glycine accelerated reaction of TTCA, whereas cysteine inhibited that of Gly-Amadori due to association forming relatively stable thiazolidines. Cys-Amadori/Gly had the highest reactivity in development of both meaty flavors and brown products. TTCA/Gly favored yielding meaty flavors, whereas Gly-Amadori/Cys favored generation of brown products. Conclusively, initial formation of TTCA and pathway involving TTCA with glycine were more applicable to efficiently produce processed-meat flavorings in a cysteine-xylose-glycine system. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Reaction Pathways in Catechol/Primary Amine Mixtures: A Window on Crosslinking Chemistry.

    Directory of Open Access Journals (Sweden)

    Juan Yang

    Full Text Available Catechol chemistry is used as a crosslinking tool abundantly in both natural organisms (e.g. mussels, sandcastle worms and synthetic systems to achieve the desired mechanical properties. Despite this abundance and success, the crosslinking chemistry is still poorly understood. In this study, to simplify the system, yet to capture the essential chemistry, model compounds 4-methyl catechol and propylamine are used. The reaction of 4-methyl catechol (2 mM with propylamine (6 mM is carried out in the presence of NaIO4 (2 mM in 10 mM Na2CO3 aqueous solution. A variety of spectroscopic/spectrometric and chromatographic methods such as 1H NMR, LC-MS, and UV-VIS are used to track the reaction and identify the products/intermediates. It is found that the crosslinking chemistry of a catechol and an amine is both fast and complicated. Within five minutes, more than 60 products are formed. These products encompass 19 different masses ranging from molecular weight of 179 to 704. By combining time-dependent data, it is inferred that the dominant reaction pathways: the majority is formed via aryloxyl-phenol coupling and Michael-type addition, whereas a small fraction of products is formed via Schiff base reactions.

  16. 75 FR 18552 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2010-04-12

    ... of Personnel Management Building, 1900 E Street, NW., Washington, DC. The Federal Prevailing Rate... business. Therefore, these caucuses will be closed to the public because of a determination made by the..., Federal Prevailing Rate Advisory Committee, Room 5H27, 1900 E Street, NW., Washington, DC 20415, (202) 606...

  17. Pump-shaped dump optimal control reveals the nuclear reaction pathway of isomerization of a photoexcited cyanine dye.

    Science.gov (United States)

    Dietzek, Benjamin; Brüggemann, Ben; Pascher, Torbjörn; Yartsev, Arkady

    2007-10-31

    Using optimal control as a spectroscopic tool we decipher the details of the molecular dynamics of the essential multidimensional excited-state photoisomerization - a fundamental chemical reaction of key importance in biology. Two distinct nuclear motions are identified in addition to the overall bond-twisting motion: Initially, the reaction is dominated by motion perpendicular to the torsion coordinate. At later times, a second optically active vibration drives the system along the reaction path to the bottom of the excited-state potential. The time scales of the wavepacket motion on a different part of the excited-state potential are detailed by pump-shaped dump optimal control. This technique offers new means to control a chemical reaction far from the Franck-Condon point of absorption and to map details of excited-state reaction pathways revealing unique insights into the underlying reaction mechanism.

  18. 7 CFR 27.35 - Lower class of two samples to prevail.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Lower class of two samples to prevail. 27.35 Section 27.35 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE... Micronaire Determinations § 27.35 Lower class of two samples to prevail. In case a sample drawn from one...

  19. Effects of Prevailing Winds on Turbidity of a Shallow Estuary

    OpenAIRE

    Cho, Hyun Jung

    2007-01-01

    Estuarine waters are generally more turbid than lakes or marine waters due to greater algal mass and continual re-suspension of sediments. The varying effects of diurnal and seasonal prevailing winds on the turbidity condition of a wind-dominated estuary were investigated by spatial and statistical analyses of wind direction, water level, turbidity, chlorophyll a, and PAR (Photosynthetically Active Radiation) collected in Lake Pontchartrain, Louisiana, USA. The prolonged prevailing winds were...

  20. Combustion modeling and kinetic rate calculations for a stoichiometric cyclohexane flame. 1. Major reaction pathways.

    Science.gov (United States)

    Zhang, Hongzhi R; Huynh, Lam K; Kungwan, Nawee; Yang, Zhiwei; Zhang, Shaowen

    2007-05-17

    The Utah Surrogate Mechanism was extended in order to model a stoichiometric premixed cyclohexane flame (P = 30 Torr). Generic rates were assigned to reaction classes of hydrogen abstraction, beta scission, and isomerization, and the resulting mechanism was found to be adequate in describing the combustion chemistry of cyclohexane. Satisfactory results were obtained in comparison with the experimental data of oxygen, major products and important intermediates, which include major soot precursors of C2-C5 unsaturated species. Measured concentrations of immediate products of fuel decomposition were also successfully reproduced. For example, the maximum concentrations of benzene and 1,3-butadiene, two major fuel decomposition products via competing pathways, were predicted within 10% of the measured values. Ring-opening reactions compete with those of cascading dehydrogenation for the decomposition of the conjugate cyclohexyl radical. The major ring-opening pathways produce 1-buten-4-yl radical, molecular ethylene, and 1,3-butadiene. The butadiene species is formed via beta scission after a 1-4 internal hydrogen migration of 1-hexen-6-yl radical. Cascading dehydrogenation also makes an important contribution to the fuel decomposition and provides the exclusive formation pathway of benzene. Benzene formation routes via combination of C2-C4 hydrocarbon fragments were found to be insignificant under current flame conditions, inferred by the later concentration peak of fulvene, in comparison with benzene, because the analogous species series for benzene formation via dehydrogenation was found to be precursors with regard to parent species of fulvene.

  1. PREVAIL-EPL alpha tool electron optics subsystem

    Science.gov (United States)

    Pfeiffer, Hans C.; Dhaliwal, Rajinder S.; Golladay, Steven D.; Doran, Samuel K.; Gordon, Michael S.; Kendall, Rodney A.; Lieberman, Jon E.; Pinckney, David J.; Quickle, Robert J.; Robinson, Christopher F.; Rockrohr, James D.; Stickel, Werner; Tressler, Eileen V.

    2001-08-01

    The IBM/Nikon alliance is continuing pursuit of an EPL stepper alpha tool based on the PREVAIL technology. This paper provides a status report of the alliance activity with particular focus on the Electron Optical Subsystem developed at IBM. We have previously reported on design features of the PREVAIL alpha system. The new state-of-the-art e-beam lithography concepts have since been reduced to practice and turned into functional building blocks of a production level lithography tool. The electron optical alpha tool subsystem has been designed, build, assembled and tested at IBM's Semiconductor Research and Development Center (SRDC) in East Fishkill, New York. After demonstrating subsystem functionality, the electron optical column and all associated control electronics hardware and software have been shipped during January 2001 to Nikon's facility in Kumagaya, Japan, for integration into the Nikon commercial e-beam stepper alpha tool. Early pre-shipment results obtained with this electron optical subsystem are presented.

  2. An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

    KAUST Repository

    Bucci, Alberto; Menendez Rodriguez, Gabriel; Bellachioma, Gianfranco; Zuccaccia, Cristiano; Poater, Albert; Cavallo, Luigi; Macchioni, Alceo

    2016-01-01

    The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.

  3. An Alternative Reaction Pathway for Iridium Catalyzed Water Oxidation Driven by CAN

    KAUST Repository

    Bucci, Alberto

    2016-06-10

    The generation of solar fuels by means of a photosynthetic apparatus strongly relies on the development of an efficient water oxidation catalyst (WOC). Cerium ammonium nitrate (CAN) is the most commonly used sacrificial oxidant to explore the potentiality of WOCs. It is usually assumed that CAN has the unique role to oxidatively energize WOCs, making them capable to offer a low energy reaction pathway to transform H2O to O2. Herein we show that CAN might have a much more relevant and direct role in WO, mainly related to the capture and liberation of O–O containing molecular moieties.

  4. Combined quantum mechanical and molecular mechanical reaction pathway calculation for aromatic hydroxylation by p-hydroxybenzoate-3-hydroxylase

    NARCIS (Netherlands)

    Ridder, L.; Mulholland, A.; Rietjens, I.M.C.M.; Vervoort, J.

    1999-01-01

    The reaction pathway for the aromatic 3-hydroxylation of p-hydroxybenzoate by the reactive C4a-hydroperoxyflavin cofactor intermediate in p-hydroxybenzoate hydroxylase (PHBH) has been investigated by a combined quantum mechanical and molecular mechanical (QM/MM) method. A structural model for the

  5. 76 FR 9694 - Prevailing Rate Systems; Redefinition of the Northeastern Arizona and Colorado Appropriated Fund...

    Science.gov (United States)

    2011-02-22

    ... 3206-AM33 Prevailing Rate Systems; Redefinition of the Northeastern Arizona and Colorado Appropriated... changes are based on recent consensus recommendations of the Federal Prevailing Rate Advisory Committee to... Northeastern Arizona wage area. The Federal Prevailing Rate Advisory Committee (FPRAC), the national labor...

  6. 76 FR 70321 - Prevailing Rate Systems; Redefinition of the Northern Mississippi and Memphis, TN, Appropriated...

    Science.gov (United States)

    2011-11-14

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM37 Prevailing Rate Systems; Redefinition... on a consensus recommendation of the Federal Prevailing Rate Advisory Committee (FPRAC) to best match... which OPM received no comments. The Federal Prevailing Rate Advisory Committee (FPRAC), the national...

  7. 78 FR 18252 - Prevailing Rate Systems; North American Industry Classification System Based Federal Wage System...

    Science.gov (United States)

    2013-03-26

    ...-AM78 Prevailing Rate Systems; North American Industry Classification System Based Federal Wage System... applicable sections. The Federal Prevailing Rate Advisory Committee, the national labor- management committee... proposing to amend 5 CFR part 532 as follows: PART 532--PREVAILING RATE SYSTEMS 0 1. The authority citation...

  8. 76 FR 31885 - Prevailing Rate Systems; Redefinition of the Northern Mississippi and Memphis, TN, Appropriated...

    Science.gov (United States)

    2011-06-02

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM37 Prevailing Rate Systems; Redefinition... Prevailing Rate Advisory Committee (FPRAC) to best match the county proposed for redefinition to a nearby FWS... Memphis wage area. The Federal Prevailing Rate Advisory Committee (FPRAC), the national labor-management...

  9. Reaction pathways of biomass-derived oxygenates on noble metal surfaces

    Science.gov (United States)

    McManus, Jesse R.

    As the global demand for energy continues to rise, the environmental concerns associated with increased fossil fuel consumption have motivated the use of biomass as an alternative, carbon-renewable energy feedstock. Controlling reactive chemistry of the sugars that comprise biomass through the use of catalysis becomes essential in effectively producing green fuels and value-added chemicals. Recent work on biomass conversion catalysts have demonstrated the efficacy of noble metal catalyst systems for the reforming of biomass to hydrogen fuel, and the hydrodeoxygenation of biomass-derived compounds to value-added chemicals. In particular, Pt and Pd surfaces have shown considerable promise as reforming catalysts in preliminary aqueous phase reforming studies. It becomes important to understand the mechanisms by which these molecules react on the catalyst surfaces in order to determine structure-activity relationships and bond scission energetics as to provide a framework for engineering more active and selective catalysts. Fundamental surface science techniques provide the tools to do this; however, work in this field has been so far limited to simple model molecules like ethanol and ethylene glycol. Herein, temperature programmed desorption and high resolution electron energy loss spectroscopy are utilized in an ultra-high vacuum surface science study of the biomass-derived sugar glucose on Pt and Pd single crystal catalysts. Overall, it was determined that the aldehyde function of a ring-open glucose molecule plays an integral part in the initial bonding and reforming reaction pathway, pointing to the use of aldoses glycolaldehyde and glyceraldehyde as the most appropriate model compounds for future studies. Furthermore, the addition of adatom Zn to a Pt(111) surface was found to significantly decrease the C-H and C-C bond scission activity in aldehyde containing compounds, resulting in a preferred deoxygenation pathway in opposition to the decarbonylation pathway

  10. Electrode Reaction Pathway in Oxide Anode for Solid Oxide Fuel Cells

    Science.gov (United States)

    Li, Wenyuan

    the electrolyte to change 3PB kinetics. Compared to Ni, Co doping activates the bulk oxygen more significantly, promoting the reaction at 2PB. The active surface reaction zone is found to be enlarged by the electrolyte with high oxygen activity (SSZ vs. YSZ) when charge transfer is one of the RDS. Due to the larger exchange current for charge transfer in 3PB with SSZ electrolyte, the adsorption gradient zone is broadened, leading to enhanced surface reaction kinetics. The potential application of such finding is demonstrated on SSZ/YSZ/SSZ sandwich, showing largely improved electrode performance, opening a wide door for the utilization of electrolytes that are too expensive, fragile or instable to be used before. The bulk path way in 2PB reaction can be affected by overpotential in terms of local vacancy concentration, built-in electrical field and stability. It is proven that an uneven distribution of lattice oxygen is established under operation conditions with overpotential by both qualitative analysis and analytic solution. An electrostatic field force is present besides the concentration gradient in the anode lattice to control the motion of oxygen ions. Compared to the usual estimation based on chemical diffusion mechanism, the real deviation of ionic defects concentration under polarization from the equilibrium state near electrode/electrolyte interface is smaller with the built-in electrical field. The overpotential is demonstrated to be able to open up or shut down the bulk pathway depending on the ionic defects of electrodes. The analysis on the bulk pathway in terms of local charged species and various potentials provides new insight in anion diffusion and electrode stability.

  11. Probabilistic pathway construction.

    Science.gov (United States)

    Yousofshahi, Mona; Lee, Kyongbum; Hassoun, Soha

    2011-07-01

    Expression of novel synthesis pathways in host organisms amenable to genetic manipulations has emerged as an attractive metabolic engineering strategy to overproduce natural products, biofuels, biopolymers and other commercially useful metabolites. We present a pathway construction algorithm for identifying viable synthesis pathways compatible with balanced cell growth. Rather than exhaustive exploration, we investigate probabilistic selection of reactions to construct the pathways. Three different selection schemes are investigated for the selection of reactions: high metabolite connectivity, low connectivity and uniformly random. For all case studies, which involved a diverse set of target metabolites, the uniformly random selection scheme resulted in the highest average maximum yield. When compared to an exhaustive search enumerating all possible reaction routes, our probabilistic algorithm returned nearly identical distributions of yields, while requiring far less computing time (minutes vs. years). The pathways identified by our algorithm have previously been confirmed in the literature as viable, high-yield synthesis routes. Prospectively, our algorithm could facilitate the design of novel, non-native synthesis routes by efficiently exploring the diversity of biochemical transformations in nature. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Genetics of Schizophrenia: Historical Insights and Prevailing Evidence.

    Science.gov (United States)

    van de Leemput, J; Hess, J L; Glatt, S J; Tsuang, M T

    2016-01-01

    Schizophrenia's (SZ's) heritability and familial transmission have been known for several decades; however, despite the clear evidence for a genetic component, it has been very difficult to pinpoint specific causative genes. Even so genetic studies have taught us a lot, even in the pregenomic era, about the molecular underpinnings and disease-relevant pathways. Recurring themes emerged revealing the involvement of neurodevelopmental processes, glutamate regulation, and immune system differential activation in SZ etiology. The recent emergence of epigenetic studies aimed at shedding light on the biological mechanisms underlying SZ has provided another layer of information in the investigation of gene and environment interactions. However, this epigenetic insight also brings forth another layer of complexity to the (epi)genomic landscape such as interactions between genetic variants, epigenetic marks-including cross-talk between DNA methylation and histone modification processes-, gene expression regulation, and environmental influences. In this review, we seek to synthesize perspectives, including limitations and obstacles yet to overcome, from genetic and epigenetic literature on SZ through a qualitative review of risk factors and prevailing hypotheses. Encouraged by the findings of both genetic and epigenetic studies to date, as well as the continued development of new technologies to collect and interpret large-scale studies, we are left with a positive outlook for the future of elucidating the molecular genetic mechanisms underlying SZ and other complex neuropsychiatric disorders. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. 75 FR 58339 - Prevailing Rate Systems; Redefinition of the Shreveport, LA; Texarkana, TX; Milwaukee, WI; and...

    Science.gov (United States)

    2010-09-24

    ... 3206-AM28 Prevailing Rate Systems; Redefinition of the Shreveport, LA; Texarkana, TX; Milwaukee, WI... area. These changes are based on recent consensus recommendations of the Federal Prevailing Rate... below. The Federal Prevailing Rate Advisory Committee (FPRAC), the national labor-management committee...

  14. A Networks Approach to Modeling Enzymatic Reactions.

    Science.gov (United States)

    Imhof, P

    2016-01-01

    Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

  15. Reaction pathway and oxidation mechanisms of dibutyl phthalate by persulfate activated with zero-valent iron

    Energy Technology Data Exchange (ETDEWEB)

    Li, Huanxuan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); Wan, Jinquan, E-mail: ppjqwan@scut.edu.cn [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Ma, Yongwen [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China); State Key Lab Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640 (China); Wang, Yan [School of Environment and Energy, South China University of Technology, Guangzhou 510006 (China); The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China, Guangzhou 510640 (China)

    2016-08-15

    This study investigated reaction pathway and oxidation mechanisms of dibutyl phthalate (DBP) by persulfate (PS) activated with zero-valent iron (ZVI). The DBP degradation was studied at three pH values (acidic, neutral and basic) in the presence of different organic scavengers. Using a chemical probe method, both sulfate radical (SO{sub 4}·{sup −}) and hydroxyl radical (·OH) were found to be primary oxidants at pH 3.0 and pH 7.0, respectively while ·OH was the major specie to oxidize DBP at pH 11.0. A similar result was found in an experiment of Electron Spin Resonance spin-trapping where in addition to ·OH, superoxide radical (O{sub 2}·{sup −}) was detected at pH 11.0. The transformation of degradation products including dimethyl phthalate (DMP), diethyl phthalate (DEP), phthalic anhydride, and acetophenone exhibited diverse variation during the reaction processes. The phthalic anhydride concentration appeared to be maximum at all pHs. Another eleven intermediate products were also found at pH 3.0 by GC–MS and HPLC analysis, and their degradation mechanisms and pathways were proposed. It was suggested that dealkylation, hydroxylation, decarboxylation and hydrogen extraction were the dominant degradation mechanisms of DBP at pH 3.0. - Highlights: • Both SO{sub 4}{sup −}· and ·OH were found to be the major active species at pH 3.0 and pH 7.0. • ·OH and ·O2– were the primary oxidants pH 11.0. • The intermediate products were investigated as well as the degradation pathway. • Dealkylation, hydroxylation, decarboxylation, H-extraction were the major mechanisms.

  16. 5 CFR 532.205 - The use of Federal, State, and local minimum wage requirements in determining prevailing rates.

    Science.gov (United States)

    2010-01-01

    ... minimum wage requirements in determining prevailing rates. 532.205 Section 532.205 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS PREVAILING RATE SYSTEMS Prevailing Rate Determinations § 532.205 The use of Federal, State, and local minimum wage requirements in determining prevailing...

  17. Reaction pathways for reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes

    International Nuclear Information System (INIS)

    Cunha, M.C.P.M. da; De Souza, J.P.I.; Nart, F.C.

    2000-01-01

    The reduction of nitrate ions on platinum, rhodium, and platinum-rhodium alloy electrodes has been investigated using differential electrochemical mass spectrometry and in situ FTIR measurements. For 3 M HNO 3 concentration it has been found that nitrate starts the reduction with partial N-O bond dissociation and N-N bond formation generating NO and N 2 O. At potentials lower than 0.2 V the reaction proceeds forming dissolved NH 4 + . For potentials lower than 0 V the reduction continues via a multiple pathway reaction leading to the nonselective production of N 2 , NH 2 OH, and N 2 H 2 . On the alloyed electrodes, the production of NO and N 2 O has been observed in both cathodic and anodic scans, while on pure platinum and rhodium electrodes the reaction has been observed only during the cathodic scan. Contrasting with the pure platinum and rhodium alloys, where the N-O bond break starts forming NO and N 2 O, on the alloys HNO 2 has been observed as the first reaction step. For alloys with higher rhodium composition, like Pt 75 Rh 25 , no N 2 has been detected for potentials lower than 0 V

  18. 78 FR 60182 - Prevailing Rate Systems; Definition of Broward County, Florida, to a Nonappropriated Fund Federal...

    Science.gov (United States)

    2013-10-01

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM83 Prevailing Rate Systems; Definition of... wage area. The Federal Prevailing Rate Advisory Committee, the national labor-management committee... follows: PART 532--PREVAILING RATE SYSTEMS 0 1. The authority citation for part 532 continues to read as...

  19. 78 FR 29658 - Prevailing Rate Systems; Definition of Broward County, Florida, to a Nonappropriated Fund Federal...

    Science.gov (United States)

    2013-05-21

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM83 Prevailing Rate Systems; Definition of... and Palm Beach Counties, FL. The Federal Prevailing Rate Advisory Committee, the national labor... 532--PREVAILING RATE SYSTEMS 0 1. The authority citation for part 532 continues to read as follows...

  20. Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

    Science.gov (United States)

    Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

    2015-04-10

    As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

  1. Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

    Directory of Open Access Journals (Sweden)

    Xue Zhang

    2015-04-01

    Full Text Available As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs and polychlorinated biphenyls (PCBs are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD. Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

  2. Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

    International Nuclear Information System (INIS)

    Jang, Keun Jo; Kweon, Dae Cheol; Kim, Myeong Goo; Yoo, Beong Gyu

    2007-01-01

    The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings

  3. Development and implementation of a critical pathway for prevention of adverse reactions to contrast media for computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Keun Jo [Presbyterian Medical Center, Seoul (Korea, Republic of); Kweon, Dae Cheol; Kim, Myeong Goo [Seoul National University Hospital, Seoul (Korea, Republic of); Yoo, Beong Gyu [Wonkwang Health Science College, Iksan (Korea, Republic of)

    2007-03-15

    The purpose of this study is to develop a critical pathway (CP) for the prevention of adverse reactions to contrast media for computed tomography. The CP was developed and implemented by a multidisciplinary group is Seoul National University Hospital. The CP was applied to CT patients. Patients who underwent CT scanning were included in the CP group from March in 2004. The satisfaction of the patients with CP was compared with non-CP groups. We also investigated the degree of satisfaction among the radiological technologists and nurses. The degree of patient satisfaction with the care process increased patient information (24%), prevention of adverse reactions to contrast media (19%), pre-cognitive effect of adverse reactions to contrast media (39%) and information degree of adverse reactions to contrast media (19%). This CP program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings.

  4. On the usefulness of 'what' and 'where' pathways in vision.

    Science.gov (United States)

    de Haan, Edward H F; Cowey, Alan

    2011-10-01

    The primate visual brain is classically portrayed as a large number of separate 'maps', each dedicated to the processing of specific visual cues, such as colour, motion or faces and their many features. In order to understand this fractionated architecture, the concept of cortical 'pathways' or 'streams' was introduced. In the currently prevailing view, the different maps are organised hierarchically into two major pathways, one involved in recognition and memory (the ventral stream or 'what' pathway) and the other in the programming of action (the dorsal stream or 'where' pathway). In this review, we question this heuristically influential but potentially misleading linear hierarchical pathway model and argue instead for a 'patchwork' or network model. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Catalytic Hydrotreatment of Fast Pyrolysis Oil: Model Studies on Reaction Pathways for the Carbohydrate Fraction

    OpenAIRE

    Wildschut, J.; Arentz, J.; Rasrendra, C. B.; Venderbosch, R. H.; Heeres, H. J.

    2009-01-01

    Fast pyrolysis oil can be upgraded by a catalytic hydrotreatment (250-400 degrees C, 100-200 bar) using heterogeneous catalysts such as Ru/C to hydrocarbon-like products that can serve as liquid transportation fuels. Insight into the complex reaction pathways of the various component fractions during hydrotreatment is desirable to reduce the formation of by-products such as char and gaseous components. This paper deals with the catalytic hydrotreatment of representative model components for t...

  6. 76 FR 9640 - Prevailing Rate Systems: Santa Clara, CA, Tulsa County, OK, and Angelina County, TX

    Science.gov (United States)

    2011-02-22

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM22 Prevailing Rate Systems: Santa Clara... County, Texas, as an area of application to the Dallas, TX, NAF FWS wage area. The Federal Prevailing.... Accordingly, the U.S. Office of Personnel Management amends 5 CFR part 532 as follows: PART 532--PREVAILING...

  7. Modeling reaction histories to study chemical pathways in condensed phase detonation

    International Nuclear Information System (INIS)

    Scott Stewart, D.; Hernández, Alberto; Lee, Kibaek

    2016-01-01

    The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art of two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.

  8. Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants.

    Science.gov (United States)

    Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng

    2017-07-06

    The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.

  9. 76 FR 70365 - Prevailing Rate Systems; Redefinition of the Austin, TX and Waco, TX, Appropriated Fund Federal...

    Science.gov (United States)

    2011-11-14

    ... 3206-AM50 Prevailing Rate Systems; Redefinition of the Austin, TX and Waco, TX, Appropriated Fund... the Federal Prevailing Rate Advisory Committee to best match the counties proposed for redefinition to... Prevailing Rate Advisory Committee (FPRAC), the national labor-management committee responsible for advising...

  10. 77 FR 68073 - Prevailing Rate Systems; Redefinition of the St. Louis, MO; Southern Missouri; Cleveland, OH; and...

    Science.gov (United States)

    2012-11-15

    ... 3206-AM70 Prevailing Rate Systems; Redefinition of the St. Louis, MO; Southern Missouri; Cleveland, OH... Cleveland wage area. These changes are based on recent consensus recommendations of the Federal Prevailing... proposing the changes described below. The Federal Prevailing Rate Advisory Committee (FPRAC), the national...

  11. 75 FR 39460 - Prevailing Rate Systems; Redefinition of the Chicago, IL; Fort Wayne-Marion, IN; Indianapolis, IN...

    Science.gov (United States)

    2010-07-09

    ...-AM21 Prevailing Rate Systems; Redefinition of the Chicago, IL; Fort Wayne-Marion, IN; Indianapolis, IN... wage area. These changes are based on recent consensus recommendations of the Federal Prevailing Rate... below. The Federal Prevailing Rate Advisory Committee (FPRAC), the national labor-management committee...

  12. One-step simultaneous differential scanning calorimetry-FTIR microspectroscopy to quickly detect continuous pathways in the solid-state glucose/asparagine Maillard reaction.

    Science.gov (United States)

    Hwang, Deng-Fwu; Hsieh, Tzu-Feng; Lin, Shan-Yang

    2013-01-01

    The stepwise reaction pathway of the solid-state Maillard reaction between glucose (Glc) and asparagine (Asn) was investigated using simultaneous differential scanning calorimetry (DSC)-FTIR microspectroscopy. The color change and FTIR spectra of Glc-Asn physical mixtures (molar ratio = 1:1) preheated to different temperatures followed by cooling were also examined. The successive reaction products such as Schiff base intermediate, Amadori product, and decarboxylated Amadori product in the solid-state Glc-Asn Maillard reaction were first simultaneously evidenced by this unique DSC-FTIR microspectroscopy. The color changed from white to yellow-brown to dark brown, and appearance of new IR peaks confirmed the formation of Maillard reaction products. The present study clearly indicates that this unique DSC-FTIR technique not only accelerates but also detects precursors and products of the Maillard reaction in real time.

  13. 78 FR 29657 - Prevailing Rate Systems; Definition of Vanderburgh County, Indiana, to a Nonappropriated Fund...

    Science.gov (United States)

    2013-05-21

    ...-AM82 Prevailing Rate Systems; Definition of Vanderburgh County, Indiana, to a Nonappropriated Fund... County, IN; and Jefferson and Pulaski Counties, MO. The Federal Prevailing Rate Advisory Committee, the... as follows: [[Page 29658

  14. Elementary steps and reaction pathways in the aqueous phase alkylation of phenol with ethanol

    Energy Technology Data Exchange (ETDEWEB)

    Eckstein, Sebastian; Hintermeier, Peter H.; Olarte, Mariefel V.; Liu, Yue; Baráth, Eszter; Lercher, Johannes A.

    2017-08-01

    The hydronium ion normalized reaction rate in aqueous phase alkylation of phenol with ethanol on H-MFI zeolites increases with decreasing concentration of acid sites. Higher rates are caused by higher concentrations of phenol in the zeolite pores, as the concentration of hydronium ions generated by zeolite Brønsted acid sites decreases. Considering the different concentrations of reacting species it is shown that the intrinsic rate constant for alkylation is independent of the concentration of hydronium ions in the zeolite pores. Alkylation at the aromatic ring of phenol and of toluene as well as O-alkylation of phenol have the same activation energy, 104 ± 5 kJ/mol. This is energetic barrier to form the ethyl carbenium ion from ethanol associated to the hydronium ion. Thus, in both the reaction pathways the catalyst involves a carbenium ion, which forms a bond to a nucleophilic oxygen (ether formation) or carbon (alkylation).

  15. Reaction between peroxynitrite and boronates: EPR spin-trapping, HPLC analyses, and quantum mechanical study of the free radical pathway

    Science.gov (United States)

    Sikora, Adam; Zielonka, Jacek; Lopez, Marcos; Dybala-Defratyka, Agnieszka; Joseph, Joy; Marcinek, Andrzej; Kalyanaraman, Balaraman

    2013-01-01

    Recently we showed that peroxynitrite (ONOO−) reacts directly and rapidly with aromatic and aliphatic boronic acids (k ≈ 106 M−1s−1). Product analyses and substrate consumption data indicated that ONOO− reacts stoichiometrically with boronates, yielding the corresponding phenols as the major product (~85–90%), and the remaining products (10–15%) were proposed to originate from free radical intermediates (phenyl and phenoxyl radicals). Here we investigated in detail the minor, free radical pathway of boronate reaction with ONOO−. The electron paramagnetic resonance (EPR) spin-trapping technique was used to characterize the free radical intermediates formed from the reaction between boronates and ONOO−. Using 2-methyl-2-nitrosopropane (MNP) and 5-diethoxyphosphoryl-5-methyl-1-pyrroline-N-oxide (DEPMPO) spin traps, phenyl radicals were trapped and detected. Although phenoxyl radicals were not detected, the positive effects of molecular oxygen, and inhibitory effects of hydrogen atom donors (acetonitrile, and 2-propanol) and general radical scavengers (GSH, NADH, ascorbic acid and tyrosine) on the formation of phenoxyl radical-derived nitrated product, suggest that phenoxyl radical was formed as the secondary species. We propose that the initial step of the reaction involves the addition of ONOO− to the boron atom in boronates. The anionic intermediate undergoes both heterolytic (major pathway) and homolytic (minor pathway) cleavage of the peroxy (O-O) bond to form phenol and nitrite as a major product (via a non-radical mechanism), or a radical pair PhB(OH)2O•−…•NO2 as a minor product. It is conceivable that phenyl radicals are formed by the fragmentation of PhB(OH)2O•− radical anion. According to the DFT quantum mechanical calculations, the energy barrier for the dissociation of PhB(OH)2O•− radical anion to form phenyl radicals is only a few kcal/mol, suggesting rapid and spontaneous fragmentation of PhB(OH)2O•− radical anion

  16. Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A: Kinetics, reaction pathways, and formation of brominated by-products

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Yuefei [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Kong, Deyang [Nanjing Institute of Environmental Science, Ministry of Environmental Protection of PRC, Nanjing 210042 (China); Lu, Junhe, E-mail: jhlu@njau.edu.cn [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China); Jin, Hao; Kang, Fuxing; Yin, Xiaoming; Zhou, Quansuo [Department of Environmental Science and Engineering, Nanjing Agricultural University, Nanjing 210095 (China)

    2016-08-05

    Highlights: • Cobalt catalyzed peroxymonosulfate oxidation of tetrabromobisphenol A. • Phenolic moiety was the reactive site for sulfate radical attack. • Pathways include β-scission, oxidation, debromination and coupling reactions. • Brominated disinfection by-products were found during TBBPA degradation. • Humic acid inhibited TBBPA degradation but promoted DBPs formation. - Abstract: Degradation of tetrabromobisphenol A (TBBPA), a flame retardant widely spread in the environment, in Co(II) catalyzed peroxymonosulfate (PMS) oxidation process was systematically explored. The second-order-rate constant for reaction of sulfate radical (SO{sub 4}{sup ·−}) with TBBPA was determined to be 5.27 × 10{sup 10} M{sup −1} s{sup −1}. Apparently, degradation of TBBPA showed first-order kinetics to the concentrations of both Co(II) and PMS. The presence of humic acid (HA) and bicarbonate inhibited TBBPA degradation, most likely due to their competition for SO{sub 4}{sup ·−}. Degradation of TBBPA was initiated by an electron abstraction from one of the phenolic rings. Detailed transformation pathways were proposed, including β-scission of isopropyl bridge, phenolic ring oxidation, debromination and coupling reactions. Further oxidative degradation of intermediates in Co(II)/PMS process yielded brominated disinfection by-products (Br-DBPs) such as bromoform and brominated acetic acids. Evolution profile of Br-DBPs showed an initially increasing and then decreasing pattern with maximum concentrations occurring around 6–10 h. The presence of HA enhanced the formation of Br-DBPs significantly. These findings reveal potentially important, but previously unrecognized, formation of Br-DBPs during sulfate radical-based oxidation of bromide-containing organic compounds that may pose toxicological risks to human health.

  17. Extracting reaction networks from databases-opening Pandora's box.

    Science.gov (United States)

    Fearnley, Liam G; Davis, Melissa J; Ragan, Mark A; Nielsen, Lars K

    2014-11-01

    Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge. © The Author 2013. Published by Oxford University Press.

  18. Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

    International Nuclear Information System (INIS)

    Wang Sufan; Smith, Sean C.

    2006-01-01

    The 'leading coordinate' approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information

  19. DFT study of benzyl alcohol/TiO2 interfacial surface complex: reaction pathway and mechanism of visible light absorption.

    Science.gov (United States)

    Zhao, Lei; Gu, Feng Long; Kim, Minjae; Miao, Maosheng; Zhang, Rui-Qin

    2017-09-24

    We propose a new pathway for the adsorption of benzyl alcohol on the surface of TiO 2 and the formation of interfacial surface complex (ISC). The reaction free energies and reaction kinetics were thoroughly investigated by density functional calculations. The TiO 2 surfaces were modeled by clusters consisting of 4 Ti atoms and 18 O atoms passivated by H, OH group and H 2 O molecules. Compared with solid-state calculations utilizing the periodicity of the materials, such cluster modeling allows inclusion of the high-order correlation effects that seem to be essential for the adsorption of organic molecules onto solid surfaces. The effects of both acidity and solvation are included in our calculations, which demonstrate that the new pathway is competitive with a previous pathway. The electronic structure calculations based on the relaxed ISC structures reveal that the chemisorption of benzyl alcohol on the TiO 2 surface greatly alters the nature of the frontier molecular orbitals. The resulted reduced energy gap in ISC matches the energy of visible light, showing how the adsorption of benzyl alcohol sensitizes the TiO 2 surface. Graphical Abstract The chemisorption of benzyl alcohol on TiO 2 surface greatly alters the nature of the frontier molecular orbitals and the formed interfacial surface complex can be sensitized by visible light.

  20. PREVAIL: latest electron optics results

    Science.gov (United States)

    Pfeiffer, Hans C.; Golladay, Steven D.; Gordon, Michael S.; Kendall, Rodney A.; Lieberman, Jon E.; Rockrohr, James D.; Stickel, Werner; Yamaguchi, Takeshi; Okamoto, Kazuya; Umemoto, Takaaki; Shimizu, Hiroyasu; Kojima, Shinichi; Hamashima, Muneki

    2002-07-01

    The PREVAIL electron optics subsystem developed by IBM has been installed at Nikon's facility in Kumagaya, Japan, for integration into the Nikon commercial EPL stepper. The cornerstone of the electron optics design is the Curvilinear Variable Axis Lens (CVAL) technique originally demonstrated with a proof of concept system. This paper presents the latest experimental results obtained with the electron optical subsystem at Nikon's facility. The results include micrographs illustrating proper CVAL operation through the spatial resolution achieved over the entire optical field of view. They also include data on the most critical issue of the EPL exposure approach: subfield stitching. The methodology of distortion correction will be described and both micrographs and metrology data of stitched subfields will be presented. This paper represents a progress report of the IBM/Nikon alliance activity on EPL.

  1. 78 FR 60181 - Prevailing Rate Systems; Redefinition of the Clayton-Cobb-Fulton, Georgia, Nonappropriated Fund...

    Science.gov (United States)

    2013-10-01

    ... OFFICE OF PERSONNEL MANAGEMENT 5 CFR Part 532 RIN 3206-AM84 Prevailing Rate Systems; Redefinition of the Clayton-Cobb-Fulton, Georgia, Nonappropriated Fund Federal Wage System Wage Area AGENCY: U.S... Counties). The Federal Prevailing Rate Advisory Committee, the national labor-management committee...

  2. Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

    Science.gov (United States)

    Zhang, Hong; Zuo, Ran; Zhang, Guoyi

    2017-11-01

    In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

  3. Is the Economic Crisis Challenging the Prevailing Gender Regime?

    DEFF Research Database (Denmark)

    Leschke, Janine; Jepsen, Maria

    2014-01-01

    and analysing the corresponding position of women and men in paid and unpaid work, the paper contains an in-depth discussion of the short- and medium-term policy responses to the crisis. Our analysis shows that independent of the prevailing gender regime, scant public attention has been directed to gender...

  4. A case for 'prevailing ecology' as premium determinant in home ...

    African Journals Online (AJOL)

    A case for 'prevailing ecology' as premium determinant in home-based child care ... Ewe mothers located in Dzemeni a migrant, lakeside community in Ghana. ... It builds a case from the analysis of definitions and concepts in care literature.

  5. Mechanisms for the inversion of chirality: Global reaction route mapping of stereochemical pathways in a probable chiral extraterrestrial molecule, 2-aminopropionitrile

    International Nuclear Information System (INIS)

    Kaur, Ramanpreet; Vikas

    2015-01-01

    2-Aminopropionitrile (APN), a probable candidate as a chiral astrophysical molecule, is a precursor to amino-acid alanine. Stereochemical pathways in 2-APN are explored using Global Reaction Route Mapping (GRRM) method employing high-level quantum-mechanical computations. Besides predicting the conventional mechanism for chiral inversion that proceeds through an achiral intermediate, a counterintuitive flipping mechanism is revealed for 2-APN through chiral intermediates explored using the GRRM. The feasibility of the proposed stereochemical pathways, in terms of the Gibbs free-energy change, is analyzed at the temperature conditions akin to the interstellar medium. Notably, the stereoinversion in 2-APN is observed to be more feasible than the dissociation of 2-APN and intermediates involved along the stereochemical pathways, and the flipping barrier is observed to be as low as 3.68 kJ/mol along one of the pathways. The pathways proposed for the inversion of chirality in 2-APN may provide significant insight into the extraterrestrial origin of life

  6. Stochasticity in the yeast mating pathway

    International Nuclear Information System (INIS)

    Hong-Li, Wang; Zheng-Ping, Fu; Xin-Hang, Xu; Qi, Ouyang

    2009-01-01

    We report stochastic simulations of the yeast mating signal transduction pathway. The effects of intrinsic and external noise, the influence of cell-to-cell difference in the pathway capacity, and noise propagation in the pathway have been examined. The stochastic temporal behaviour of the pathway is found to be robust to the influence of inherent fluctuations, and intrinsic noise propagates in the pathway in a uniform pattern when the yeasts are treated with pheromones of different stimulus strengths and of varied fluctuations. In agreement with recent experimental findings, extrinsic noise is found to play a more prominent role than intrinsic noise in the variability of proteins. The occurrence frequency for the reactions in the pathway are also examined and a more compact network is obtained by dropping most of the reactions of least occurrence

  7. Dexmedetomidine Inhibits Inflammatory Reaction in Lung Tissues of Septic Rats by Suppressing TLR4/NF-κB Pathway

    Directory of Open Access Journals (Sweden)

    Yuqing Wu

    2013-01-01

    and 20 μg/kg significantly decreased mortality and pulmonary inflammation of septic rats, as well as suppressed CLP-induced elevation of TNF-α and IL-6 and inhibited TLR4/MyD88 expression and NF-κB activation. These results suggest that dexmedetomidine may decrease mortality and inhibit inflammatory reaction in lung tissues of septic rats by suppressing TLR4/MyD88/NF-κB pathway.

  8. Primary Metabolic Pathways and Metabolic Flux Analysis

    DEFF Research Database (Denmark)

    Villadsen, John

    2015-01-01

    his chapter introduces the metabolic flux analysis (MFA) or stoichiometry-based MFA, and describes the quantitative basis for MFA. It discusses the catabolic pathways in which free energy is produced to drive the cell-building anabolic pathways. An overview of these primary pathways provides...... the reader who is primarily trained in the engineering sciences with atleast a preliminary introduction to biochemistry and also shows how carbon is drained off the catabolic pathways to provide precursors for cell mass building and sometimes for important industrial products. The primary pathways...... to be examined in the following are: glycolysis, primarily by the EMP pathway, but other glycolytic pathways is also mentioned; fermentative pathways in which the redox generated in the glycolytic reactions are consumed; reactions in the tricarboxylic acid (TCA) cycle, which produce biomass precursors and redox...

  9. Analyzing atmospheric kinetic pathways using PumpKin

    Science.gov (United States)

    Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

    2013-09-01

    In the present work we show the application of our software tool called PumpKin (pathway reduction method for plasma kinetic models) to find all principal pathways of atmospheric kinetic system, i.e. the dominant reaction sequences, in chemical reaction systems. The goal was to reduce a complex plasma chemistry model. Recent kinetic models of atmospheric chemistry, or any industrial application, contain thousands of chemical reactions and species. The main difficulty is that these reduced chemical pathways depend on timescales, electric field, temperature, pressure etc. PumpKin is a universal tool, which only requires from user the temporal profile of the densities of species and the reaction rates, as well the stoichiometric matrix of the system. Also, the user should specify the timescale of interest.

  10. ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

    Science.gov (United States)

    Kayala, Matthew A; Baldi, Pierre

    2012-10-22

    Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

  11. Electrophilic properties of patulin. Adduct structures and reaction pathways with 4-bromothiophenol and other model nucleophiles.

    Science.gov (United States)

    Fliege, R; Metzler, M

    2000-05-01

    The mycotoxin patulin (PAT) is believed to exert its cytotoxic and chromosome-damaging effects by forming covalent adducts with essential cellular thiols. Since the chemical structures of such adducts are unknown to date, we have studied the reaction of PAT and its O-acetylated derivative with the monofunctional thiol model compound 4-bromothiophenol (BTP), which was chosen due to analytical advantages. By means of analytical and preparative high-performance liquid chromatography, 16 adducts of PAT and 3 adducts of acetyl-PAT were isolated and their chemical structures elucidated by (1)H and (13)C NMR, IR, and UV spectroscopy. Time course studies and analysis of daughter product formation from isolated intermediate adducts led to a detailed scheme for the reaction of PAT with BTP. The structures of adducts of PAT formed with other model nucleophiles, e. g., the aliphatic thiol 2-mercaptoethanol and the aromatic amine 4-bromoaniline, were also elucidated and found to corroborate the reaction scheme. In addition, one further reaction pathway was observed with 2-mercaptoethanol, which appears to be independent from those found for BTP. Our study with model nucleophiles provides insights into the electrophilic reactivity of PAT and proved to be useful for the structure elucidation of PAT adducts with biological nucleophiles of toxicological relevance, as will be reported by Fliege and Metzler [(2000) Chem. Res. Toxicol. 13, 373-381].

  12. Degradation of γ-HCH spiked soil using stabilized Pd/Fe0 bimetallic nanoparticles: Pathways, kinetics and effect of reaction conditions

    International Nuclear Information System (INIS)

    Singh, Ritu; Misra, Virendra; Mudiam, Mohana Krishna Reddy; Chauhan, Lalit Kumar Singh; Singh, Rana Pratap

    2012-01-01

    Highlights: ► This study explores the potential of CMC-Pd/nFe 0 to degrade γ-HCH in spiked soil. ► Sorption–desorption characteristics and partitioning of γ-HCH is investigated. ► Three degradation pathways has been proposed and discussed. ► γ-HCH degradation mechanism and kinetics is elucidated. ► Activation energy reveals that γ-HCH degradation is a surface mediated reaction. - Abstract: This study investigates the degradation pathway of gamma-hexachlorocyclohexane (γ-HCH) in spiked soil using carboxymethyl cellulose stabilized Pd/Fe 0 bimetallic nanoparticles (CMC-Pd/nFe 0 ). GC–MS analysis of γ-HCH degradation products showed the formation of pentachlorocyclohexene, tri- and di-chlorobenzene as intermediate products while benzene was formed as the most stable end product. On the basis of identified intermediates and final products, degradation pathway of γ-HCH has been proposed. Batch studies showed complete γ-HCH degradation at a loading of 0.20 g/L CMC-Pd/nFe 0 within 6 h of incubation. The surface area normalized rate constant (k SA ) was found to be 7.6 × 10 −2 L min −1 m −2 . CMC-Pd/nFe 0 displayed ∼7-fold greater efficiency for γ-HCH degradation in comparison to Fe 0 nanoparticles (nFe 0 ), synthesized without CMC and Pd. Further studies showed that increase in CMC-Pd/nFe 0 loading and reaction temperature facilitates γ-HCH degradation, whereas a declining trend in degradation was noticed with the increase in pH, initial γ-HCH concentration and in the presence of cations. The data on activation energy (33.7 kJ/mol) suggests that γ-HCH degradation is a surface mediated reaction. The significance of the study with respect to remediation of γ-HCH contaminated soil using CMC-Pd/nFe 0 has been discussed.

  13. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

    KAUST Repository

    Mohamed, Samah; Cai, Liming; Khaled, Fathi; Banyon, Colin; Wang, Zhandong; Rachidi, Mariam El; Pitsch, Heinz; Curran, Henry J.; Farooq, Aamir; Sarathy, Mani

    2016-01-01

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

  14. Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

    KAUST Repository

    Mohamed, Samah

    2016-03-21

    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

  15. Pathways for the reaction of the butadiene radical cation, [C{sub 4}H{sub 6}]{sup {sm{underscore}bullet}+}, with ethylene

    Energy Technology Data Exchange (ETDEWEB)

    Hofmann, M.; Schaefer, H.F. III

    1999-11-04

    The Diels-Alder (DA) reaction, a [4+2] cycloaddition used to build six membered rings, is one of the most valuable cycloadditions in organic chemistry. In cases where the ene does not add to the diene (even with the help of Lewis acids which may reduce the electron density of one reactant by complexation) one electron oxidation (by an oxidizing agent or by photoinduced electron transfer (PET)) may accelerate the reaction. Reaction pathways for the addition of ethylene, 1, to butadiene radical cation, 2, involving H-shifts have been investigated at the coupled cluster UCCSD(T)/DZP//UMP2(fc)/DZP + ZPE level of theory. Activation energies are relatively low for [1,2]- (10.0 kcal mol{sup {minus}1}, TS-4/20) and [1,5]-hydrogen shifts (7.7 kcal mol{sup {minus}1}, TS-4/26) but are relatively high for [1,4]-(33.8 kcal mol{sup {minus}1}, TS-4/14) and [1,3]-H shifts (e.g., 42.2 kcal mol{sup {minus}1}, TS-12/13; 57.2 kcal mol{sup {minus}1}, TS-16/21). Several rearrangement reactions have been found to occur below the energy limit of separated 1 + 2. The cyclopentenyl cation, [C{sub 5}{sub 7}]{sup +}, 18, experimentally observed as reaction product of the butadiene radical cation, 2, and ethylene, 1, in the gas phase may origin from various reaction pathways. The following reaction sequence has been identified as the lowest in energy path from 1 + 2 to 18 with all relative energies ({Delta}E{degree}) of transition structures below that of 1 + 2: (a) ethylene adds to the butadiene radical cation to form an open-chain distonic intermediate, that undergoes a [1,5]-H shift to the 1,4-hexadiene radical cation; (b) intramolecular [2+1] cycloaddition to methyl-cyclopenta-1,3-diyl intermediates, which can interconvert through a bicyclo[2.1.0]pentane radical cation; (c) [1,2]-H shift to the 3-methyl cyclopentene radical cation; (d) methyl radical loss to give cyclopenten-3-yl cation. Along this reaction pathway, {Delta}H{sup 298} is below that of 1 + 2; max. ({Delta}G{sup 298} by

  16. Effects of Prevailing Winds on Turbidity of a Shallow Estuary

    Directory of Open Access Journals (Sweden)

    Hyun Jung Cho

    2007-06-01

    Full Text Available Estuarine waters are generally more turbid than lakes or marine waters due to greater algal mass and continual re-suspension of sediments. The varying effects of diurnal and seasonal prevailing winds on the turbidity condition of a wind-dominated estuary were investigated by spatial and statistical analyses of wind direction, water level, turbidity, chlorophyll a, and PAR (Photosynthetically Active Radiation collected in Lake Pontchartrain, Louisiana, USA. The prolonged prevailing winds were responsible for the long-term, large-scale turbidity pattern of the estuary, whereas the short-term changes in wind direction had differential effects on turbidity and water level in varying locations. There were temporal and spatial changes in the relationship between vertical light attenuation coefficient (Kd and turbidity, which indicate difference in phytoplankton and color also affect Kd. This study demonstrates that the effect of wind on turbidity and water level on different shores can be identified through system-specific analyses of turbidity patterns.

  17. 76 FR 14679 - Prevailing Wage Rates for Construction Occupations on Guam for Purposes of the H-2B Temporary...

    Science.gov (United States)

    2011-03-17

    ...)(v)(E) and (F). If the prevailing wage rate is too low, available U.S. workers may be dissuaded from... Docket No. USCIS-2010-0006] RIN 1615-ZA98 Prevailing Wage Rates for Construction Occupations on Guam for... the public on the system that the Governor of Guam is using to determine prevailing wage rates for...

  18. Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

    Science.gov (United States)

    Flamholz, Avi; Reznik, Ed; Liebermeister, Wolfram; Milo, Ron

    2014-01-01

    In metabolism research, thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway. However, the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions through the flux-force relationship, which states that the logarithm of the ratio between the forward and reverse fluxes is directly proportional to the change in Gibbs energy due to a reaction (ΔrG′). Accordingly, if an enzyme catalyzes a reaction with a ΔrG′ of -5.7 kJ/mol then the forward flux will be roughly ten times the reverse flux. As ΔrG′ approaches equilibrium (ΔrG′ = 0 kJ/mol), exponentially more enzyme counterproductively catalyzes the reverse reaction, reducing the net rate at which the reaction proceeds. Thus, the enzyme level required to achieve a given flux increases dramatically near equilibrium. Here, we develop a framework for quantifying the degree to which pathways suffer these thermodynamic limitations on flux. For each pathway, we calculate a single thermodynamically-derived metric (the Max-min Driving Force, MDF), which enables objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force. Our framework accounts for the effect of pH, ionic strength and metabolite concentration ranges and allows us to quantify how alterations to the pathway structure affect the pathway's thermodynamics. Applying this methodology to pathways of central metabolism sheds light on some of their features, including metabolic bypasses (e.g., fermentation pathways bypassing substrate-level phosphorylation), substrate channeling (e.g., of oxaloacetate from malate dehydrogenase to citrate synthase), and use of alternative cofactors (e.g., quinone as an electron acceptor instead of NAD). The methods presented here place another arrow in metabolic engineers' quiver, providing a simple means of evaluating

  19. NMR studies of stock process water and reaction pathways in hydrothermal carbonization of furfural residue

    Directory of Open Access Journals (Sweden)

    Fen Yue

    2018-04-01

    Full Text Available Hydrothermal carbonization (HTC is a valuable approach to convert furfural residue (FR into carbon material. The prepared biochars are usually characterized comprehensively, while the stock process water still remains to be studied in detail. Herein, a NMR study of the main components in stock process water generated at different HTC reaction conditions was reported. Various qualitative and quantitative NMR techniques (1H and 13C NMR, 1H–1H COSY and 1H13C HSQC etc. especially 1D selective gradient total correlation spectroscopy (TOCSY NMR were strategically applied in the analysis of HTC stock process water. Without separation and purification, it was demonstrated that the main detectable compounds are 5-hydroxymethylfurfural, formic acid, methanol, acetic acid, levulinic acid, glycerol, hydroxyacetone and acetaldehyde in this complicate mixture. Furthermore, the relationship between the concentration of major products and the reaction conditions (180–240 °C at 8 h, and 1–24 h at 240 °C was established. Finally, reasonable reaction pathways for hydrothermal conversion of FR were proposed based on this result and our previously obtained characteristics of biochars. The routine and challenging NMR methods utilized here would be an alternative other than HPLC or GC for biomass conversion research and can be extended to more studies. Keywords: NMR, Hydrothermal carbonization, Furfural residue, Stock process water

  20. [Effects and mechanisms of the inflammatory reaction related to NASH and induced by activation of the cholinergic anti-inflammatory pathway].

    Science.gov (United States)

    Zhou, Zhou; Chen, Xiaomei; Li, Fuqiang; Tang, Cuilan

    2015-01-01

    To investigate the effects and mechanisms of the inflammatory reaction related to nonalcoholic steatohepatitis (NASH) and induced by activation of the cholinergic anti-inflammatory pathway. A mouse model of NASH was established by feeding a high-fat and high-sugar diet.Activation of the cholinergic anti-inflammatory pathway was achieved by nicotine administration to the NASH modeled mice and normal controls. Liver biopsies were taken and the concentrations of cytokines were measured. Isolated liver primary Kupffer cells and RAw264.7 cells were cultured, pre-treated or not with lipopolysaccharide (LPS) and exposed to nicotine, after which the supernatant concentrations of IL-6 and TNFa were determined by ELISA. The protein expression levels of phosphorylated (p)-NF-kB and I k B were detected in primary cultured Kupffer cells by western blotting. The mouse model of NASH was successfully established, as evidenced by findings from liver biopsy and serum liver function tests. The degree of liver inflammation in the NASH mice decreased after nicotine administration, and the level of serum TNFa also significantly decreased. The levels of serum TNFa were 21.95+/-0.8 pg/mL in nicotine-treated mice and 38.07+/-1.7 pg/mL in the non-nicotine-treated NASH mice (P less than 0.05). The nicotine treatment also significantly reduced the concentration of TNFa in the culture supernatants of Kupffer cells after LPS stimulation; moreover, the supernatant level of TNFa decreased significantly after the nicotine treatment (Pless than 0.05). LPS stimulation of the RAw264.7 cells led to an increased level ofp-NF-kB and a reduced level ofI-kB, suggesting that the NF-kB pathway had been activated; different doses of nicotine pre-treatment led to down-regulation of the p-NF-kB level and up-regulation of the I-kB level, both in dose-dependent manners. Activating the cholinergic anti-inflammatory pathway inhibits the NASH-related inflammatory reaction, and the mechanism for this inhibition

  1. Functional Dissociations within the Ventral Object Processing Pathway: Cognitive Modules or a Hierarchical Continuum?

    Science.gov (United States)

    Cowell, Rosemary A.; Bussey, Timothy J.; Saksida, Lisa M.

    2010-01-01

    We examined the organization and function of the ventral object processing pathway. The prevailing theoretical approach in this field holds that the ventral object processing stream has a modular organization, in which visual perception is carried out in posterior regions and visual memory is carried out, independently, in the anterior temporal…

  2. Reaction Decoder Tool (RDT): extracting features from chemical reactions.

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

    2016-07-01

    Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

  3. Post hoc analyses of East Asian patients from the randomized placebo-controlled PREVAIL trial of enzalutamide in patients with chemotherapy-naïve, metastatic castration-resistant prostate cancer.

    Science.gov (United States)

    Kim, Choung Soo; Choi, Young Deuk; Lee, Sang Eun; Lee, Hyun Moo; Ueda, Takeshi; Yonese, Junji; Fukagai, Takashi; Chiong, Edmund; Lau, Weber; Abhyankar, Sarang; Theeuwes, Ad; Tombal, Bertrand; Beer, Tomasz M; Kimura, Go

    2017-07-01

    Enzalutamide is an androgen receptor (AR) inhibitor that acts on different steps in the AR signaling pathway. In PREVAIL, an international, phase III, double-blind, placebo-controlled trial, enzalutamide significantly reduced the risk of radiographic progression by 81% (hazard ratio [HR], 0.19; P PREVAIL trial, we performed a post hoc analysis of the Japanese, Korean, and Singaporean patients. PREVAIL enrolled patients with asymptomatic or mildly symptomatic chemotherapy-naïve metastatic castration-resistant prostate cancer who had progressed on androgen deprivation therapy. During the study, patients received enzalutamide (160 mg/d) or placebo (1:1) until death or discontinuation because of radiographic progression or skeletal-related event and initiation of subsequent therapy. Centrally assessed radiographic progression-free survival (rPFS) and overall survival (OS) were coprimary endpoints. The secondary endpoints of the PREVAIL trial were investigator-assessed rPFS, time to initiation of chemotherapy, time to prostate-specific antigen (PSA) progression, and PSA response (≥50% decline). Of 1717 patients, 148 patients were enrolled at sites in East Asia (enzalutamide 73, placebo 75). Treatment effect of enzalutamide versus placebo was consistent with that for the overall population as indicated by the HRs (95% confidence interval) of 0.38 (0.10-1.44) for centrally assessed rPFS, 0.59 (0.29-1.23) for OS, 0.33 (0.19-0.60) for time to chemotherapy, and 0.32 (0.20-0.50) for time to PSA progression. In East Asian patients, PSA responses were observed in 68.5% and 14.7% of enzalutamide- and placebo-treated patients, respectively. The enzalutamide plasma concentration ratio (East Asian:non-Asian patients) was 1.12 (90% confidence interval, 1.05-1.20) at 13 weeks. Treatment-related adverse events grade ≥ 3 occurred in 1.4% and 2.7% of enzalutamide- and placebo-treated East Asian patients, respectively. Treatment effects and safety of enzalutamide in East Asian

  4. Kinetic and thermodynamic study of the reaction catalyzed by glucose-6-phosphate dehydrogenase with nicotinamide adenine dinucleotide

    International Nuclear Information System (INIS)

    Martin del Campo, Julia S.; Patino, Rodrigo

    2011-01-01

    Research highlights: → The reaction catalyzed by one enzyme of the pentose phosphate pathway was studied. → A spectrophotometric method is proposed for kinetic and thermodynamic analysis. → The pH and the temperature influences are reported on physical chemical properties. → Relative concentrations of substrates are also important in the catalytic process. - Abstract: The enzyme glucose-6-phosphate dehydrogenase (G6PD, EC 1.1.1.49) from Leuconostoc mesenteroides has a dual coenzyme specificity with oxidized nicotinamide adenine dinucleotide (NAD ox ) and oxidized nicotinamide adenine dinucleotide phosphate as electron acceptors. The G6PD coenzyme selection is determined by the metabolic cellular prevailing conditions. In this study a kinetic and thermodynamic analysis is presented for the reaction catalyzed by G6PD from L. mesenteroides with NAD ox as coenzyme in phosphate buffer. For this work, an in situ spectrophotometric technique was employed based on the detection of one product of the reaction. Substrate and coenzyme concentrations as well as temperature and pH effects were evaluated. The apparent equilibrium constant, the Michaelis constant, and the turnover number were determined as a function of each experimental condition. The standard transformed Gibbs energy of reaction was determined from equilibrium constants at different initial conditions. For the product 6-phospho-D-glucono-1,5-lactone, a value of the standard Gibbs energy of formation is proposed, Δ f G o = -1784 ± 5 kJ mol -1 .

  5. Kinetic and thermodynamic study of the reaction catalyzed by glucose-6-phosphate dehydrogenase with nicotinamide adenine dinucleotide

    Energy Technology Data Exchange (ETDEWEB)

    Martin del Campo, Julia S. [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados - Unidad Merida, Carretera antigua a Progreso Km. 6, A.P. 73 Cordemex, 97310, Merida, Yucatan (Mexico); Patino, Rodrigo, E-mail: rtarkus@mda.cinvestav.mx [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados - Unidad Merida, Carretera antigua a Progreso Km. 6, A.P. 73 Cordemex, 97310, Merida, Yucatan (Mexico)

    2011-04-20

    Research highlights: {yields} The reaction catalyzed by one enzyme of the pentose phosphate pathway was studied. {yields} A spectrophotometric method is proposed for kinetic and thermodynamic analysis. {yields} The pH and the temperature influences are reported on physical chemical properties. {yields} Relative concentrations of substrates are also important in the catalytic process. - Abstract: The enzyme glucose-6-phosphate dehydrogenase (G6PD, EC 1.1.1.49) from Leuconostoc mesenteroides has a dual coenzyme specificity with oxidized nicotinamide adenine dinucleotide (NAD{sub ox}) and oxidized nicotinamide adenine dinucleotide phosphate as electron acceptors. The G6PD coenzyme selection is determined by the metabolic cellular prevailing conditions. In this study a kinetic and thermodynamic analysis is presented for the reaction catalyzed by G6PD from L. mesenteroides with NAD{sub ox} as coenzyme in phosphate buffer. For this work, an in situ spectrophotometric technique was employed based on the detection of one product of the reaction. Substrate and coenzyme concentrations as well as temperature and pH effects were evaluated. The apparent equilibrium constant, the Michaelis constant, and the turnover number were determined as a function of each experimental condition. The standard transformed Gibbs energy of reaction was determined from equilibrium constants at different initial conditions. For the product 6-phospho-D-glucono-1,5-lactone, a value of the standard Gibbs energy of formation is proposed, {Delta}{sub f}G{sup o} = -1784 {+-} 5 kJ mol{sup -1}.

  6. Predicting metabolic pathways by sub-network extraction.

    Science.gov (United States)

    Faust, Karoline; van Helden, Jacques

    2012-01-01

    Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.

  7. Application of Enzyme Coupling Reactions to Shift Thermodynamically Limited Biocatalytic Reactions

    DEFF Research Database (Denmark)

    Abu, Rohana; Woodley, John M.

    2015-01-01

    , it can be challenging to combine several engineered enzymes in vitro for the conversion of non-natural substrates. In this mini-review we focus on enzyme coupling reactions as a tool to alleviate thermodynamic constraints in synthetically useful biocatalytic reactions. The implications of thermodynamic...... shift the equilibrium of otherwise thermodynamically unfavourable reactions to give a higher conversion of the target product. By coupling an energetically unfavourable reaction with a more favourable one, the multi-enzyme cascade mimics the approach taken in nature in metabolic pathways. Nevertheless...

  8. Metabolic signature of sun exposed skin suggests catabolic pathway overweighs anabolic pathway.

    Directory of Open Access Journals (Sweden)

    Manpreet Randhawa

    Full Text Available Skin chronically exposed to sun results in phenotypic changes referred as photoaging. This aspect of aging has been studied extensively through genomic and proteomic tools. Metabolites, the end product are generated as a result of biochemical reactions are often studied as a culmination of complex interplay of gene and protein expression. In this study, we focused exclusively on the metabolome to study effects from sun-exposed and sun-protected skin sites from 25 human subjects. We generated a highly accurate metabolomic signature for the skin that is exposed to sun. Biochemical pathway analysis from this data set showed that sun-exposed skin resides under high oxidative stress and the chains of reactions to produce these metabolites are inclined toward catabolism rather than anabolism. These catabolic activities persuade the skin cells to generate metabolites through the salvage pathway instead of de novo synthesis pathways. Metabolomic profile suggests catabolic pathways and reactive oxygen species operate in a feed forward fashion to alter the biology of sun exposed skin.

  9. Synthetic Control of Kinetic Reaction Pathway and Cationic Ordering in High-Ni Layered Oxide Cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Dawei [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory Physical Chemistry Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen Fujian 361005 China; Kou, Ronghui [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Ren, Yang [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Sun, Cheng-Jun [X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne IL 60439 USA; Zhao, Hu [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; Zhang, Ming-Jian [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA; School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen Guangdong 518055 P. R. China; Li, Yan [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Huq, Ashifia [Chemical and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge TN 37831 USA; Ko, J. Y. Peter [The Cornell High Energy Synchrotron Source, Cornell University, Ithaca NY 14853 USA; Pan, Feng [School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen Guangdong 518055 P. R. China; Sun, Yang-Kook [Department of Energy Engineering, Hanyang University, Seoul 133-791 South Korea; Yang, Yong [Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory Physical Chemistry Solid Surfaces, Department of Chemistry, Xiamen University, Xiamen Fujian 361005 China; Amine, Khalil [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Bai, Jianming [National Synchrotron Light Source II, Brookhaven National Laboratory, Upton NY 11973 USA; Chen, Zonghai [Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne IL 60439 USA; Wang, Feng [Sustainable Energy Technologies Department, Brookhaven National Laboratory, Upton NY 11973 USA

    2017-08-25

    Nickel-rich layered transition metal oxides, LiNi1-x(MnCo)(x)O-2 (1-x >= 0.5), are appealing candidates for cathodes in next-generation lithium-ion batteries (LIBs) for electric vehicles and other large-scale applications, due to their high capacity and low cost. However, synthetic control of the structural ordering in such a complex quaternary system has been a great challenge, especially in the presence of high Ni content. Herein, synthesis reactions for preparing layered LiNi0.7Mn0.15Co0.15O2 (NMC71515) by solid-state methods are investigated through a combination of time-resolved in situ high-energy X-ray diffraction and absorption spectroscopy measurements. The real-time observation reveals a strong temperature dependence of the kinetics of cationic ordering in NMC71515 as a result of thermal-driven oxidation of transition metals and lithium/oxygen loss that concomitantly occur during heat treatment. Through synthetic control of the kinetic reaction pathway, a layered NMC71515 with low cationic disordering and a high reversible capacity is prepared in air. The findings may help to pave the way for designing high-Ni layered oxide cathodes for LIBs.

  10. Interfacial reactions in intermetallic matrix composites

    International Nuclear Information System (INIS)

    Cantrell, L.B.; Clevenger, E.M.; Perepezko, J.H.

    1993-01-01

    The thermal stability of advanced composites is dominated by the behavior of internal interfaces. Analysis of these internal interfaces often involves consideration of at least ternary order phase equilibria. Limited thermodynamic data exists for ternary and higher order systems. However, a combined approach based upon the use of binary data to estimate ternary phase equilibria and experimentally determined reaction pathways is effective in the analysis of interface reactions in composite systems. In blended powder samples, thermal analysis was used to find possible reaction temperatures, while X-ray analysis, EDS, and EPMA of diffusion couples were used to assess interdiffusion reaction pathways. The approach is illustrated by compatibility studies between TiAl and TiSi 2 at 1,100 C, and in-situ reactions between B 4 C and TiAl at 1300 C where multiple reaction sequences have been analyzed to provide guidance for the design of in-situ reaction processing of composites

  11. Reactions of ferrate(VI) with iodide and hypoiodous acid: kinetics, pathways, and implications for the fate of iodine during water treatment.

    Science.gov (United States)

    Shin, Jaedon; von Gunten, Urs; Reckhow, David A; Allard, Sebastien; Lee, Yunho

    2018-06-01

    Oxidative treatment of iodide-containing waters can form iodinated disinfection by-products (I-DBPs) that are more toxic than the regulated DBPs. To better understand the fate of iodine during water treatment with ferrate(VI), kinetics, products, and stoichiometries for the reactions of ferrate(VI) with iodide (I - ) and hypoiodous acid (HOI) were determined. Ferrate(VI) showed considerable reactivities to both I - and HOI with higher reactivities at lower pH. Interestingly, the reaction of ferrate(VI) with HOI ( k = 6.0×10 3 M -1 s -1 at pH 9) was much faster than with I - ( k = 5.6×10 M -1 s -1 at pH 9). The main reaction pathway during treatment of I - -containing waters was the oxidation of I - to HOI and its further oxidation to IO 3 - by ferrate(VI). However, for pH > 9, the HOI disproportionation catalyzed by ferrate(VI) became an additional transformation pathway forming I - and IO 3 - . The reduction of HOI by hydrogen peroxide ( k = 2.0×10 8 M -1 s -1 for the reaction, HOI + HO 2 - → I - + O 2 + 2H + ), the latter being produced from ferrate(VI) decomposition, also contributes to the I - regeneration in the pH range 9 - 11. A kinetic model was developed that could well simulate the fate of iodine in the ferrate(VI)-I - system. Overall, due to a rapid oxidation of I - to IO 3 - with short-lifetimes of HOI, ferrate(VI) oxidation appears to be a promising option for I-DBP mitigation during treatment of I - -containing waters.

  12. Vets prevail online intervention reduces PTSD and depression in veterans with mild-to-moderate symptoms.

    Science.gov (United States)

    Hobfoll, Stevan E; Blais, Rebecca K; Stevens, Natalie R; Walt, Lisa; Gengler, Richard

    2016-01-01

    Despite heightened rates of depression and posttraumatic stress disorder (PTSD) among in Iraq/Afghanistan veterans, the majority of distressed veterans will not receive mental health care. Overcoming barriers to mental health services requires innovative approaches to broaden the reach of evidence-based treatment. The current study examined the efficacy and acceptability of an innovative and dynamic online cognitive-behavioral therapy intervention for PTSD and depression called Vets Prevail. A randomized clinical trial conducted between 2011 and 2013 assessed changes in PTSD and depression in veterans with mild-to-moderate distress. Veterans randomized to Vets Prevail (n = 209) were aged 34.2 ± 7.6 years, mostly male (81.3%), and nonminority (73.7%). Veterans randomized to adjustment as usual (n = 94) were aged 34.7 ± 8.9, mostly male (81.9%), and White (67.0%). Veterans completed the PTSD Checklist-Military Version and the Center for Epidemiological Studies Depression scale (10-item version) postintervention and at 12-week follow-up. Veterans in the Vets Prevail condition reported significantly greater reductions in PTSD, t(250) = 3.24, p = .001 (Mreduction = 5.51, SD = 9.63), and depression, t(252) = 4.37, p = .001 (Mreduction = 2.31, SD = 5.34), at 12-week follow-up compared with veterans in the adjustment as usual condition (PTSD Mreduction = 1.00, SD = 7.32; depression Mreduction = 0.48, SD = 4.95), with moderate effect sizes for PTSD (Cohen's d = 0.42) and depression (Cohen's d = 0.56). Exploratory analysis shows that Vets Prevail may be effective regardless of combat trauma exposure, gender, and ethnic minority status. Vets Prevail circumvents many barriers to care and effectively addresses the dire mental health needs of veterans. (c) 2015 APA, all rights reserved).

  13. 78 FR 70599 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2013-11-26

    ... of Personnel Management Building, 1900 E Street NW., Washington, DC. The Federal Prevailing Rate... the matters being considered and would disrupt substantially the disposition of its business... Advisory Committee, Room 5H27, 1900 E Street NW., Washington, DC 20415, (202) 606-9400. U.S. Office of...

  14. Reaction pathways of furfural, furfuryl alcohol and 2-methylfuran on Cu(111) and NiCu bimetallic surfaces

    Science.gov (United States)

    Xiong, Ke; Wan, Weiming; Chen, Jingguang G.

    2016-10-01

    Hydrodeoxygenation (HDO) is an important reaction for converting biomass-derived furfural to value-added 2-methylfuran, which is a promising fuel additive. In this work, the HDO of furfural to produce 2-methylfuran occurred on the NiCu bimetallic surfaces prepared on either Ni(111) or Cu(111). The reaction pathways of furfural were investigated on Cu(111) and Ni/Cu(111) surfaces using density functional theory (DFT) calculations, temperature-programmed desorption (TPD) and high-resolution electron energy loss spectroscopy (HREELS) experiments. These studies provided mechanistic insights into the effects of bimetallic formation on enhancing the HDO activity. Specifically, furfural weakly adsorbed on Cu(111), while it strongly adsorbed on Ni/Cu(111) through an η2(C,O) configuration, which led to the HDO of furfural on Ni/Cu(111). The ability to dissociate H2 on Ni/Cu(111) is also an important factor for enhancing the HDO activity over Cu(111).

  15. Reaction pathway of the degradation of the p-hydroxybenzoic acid by sulfate radical generated by ionizing radiations

    International Nuclear Information System (INIS)

    Criquet, Justine; Leitner, Nathalie Karpel Vel

    2015-01-01

    The degradation of p-hydroxybenzoic acid (HBA) in aqueous solutions by ionizing radiation was studied. The phenolic pollutant was easily removed by the electron beam irradiation, as more than 80% of the initial 100 µM introduced was degraded for a dose of 600 Gy. It was shown that the addition of persulfate, producing the sulfate radical as additional reactive species, induced a change in the reaction pathway. LC–MS analyses were performed in order to identify the different by-products formed. In the absence of persulfate, the main by-product formed was 3,4-dihydroxybenzoic acid, while in presence of persulfate, 1,4-benzoquinone was detected and the hydroxylated by-products were not present. A reaction pathway of HBA degradation by hydroxyl and sulfate radicals was proposed from the identification of the chemical structure of the different by-products detected. The influences of pH and dissolved oxygen were also studied. A high decline of HBA degradation was observed at pH 11 compared to pH 4.5, this decrease was minimized in the presence of persulfate. The dissolved oxygen concentration was found to be a limiting parameter of HBA degradation, however an excess of dissolved oxygen in solution did not improve the degradation to a large extent. - Highlights: • p-Hydroxybenzoic acid (HBA) is easily removed by e-beam irradiation. • The sulfate radicals formed from persulfate induce loss of the benzoic acid skeleton. • The dissolved oxygen concentration is a limiting parameter of the HBA degradation. • The effect of pH is minimized in presence of persulfate

  16. Reaction paths based on mean first-passage times

    International Nuclear Information System (INIS)

    Park, Sanghyun; Sener, Melih K.; Lu Deyu; Schulten, Klaus

    2003-01-01

    Finding representative reaction pathways is important for understanding the mechanism of molecular processes. We propose a new approach for constructing reaction paths based on mean first-passage times. This approach incorporates information about all possible reaction events as well as the effect of temperature. As an application of this method, we study representative pathways of excitation migration in a photosynthetic light-harvesting complex, photosystem I. The paths thus computed provide a complete, yet distilled, representation of the kinetic flow of excitation toward the reaction center, thereby succinctly characterizing the function of the system

  17. High-pressure vapor-phase hydrodeoxygenation of lignin-derived oxygenates to hydrocarbons by a PtMo bimetallic catalyst: Product selectivity, reaction pathway, and structural characterization

    Energy Technology Data Exchange (ETDEWEB)

    Yohe, Sara L.; Choudhari, Harshavardhan J.; Mehta, Dhairya D.; Dietrich, Paul J.; Detwiler, Michael D.; Akatay, Cem M.; Stach, Eric A.; Miller, Jeffrey T.; Delgass, W. Nicholas; Agrawal, Rakesh; Ribeiro, Fabio H.

    2016-12-01

    High-pressure, vapor-phase, hydrodeoxygenation (HDO) reactions of dihydroeugenol (2-methoxy-4-propylphenol), as well as other phenolic, lignin-derived compounds, were investigated over a bimetallic platinum and molybdenum catalyst supported on multi-walled carbon nanotubes (5%Pt2.5%Mo/MWCNT). Hydrocarbons were obtained in 100% yield from dihydroeugenol, including 98% yield of the hydrocarbon propylcyclohexane. The final hydrocarbon distribution was shown to be a strong function of hydrogen partial pressure. Kinetic analysis showed three main dihydroeugenol reaction pathways: HDO, hydrogenation, and alkylation. The major pathway occurred via Pt catalyzed hydrogenation of the aromatic ring and methoxy group cleavage to form 4-propylcyclohexanol, then Mo catalyzed removal of the hydroxyl group by dehydration to form propylcyclohexene, followed by hydrogenation of propylcyclohexene on either the Pt or Mo to form the propylcyclohexane. Transalkylation by the methoxy group occurred as a minor side reaction. Catalyst characterization techniques including chemisorption, scanning transmission electron microscopy, X-ray absorption spectroscopy, and X-ray photoelectron spectroscopy were employed to characterize the catalyst structure. Catalyst components identified were Pt particles, bimetallic PtMo particles, a Mo carbide-like phase, and Mo oxide phases.

  18. 77 FR 8926 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2012-02-15

    ... Personnel Management Building, 1900 E Street NW., Washington, DC. The Federal Prevailing Rate Advisory... considered and would disrupt substantially the disposition of its business. Therefore, these caucuses will be... 5H27, 1900 E Street NW., Washington, DC 20415, (202) 606-9400. U.S. Office of Personnel Management...

  19. 77 FR 76304 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2012-12-27

    ... 5A06A, U.S. Office of Personnel Management Building, 1900 E Street NW., Washington, DC. The Federal... the matters being considered and would disrupt substantially the disposition of its business... Management, Federal Prevailing Rate Advisory Committee, Room 5H27, 1900 E Street NW., Washington, DC 20415...

  20. Reconstructing biochemical pathways from time course data.

    Science.gov (United States)

    Srividhya, Jeyaraman; Crampin, Edmund J; McSharry, Patrick E; Schnell, Santiago

    2007-03-01

    Time series data on biochemical reactions reveal transient behavior, away from chemical equilibrium, and contain information on the dynamic interactions among reacting components. However, this information can be difficult to extract using conventional analysis techniques. We present a new method to infer biochemical pathway mechanisms from time course data using a global nonlinear modeling technique to identify the elementary reaction steps which constitute the pathway. The method involves the generation of a complete dictionary of polynomial basis functions based on the law of mass action. Using these basis functions, there are two approaches to model construction, namely the general to specific and the specific to general approach. We demonstrate that our new methodology reconstructs the chemical reaction steps and connectivity of the glycolytic pathway of Lactococcus lactis from time course experimental data.

  1. Automated pathway and reaction prediction facilitates in silico identification of unknown metabolites in human cohort studies.

    Science.gov (United States)

    Quell, Jan D; Römisch-Margl, Werner; Colombo, Marco; Krumsiek, Jan; Evans, Anne M; Mohney, Robert; Salomaa, Veikko; de Faire, Ulf; Groop, Leif C; Agakov, Felix; Looker, Helen C; McKeigue, Paul; Colhoun, Helen M; Kastenmüller, Gabi

    2017-12-15

    Identification of metabolites in non-targeted metabolomics continues to be a bottleneck in metabolomics studies in large human cohorts. Unidentified metabolites frequently emerge in the results of association studies linking metabolite levels to, for example, clinical phenotypes. For further analyses these unknown metabolites must be identified. Current approaches utilize chemical information, such as spectral details and fragmentation characteristics to determine components of unknown metabolites. Here, we propose a systems biology model exploiting the internal correlation structure of metabolite levels in combination with existing biochemical and genetic information to characterize properties of unknown molecules. Levels of 758 metabolites (439 known, 319 unknown) in human blood samples of 2279 subjects were measured using a non-targeted metabolomics platform (LC-MS and GC-MS). We reconstructed the structure of biochemical pathways that are imprinted in these metabolomics data by building an empirical network model based on 1040 significant partial correlations between metabolites. We further added associations of these metabolites to 134 genes from genome-wide association studies as well as reactions and functional relations to genes from the public database Recon 2 to the network model. From the local neighborhood in the network, we were able to predict the pathway annotation of 180 unknown metabolites. Furthermore, we classified 100 pairs of known and unknown and 45 pairs of unknown metabolites to 21 types of reactions based on their mass differences. As a proof of concept, we then looked further into the special case of predicted dehydrogenation reactions leading us to the selection of 39 candidate molecules for 5 unknown metabolites. Finally, we could verify 2 of those candidates by applying LC-MS analyses of commercially available candidate substances. The formerly unknown metabolites X-13891 and X-13069 were shown to be 2-dodecendioic acid and 9

  2. Computational Investigation of the Competition between the Concerted Diels-Alder Reaction and Formation of Diradicals in Reactions of Acrylonitrile with Non-Polar Dienes

    Science.gov (United States)

    James, Natalie C.; Um, Joann M.; Padias, Anne B.; Hall, H. K.; Houk, K. N.

    2013-01-01

    The energetics of the Diels-Alder cycloaddition reactions of several 1,3-dienes with acrylonitrile, and the energetics of formation of diradicals, were investigated with density functional theory (B3LYP and M06-2X) and compared to experimental data. For the reaction of 2,3-dimethyl-1,3-butadiene with acrylonitrile, the concerted reaction is favored over the diradical pathway by 2.5 kcal/mol using B3LYP/6-31G(d); experimentally this reaction gives both cycloadduct and copolymer. The concerted cycloaddition of cyclopentadiene with acrylonitrile is preferred computationally over the stepwise pathway by 5.9 kcal/mol; experimentally, only the Diels-Alder adduct is formed. For the reactions of (E)-1,3-pentadiene and acrylonitrile, both cycloaddition and copolymerization were observed experimentally; these trends were mimicked by the computational results, which showed only a 1.2 kcal/mol preference for the concerted pathway. For the reactions of (Z)-1,3-pentadiene and acrylonitrile, the stepwise pathway is preferred by 3.9 kcal/mol, in agreement with previous experimental findings that only polymerization occurs. M06-2X is known to give more accurate activation and reaction energetics but the energies of diradicals are too high. PMID:23758325

  3. 75 FR 75706 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2010-12-06

    ... Building, 1900 E Street, NW., Washington, DC. The Federal Prevailing Rate Advisory Committee is composed of... considered and would disrupt substantially the disposition of its business. Therefore, these caucuses will be... 5H27, 1900 E Street, NW., Washington, DC 20415, (202) 606-9400. U.S. Office of Personnel Management...

  4. 76 FR 75567 - Federal Prevailing Rate Advisory Committee; Open Committee Meetings

    Science.gov (United States)

    2011-12-02

    ..., 1900 E Street, NW., Washington, DC. The Federal Prevailing Rate Advisory Committee is composed of a... disrupt substantially the disposition of its business. Therefore, these caucuses will be closed to the... 5H27, 1900 E Street, NW., Washington, DC 20415, (202) 606-9400. U.S. Office of Personnel Management...

  5. Prevailing of sensitive blood driving to AIDS/HIV. Provincial Blood Bank of Sancti Spíritus. 2007-2008.

    Directory of Open Access Journals (Sweden)

    Martha Quesada Concepción

    2011-09-01

    Full Text Available Because of blood transfusions are one of the ways of transmitting the immune deficiency syndrome (AIDS/HIV; it constitutes warriness from the epidemiological point of view. A descriptive research was done with the objective of determining the prevailing of sensitive blood driving AIDS/HIV in the Provincial Blood Bank from Sancti Spíritus from January 1 st , 2007 to December 31 st, 2008. The sample was conformed by 312 donants with positive diagnosis to AIDS/HIV. Some variables were used such as prevailing, age, sex, race, home town. The scores of higher prevailing to AIDS/HIV were shown by the male sex (4,42, the 26-33 year old group (1,55; it prevailing volunteer blood driving (81,0 % , and Sancti Spíritus municipality gave more cases (27,5% .Just because sensibility to tests based on antibody, that is why it is important the constant checking of all processes that guarantee blood driving to be sired.

  6. The concern of emergence of multi-station reaction pathways that might make stepwise the mechanism of the 1,3-dipolar cycloadditions of azides and alkynes

    Science.gov (United States)

    Mohtat, Bita; Siadati, Seyyed Amir; Khalilzadeh, Mohammad Ali; Zareyee, Daryoush

    2018-03-01

    After hot debates on the concerted or stepwise nature of the mechanism of the catalyst-free 1,3-dipolar cycloadditions (DC)s, nowadays, it is being believed that for the reaction of each dipole and dipolarophile, there is a possibility that the reaction mechanism becomes stepwise, intermediates emerge, and the reaction becomes non-stereospecific. Yield of even minimal amounts of unwanted side products or stereoisomers as impurities could bring many troubles like difficult purification steps. In this project, we have made attempts to study all probable reaction channels of the azide cycloadditions with two functionalized alkynes, in order to answer this question: "is there any possibility that intermediates evolve in the catalyst-free click 1,3-DC reaction of azide-alkynes?". During the calculations, several multi-station reaction pathways supporting the stepwise and concerted mechanisms were detected. Also, the born-oppenheimer molecular dynamic (BOMD) simulation was used to find trustable geometries which could be emerged during the reaction coordinate.

  7. Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment.

    Directory of Open Access Journals (Sweden)

    Ruijuan Qu

    Full Text Available Tetrabromobisphenol A (TBBPA is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters.

  8. Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

    Science.gov (United States)

    Wang, Xinghao; Huang, Qingguo; Lu, Junhe; Wang, Liansheng; Wang, Zunyao

    2015-01-01

    Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters. PMID:26430733

  9. From simple to complex and backwards. Chemical reactions under very high pressure

    International Nuclear Information System (INIS)

    Bini, Roberto; Ceppatelli, Matteo; Citroni, Margherita; Schettino, Vincenzo

    2012-01-01

    Highlights: ► High pressure reactivity of several molecular systems. ► Reaction kinetics and dynamics in high density conditions. ► Key role of optical pumping and electronic excitation. ► Perspectives for the synthesis of hydrogen. - Abstract: High pressure chemical reactions of molecular systems are discussed considering the various factors that can affect the reactivity. These include steric hindrance and geometrical constraints in the confined environment of crystals at high pressure, changes of the free energy landscape with pressure, photoactivation by two-photon absorption, local and collective effects. A classification of the chemical reactions at high pressure is attempted on the basis of the prevailing factors.

  10. Prevailing Wage Regulations and School Construction Costs: Evidence from British Columbia.

    Science.gov (United States)

    Bilginsoy, Cihan; Philips, Peter

    2000-01-01

    Examines effects of prevailing wage laws on school construction costs, using final cost data from six British Columbia school districts. When controlling for factors such as construction business cycle, number of competitors, and school type, there was no significant unit cost change following the Skill Development and Fair Wage Policy Act.…

  11. Radical Rearrangement Chemistry in Ultraviolet Photodissociation of Iodotyrosine Systems: Insights from Metastable Dissociation, Infrared Ion Spectroscopy, and Reaction Pathway Calculations.

    Science.gov (United States)

    Ranka, Karnamohit; Zhao, Ning; Yu, Long; Stanton, John F; Polfer, Nicolas C

    2018-05-29

    We report on the ultraviolet photodissociation (UVPD) chemistry of protonated tyrosine, iodotyrosine, and diiodotyrosine. Distonic loss of the iodine creates a high-energy radical at the aromatic ring that engages in hydrogen/proton rearrangement chemistry. Based on UVPD kinetics measurements, the appearance of this radical is coincident with the UV irradiation pulse (8 ns). Conversely, sequential UVPD product ions exhibit metastable decay on ca. 100 ns timescales. Infrared ion spectroscopy is capable of confirming putative structures of the rearrangement products as proton transfers from the imine and β-carbon hydrogens. Potential energy surfaces for the various reaction pathways indicate that the rearrangement chemistry is highly complex, compatible with a cascade of rearrangements, and that there is no preferred rearrangement pathway even in small molecular systems like these. Graphical Abstract.

  12. Uranium oxidation: characterization of oxides formed by reaction with water

    International Nuclear Information System (INIS)

    Fuller, E.L. Jr.; Smyrl, N.R.; Condon, J.B.; Eager, M.H.

    1983-01-01

    Three different uranium oxide samples have been characterized with respect to the different preparation techniques. Results show that the water reaction with uranium metal occurs cyclically forming laminar layers of oxide which spall off due to the strain at the oxide/metal interface. Single laminae are released if liquid water is present due to the prizing penetration at the reaction zone. The rate of reaction of water with uranium is directly proportional to the amount of adsorbed water on the oxide product. Rapid transport is effected through the open hydrous oxide product. Dehydration of the hydrous oxide irreversibly forms a more inert oxide which cannot be rehydrated to the degree that prevails in the original hydrous product of uranium oxidation with water. 27 figures

  13. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

    Science.gov (United States)

    Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

    2010-01-01

    The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

  14. Confirmation of the reaction pathway for obtaining 1-(stearamidoethyl-2-hepta-decyl-2-i midazoline

    Directory of Open Access Journals (Sweden)

    Ružić Nenad Lj.

    2002-01-01

    Full Text Available 2-lmidazolines are components of many products, used in industry and households. 1-(Stearamidoethyl-2-heptadecyl-2-imidazoline is a surface active compound, which after quaternization with dimethyl sulfate, is used in lubricants, detergents, shampoos, softeners and cosmetics products. Due to its importance, it was essential to establish the exact reaction pathway for obtaining this compound. Diethylene triamine and stearic acid were used as the starting components. Using titrimetric analysis, and IR and 1H NMR spectros-copic analysis, as well as UV-Vis spectrophotometry it was established that the main intermediate was the 1,3-diamide bis(stearamidoethylamine. Earlier investigations conducted by some authors, using exclusively titrimetric analysis, showed that the main intermediate was the 1,2-diamide. In this paper it was proved that the assumption of these authors that salicylaldehiyde would react only with the primary and not the secondary amine groups was wrong. 1,2-Diamide is the main product of the hydrolysis of 1-(stearamido-ethyl-2-heptadecyl-2-imidazoline. It was shown, in this paper that the reaction of diethylene triamine with stearic acid in xylene at the reflux temperature, yields the salt of 1-(stearamidoethyl-2-heptadecyl-2-imidazoline and stearic acid.

  15. Chemical pathways for the formation of ammonia in Hanford wastes

    Energy Technology Data Exchange (ETDEWEB)

    Stock, L.M.; Pederson, L.R.

    1997-09-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence.

  16. Chemical pathways for the formation of ammonia in Hanford wastes

    International Nuclear Information System (INIS)

    Stock, L.M.; Pederson, L.R.

    1997-09-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important). Reduction of nitrite ions is believed to be the most important source of ammonia. Whether by radiolytic or thermal routes, nitrite reduction reactions proceed through nitrogen dioxide, nitric oxide, the nitrosyl anion, and the hyponitrite anion. Nitrite ion is also converted into hydroxylamine, another important intermediate on the pathway to form ammonia. These reaction pathways additionally result in the formation of nitrous oxide and molecular nitrogen, whereas hydrogen formation is produced in a separate reaction sequence

  17. Modeling chemical reactions for drug design.

    Science.gov (United States)

    Gasteiger, Johann

    2007-01-01

    Chemical reactions are involved at many stages of the drug design process. This starts with the analysis of biochemical pathways that are controlled by enzymes that might be downregulated in certain diseases. In the lead discovery and lead optimization process compounds have to be synthesized in order to test them for their biological activity. And finally, the metabolism of a drug has to be established. A better understanding of chemical reactions could strongly help in making the drug design process more efficient. We have developed methods for quantifying the concepts an organic chemist is using in rationalizing reaction mechanisms. These methods allow a comprehensive modeling of chemical reactivity and thus are applicable to a wide variety of chemical reactions, from gas phase reactions to biochemical pathways. They are empirical in nature and therefore allow the rapid processing of large sets of structures and reactions. We will show here how methods have been developed for the prediction of acidity values and of the regioselectivity in organic reactions, for designing the synthesis of organic molecules and of combinatorial libraries, and for furthering our understanding of enzyme-catalyzed reactions and of the metabolism of drugs.

  18. An unexpected reaction pathway in the synthesis of the ABCE framework of strychnine-type alkaloids - A multidisciplinary study

    Science.gov (United States)

    Šoral, Michal; Markus, Jozef; Doháňošová, Jana; Šoralová, Stanislava; Dvoranová, Dana; Chyba, Andrej; Moncol, Ján; Berkeš, Dušan; Liptaj, Tibor

    2017-01-01

    Acid-catalyzed cyclization of spirocyclic 1‧-benzyl-2‧-(prop-2-en-1-yl)spiro[indole-3,3‧-pyrrolidine]-5‧-one (1) was performed. The pentacyclic product of Povarov-like imino-Diels-Alder reaction was isolated in high yield instead of expected tetracyclic aza-Prins intermediate. The unusual exotic alkaloid-type structure of the resulting molecule 2 was unambiguously confirmed by a detailed NMR analysis using a set of 2D NMR spectra including an INADEQUATE experiment. The relative configuration of 2 was predicted from the synthesis mechanism and DFT geometry calculations and independently confirmed using NOESY and residual dipolar coupling (RDC) assisted NMR analysis in stretched crosslinked polystyrene gels. The reversibility of the cycloaddition in aprotic solvents was observed. A new reaction pathway yielding a rare 6-5-5-5 tetracyclic spiroindoline 3 was suggested. The relative configuration within the tetracyclic framework was ultimately proved using Single-crystal X-ray diffraction analysis of compound 4.

  19. Progranulin protects vascular endothelium against atherosclerotic inflammatory reaction via Akt/eNOS and nuclear factor-κB pathways.

    Science.gov (United States)

    Hwang, Hwan-Jin; Jung, Tae Woo; Hong, Ho Cheol; Choi, Hae Yoon; Seo, Ji-A; Kim, Sin Gon; Kim, Nan Hee; Choi, Kyung Mook; Choi, Dong Seop; Baik, Sei Hyun; Yoo, Hye Jin

    2013-01-01

    Atherosclerosis is considered a chronic inflammatory disease, initiated by activation and dysfunction of the endothelium. Recently, progranulin has been regarded as an important modulator of inflammatory processes; however, the role for prgranulin in regulating inflammation in vascular endothelial cells has not been described. Signaling pathways mediated by progranulin were analyzed in human umbilical vein endothelial cells (HUVECs) treated with progranulin. Progranulin significantly induced Akt and endothelial nitric oxide synthase (eNOS) phosphorylation in HUVECs, an effect that was blocked with Akt inhibitor. Furthermore, nitric oxide (NO) level, the end product of Akt/eNOS pathway, was significantly upregulated after progranulin treatment. Next, we showed that progranulin efficiently inhibited lipopolysaccharide (LPS)-mediated pro-inflammatory signaling. LPS-induced phosphorylation of IκB and nuclear factor-κB (NF-κB) levels decreased after progranulin treatment. Also, progranulin blocked translocation of NF-κB from the cytosol to the nucleus. In addition, progranulin significantly reduced the expression of vascular cell adhesion molecule-1 (VCAM-1) and intercellular adhesion molecule-1 (ICAM-1) by inhibiting binding of NF- κB to their promoter regions and blocked attachment of monocytes to HUVECs. Progranulin also significantly reduced the expression of tumor necrosis factor receptor-α (TNF-α) and monocyte chemo-attractant protein-1 (MCP-1), the crucial inflammatory molecules known to aggravate atherosclerosis. Progranulin efficiently inhibited LPS-mediated pro-inflammatory signaling in endothelial cells through activation of the Akt/eNOS pathway and attenuation of the NF-κB pathway, suggesting its protective roles in vascular endothelium against inflammatory reaction underlying atherosclerosis.

  20. Evaluate prevailing climate change on Great Lakes water levels

    International Nuclear Information System (INIS)

    Islam, M.

    2009-01-01

    'Full text:'In this paper, results of a comprehensive water mass balance modeling for the Great Lakes against prevailing and different anticipated climate change scenarios would be presented. Modeling is done in evaluating the changes in the lake storages and then changes in the lake's water level considering present condition, uncertainty and variability of climate and hydrologic conditions in the future. Inflow-outflow and consequent changes in the five Great Lake's storages are simulated for the last 30 years and then projected to evaluate the changes in the lake storages for the next 50 years. From the predicted changes in the lake storage data, water level is calculated using mass to linear conversion equation. Modeling and analysis results are expected to be helpful in understanding the possible impacts of the climate change on the Great Lakes water environment and preparing strategic plan for the sustainable management of lake's water resources. From the recent past, it is observed that there is a depleting trend in the lakes water level and hence there is a potential threat to lake's water environment and uncertainty of the availability of quality and quantity of water for the future generations, especially against prevailing and anticipated climate changes. For this reason, it is an urgent issue of understanding and quantifying the potential impacts of climate change on the Great Lake's water levels and storages. (author)

  1. Evaluation of a setting reaction pathway in the novel composite TiHA-CSD bone cement by FT-Raman and FT-IR spectroscopy

    Science.gov (United States)

    Paluszkiewicz, Czesława; Czechowska, Joanna; Ślósarczyk, Anna; Paszkiewicz, Zofia

    2013-02-01

    The aim of this study was to determine a setting reaction pathway in a novel, surgically handy implant material, based on calcium sulfate hemihydrate (CSH) and titanium doped hydroxyapatite (TiHA). The previous studies confirmed superior biological properties of TiHA in comparison to the undoped hydroxyapatite (HA) what makes it highly attractive for future medical applications. In this study the three types of titanium modified HA powders: untreated, calcined at 800 °C, sintered at 1250 °C and CSH were used to produce bone cements. The Fourier Transform-InfraRed (FT-IR) spectroscopy and Raman spectroscopy were applied to evaluate processes taking place during the setting of the studied materials. Our results undoubtedly confirmed that the reaction pathways and the phase compositions differed significantly for set cements and were dependent on the initial heat treatment of TiHA powder. Final materials were multiphase composites consisting of calcium sulfate dihydrate, bassanite, tricalcium phosphate, hydroxyapatite and calcium titanate (perovskite). The FT-IR and Scanning Electron Microscopy (SEM) measurements performed after the incubation of the cement samples in the simulated body fluid (SBF), indicate on high bioactive potential of the obtained bone cements.

  2. Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

    International Nuclear Information System (INIS)

    Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas; Goulding, Celia W.

    2014-01-01

    The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully

  3. Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Rodrigo; Lan, Benson; Latif, Yama; Chim, Nicholas [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); Goulding, Celia W., E-mail: celia.goulding@uci.edu [UC Irvine, 2212 Natural Sciences I, Irvine, CA 92697 (United States); UC Irvine, 2302 Natural Sciences I, Irvine, CA 92697 (United States)

    2014-04-01

    The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NO levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully

  4. DEOP: a database on osmoprotectants and associated pathways

    KAUST Repository

    Bougouffa, S.

    2014-10-17

    Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at.

  5. DEOP: a database on osmoprotectants and associated pathways

    KAUST Repository

    Bougouffa, S.; Radovanovic, A.; Essack, M.; Bajic, Vladimir B.

    2014-01-01

    Microorganisms are known to counteract salt stress through salt influx or by the accumulation of osmoprotectants (also called compatible solutes). Understanding the pathways that synthesize and/or breakdown these osmoprotectants is of interest to studies of crops halotolerance and to biotechnology applications that use microbes as cell factories for production of biomass or commercial chemicals. To facilitate the exploration of osmoprotectants, we have developed the first online resource, ‘Dragon Explorer of Osmoprotection associated Pathways’ (DEOP) that gathers and presents curated information about osmoprotectants, complemented by information about reactions and pathways that use or affect them. A combined total of 141 compounds were confirmed osmoprotectants, which were matched to 1883 reactions and 834 pathways. DEOP can also be used to map genes or microbial genomes to potential osmoprotection-associated pathways, and thus link genes and genomes to other associated osmoprotection information. Moreover, DEOP provides a text-mining utility to search deeper into the scientific literature for supporting evidence or for new associations of osmoprotectants to pathways, reactions, enzymes, genes or organisms. Two case studies are provided to demonstrate the usefulness of DEOP. The system can be accessed at.

  6. Bacterial variations on the methionine salvage pathway

    Directory of Open Access Journals (Sweden)

    Haas Dieter

    2004-03-01

    Full Text Available Abstract Background The thiomethyl group of S-adenosylmethionine is often recycled as methionine from methylthioadenosine. The corresponding pathway has been unravelled in Bacillus subtilis. However methylthioadenosine is subjected to alternative degradative pathways depending on the organism. Results This work uses genome in silico analysis to propose methionine salvage pathways for Klebsiella pneumoniae, Leptospira interrogans, Thermoanaerobacter tengcongensis and Xylella fastidiosa. Experiments performed with mutants of B. subtilis and Pseudomonas aeruginosa substantiate the hypotheses proposed. The enzymes that catalyze the reactions are recruited from a variety of origins. The first, ubiquitous, enzyme of the pathway, MtnA (methylthioribose-1-phosphate isomerase, belongs to a family of proteins related to eukaryotic intiation factor 2B alpha. mtnB codes for a methylthioribulose-1-phosphate dehydratase. Two reactions follow, that of an enolase and that of a phosphatase. While in B. subtilis this is performed by two distinct polypeptides, in the other organisms analyzed here an enolase-phosphatase yields 1,2-dihydroxy-3-keto-5-methylthiopentene. In the presence of dioxygen an aci-reductone dioxygenase yields the immediate precursor of methionine, ketomethylthiobutyrate. Under some conditions this enzyme produces carbon monoxide in B. subtilis, suggesting a route for a new gaseous mediator in bacteria. Ketomethylthiobutyrate is finally transaminated by an aminotransferase that exists usually as a broad specificity enzyme (often able to transaminate aromatic aminoacid keto-acid precursors or histidinol-phosphate. Conclusion A functional methionine salvage pathway was experimentally demonstrated, for the first time, in P. aeruginosa. Apparently, methionine salvage pathways are frequent in Bacteria (and in Eukarya, with recruitment of different polypeptides to perform the needed reactions (an ancestor of a translation initiation factor and Ru

  7. Synergistic reaction between SO2 and NO2 on mineral oxides: a potential formation pathway of sulfate aerosol.

    Science.gov (United States)

    Liu, Chang; Ma, Qingxin; Liu, Yongchun; Ma, Jinzhu; He, Hong

    2012-02-07

    Sulfate is one of the most important aerosols in the atmosphere. A new sulfate formation pathway via synergistic reactions between SO(2) and NO(2) on mineral oxides was proposed. The heterogeneous reactions of SO(2) and NO(2) on CaO, α-Fe(2)O(3), ZnO, MgO, α-Al(2)O(3), TiO(2), and SiO(2) were investigated by in situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (in situ DRIFTS) at ambient temperature. Formation of sulfate from adsorbed SO(2) was promoted by the coexisting NO(2), while surface N(2)O(4) was observed as the crucial oxidant for the oxidation of surface sulfite. This process was significantly promoted by the presence of O(2). The synergistic effect between SO(2) and NO(2) was not observed on other mineral particles (such as CaCO(3) and CaSO(4)) probably due to the lack of the surface reactive oxygen sites. The synergistic reaction between SO(2) and NO(2) on mineral oxides resulted in the formation of internal mixtures of sulfate, nitrate, and mineral oxides. The change of mixture state will affect the physicochemical properties of atmospheric particles and therefore further influence their environmental and climate effects.

  8. Fluid flow pathways through the oceanic crust: reaction permeability and isotopic tracing

    Science.gov (United States)

    McCaig, Andrew; Castelain, Teddy; Klein, Frieder

    2013-04-01

    It is generally assumed that the dominant means of creating permeability in ocean floor hydrothermal systems is fracturing, induced either by cooling or by tectonic stress. Here we show textural evidence that metamorphic reactions can create a hierarchy of permeable pathways through gabbroic rocks similar to a fracture hierarchy. Isotopic microsampling shows that just as with fractures, most flow occurs through the larger channelways, and that even at the microscale, flow can be extremely heterogeneous with alteration affecting only certain minerals in the framework, leaving others untouched. Reaction permeability is created in three ways; dissolution creating open porosity, microcracking due to volume increase reactions involving olivine, and expansion of water due to rapid heating in dyke margins, particularly when intruded into brecciated rocks. Our data comes from IODP Hole U1309D, which was drilled to 1400 mbsf in the footwall of the Atlantis Massif detachment fault at the Mid-Atlantic Ridge 30°N. The core is composed of gabbroic rocks interlayered with olivine rich troctolites, with several basalt/diabase sills in the top 130 m. The dominant alteration occurred in the greenschist facies, at depths at least 1 km below seafloor, and decreases in intensity downhole. Whole rock oxygen isotope values range from +5.5 permil to +1.5 permil, indicating variable degrees of interaction with seawater at temperatures generally > 250 °C. Gabbroic rocks and diabases exhibit a range of Sr isotope ratios from MORB values (0.70261) to intermediate ratios (0.70429). Microsampling shows that amphiboles are often more radiogenic than coexisting plagioclase and can sometimes be isotopically altered in the same rock as completely unaltered primary minerals. Large (10 cm) amphibole-filled vugs show values ranging up to 0.708, close to seawater. In some cases however the secondary minerals are virtually unaltered indicating low fluid fluxes in pervasive alteration. SEM textures in

  9. Fragmentation Pathways of Lithiated Hexose Monosaccharides

    Science.gov (United States)

    Abutokaikah, Maha T.; Frye, Joseph W.; Tschampel, John; Rabus, Jordan M.; Bythell, Benjamin J.

    2018-05-01

    We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. [Figure not available: see fulltext.

  10. OECOSYS prevailing exercise applications

    International Nuclear Information System (INIS)

    Mueck, K.; Suda, M.

    1999-10-01

    In the Research Center Seibersdorf the computer simulation code OECOSYS was installed in 1989 which represents a version of the model ECOSYS-87 developed by GSF in Neuherberg, and adapted to the Austrian situation. The model available since then simulates from input parameters such as the integral of the activity concentration in air and the ground deposition of each radionuclide as well as the precipitation values via the interception on plants and deposition on soil and the transfer of radionuclides into the various ecosystems and fodder-food chains into the various foodstuffs and calculates in this way the course of the activity concentration in these foodstuffs. Via the consumption rates of each foodstuff the contribution of the ingestion of each foodstuff and by that the total ingestion dose may be evaluated. Further, the simulation model permits the calculation of the various exposure pathways as inhalation and external irradiation from the plume and ground and enable the user to obtain a fast comparison of the various exposure pathways. In order to ensure the availability of the code and the accompanying infrastructure, by order of the federal chancellery sect. VI the computer code is run in certain intervals and test calculations are performed with it. Each exercise run was based on scenarios which could result in case of severe accidents in neighboring nuclear power plants. Generally, extremely unrealistic scenarios were assumed which do not correspond to the safety standard of the respective nuclear power plant in order to obtain calculation examples which may serve the emergency units in their planning for emergency situations. Furthermore, by these exercise runs a demonstration of the contribution of the various exposure pathways for the persons responsible for emergency management in case of a crisis shall be given to enable them to appropriately design the respective planning features. In the present report the calculations performed up to now are

  11. Progranulin protects vascular endothelium against atherosclerotic inflammatory reaction via Akt/eNOS and nuclear factor-κB pathways.

    Directory of Open Access Journals (Sweden)

    Hwan-Jin Hwang

    Full Text Available OBJECTIVE: Atherosclerosis is considered a chronic inflammatory disease, initiated by activation and dysfunction of the endothelium. Recently, progranulin has been regarded as an important modulator of inflammatory processes; however, the role for prgranulin in regulating inflammation in vascular endothelial cells has not been described. METHOD AND RESULTS: Signaling pathways mediated by progranulin were analyzed in human umbilical vein endothelial cells (HUVECs treated with progranulin. Progranulin significantly induced Akt and endothelial nitric oxide synthase (eNOS phosphorylation in HUVECs, an effect that was blocked with Akt inhibitor. Furthermore, nitric oxide (NO level, the end product of Akt/eNOS pathway, was significantly upregulated after progranulin treatment. Next, we showed that progranulin efficiently inhibited lipopolysaccharide (LPS-mediated pro-inflammatory signaling. LPS-induced phosphorylation of IκB and nuclear factor-κB (NF-κB levels decreased after progranulin treatment. Also, progranulin blocked translocation of NF-κB from the cytosol to the nucleus. In addition, progranulin significantly reduced the expression of vascular cell adhesion molecule-1 (VCAM-1 and intercellular adhesion molecule-1 (ICAM-1 by inhibiting binding of NF- κB to their promoter regions and blocked attachment of monocytes to HUVECs. Progranulin also significantly reduced the expression of tumor necrosis factor receptor-α (TNF-α and monocyte chemo-attractant protein-1 (MCP-1, the crucial inflammatory molecules known to aggravate atherosclerosis. CONCLUSION: Progranulin efficiently inhibited LPS-mediated pro-inflammatory signaling in endothelial cells through activation of the Akt/eNOS pathway and attenuation of the NF-κB pathway, suggesting its protective roles in vascular endothelium against inflammatory reaction underlying atherosclerosis.

  12. Between affiliation and autonomy: navigating pathways of women's empowerment and gender justice in rural Bangladesh.

    Science.gov (United States)

    Kabeer, Naila

    2011-01-01

    Inasmuch as women's subordinate status is a product of the patriarchal structures of constraint that prevail in specific contexts, pathways of women's empowerment are likely to be "path dependent." They will be shaped by women's struggles to act on the constraints that prevail in their societies, as much by what they seek to defend as by what they seek to change. The universal value that many feminists claim for individual autonomy may not therefore have the same purchase in all contexts. This article examines processes of empowerment as they play out in the lives of women associated with social mobilization organizations in the specific context of rural Bangladesh. It draws on their narratives to explore the collective strategies through which these organizations sought to empower the women and how they in turn drew on their newly established "communities of practice" to navigate their own pathways to wider social change. It concludes that while the value attached to social affiliations by the women in the study is clearly a product of the societies in which they have grown up, it may be no more context-specific than the apparently universal value attached to individual autonomy by many feminists.

  13. The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

    Science.gov (United States)

    Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

    2017-12-01

    The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

  14. An optimization model for metabolic pathways.

    Science.gov (United States)

    Planes, F J; Beasley, J E

    2009-10-15

    Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner.

  15. Method for determining heterologous biosynthesis pathways

    KAUST Repository

    Gao, Xin

    2017-08-10

    The present invention relates to a method and system for dynamically analyzing, determining, predicting and displaying ranked suitable heterologous biosynthesis pathways for a specified host. The present invention addresses the problem of finding suitable pathways for the endogenous metabolism of a host organism because the efficacy of heterologous biosynthesis is affected by competing endogenous pathways. The present invention is called MRE (Metabolic Route Explorer), and it was conceived and developed to systematically and dynamically search for, determine, analyze, and display promising heterologous pathways while considering competing endogenous reactions in a given host organism.

  16. Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

    Directory of Open Access Journals (Sweden)

    de Ridder Dick

    2008-12-01

    Full Text Available Abstract Background Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the variations between them. Results We present an efficient framework, Metabolic Pathway Alignment and Scoring (M-PAS, for identifying and ranking conserved metabolic pathways. M-PAS aligns all reactions in entire metabolic networks of two species and assembles them into pathways, taking mismatches, gaps and crossovers into account. It uses a comprehensive scoring function, which quantifies pathway similarity such that we can focus on different pathways given different biological motivations. Using M-PAS, we detected 1198 length-four pathways fully conserved between Saccharomyces cerevisiae and Escherichia coli, and also revealed 1399 cases of a species using a unique route in otherwise highly conserved pathways. Conclusion Our method efficiently automates the process of exploring reaction arrangement possibilities, both between species and within species, to find conserved pathways. We not only reconstruct conventional pathways such as those found in KEGG, but also discover new pathway possibilities. Our results can help to generate hypotheses on missing reactions and manifest differences in highly conserved pathways, which is useful for biology and life science applications.

  17. Protective Effects of Maillard Reaction Products of Whey Protein Concentrate against Oxidative Stress through an Nrf2-Dependent Pathway in HepG2 Cells.

    Science.gov (United States)

    Pyo, Min Cheol; Yang, Sung-Yong; Chun, Su-Hyun; Oh, Nam Su; Lee, Kwang-Won

    2016-09-01

    Whey protein concentrate (WPC), which contains α-lactalbumin and β-lactoglobulin, is utilized widely in the food industry. The Maillard reaction is a complex reaction that produces Maillard reaction products (MRPs), which are associated with the formation of antioxidant compounds. In this study, the hepatoprotection activity of MRPs of WPC against oxidative stress through the nuclear factor-E2-related factor 2 (Nrf2)-dependent antioxidant pathway in HepG2 cells was examined. Glucose-whey protein concentrate conjugate (Glc-WPC) was obtained from Maillard reaction between WPC and glucose. The fluorescence intensity of Glc-WPC increased after 7 d compared to native WPC, and resulted in loss of 48% of the free amino groups of WPC. The sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of Glc-WPC showed the presence of a high-molecular-weight portion. Treatment of HepG2 cells with Glc-WPC increased cell viability in the presence of oxidative stress, inhibited the generation of intracellular reactive oxygen species by tert-butyl hydroperoxide (t-BHP), and increased the glutathione level. Nrf2 translocation and Nrf2, reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H)-quinone oxidoreductase 1 (NOQ1), heme oxygenase-1 (HO-1), glutamate-L-cysteine ligase (GCL)M and GCLC mRNA levels were increased by Glc-WPC. Also, Glc-WPC increased the phosphorylation of extracellular signal-regulated kinase (ERK) 1/2 and c-Jun N-terminal kinase (JNK). The results of this study demonstrate that Glc-WPC activates the Nrf2-dependent pathway through the phosphorylation of ERK1/2 and JNK in HepG2 cells, and induces production of antioxidant enzymes and phase II enzymes.

  18. Catalytic hydroconversion of tricaprylin and caprylic acid as model reaction for biofuel production from triglycerides

    Energy Technology Data Exchange (ETDEWEB)

    Boda, L.; Thernesz, A. [MOL Hungarian Oil and Gas Co. Plc., Szazhalombatta (Hungary); Onyestyak, G.; Solt, H.; Lonyi, F.; Valyon, J. [Hungarian Academy of Sciences, Budapest (Hungary). Inst. of Nanochemistry and Catalysis

    2010-07-01

    Palladium/activated carbon (Pd/C) and non-sulfided Ni,Mo/{gamma}-Al{sub 2}O{sub 3} catalysts were used. The hydroconversion was found to proceed in consecutive steps of tricaprylin (TC) hydrogenolysis (HYS) to caprylic acid (CA) and propane, and hydrodeoxygenation (HDO) of the acid intermediate to get hydrocarbon. Two HDO routes were distinguished: (i) over Pd/C the prevailing reaction route was the decarbonylation, whereas (ii) over molybdena-alumina catalysts the main reaction was the reduction of oxygen to get water. (orig.)

  19. Reaction kinetics of dolomite rim growth

    Science.gov (United States)

    Helpa, V.; Rybacki, E.; Abart, R.; Morales, L. F. G.; Rhede, D.; Jeřábek, P.; Dresen, G.

    2014-04-01

    Reaction rims of dolomite (CaMg[CO3]2) were produced by solid-state reactions at the contacts of oriented calcite (CaCO3) and magnesite (MgCO3) single crystals at 400 MPa pressure, 750-850 °C temperature, and 3-146 h annealing time to determine the reaction kinetics. The dolomite reaction rims show two different microstructural domains. Elongated palisades of dolomite grew perpendicular into the MgCO3 interface with length ranging from about 6 to 41 µm. At the same time, a 5-71 µm wide rim of equiaxed granular dolomite grew at the contact with CaCO3. Platinum markers showed that the original interface is located at the boundary between the granular and palisade-forming dolomite. In addition to dolomite, a 12-80 µm thick magnesio-calcite layer formed between the dolomite reaction rims and the calcite single crystals. All reaction products show at least an axiotactic crystallographic relationship with respect to calcite reactant, while full topotaxy to calcite prevails within the granular dolomite and magnesio-calcite. Dolomite grains frequently exhibit growth twins characterized by a rotation of 180° around one of the equivalent axis. From mass balance considerations, it is inferred that the reaction rim of dolomite grew by counter diffusion of MgO and CaO. Assuming an Arrhenius-type temperature dependence, activation energies for diffusion of CaO and MgO are E a (CaO) = 192 ± 54 kJ/mol and E a (MgO) = 198 ± 44 kJ/mol, respectively.

  20. Precise generation of systems biology models from KEGG pathways.

    Science.gov (United States)

    Wrzodek, Clemens; Büchel, Finja; Ruff, Manuel; Dräger, Andreas; Zell, Andreas

    2013-02-21

    The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with an enormous amount of information and provide a foundation for initial structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and often omit important details for the sake of a clear arrangement of its entries. Thus, a direct conversion into systems biology models would produce incomplete and erroneous models. Here, we present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded in the standardized community pathway formats SBML (Levels 2 and 3) and BioPAX (Levels 2 and 3). This method involves correcting invalid or incomplete KGML content, creating complete and valid stoichiometric reactions, translating relations to signaling models and augmenting the pathway content with various information, such as cross-references to Entrez Gene, OMIM, UniProt ChEBI, and many more.Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG to BioPAX does not involve a loss of information, whilst lossless translations to SBML can only be performed using SBML Level 3, including its recently proposed qualitative models and groups extension packages. Building correct BioPAX and SBML signaling models from the KEGG database is a unique characteristic of the proposed method. Further, there is no other approach that is able to appropriately construct metabolic models from KEGG pathways, including correct reactions with stoichiometry. The resulting initial models, which contain valid and comprehensive SBML or BioPAX code and a multitude of cross-references, lay the foundation to facilitate further modeling steps.

  1. Concise Synthesis of Macrocycles by Multicomponent Reactions

    NARCIS (Netherlands)

    Abdelraheem, Eman M. M.; Khaksar, Samad; Dömling, Alexander

    2018-01-01

    A short reaction pathway was devised to synthesize a library of artificial 18-27-membered macrocycles. The five-step reaction sequence involves ring opening of a cyclic anhydride with a diamine, esterification, coupling with an amino acid isocyanide, saponification, and, finally, macro-ring closure

  2. Aromatic products from reaction of lignin model compounds with UV-alkaline peroxide

    International Nuclear Information System (INIS)

    Sun, Y.P.; Wallis, A.F.A.; Nguyen, K.L.

    1997-01-01

    A series of guaiacyl and syringyl lignin model compounds and their methylated analogues were reacted with alkaline hydrogen peroxide while irradiating with UV light at 254 nm. The aromatic products obtained were investigated by gas chromatography-mass spectrometry (GC-MS). Guaiacol, syringol and veratrol gave no detectable aromatic products. However, syringol methyl ether gave small amounts of aromatic products, resulting from ring substitution and methoxyl displacement by hydroxyl radicals. Reaction of vanillin and syringaldehyde gave the Dakin reaction products, methoxy-1,4-hydroquinones, while reaction of their methyl ethers yielded benzoic acids. Acetoguaiacone, acetosyringone and their methyl ethers afforded several hydroxylated aromatic products, but no aromatic products were identified in the reaction mixtures from guaiacylpropane and syringylpropane. In contrast, veratrylpropane gave a mixture from which 17 aromatic hydroxylated compounds were identified. It is concluded that for phenolic lignin model compounds, particularly those possessing electrondonating aromatic ring substituents, ring-cleavage reactions involving superoxide radical anions are dominant, whereas for non-phenolic lignin models, hydroxylation reactions through attack of hydroxyl radicals prevail

  3. The Paterno-Buchi reaction

    DEFF Research Database (Denmark)

    Brogaard, Rasmus Yding; Schalk, Oliver; Boguslavskiy, Andrey E.

    2012-01-01

    The Paternò-Büchi (PB) reaction between an excited carbonyl compound and an alkene has been widely studied, but so far little is known about the excited-state dynamics of the reaction. In this investigation, we used a compound in which a formyl and a vinyl group are attached to a [2.......2]paracyclophane in order to obtain a model system in pre-reactive conformation for the PB reaction. We studied the excited-state dynamics of the isolated molecule in a molecular beam using femtosecond time-resolved photoelectron spectroscopy and ab initio calculations. The results show that inter-system crossing...... within two picoseconds competes efficiently with the reaction in the singlet manifold. Thus, the PB reaction in this model system takes place in the triplet state on a time scale of nanoseconds. This result stresses the importance of triplet states in the excited-state pathway of the PB reaction...

  4. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

    Directory of Open Access Journals (Sweden)

    Karp Peter D

    2004-06-01

    Full Text Available Abstract Background The PathoLogic program constructs Pathway/Genome databases by using a genome's annotation to predict the set of metabolic pathways present in an organism. PathoLogic determines the set of reactions composing those pathways from the enzymes annotated in the organism's genome. Most annotation efforts fail to assign function to 40–60% of sequences. In addition, large numbers of sequences may have non-specific annotations (e.g., thiolase family protein. Pathway holes occur when a genome appears to lack the enzymes needed to catalyze reactions in a pathway. If a protein has not been assigned a specific function during the annotation process, any reaction catalyzed by that protein will appear as a missing enzyme or pathway hole in a Pathway/Genome database. Results We have developed a method that efficiently combines homology and pathway-based evidence to identify candidates for filling pathway holes in Pathway/Genome databases. Our program not only identifies potential candidate sequences for pathway holes, but combines data from multiple, heterogeneous sources to assess the likelihood that a candidate has the required function. Our algorithm emulates the manual sequence annotation process, considering not only evidence from homology searches, but also considering evidence from genomic context (i.e., is the gene part of an operon? and functional context (e.g., are there functionally-related genes nearby in the genome? to determine the posterior belief that a candidate has the required function. The method can be applied across an entire metabolic pathway network and is generally applicable to any pathway database. The program uses a set of sequences encoding the required activity in other genomes to identify candidate proteins in the genome of interest, and then evaluates each candidate by using a simple Bayes classifier to determine the probability that the candidate has the desired function. We achieved 71% precision at a

  5. Use of ESI-MS to determine reaction pathway for hydrogen sulphide scavenging with 1,3,5-tri-(2-hydroxyethyl)-hexahydro-s-triazine.

    Science.gov (United States)

    Madsen, Henrik T; Søgaard, Erik G

    2012-01-01

    To study the reaction between hydrogen sulphide and 1,3,5-tri-(2-hydroxyethyl)-hexahydro-s-triazine, which is an often used hydrogen sulphide scavenger, electro spray ionisation mass spectrometry (ESI-MS) was used. The investigation was carried out in positive mode, and tandem mass spectrometry was used to investigate the nature of unknown peaks in the mass spectra. The reaction was found to proceed as expected from theory with the triazine reacting with hydrogen sulphide to form the corresponding thiadiazine. This species subsequently reacted with a second hydrogen sulphide molecule to form the dithiazine species, hereby confirming previously obtained results and showing the ability of the ESI-MS method for studying the scavenging reaction. The final theoretical product s-trithiane was not detected. Furthermore, fragmentation products of thiadiazine and dithiazine were detected in the solution, and possible pathways and structures were suggested to describe the observed fragments. In these, thiadiazine fragmented to 2-(methylidene amino)-ethanol and 2-(1,3-thiazetidin-3-yl)-ethanol and N-(2-hydroxyethyl)-N-(sulfanylmethyl)-ethaniminium, which underwent a further fragmentation to N-methyl-N-(2-oxoethyl)-methaniminium. Dithiazine fragmented to N-methyl-N-(2-oxoethyl)-methaniminium as well. The by-product from this reaction is methanedithiol, which was not detected due to its low polarity.

  6. Rate coefficients for hydrogen abstraction reaction of pinonaldehyde

    Indian Academy of Sciences (India)

    The H abstraction reaction from the –CHO group was found to be the most dominant reaction channelamong all the possible reaction pathways and its corresponding rate coefficient at 300 K is kEckart's unsymmetrical= 3.86 ×10-10 cm3 molecule-1 s-1. Whereas the channel with immediate lower activation energy is the ...

  7. Developmentally programmed DNA deletion in Tetrahymena thermophila by a transposition-like reaction pathway.

    Science.gov (United States)

    Saveliev, S V; Cox, M M

    1996-01-01

    We provide a molecular description of key intermediates in the deletion of two internal eliminated sequences (IES elements), the M and R regions, during macronuclear development in Tetrahymena thermophila. Using a variety of PCR-based methods in vivo, double-strand breaks are detected that are generated by hydrolytic cleavage and correspond closely to the observed chromosomal junctions left behind in the macronuclei. The breaks exhibit a temporal and structural relationship to the deletion reaction that provides strong evidence that they are intermediates in the deletion pathway. Breaks in the individual strands are staggered by 4 bp, producing a four nucleotide 5' extension. Evidence is presented that breaks do not occur simultaneously at both ends. The results are most consistent with a deletion mechanism featuring initiation by double-strand cleavage at one end of the deleted element, followed by transesterification to generate the macronuclear junction on one DNA strand. An adenosine residue is found at all the nucleophilic 3' ends used in the postulated transesterification step. Evidence for the transesterification step is provided by detection of a 3' hydroxyl that would be liberated by such a step at a deletion boundary where no other DNA strand ends are detected. Images PMID:8654384

  8. Surface-Activated Coupling Reactions Confined on a Surface.

    Science.gov (United States)

    Dong, Lei; Liu, Pei Nian; Lin, Nian

    2015-10-20

    Chemical reactions may take place in a pure phase of gas or liquid or at the interface of two phases (gas-solid or liquid-solid). Recently, the emerging field of "surface-confined coupling reactions" has attracted intensive attention. In this process, reactants, intermediates, and products of a coupling reaction are adsorbed on a solid-vacuum or a solid-liquid interface. The solid surface restricts all reaction steps on the interface, in other words, the reaction takes place within a lower-dimensional, for example, two-dimensional, space. Surface atoms that are fixed in the surface and adatoms that move on the surface often activate the surface-confined coupling reactions. The synergy of surface morphology and activity allow some reactions that are inefficient or prohibited in the gas or liquid phase to proceed efficiently when the reactions are confined on a surface. Over the past decade, dozens of well-known "textbook" coupling reactions have been shown to proceed as surface-confined coupling reactions. In most cases, the surface-confined coupling reactions were discovered by trial and error, and the reaction pathways are largely unknown. It is thus highly desirable to unravel the mechanisms, mechanisms of surface activation in particular, of the surface-confined coupling reactions. Because the reactions take place on surfaces, advanced surface science techniques can be applied to study the surface-confined coupling reactions. Among them, scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) are the two most extensively used experimental tools. The former resolves submolecular structures of individual reactants, intermediates, and products in real space, while the latter monitors the chemical states during the reactions in real time. Combination of the two methods provides unprecedented spatial and temporal information on the reaction pathways. The experimental findings are complemented by theoretical modeling. In particular, density

  9. Nuclear energy is not the prevailing energy in the French energetic mix

    International Nuclear Information System (INIS)

    Destais, G.

    2011-01-01

    The author first shows that the share of nuclear energy in the French electricity production is in fact of 76% (and not 80% as usually said), and that the share of this energy in the final electricity consumption was 69% in 2009. She also outlines that nuclear electricity is only 16,5% of the total final energy consumption in France in 2009, whereas oil still prevails with 42%

  10. Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows

    DEFF Research Database (Denmark)

    Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel

    2018-01-01

    analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimised. We then use a model of sugar...... chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest....

  11. Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.

    Science.gov (United States)

    Singh, Raman K; Tsuneda, Takao

    2013-02-15

    The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.

  12. Rate coefficient for the reaction N + NO

    Science.gov (United States)

    Fox, J. L.

    1994-01-01

    Evidence has been advanced that the rate coefficient for the reaction N + NO right arrow N2 + O has a small positive temperature dependence at the high temperatures (900 to 1500 K) that prevail in the terrestrial middle and upper thermosphere by Siskind and Rusch (1992), and at the low temperatures (100 to 200 K) of the Martian lower thermosphere by Fox (1993). Assuming that the rate coefficient recommended by the Jet Propulsion Laboratory evaluation (DeMore et al., 1992) is accurate at 300 K, we derive here the low temperature value of the activation energy for this reaction and thus the rate coefficient that best fits the Viking 1 measured NO densities. We find that the fit is acceptable for a rate coefficient of about 1.3 x 10(exp -10)(T/300)(exp 0.5)exp(-400/T) and better for a value of about 2.5 x 10(exp -10)(T/300)(exp 0.5)exp(-600/T)cu cm/s.

  13. MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

    Science.gov (United States)

    Konwar, Kishori M; Hanson, Niels W; Bhatia, Maya P; Kim, Dongjae; Wu, Shang-Ju; Hahn, Aria S; Morgan-Lang, Connor; Cheung, Hiu Kan; Hallam, Steven J

    2015-10-15

    Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  14. Chemical pathways for the formation of ammonia in Hanford wastes

    International Nuclear Information System (INIS)

    Stock, L.M.; Pederson, L.R.

    1997-12-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important)

  15. Chemical pathways for the formation of ammonia in Hanford wastes

    Energy Technology Data Exchange (ETDEWEB)

    Stock, L.M.; Pederson, L.R.

    1997-12-01

    This report reviews chemical reactions leading to the formation of ammonia in Hanford wastes. The general features of the chemistry of the organic compounds in the Hanford wastes are briefly outlined. The radiolytic and thermal free radical reactions that are responsible for the initiation and propagation of the oxidative degradation reactions of the nitrogen-containing complexants, trisodium HEDTA and tetrasodium EDTA, are outlined. In addition, the roles played by three different ionic reaction pathways for the oxidation of the same compounds and their degradation products are described as a prelude to the discussion of the formation of ammonia. The reaction pathways postulated for its formation are based on tank observations, laboratory studies with simulated and actual wastes, and the review of the scientific literature. Ammonia derives from the reduction of nitrite ion (most important), from the conversion of organic nitrogen in the complexants and their degradation products, and from radiolytic reactions of nitrous oxide and nitrogen (least important).

  16. Analysis of Chlorogenic Acid Oxidation Pathway in Simulated ...

    African Journals Online (AJOL)

    Purpose: To investigate the pathways involved in the oxidation of chlorogenic acid (CA) and phenol metabolism in honeysuckle buds. Methods: A model that mimics CA oxidation by honeysuckle polyphenol oxidase (PPO) by controlling the reaction temperature or reaction duration was employed, and the resulting products ...

  17. False-positive findings in mammography screening induces short-term distress - breast cancer-specific concern prevails longer

    DEFF Research Database (Denmark)

    Aro, A R; Pilvikki Absetz, S; van Elderen, T M

    2000-01-01

    -ups at 2 and 12 months postscreening. At 2 months, there was a moderate multivariate effect of group on distress; and intrusive thinking and worry about breast cancer, in particular, were most frequent amongst the false positives. Intrusive thinking still prevailed at 12 months, in addition to a higher...... findings (n=1407), false-positive findings (n=492) and referents from outside the screening programme (n=1718, age 48-49 years). Distress was measured as illness worry, anxiety, depression, cancer beliefs and early detection behaviour. Measurements were one month before screening invitation with follow...... perceived breast cancer risk and susceptibility. Distress related to screening and false-positive findings seems to be moderate, but prevailing cancer-specific concerns call for improvements in screening programmes....

  18. Simulation studies in biochemical signaling and enzyme reactions

    Science.gov (United States)

    Nelatury, Sudarshan R.; Vagula, Mary C.

    2014-06-01

    Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

  19. Tin-Containing Silicates: Identification of a Glycolytic Pathway via 3-Deoxyglucosone

    DEFF Research Database (Denmark)

    Tolborg, Søren; Meier, Sebastian; Sádaba, I.

    2016-01-01

    a cascade of four to five sequential steps. Currently, there is a limited understanding of the competing glycolytic pathways within these systems. Here we identify dehydration of glucose to 3-deoxyglucosone as an important pathway that occurs in addition to retro-aldol reaction of hexoses when using tin......-containing silicates. It is possible to influence the relative carbon flux through these pathways by controlling the amount of alkali metal salts present in the reaction mixture. In the absence of added potassium carbonate, at least 15–30% carbon flux via 3-deoxyglucosone is observed. Addition of just a few ppm...

  20. The Reactome pathway knowledgebase.

    Science.gov (United States)

    Croft, David; Mundo, Antonio Fabregat; Haw, Robin; Milacic, Marija; Weiser, Joel; Wu, Guanming; Caudy, Michael; Garapati, Phani; Gillespie, Marc; Kamdar, Maulik R; Jassal, Bijay; Jupe, Steven; Matthews, Lisa; May, Bruce; Palatnik, Stanislav; Rothfels, Karen; Shamovsky, Veronica; Song, Heeyeon; Williams, Mark; Birney, Ewan; Hermjakob, Henning; Stein, Lincoln; D'Eustachio, Peter

    2014-01-01

    Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.

  1. Subcritical hydrothermal conversion of organic wastes and biomass. Reaction pathways

    Directory of Open Access Journals (Sweden)

    Alejandro Amadeus Castro Vega

    2007-01-01

    Full Text Available Hydrothermal conversion is a procedure which emulates organic matter’s natural conversion into bio-crude having physical and chemical properties analogous to petroleum. The artificial transformation of biomass requi- res previous knowledge of the main reaction routes and product availability. The main component of biomass (depolymerisation by hydrolysis is presented in hydrothermal cellulose conversion, producing oligosaccharides which exhibit dehydration and retro-aldol condensation reactions for transforming into furfurals and carboxylic acids. Other biomass components (such as lignin, proteins, and fat esters present both hydrolysis and pyrolysis reaction routes. As long as biomass mainly contains carbohydrates, subcritical hydrothermal conversion products and their wastes will be fundamentally analogous to those displaying cellulose. These substances have added- value by far surpassing raw material’s acquisition cost. When the main hydrothermal conversion products’ O/C, H/C molar ratios as reported in literature are plotted, an evolutionary tralectory for conversion products appears to be closely or even overlapped with fossil fuels’ geological evolution.

  2. Hygienic features of working conditions prevailing in X-ray cabinets

    International Nuclear Information System (INIS)

    Usol'tsev, V.I.; Serebryanyj, V.A.

    1975-01-01

    The results of an investigation of 352 x-ray cabinets showed that their personnel is subjected to simultaneous action of a number of factors: discomfortable microclimate, small concentrations of ozone and nitrogen oxides (within 0.1 of the maximum permissible concentration). The hands of the personnel, especially those of the x-ray laboratory assistants are contaminated with lead (2.38mg in the hands washings). Therefore the assessment of labour conditions prevailing in an x-ray cabinet and the accomplishment of measures of their provement should be carried out with due regards to all the complex of the above mentioned factors besides the ionizing radiation

  3. Skeletal-related events significantly impact health-related quality of life in metastatic castration-resistant prostate cancer: data from PREVAIL and AFFIRM trials.

    Science.gov (United States)

    Saad, F; Ivanescu, C; Phung, D; Loriot, Y; Abhyankar, S; Beer, T M; Tombal, B; Holmstrom, S

    2017-03-01

    We investigated the impact of skeletal-related events (SREs) on health-related quality of life (HRQoL) in patients with metastatic castration-resistant prostate cancer (mCRPC) in phase III trials of enzalutamide versus placebo. Patients with mCRPC experiencing at least one SRE during AFFIRM and PREVAIL were assessed for trajectory-adjusted mean change in HRQoL by first SRE using Functional Assessment of Cancer Therapy-Prostate (FACT-P; AFFIRM, three domains, and PREVAIL, nine domains) and EQ-5D (PREVAIL) instruments. First SREs caused HRQoL deterioration in both trials. Spinal cord compression had the largest impact, with clinically meaningful reductions in seven of nine FACT-P domains in PREVAIL and all three in AFFIRM (mean (95% confidence interval (CI)) change in FACT-P total score -16.95 (-26.47, -7.44) and -9.69 (-16.10, -3.27), respectively). In PREVAIL, first SREs caused clinically meaningful declines in EQ-5D utility index, irrespective of category; spinal cord compression had the largest impact (mean (95% CI) change -0.24 (-0.39, -0.08)). In AFFIRM, FACT-P and FACT-General total scores showed clinically meaningful declines after radiation/surgery to bone. SREs were associated with clinically meaningful functional declines in the daily lives of patients with mCRPC. Spinal cord compression had the largest impact on HRQoL.

  4. 5-Year Outcomes After Left Atrial Appendage Closure: From the PREVAIL and PROTECT AF Trials.

    Science.gov (United States)

    Reddy, Vivek Y; Doshi, Shephal K; Kar, Saibal; Gibson, Douglas N; Price, Matthew J; Huber, Kenneth; Horton, Rodney P; Buchbinder, Maurice; Neuzil, Petr; Gordon, Nicole T; Holmes, David R

    2017-12-19

    The PROTECT AF (WATCHMAN Left Atrial Appendage System for Embolic Protection in Patients With Atrial Fibrillation) trial demonstrated that left atrial appendage closure (LAAC) with the Watchman device (Boston Scientific, St. Paul, Minnesota) was equivalent to warfarin for preventing stroke in atrial fibrillation, but had a high rate of complications. In a second randomized trial, PREVAIL (Evaluation of the WATCHMAN LAA Closure Device in Patients With Atrial Fibrillation Versus Long Term Warfarin Therapy), the complication rate was low. The warfarin cohort experienced an unexpectedly low ischemic stroke rate, rendering the efficacy endpoints inconclusive. However, these outcomes were based on relatively few patients followed for a relatively short time. The final results of the PREVAIL trial, both alone and as part of a patient-level meta-analysis with the PROTECT AF trial, are reported with patients in both trials followed for 5 years. PREVAIL and PROTECT AF are prospective randomized clinical trials with patients randomized 2:1 to LAAC or warfarin; together, they enrolled 1,114 patients for 4,343 patient-years. Analyses are by intention-to-treat, and rates are events per 100 patient-years. For the PREVAIL trial, the first composite coprimary endpoint of stroke, systemic embolism (SE), or cardiovascular/unexplained death did not achieve noninferiority (posterior probability for noninferiority = 88.4%), whereas the second coprimary endpoint of post-procedure ischemic stroke/SE did achieve noninferiority (posterior probability for noninferiority = 97.5%); the warfarin arm maintained an unusually low ischemic stroke rate (0.73%). In the meta-analysis, the composite endpoint was similar between groups (hazard ratio [HR]: 0.820; p = 0.27), as were all-stroke/SE (HR: 0.961; p = 0.87). The ischemic stroke/SE rate was numerically higher with LAAC, but this difference did not reach statistical significance (HR: 1.71; p = 0.080). However, differences in

  5. Thermal decomposition pathways of hydroxylamine: theoretical investigation on the initial steps.

    Science.gov (United States)

    Wang, Qingsheng; Wei, Chunyang; Pérez, Lisa M; Rogers, William J; Hall, Michael B; Mannan, M Sam

    2010-09-02

    Hydroxylamine (NH(2)OH) is an unstable compound at room temperature, and it has been involved in two tragic industrial incidents. Although experimental studies have been carried out to study the thermal stability of hydroxylamine, the detailed decomposition mechanism is still in debate. In this work, several density functional and ab initio methods were used in conjunction with several basis sets to investigate the initial thermal decomposition steps of hydroxylamine, including both unimolecular and bimolecular reaction pathways. The theoretical investigation shows that simple bond dissociations and unimolecular reactions are unlikely to occur. The energetically favorable initial step of decomposition pathways was determined as a bimolecular isomerization of hydroxylamine into ammonia oxide with an activation barrier of approximately 25 kcal/mol at the MPW1K level of theory. Because hydroxylamine is available only in aqueous solutions, solvent effects on the initial decomposition pathways were also studied using water cluster methods and the polarizable continuum model (PCM). In water, the activation barrier of the bimolecular isomerization reaction decreases to approximately 16 kcal/mol. The results indicate that the bimolecular isomerization pathway of hydroxylamine is more favorable in aqueous solutions. However, the bimolecular nature of this reaction means that more dilute aqueous solution will be more stable.

  6. Theoretical studies of the reactions of HCN with atomic hydrogen

    International Nuclear Information System (INIS)

    Bair, R.A.; Dunning, T.H. Jr.

    1985-01-01

    A comprehensive theoretical study has been made of the energetics of the important pathways involved in the reaction of hydrogen atoms with hydrogen cyanide. For each reaction ab initio GVB-CI calculations were carried out to determine the structures and vibrational frequencies of the reactants, transition states, and products; then POL-CI calculations were carried out to more accurately estimate the electronic contribution to the energetics of the reactions. The hydrogen abstraction reaction is calculated to be endoergic by 24 kcal/mol [expt. ΔH (0 K) = 16--19 kcal/mol] with a barrier of 31 kcal/mol in the forward direction and 6 kcal/mol in the reverse direction. For the hydrogen addition reactions, addition to the carbon atom is calculated to be exoergic by 19 kcal/mol with a barrier of 11 kcal/mol, while addition to the nitrogen center is essentially thermoneutral with a barrier of 17 kcal/mol. Calculations were also carried out on the isomerization reactions of the addition products. The cis→trans isomerization of HCNH has a barrier of only 10 kcal/mol with the trans isomer being more stable by 5 kcal/mol. The (1,2)-hydrogen migration reaction, converting H 2 CN to trans-HCNH, is endoergic by only 14 kcal/mol, but the calculated barrier for the transfer is 52 kcal/mol. The energy of the migration pathway thus lies above that of the dissociation--recombination pathway

  7. Reaction progress pathways for glass and spent fuel under unsaturated conditions

    International Nuclear Information System (INIS)

    Bates, J.; Finn, P.; Bourcier, W.; Stout, R.

    1994-10-01

    The source term for the release of radionuclides from a nuclear waste repository is the waste form. In order to assess the performance of the repository and the engineered barrier system (EBS) compared to regulations established by the Nuclear Regulatory Commission and the Environmental Protection Agency it is necessary (1) to use available data to place bounding limits on release rates from the EBS, and (2) to develop a mechanistic predictive model of the radionuclide release and validate the model against tests done under a variety of different potential reaction conditions. The problem with (1) is that there is little experience to use when evaluating waste form reaction under unsaturated conditions such that errors in applying expert judgment to the problem may be significant. The second approach, to test and model the waste form reaction, is a more defensible means of providing input to the prediction of radionuclide release. In this approach, information related to the source term has a technical basis and provides a starting point to make reasonable assumptions for long-term behavior. Key aspects of this approach are an understanding of the reaction progress mechanism and the ability to model the tests using a geochemical code such as EQ3/6. Current knowledge of glass, UO 2 , and spent fuel reactions under different conditions are described below

  8. PumpKin: A tool to find principal pathways in plasma chemical models

    Science.gov (United States)

    Markosyan, A. H.; Luque, A.; Gordillo-Vázquez, F. J.; Ebert, U.

    2014-10-01

    PumpKin is a software package to find all principal pathways, i.e. the dominant reaction sequences, in chemical reaction systems. Although many tools are available to integrate numerically arbitrarily complex chemical reaction systems, few tools exist in order to analyze the results and interpret them in relatively simple terms. In particular, due to the large disparity in the lifetimes of the interacting components, it is often useful to group reactions into pathways that recycle the fastest species. This allows a researcher to focus on the slow chemical dynamics, eliminating the shortest timescales. Based on the algorithm described by Lehmann (2004), PumpKin automates the process of finding such pathways, allowing the user to analyze complex kinetics and to understand the consumption and production of a certain species of interest. We designed PumpKin with an emphasis on plasma chemical systems but it can also be applied to atmospheric modeling and to industrial applications such as plasma medicine and plasma-assisted combustion.

  9. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions and novel technologies

    Directory of Open Access Journals (Sweden)

    Frank eSchreiber

    2012-10-01

    Full Text Available Nitrous oxide (N2O is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH or the reduction of nitrite (NO2- to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO2- to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria. In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO2-, NH2OH and nitroxyl (HNO. Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser based absorption spectroscopy. In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build-up.

  10. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    Science.gov (United States)

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  11. Discrete event simulations for glycolysis pathway and energy balance

    NARCIS (Netherlands)

    Zwieten, van D.A.J.; Rooda, J.E.; Armbruster, H.D.; Nagy, J.D.

    2010-01-01

    In this report, the biological network of the glycolysis pathway has been modeled using discrete event models (DEMs). The most important feature of this pathway is that energy is released. To create a stable steady-state system an energy molecule equilibrating enzyme and metabolic reactions have

  12. Statistical properties of deep inelastic reactions

    International Nuclear Information System (INIS)

    Moretto, L.G.

    1983-08-01

    The multifaceted aspects of deep-inelastic heavy-ion collisions are discussed in terms of the statistical equilibrium limit. It is shown that a conditional statistical equilibrium, where a number of degrees of freedom are thermalized while others are still relaxing, prevails in most of these reactions. The individual degrees of freedom that have been explored experimentally are considered in their statistical equilibrium limit, and the extent to which they appear to be thermalized is discussed. The interaction between degrees of freedom on their way towards equilibrium is shown to create complex feedback phenomena that may lead to self-regulation. A possible example of self-regulation is shown for the process of energy partition between fragments promoted by particle exchange. 35 references

  13. New challenges for text mining: mapping between text and manually curated pathways

    Science.gov (United States)

    Oda, Kanae; Kim, Jin-Dong; Ohta, Tomoko; Okanohara, Daisuke; Matsuzaki, Takuya; Tateisi, Yuka; Tsujii, Jun'ichi

    2008-01-01

    Background Associating literature with pathways poses new challenges to the Text Mining (TM) community. There are three main challenges to this task: (1) the identification of the mapping position of a specific entity or reaction in a given pathway, (2) the recognition of the causal relationships among multiple reactions, and (3) the formulation and implementation of required inferences based on biological domain knowledge. Results To address these challenges, we constructed new resources to link the text with a model pathway; they are: the GENIA pathway corpus with event annotation and NF-kB pathway. Through their detailed analysis, we address the untapped resource, ‘bio-inference,’ as well as the differences between text and pathway representation. Here, we show the precise comparisons of their representations and the nine classes of ‘bio-inference’ schemes observed in the pathway corpus. Conclusions We believe that the creation of such rich resources and their detailed analysis is the significant first step for accelerating the research of the automatic construction of pathway from text. PMID:18426550

  14. Dealkylation of alkylbenzenes: a significant pathway in the toluene, o-, m-, p-xylene + OH reaction.

    Science.gov (United States)

    Noda, Jun; Volkamer, Rainer; Molina, Mario J

    2009-09-03

    The OH-radical initiated oxidation of a series of monocyclic aromatic hydrocarbons (benzene, toluene, o-, m-, and p-xylene) in the presence of oxygen and NO(x) was investigated in a flowtube coupled with a chemical ionization mass spectrometer (CIMS). OH-radical addition to the aromatic ring--the major reaction pathway--has previously been shown to have a particular sensitivity to experimental conditions. This is the first flowtube study that demonstrates the atmospheric relevance of product yields from the OH-addition channel on the millisecond time scale (35-75 ms); the phenol yield from benzene and cresol yields from toluene are found to be 51.0 +/- 4.3% and 17.7 +/- 2.1%, in excellent agreement with previous studies under close to atmospheric conditions. We further report unambiguous experimental evidence that dealkylation is a novel and significant pathway for toluene and o-, m-, and p-xylene oxidation. At 150 Torr of O2 partial pressure, toluene is found to dealkylate with a yield of 5.4 +/- 1.2% phenol; similarly, m-, o-, and p-xylene dealkylate with yields of 11.2 +/- 3.8%, 4.5 +/- 3.2%, and 4.3 +/- 3.1% cresol, respectively. A dealkylation mechanism via OH-addition in the ipso position is feasible (DeltaH = -9 kcal/mol for phenol formation from toluene) but does not lend itself easily to explain the significant isomer effect observed among xylenes; instead an alternative mechanism is presented that can explain this isomer effect and forms phenol and likely epoxide type products with identical m/z (indistinguishable in our CIMS analysis) via a carbene-type intermediate. Dealkylation adds to the atmospheric production of phenol- and likely epoxide-type products, with aldehydes as expected co-products, and helps improve the carbon balance in the initial stages of aromatic oxidation.

  15. Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

    NARCIS (Netherlands)

    De Wispelaere, K.; Ensing, B.; Ghysels, A.; Meijer, E.J.; van Van Speybroeck, V.

    2015-01-01

    The methanol-to-olefin process is a showcase example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first

  16. Prevailence of Patch Test Positivity with Some Bases

    Directory of Open Access Journals (Sweden)

    J S Pasricha

    1987-01-01

    Full Text Available To evaluate the suitability of some chemicals to act as bases for antigens for patch tests, patch tests were performed with these agents in patients having contact dermatitis. Propylene glycol′used as such produced positive reactions in 25 (50% patients of which 12 were 2 + or more, polyethylene glycol 200 produced positive reactions in 9 (18% cases of which 4 cases were 2 + or more, a mixture of liquid paraffin and hard paraffin gave rise to positive reactions in 10 (10% cases 3 of these being 2 +, a mixture of liquid paraffin and bees wax was positive in 14 (14,Yo cases 3 of these being 2 +, yellow petrolatum was positive in 4 (8% cases, one of which was 2 +, white petrolatum was positive in S (6% cases all of these being + reactions only, and glycerol gave rise to a I + reaction in only one (2% caw. In tropical countries, water should be as base for as many antigens as possible for others, a control test with the b must be included.

  17. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

    Science.gov (United States)

    Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

    2011-08-15

    The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

  18. Molecular weight growth in Titan's atmosphere: branching pathways for the reaction of 1-propynyl radical (H3CC≡C˙) with small alkenes and alkynes.

    Science.gov (United States)

    Kirk, Benjamin B; Savee, John D; Trevitt, Adam J; Osborn, David L; Wilson, Kevin R

    2015-08-28

    The reaction of small hydrocarbon radicals (i.e.˙CN, ˙C2H) with trace alkenes and alkynes is believed to play an important role in molecular weight growth and ultimately the formation of Titan's characteristic haze. Current photochemical models of Titan's atmosphere largely assume hydrogen atom abstraction or unimolecular hydrogen elimination reactions dominate the mechanism, in contrast to recent experiments that reveal significant alkyl radical loss pathways during reaction of ethynyl radical (˙C2H) with alkenes and alkynes. In this study, the trend is explored for the case of a larger ethynyl radical analogue, the 1-propynyl radical (H3CC[triple bond, length as m-dash]C˙), a likely product from the high-energy photolysis of propyne in Titan's atmosphere. Using synchrotron vacuum ultraviolet photoionization mass spectrometry, product branching ratios are measured for the reactions of 1-propynyl radical with a suite of small alkenes (ethylene and propene) and alkynes (acetylene and d4-propyne) at 4 Torr and 300 K. Reactions of 1-propynyl radical with acetylene and ethylene form single products, identified as penta-1,3-diyne and pent-1-en-3-yne, respectively. These products form by hydrogen atom loss from the radical-adduct intermediates. The reactions of 1-propynyl radical with d4-propyne and propene form products from both hydrogen atom and methyl loss, (-H = 27%, -CH3 = 73%) and (-H = 14%, -CH3 = 86%), respectively. Together, these results indicate that reactions of ethynyl radical analogues with alkenes and alkynes form significant quantities of products by alkyl loss channels, suggesting that current photochemical models of Titan over predict both hydrogen atom production as well as the efficiency of molecular weight growth in these reactions.

  19. Quantum chemical investigation of the reaction of O( P2) with certain ...

    Indian Academy of Sciences (India)

    WINTEC

    In the case of methyl radical the minimum energy reaction pathway leads to the products CO + H2 + H. In ... Reactions of atomic oxygen with hydrocarbon radicals play an important role in ..... The reaction between singlet oxygen and propyl ...

  20. [Polyketone Reaction in Biosynthetic Pathways of 2, 3, 5, 4'-Tetrahydroxy Stilhene-2-O-β-D-glucoside in Polygonum multiflorum by Biocatalysis].

    Science.gov (United States)

    Lei, Lei; Xia, Wan-xia; Shao, Li; Zhao, Shu-jin

    2015-10-01

    2, 3, 5, 4'-Tetrahydroxy stilbene-2-O-β-D-glucoside (THSG), the active ingredient of Polygonum multiflorum, its polyketone reaction in the biosynthesis pathways was studied by biocatalysis method. The substrates 4-coumaroyl-CoA and malonyl-CoA were catalyzed in vitro by the crude enzyme extracted from Polygonum multiflorum callus, then the products were verified by HPLC and LC-MS methods. And the crude enzyme was analyzed by ammonium sulfate precipitation method and SDS-PAGE. HPLC chromatogram showed the same retention time of both the product and resveratrol standards; LC-MS spectra showed that the m/z of product was 227, which was consistent with resveratrol standards under the mode of negative ion; Ammonium sulfate (AS) precipitation method showed AS of 40% - 70% had catalytic activity,and 50% - 60% was the optimum; SDS-PAGE showed protein bands were obviously different among different AS concentration between 20% - 80%, the protein band of 42 kDa was found in AS of 50% - 60%, which had the same molecular weight with stilbene synthase. The product of polyketone reaction in the biosynthesis of THSG is resveratrol rather than THSG, so it is speculated that THSG is the conversion product of resveratrol instead of the direct product of the polyketone reaction.

  1. Parallel proton transfer pathways in aqueous acid-base reactions

    NARCIS (Netherlands)

    Cox, M.J.; Bakker, H.J.

    2008-01-01

    We study the mechanism of proton transfer (PT) between the photoacid 8-hydroxy-1,3, 6-pyrenetrisulfonic acid (HPTS) and the base chloroacetate in aqueous solution. We investigate both proton and deuteron transfer reactions in solutions with base concentrations ranging from 0.25M to 4M. Using

  2. Direct projectile break up its relation to the astrophysically revelant fusion reactions

    International Nuclear Information System (INIS)

    Bertulani, C.A.; Hussein, M.S.

    1990-05-01

    The break-up into two pieces of weakly bound nuclei passing by the Coulomb field of a large Z nucleus can provide useful information on the inverse fusion reactions which are important for the elemental formation in the stars. However, the nuclear interaction complicates considerably the extraction of such information. A study is made of the contributions of the Coulomb and nuclear interaction to the process, showing when the Coulomb break-up prevails and how a reliable separation of multipolarities can be done. (author)

  3. An autonomous organic reaction search engine for chemical reactivity

    Science.gov (United States)

    Dragone, Vincenza; Sans, Victor; Henson, Alon B.; Granda, Jaroslaw M.; Cronin, Leroy

    2017-06-01

    The exploration of chemical space for new reactivity, reactions and molecules is limited by the need for separate work-up-separation steps searching for molecules rather than reactivity. Herein we present a system that can autonomously evaluate chemical reactivity within a network of 64 possible reaction combinations and aims for new reactivity, rather than a predefined set of targets. The robotic system combines chemical handling, in-line spectroscopy and real-time feedback and analysis with an algorithm that is able to distinguish and select the most reactive pathways, generating a reaction selection index (RSI) without need for separate work-up or purification steps. This allows the automatic navigation of a chemical network, leading to previously unreported molecules while needing only to do a fraction of the total possible reactions without any prior knowledge of the chemistry. We show the RSI correlates with reactivity and is able to search chemical space using the most reactive pathways.

  4. A Theoretical Investigation of the Plausibility of Reactions Between Ammonia and Carbonyl Species (Formaldehyde, Acetaldehyde, and Acetone) in Interstellar Ice Analogs at Ultracold Temperatures

    Science.gov (United States)

    Chen, Lina; Woon, David E.

    2011-01-01

    We have reexamined the reaction between formaldehyde and ammonia, which was previously studied by us and other workers in modestly sized cluster calculations. Larger model systems with up to 12H2O were employed, and reactions of two more carbonyl species, acetaldehyde and acetone, were also carried out. Calculations were performed at the B3LYP/6-31+G** level with bulk solvent effects treated with a polarizable continuum model; limited MP2/6-31+G** calculations were also performed. We found that while the barrier for the concerted proton relay mechanism described in previous work remains modest, it is still prohibitively high for the reaction to occur under the ultracold conditions that prevail in dense interstellar clouds. However, a new pathway emerged in more realistic clusters that involves at least one barrierless step for two of the carbonyl species considered here: ammonia reacts with formaldehyde and acetaldehyde to form a partial charge transfer species in small clusters (4H2O) and a protonated hydroxyamino intermediate species in large clusters (9H2O, 12H2O); modest barriers that decrease sharply with cluster size are found for the analogous processes for the acetone-NH3 reaction. Furthermore, if a second ammonia replaces one of the water molecules in calculations in the 9H2O clusters, deprotonation can occur to yield the same neutral hydroxyamino species that is formed via the original concerted proton relay mechanism. In at least one position, deprotonation is barrierless when zero-point energy is included. In addition to describing the structures and energetics of the reactions between formaldehyde, acetaldehyde, and acetone with ammonia, we report spectroscopic predictions of the observable vibrational features that are expected to be present in ice mixtures of different composition.

  5. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.

    Science.gov (United States)

    Dailey, Harry A; Dailey, Tamara A; Gerdes, Svetlana; Jahn, Dieter; Jahn, Martina; O'Brian, Mark R; Warren, Martin J

    2017-03-01

    The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized. Copyright © 2017 American Society for Microbiology.

  6. Further analysis of PREVAIL: enzalutamide use in chemotherapy-naïve men with metastatic castration-resistant prostate cancer.

    Science.gov (United States)

    Aragon-Ching, Jeanny B

    2014-01-01

    PREVAIL was a phase III multinational, double-blind, placebo-controlled trial that enrolled chemotherapy-naïve men with metastatic castration-resistant prostate cancer (mCRPC), which showed remarkable improvement in co-primary endpoints with an overall 81% reduction in the risk of radiographic progression, as well as 29% reduction in the risk of death in favor of the enzalutamide arm over placebo. All secondary endpoints including time to subsequent chemotherapy initiation and prostate specific antigen (PSA) progression were in favor of the enzalutamide arm. The results of PREVAIL shows the utility of enzalutamide that would likely soon expand the indication to asymptomatic or minimally symptomatic men with mCRPC not previously treated with chemotherapy.

  7. Alternative reaction routes during coal hydrogenation and coal derived oil upgrading

    Energy Technology Data Exchange (ETDEWEB)

    Schulz, H.; Kordokuzis, G.; Langner, M. (University of Karlsruhe, Karlsruhe (Germany, F.R.). Engler-Bunte-Institute)

    1989-10-01

    Alternative reaction routes have been traced for the hydrodenitrogenation and hydrodeoxygenation of coal structure related model compounds. Reaction pathways are very structure specific. It is shown how reaction mechanisms switch from one route to another with changes in reaction conditions and catalyst features. Optimization of coal liquefaction processes can make use of this detailed understanding of selectivity. 5 refs., 7 figs.

  8. Vapor-Phase Hydrodeoxygenation of Guaiacol to Aromatics over Pt/HBeta: Identification of the Role of Acid Sites and Metal Sites on the Reaction Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Nie, Lei [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China; Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Peng, Bo [Institute for Integrated Catalysis, Pacific Northwest National Laboratory, P.O. Box 999 Richland WA 99352 USA; Zhu, Xinli [Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 P.R. China

    2018-02-05

    Hydrodeoxygenation of guaiacol, a phenolic compound derived from lignin fraction of biomass, over a Pt/HBeta catalyst at 350 °C and atmospheric pressure produces benzene, toluene, xylenes, and C9+ aromatics with yield of 42%, 29%, 12%, and 5%, respectively. Reaction pathways for conversion of two functional groups (hydroxyl and methoxyl) over the bifunctional catalyst were studied. Both guaiacol and intermediate products (catechol and cyclopentanone) were fed onto zeolite HBeta and Pt/SiO2 to identify the individual role of acid site and metal site. Acid sites (mainly Brønsted acid site, BAS) catalyze transalkylation and dehydroxylation reactions in sequence, producing phenol, cresols and xylenols as the major products at high conversion. Pt sites catalyze demethylation reaction resulting in catechol as the primary product, which can either be deoxygenated to phenol followed by phenol to benzene, or decarbonylated to cyclopentanone and further to butane. The close proximity of Pt and BAS in bifunctional Pt/HBeta enables both transalkylation and deoxygenation reactions with inhibited demethylation and decarbonylation reactions, producing aromatics as major final products with a total yield > 85%. Both activity and stability of bifunctional Pt/HBeta during hydrodeoxygenation of guaiacol is improved compared to HBeta and Pt/SiO2. The addition of water to the feed further improves the activity and stability via hydrolysis of O-CH3 bond of guaiacol on BAS and removing coke around Pt.

  9. Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus

    DEFF Research Database (Denmark)

    Thykær, Jette; Andersen, Mikael Rørdam; Baker, S. E.

    2009-01-01

    with the reactions, we identified orthologous candidate essential genes in Aspergillus fumigatus. Our predictions are validated in part by the modes of action for some antifungal drugs and by molecular genetic studies of essential genes in A. fumigatus and other fungi. The use of metabolic models to predict...... of 1190 biochemically unique reactions that are associated with 871 open reading frames. Through a systematic in silico deletion of single metabolic reactions using this model, several essential metabolic pathways were identified for A. niger. A total of 138 reactions were identified as being essential...... biochemical reactions during growth on a minimal glucose medium. The majority of the reactions grouped into essential biochemical pathways covering cell wall biosynthesis, amino acid biosynthesis, energy metabolism and purine and pyrimidine metabolism. Based on the A. niger open reading frames associated...

  10. 76 FR 21036 - Application of the Prevailing Wage Methodology in the H-2B Program

    Science.gov (United States)

    2011-04-14

    ... Department to ``promulgate new rules concerning the calculation of the prevailing wage rate in the H-2B... wage methodology set forth in this Rule applies only to wages paid for work performed on or after...: Notice. SUMMARY: On January 19, 2011, the Department of Labor (Department) published a final rule, Wage...

  11. Back-reactions, short-circuits, leaks and other energy wasteful reactions in biological electron transfer: redox tuning to survive life in O(2).

    Science.gov (United States)

    Rutherford, A William; Osyczka, Artur; Rappaport, Fabrice

    2012-03-09

    The energy-converting redox enzymes perform productive reactions efficiently despite the involvement of high energy intermediates in their catalytic cycles. This is achieved by kinetic control: with forward reactions being faster than competing, energy-wasteful reactions. This requires appropriate cofactor spacing, driving forces and reorganizational energies. These features evolved in ancestral enzymes in a low O(2) environment. When O(2) appeared, energy-converting enzymes had to deal with its troublesome chemistry. Various protective mechanisms duly evolved that are not directly related to the enzymes' principal redox roles. These protective mechanisms involve fine-tuning of reduction potentials, switching of pathways and the use of short circuits, back-reactions and side-paths, all of which compromise efficiency. This energetic loss is worth it since it minimises damage from reactive derivatives of O(2) and thus gives the organism a better chance of survival. We examine photosynthetic reaction centres, bc(1) and b(6)f complexes from this view point. In particular, the evolution of the heterodimeric PSI from its homodimeric ancestors is explained as providing a protective back-reaction pathway. This "sacrifice-of-efficiency-for-protection" concept should be generally applicable to bioenergetic enzymes in aerobic environments. Copyright © 2012 Federation of European Biochemical Societies. All rights reserved.

  12. Lifecycle impacts of natural gas to hydrogen pathways on urban air quality

    International Nuclear Information System (INIS)

    Wang, Guihua; Ogden, Joan M.; Nicholas, Michael A.

    2007-01-01

    In this paper we examine the potential air quality impacts of hydrogen transportation fuel from a lifecycle analysis perspective, including impacts from fuel production, delivery, and vehicle use. We assume that hydrogen fuel cell vehicles are introduced in a specific region, Sacramento County, California. We consider two levels of market penetration where 9% or 20% of the light duty fleet are hydrogen fuel cell vehicles. The following three natural gas to hydrogen supply pathways are assessed in detail and compared in terms of emissions and the resulting changes in ambient air quality: (1) onsite hydrogen production; (2) centralized hydrogen production with gaseous hydrogen pipeline delivery systems; and (3) centralized hydrogen production with liquid hydrogen truck delivery systems. All the pathways examined use steam methane reforming (SMR) of natural gas to produce hydrogen. The source contributions to incremental air pollution are estimated and compared among hydrogen pathways. All of the hydrogen pathways result in extremely low contributions to ambient air concentrations of NO x , CO, particulates, and SO x , typically less than 0.1% of the current ambient pollution for both levels of market penetration. Among the hydrogen supply options, it is found that the central SMR with pipeline delivery systems is the lowest pollution option available provided the plant is located to avoid transport of pollutants into the city via prevailing winds. The onsite hydrogen pathway is comparable to the central hydrogen pathway with pipeline systems in terms of the resulting air pollution. The pathway with liquid hydrogen trucks has a greater impact on air quality relative to the other pathways due to emissions associated with diesel trucks and electricity consumption to liquefy hydrogen. However, all three hydrogen pathways result in negligible air pollution in the region. (author)

  13. Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

    Science.gov (United States)

    Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

    2014-12-02

    Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

  14. A thermodynamic solution model for calcium carbonate: Towards an understanding of multi-equilibria precipitation pathways.

    Science.gov (United States)

    Donnet, Marcel; Bowen, Paul; Lemaître, Jacques

    2009-12-15

    Thermodynamic solubility calculations are normally only related to thermodynamic equilibria in solution. In this paper, we extend the use of such solubility calculations to help elucidate possible precipitation reaction pathways during the entire reaction. We also estimate the interfacial energy of particles using only solubility data by a modification of Mersmann's approach. We have carried this out by considering precipitation reactions as a succession of small quasi-equilibrium states. Thus possible equilibrium precipitation pathways can be evaluated by calculating the evolution of surface charge, particle size and/or interfacial energy during the ongoing reaction. The approach includes the use of the Kelvin's law to express the influence of particle size on the solubility constant of precipitates, the use of Nernst's law to calculate surface potentials from solubility calculations and relate this to experimentally measured zeta potentials. Calcium carbonate precipitation and zeta potential measurements of well characterised high purity calcite have been used as a model system to validate the calculated values. The clarification of the change in zeta potential on titration illustrates the power of this approach as a tool for reaction pathway prediction and hence knowledge based tailoring of precipitation reactions.

  15. Accurate atom-mapping computation for biochemical reactions.

    Science.gov (United States)

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  16. Quantum state-resolved gas/surface reaction dynamics probed by reflection absorption infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chen Li [Department of Dynamics at Surfaces, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen (Germany); Ueta, Hirokazu; Beck, Rainer D. [Laboratoire de Chimie Physique Moleculaire, Ecole Polytechnique Federale de Lausanne (Switzerland); Bisson, Regis [Aix-Marseille Universite, PIIM, CNRS, UMR 7345, 13397 Marseille (France)

    2013-05-15

    We report the design and characterization of a new molecular-beam/surface-science apparatus for quantum state-resolved studies of gas/surface reaction dynamics combining optical state-specific reactant preparation in a molecular beam by rapid adiabatic passage with detection of surface-bound reaction products by reflection absorption infrared spectroscopy (RAIRS). RAIRS is a non-invasive infrared spectroscopic detection technique that enables online monitoring of the buildup of reaction products on the target surface during reactant deposition by a molecular beam. The product uptake rate obtained by calibrated RAIRS detection yields the coverage dependent state-resolved reaction probability S({theta}). Furthermore, the infrared absorption spectra of the adsorbed products obtained by the RAIRS technique provide structural information, which help to identify nascent reaction products, investigate reaction pathways, and determine branching ratios for different pathways of a chemisorption reaction. Measurements of the dissociative chemisorption of methane on Pt(111) with this new apparatus are presented to illustrate the utility of RAIRS detection for highly detailed studies of chemical reactions at the gas/surface interface.

  17. Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".

    Science.gov (United States)

    Liu, Mengjin; Bienfait, Bruno; Sacher, Oliver; Gasteiger, Johann; Siezen, Roland J; Nauta, Arjen; Geurts, Jan M W

    2014-01-01

    The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the "missing links" between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.

  18. Uranium fluoride chemistry. Part 1. The gas phase reaction of uranium hexafluoride with alcohols

    International Nuclear Information System (INIS)

    Schnautz, N.G.; Venter, P.J.

    1992-01-01

    The reaction between uranium hexafluoride (UF 6 ) and simple alcohols in the gas phase was observed to proceed by way of three possible reaction pathways involving dehydration, deoxygenative fluorination, and ether formation. These reactions can best be explained by assuming that alcohols first react with UF 6 to afford the alkoxy uranium pentafluoride intermediate ROUF 5 , which reacts further to give the dehydration, deoxygenative fluorination, and ether products. In each of the above three reaction pathways, UF 6 is transformed to UOF 4 , which being as reactive toward alcohols as UF 6 , reacts further with the alcohol in question to finally afford the unreactive uranyl fluoride (UO 2 F 2 ). 6 refs., 2 tabs

  19. Correcting ligands, metabolites, and pathways

    Directory of Open Access Journals (Sweden)

    Vriend Gert

    2006-11-01

    Full Text Available Abstract Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry and that a considerable number (about one third had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and

  20. Redox reactions in food fermentations

    DEFF Research Database (Denmark)

    Hansen, Egon Bech

    2018-01-01

    involves oxidative steps in the early part of the pathways whereas a multitude of different reactions are used as compensating reductions. Much of the diversity seen between food fermentations arise from the different routes and the different electron acceptors used by microorganisms to counterbalance...... and this contributes to the diversity in flavor, color, texture, and shelf life. The review concludes that these reactions are still only incompletely understood and that they represent an interesting area for fundamental research and also represent a fertile field for product development through a more conscious use...... of the redox properties of strains used to compose food cultures....

  1. Prediction of novel synthetic pathways for the production of desired chemicals

    Directory of Open Access Journals (Sweden)

    Park Jin

    2010-03-01

    Full Text Available Abstract Background There have been several methods developed for the prediction of synthetic metabolic pathways leading to the production of desired chemicals. In these approaches, novel pathways were predicted based on chemical structure changes, enzymatic information, and/or reaction mechanisms, but the approaches generating a huge number of predicted results are difficult to be applied to real experiments. Also, some of these methods focus on specific pathways, and thus are limited to expansion to the whole metabolism. Results In the present study, we propose a system framework employing a retrosynthesis model with a prioritization scoring algorithm. This new strategy allows deducing the novel promising pathways for the synthesis of a desired chemical together with information on enzymes involved based on structural changes and reaction mechanisms present in the system database. The prioritization scoring algorithm employing Tanimoto coefficient and group contribution method allows examination of structurally qualified pathways to recognize which pathway is more appropriate. In addition, new concepts of binding site covalence, estimation of pathway distance and organism specificity were taken into account to identify the best synthetic pathway. Parameters of these factors can be evolutionarily optimized when a newly proven synthetic pathway is registered. As the proofs of concept, the novel synthetic pathways for the production of isobutanol, 3-hydroxypropionate, and butyryl-CoA were predicted. The prediction shows a high reliability, in which experimentally verified synthetic pathways were listed within the top 0.089% of the identified pathway candidates. Conclusions It is expected that the system framework developed in this study would be useful for the in silico design of novel metabolic pathways to be employed for the efficient production of chemicals, fuels and materials.

  2. Post hoc analysis of Japanese patients from the placebo-controlled PREVAIL trial of enzalutamide in patients with chemotherapy-naive, metastatic castration-resistant prostate cancer—updated results

    Science.gov (United States)

    Ueda, Takeshi

    2017-01-01

    Abstract A post hoc analysis of interim results from PREVAIL, a Phase III, double-blind, placebo-controlled trial of men with metastatic castration-resistant prostate cancer, demonstrated that the treatment effects, safety and pharmacokinetics of enzalutamide in Japanese patients were generally consistent with those of the overall population. A recent longer term analysis of PREVAIL demonstrated continued benefit of enzalutamide treatment over placebo. Here, we report results from a post hoc analysis of Japanese patients enrolled in PREVAIL at the prespecified number of deaths for the final analysis. In Japanese patients, enzalutamide reduced the risk of death by 35% (hazard ratio, 0.65; 95% confidence interval, 0.28–1.51) and the risk of investigator-assessed radiographic progression or death by 60% (hazard ratio, 0.40; 95% confidence interval, 0.18–0.90). These results show that treatment effects and safety in Japanese patients in the final analysis of PREVAIL continued to be generally consistent with those of the overall population. PMID:28003320

  3. Enzalutamide in Men with Chemotherapy-naïve Metastatic Castration-resistant Prostate Cancer: Extended Analysis of the Phase 3 PREVAIL Study.

    Science.gov (United States)

    Beer, Tomasz M; Armstrong, Andrew J; Rathkopf, Dana; Loriot, Yohann; Sternberg, Cora N; Higano, Celestia S; Iversen, Peter; Evans, Christopher P; Kim, Choung-Soo; Kimura, Go; Miller, Kurt; Saad, Fred; Bjartell, Anders S; Borre, Michael; Mulders, Peter; Tammela, Teuvo L; Parli, Teresa; Sari, Suha; van Os, Steve; Theeuwes, Ad; Tombal, Bertrand

    2017-02-01

    Enzalutamide significantly improved radiographic progression-free survival (rPFS) and overall survival (OS) among men with chemotherapy-naïve metastatic castration-resistant prostate cancer at the prespecified interim analysis of PREVAIL, a phase 3, double-blind, randomized study. We evaluated the longer-term efficacy and safety of enzalutamide up to the prespecified number of deaths in the final analysis, which included an additional 20 mo of follow-up for investigator-assessed rPFS, 9 mo of follow-up for OS, and 4 mo of follow-up for safety. Enzalutamide reduced the risk of radiographic progression or death by 68% (hazard ratio [HR] 0.32, 95% confidence interval [CI] 0.28-0.37; pPREVAIL provides more complete assessment of the clinical benefit of enzalutamide. PREVAIL is registered on ClinicalTrials.gov as NCT01212991. According to data from longer follow-up, enzalutamide continued to provide benefit over placebo in patients with metastatic castration-resistant prostate cancer. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

  4. Theoretical investigation of the gas-phase reactions of CrO(+) with ethylene.

    Science.gov (United States)

    Scupp, Thomas M; Dudley, Timothy J

    2010-01-21

    The potential energy surfaces associated with the reactions of chromium oxide cation (CrO(+)) with ethylene have been characterized using density functional, coupled-cluster, and multireference methods. Our calculations show that the most probable reaction involves the formation of acetaldehyde and Cr(+) via a hydride transfer involving the metal center. Our calculations support previous experimental hypotheses that a four-membered ring intermediate plays an important role in the reactivity of the system. We have also characterized a number of viable reaction pathways that lead to other products, including ethylene oxide. Due to the experimental observation that CrO(+) can activate carbon-carbon bonds, a reaction pathway involving C-C bond cleavage has also been characterized. Since many of the reactions involve a change in the spin state in going from reactants to products, locations of these spin surface crossings are presented and discussed. The applicability of methods based on Hartree-Fock orbitals is also discussed.

  5. Isolation of an oxomanganese(V) porphyrin intermediate in the reaction of a manganese(III) porphyrin complex and H2O2 in aqueous solution.

    Science.gov (United States)

    Nam, Wonwoo; Kim, Inwoo; Lim, Mi Hee; Choi, Hye Jin; Lee, Je Seung; Jang, Ho G

    2002-05-03

    The reaction of [Mn(TF(4)TMAP)](CF(3)SO(3))(5) (TF(4)TMAP=meso-tetrakis(2,3,5,6-tetrafluoro-N,N,N-trimethyl-4-aniliniumyl)porphinato dianion) with H(2)O(2) (2 equiv) at pH 10.5 and 0 degrees C yielded an oxomanganese(V) porphyrin complex 1 in aqueous solution, whereas an oxomanganese(IV) porphyrin complex 2 was generated in the reactions of tert-alkyl hydroperoxides such as tert-butyl hydroperoxide and 2-methyl-1-phenyl-2-propyl hydroperoxide. Complex 1 was capable of epoxidizing olefins and exchanging its oxygen with H(2) (18)O, whereas 2 did not epoxidize olefins. From the reactions of [Mn(TF(4)TMAP)](5+) with various oxidants in the pH range 3-11, the O-O bond cleavage of hydroperoxides was found to be sensitive to the hydroperoxide substituent and the pH of the reaction solution. Whereas the O-O bond of hydroperoxides containing an electron-donating tert-alkyl group is cleaved homolytically, an electron-withdrawing substituent such as an acyl group in m-chloroperoxybenzoic acid (m-CPBA) facilitates O-O bond heterolysis. The mechanism of the O-O bond cleavage of H(2)O(2) depends on the pH of the reaction solution: O-O bond homolysis prevails at low pH and O-O bond heterolysis becomes a predominant pathway at high pH. The effect of pH on (18)O incorporation from H(2) (18)O into oxygenated products was examined over a wide pH range, by carrying out the epoxidation of carbamazepine (CBZ) with [Mn(TF(4)TMAP)](5+) and KHSO(5) in buffered H(2) (18)O solutions. A high proportion of (18)O was incorporated into the CBZ-10,11-oxide product at all pH values but this proportion was not affected significantly by the pH of the reaction solution.

  6. Enzymatic description of the anhydrofructose pathway of glycogen degradation. I

    DEFF Research Database (Denmark)

    Yu, Shukun; Refdahl, Charlotte; Lundt, Inge

    2004-01-01

    The anhydrofructose pathway describes the degradation of glycogen and starch to metabolites via 1,5-anhydro-D-fructose (1,5AnFru). The enzyme catalyzing the first reaction step of this pathway, i.e., a-1,4-glucan lyase (EC 4.2.1.13), has been purified, cloned and characterized from fungi and red...... possessed all enzymes needed for conversion of glycogen to APP, an a-1,4-glucan lyase from this fungus was isolated and partially sequenced. Based on this work, a scheme of the enzymatic description of the anhydrofructose pathway in A. melaloma was proposed. Keywords: Anhydrofructose pathway; Anthracobia...

  7. A kinetic model for the glucose/glycine Maillard reaction pathways

    NARCIS (Netherlands)

    Martins, S.I.F.S.; Boekel, van M.A.J.S.

    2005-01-01

    A comprehensive kinetic model for the glucose/glycine Maillard reaction is proposed based on an approach called multiresponse kinetic modelling. Special attention was paid to reactants, intermediates and end products: -fructose, N-(1-deoxy--fructos-1-yl)-glycine (DFG), 1-deoxy-2,3-hexodiulose and

  8. Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

    International Nuclear Information System (INIS)

    Osborn, David L.

    2017-01-01

    Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low temperature combustion and the oxidation of volatile organic compounds in earth’s atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization make characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, while master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

  9. Reaction Mechanisms on Multiwell Potential Energy Surfaces in Combustion (and Atmospheric) Chemistry

    Science.gov (United States)

    Osborn, David L.

    2017-05-01

    Chemical reactions occurring on a potential energy surface with multiple wells are ubiquitous in low-temperature combustion and in the oxidation of volatile organic compounds in Earth's atmosphere. The rich variety of structural isomerizations that compete with collisional stabilization makes characterizing such complex-forming reactions challenging. This review describes recent experimental and theoretical advances that deliver increasingly complete views of their reaction mechanisms. New methods for creating reactive intermediates coupled with multiplexed measurements provide many experimental observables simultaneously. Automated methods to explore potential energy surfaces can uncover hidden reactive pathways, and master equation methods enable a holistic treatment of both sequential and well-skipping pathways. Our ability to probe and understand nonequilibrium effects and reaction sequences is increasing. These advances provide the fundamental science base for predictive models of combustion and the atmosphere that are crucial to address global challenges.

  10. Covalent bonding of chloroanilines to humic constituents: Pathways, kinetics, and stability

    International Nuclear Information System (INIS)

    Kong, Deyang; Xia, Qing; Liu, Guoqiang; Huang, Qingguo; Lu, Junhe

    2013-01-01

    Covalent coupling to natural humic constituents comprises an important transformation pathway for anilinic pollutants in the environment. We systematically investigated the reactions of chlorine substituted anilines with catechol and syringic acid in horseradish peroxidase (HRP) catalyzed systems. It was demonstrated that although nucleophilic addition was the mechanism of covalent bonding to both catechol and syringic acid, chloroanilines coupled to the 2 humic constituents via slightly different pathways. 1,4-addition and 1,2-addition are involved to catechol and syringic acid, respectively. 1,4-addition showed empirical 2nd order kinetics and this pathway seemed to be more permanent than 1,2-addition. Stability experiments demonstrated that cross-coupling products with syringic acid could be easily released in acidic conditions. However, cross-coupling with catechol was relatively stable at similar conditions. Thus, the environmental behavior and bioavailability of the coupling products should be carefully assessed. -- Highlights: •Chloroanilines covalently coupled to humic constituents in HRP catalyzed processes, which facilitated their transformation. •MS technique was employed to analyze the coupling products and therefore elucidate the reaction pathways. •Chloroanilines couple to catechol and syringic acid via 1,4- and 1,2-nucleophilic addition pathways, respectively. •Cross-coupling products formed via 1,4-nucleophilic addition pathway were more stable than those via 1,2-addition pathway. -- Bound residues of chloroanilines formed via 1,2- and 1,4-nucleophilic addition pathways showed different stability

  11. Temperature dependence of muonium reaction rates in the gas phase

    International Nuclear Information System (INIS)

    Fleming, D.G.; Garner, D.M.; Mikula, R.J.; British Columbia Univ., Vancouver

    1981-01-01

    A study of the temperature dependence of reaction rates has long been an important tool in establishing reaction pathways in chemical reactions. This is particularly true for the reactions of muonium (in comparison with those of hydrogen) since a measurement of the activation energy for chemical reaction is sensitive to both the height and the position of the potential barrier in the reaction plane. For collision controlled reactions, on the other hand, the reaction rate is expected to exhibit a weak T 1 sup(/) 2 dependence characteristic of the mean collision velocity. These concepts are discussed and their effects illustrated in a comparison of the chemical and spin exchange reaction rates of muonium and hydrogen in the temperature range approx.300-approx.500 K. (orig.)

  12. Uranium oxidation: Characterization of oxides formed by reaction with water by infrared and sorption analyses

    Science.gov (United States)

    Fuller, E. L.; Smyrl, N. R.; Condon, J. B.; Eager, M. H.

    1984-04-01

    Three different uranium oxide samples have been characterized with respect to the different preparation techniques. The results show that the water reaction with uranium metal occurs cyclically forming laminar layers of oxide which spall off due to the strain at the oxide/metal interface. Single laminae are released if liquid water is present due to the prizing penetration at the reaction zone. The rate of reaction of water with uranium is directly proportional to the amount of adsorbed water on the oxide product. Rapid transport is effected through the open hydrous oxide product. Dehydration of the hydrous oxide irreversibly forms a more inert oxide which cannot be rehydrated to the degree that prevails in the original hydrous product of uranium oxidation with water. Inert gas sorption analyses and diffuse reflectance infrared studies combined with electron microscopy prove valuable in defining the chemistry and morphology of the oxidic products and hydrated intermediates.

  13. Vanillin biosynthetic pathways in plants.

    Science.gov (United States)

    Kundu, Anish

    2017-06-01

    The present review compiles the up-to-date knowledge on vanillin biosynthesis in plant systems to focus principally on the enzymatic reactions of in planta vanillin biosynthetic pathway and to find out its impact and prospect in future research in this field. Vanillin, a very popular flavouring compound, is widely used throughout the world. The principal natural resource of vanillin is the cured vanilla pods. Due to the high demand of vanillin as a flavouring agent, it is necessary to explore its biosynthetic enzymes and genes, so that improvement in its commercial production can be achieved through metabolic engineering. In spite of significant advancement in elucidating vanillin biosynthetic pathway in the last two decades, no conclusive demonstration had been reported yet for plant system. Several biosynthetic enzymes have been worked upon but divergences in published reports, particularly in characterizing the crucial biochemical steps of vanillin biosynthesis, such as side-chain shortening, methylation, and glucoside formation and have created a space for discussion. Recently, published reviews on vanillin biosynthesis have focused mainly on the biotechnological approaches and bioconversion in microbial systems. This review, however, aims to compile in brief the overall vanillin biosynthetic route and present a comparative as well as comprehensive description of enzymes involved in the pathway in Vanilla planifolia and other plants. Special emphasis has been given on the key enzymatic biochemical reactions that have been investigated extensively. Finally, the present standpoint and future prospects have been highlighted.

  14. Directing reaction pathways by catalyst active-site selection using self-assembled monolayers.

    Science.gov (United States)

    Pang, Simon H; Schoenbaum, Carolyn A; Schwartz, Daniel K; Medlin, J Will

    2013-01-01

    One key route for controlling reaction selectivity in heterogeneous catalysis is to prepare catalysts that exhibit only specific types of sites required for desired product formation. Here we show that alkanethiolate self-assembled monolayers with varying surface densities can be used to tune selectivity to desired hydrogenation and hydrodeoxygenation products during the reaction of furfural on supported palladium catalysts. Vibrational spectroscopic studies demonstrate that the selectivity improvement is achieved by controlling the availability of specific sites for the hydrogenation of furfural on supported palladium catalysts through the selection of an appropriate alkanethiolate. Increasing self-assembled monolayer density by controlling the steric bulk of the organic tail ligand restricts adsorption on terrace sites and dramatically increases selectivity to desired products furfuryl alcohol and methylfuran. This technique of active-site selection simultaneously serves both to enhance selectivity and provide insight into the reaction mechanism.

  15. CONSTRUCTION TECHNOLOGY DIFFUSION IN DEVELOPING COUNTRIES: LIMITATIONS OF PREVAILING INNOVATION SYSTEMS

    Directory of Open Access Journals (Sweden)

    Emilia van Egmond-deWilde de Ligny

    2008-12-01

    Full Text Available The diffusion of innovative technologies in the market is usually a complex and difficult process with a varying degree of success and the effects of the diffused innovative technologies are very un-balanced. The objective of our research is to gain insight into the reasons why the diffusion of innovative technology fails, even though they promise a superior performance compared to incumbent technologies. Drawing on innovation systems theories, we have identified and used the concepts of technological regime, actor network and technology sets to analyze technology diffusion in a case study in the dwelling construction industry in Costa Rica. The results showed bottlenecks in the prevailing innovation system that curtailed the diffusion of an innovative construction technology.

  16. Visible-light-induced, Ir-catalyzed reactions of N-methyl-N-((trimethylsilylmethylaniline with cyclic α,β-unsaturated carbonyl compounds

    Directory of Open Access Journals (Sweden)

    Dominik Lenhart

    2014-04-01

    Full Text Available N-Methyl-N-((trimethylsilylmethylaniline was employed as reagent in visible-light-induced, iridium-catalyzed addition reactions to cyclic α,β-unsaturated carbonyl compounds. Typical reaction conditions included the use of one equivalent of the reaction substrate, 1.5 equivalents of the aniline and 2.5 mol % (in MeOH or 1.0 mol % (in CH2Cl2 [Ir(ppy2(dtbbpy]BF4 as the catalyst. Two major reaction products were obtained in combined yields of 30–67%. One product resulted from aminomethyl radical addition, the other product was a tricyclic compound, which is likely formed by attack of the intermediately formed α-carbonyl radical at the phenyl ring. For five-membered α,β-unsaturated lactone and lactam substrates, the latter products were the only products isolated. For the six-membered lactones and lactams and for cyclopentenone the simple addition products prevailed.

  17. Degradation of Nicotine in Chlorinated Water: Pathways and ...

    Science.gov (United States)

    Report The objective of the study is to illustrate how drinking water would affect alkaloid pesticides, and to address the issue by (a) investigating the fate of nicotine in chlorinated drinking water and deionized water, (b) determining the reaction rate and pathway of the reaction between nicotine and aqueous chlorine, (c) identifying nicotine’s degradation products, and (d) providing data that can be used to assess the potential threat from nicotine in drinking water.

  18. A SNARE-protein has opposing functions in penetration resistance and defence signalling pathways

    DEFF Research Database (Denmark)

    Zhang, Ziguo; Feechan, Angela; Pedersen, Carsten

    2007-01-01

    Penetration resistance is often the first line of defence against fungal pathogens. Subsequently induced defences are mediated by the programmed cell death (PCD) reaction pathway and the salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) signalling pathways. We previously demonstrated...

  19. Fast and quantitative differentiation of single-base mismatched DNA by initial reaction rate of catalytic hairpin assembly.

    Science.gov (United States)

    Li, Chenxi; Li, Yixin; Xu, Xiao; Wang, Xinyi; Chen, Yang; Yang, Xiaoda; Liu, Feng; Li, Na

    2014-10-15

    The widely used catalytic hairpin assembly (CHA) amplification strategy generally needs several hours to accomplish one measurement based on the prevailingly used maximum intensity detection mode, making it less practical for assays where high throughput or speed is desired. To make the best use of the kinetic specificity of toehold domain for circuit reaction initiation, we developed a mathematical model and proposed an initial reaction rate detection mode to quantitatively differentiate the single-base mismatch. Using the kinetic mode, assay time can be reduced substantially to 10 min for one measurement with the comparable sensitivity and single-base mismatch differentiating ability as were obtained by the maximum intensity detection mode. This initial reaction rate based approach not only provided a fast and quantitative differentiation of single-base mismatch, but also helped in-depth understanding of the CHA system, which will be beneficial to the design of highly sensitive and specific toehold-mediated hybridization reactions. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Analysis of the prevailing standard and technical documents for their applicability under conditions of the 'Ukrytie' operation and technical proposals relating to the elaboration of new ones concerning fire safety

    International Nuclear Information System (INIS)

    Nazarenko, B.S.; Emets, V.G.

    1998-01-01

    An analysis of the prevailing laws and standards and technical documents (STD) to ensure safe operation of nuclear power installations, with requirements of nuclear, radiation and fire safety taken into account, has been performed. Proposals on application of some items of prevailing STD under conditions of the 'Ukrytie' operation are presented. Also given are technical proposals on correction of the prevailing operational standard documents and elaboration of special STD

  1. TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling.

    Science.gov (United States)

    Zhong, Jun; Sharma, Jyoti; Raju, Rajesh; Palapetta, Shyam Mohan; Prasad, T S Keshava; Huang, Tai-Chung; Yoda, Akinori; Tyner, Jeffrey W; van Bodegom, Diederik; Weinstock, David M; Ziegler, Steven F; Pandey, Akhilesh

    2014-01-01

    Thymic stromal lymphopoietin (TSLP) is a four-helix bundle cytokine that plays a critical role in the regulation of immune responses and in the differentiation of hematopoietic cells. TSLP signals through a heterodimeric receptor complex consisting of an interleukin-7 receptor α chain and a unique TSLP receptor (TSLPR) [also known as cytokine receptor-like factor 2 (CRLF2)]. Cellular targets of TSLP include dendritic cells, B cells, mast cells, regulatory T (Treg) cells and CD4+ and CD8+ T cells. The TSLP/TSLPR axis can activate multiple signaling transduction pathways including the JAK/STAT pathway and the PI-3 kinase pathway. Aberrant TSLP/TSLPR signaling has been associated with a variety of human diseases including asthma, atopic dermatitis, nasal polyposis, inflammatory bowel disease, eosinophilic eosophagitis and, most recently, acute lymphoblastic leukemia. A centralized resource of the TSLP signaling pathway cataloging signaling events is not yet available. In this study, we present a literature-annotated resource of reactions in the TSLP signaling pathway. This pathway map is publicly available through NetPath (http://www.netpath.org/), an open access signal transduction pathway resource developed previously by our group. This map includes 236 molecules and 252 reactions that are involved in TSLP/TSLPR signaling pathway. We expect that the TSLP signaling pathway map will provide a rich resource to study the biology of this important cytokine as well as to identify novel therapeutic targets for diseases associated with dysregulated TSLP/TSLPR signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_24.

  2. Intermolecula transfer and elimination of molecular hydrogen in thermal reactions of unsaturated organic compounds

    Energy Technology Data Exchange (ETDEWEB)

    Suria, Sabartanty [Iowa State Univ., Ames, IA (United States)

    1995-02-10

    Two reactions which are important to coal liquefaction include intermolecular transfer and the elimination of two hydrogen atoms. We have designed several model reactions to probe the viability of several hydrogen transfer and elimination pathways. This report described studies on these reactions using organic model compounds.

  3. Does undernutrition still prevail among nursing home residents?

    Science.gov (United States)

    Törmä, Johanna; Winblad, Ulrika; Cederholm, Tommy; Saletti, Anja

    2013-08-01

    During recent years public awareness about malnutrition has increased and collective initiatives have been undertaken. Simultaneously, the number of older adults is increasing, and the elderly care has been placed under pressure. The aim was to assess the nutritional situation and one-year mortality among nursing home (NH) residents, and compare with historical data. Mini Nutritional Assessment-Short Form (MNA-SF), ADL Barthel Index (BI), Short Portable Mental Status Questionnaire (SPMSQ), EQ-5D, Charlson Comorbidity Index (CCI), and blood samples were collected from 172 NH residents (86.3 ± 8 years, 70% women). Mortality data was taken from NH records. Nutritional data from 166 NH residents (83.8 ± 8 years, 61% women) examined in 1996 was retrieved for historical comparison. The prevalence of malnutrition was 30%, as compared to 71% in the historical data set, corresponding to a present average body mass index of 23.7 ± 5.1 compared with 22.3 ± 4.2 kg/m(2) (p prevails and is associated with deteriorated cognition, function and increased mortality. A possible improvement in nutritional status in NH residents over time was observed. Copyright © 2012 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  4. Post hoc analysis of Japanese patients from the placebo-controlled PREVAIL trial of enzalutamide in patients with chemotherapy-naive, metastatic castration-resistant prostate cancer-updated results.

    Science.gov (United States)

    Kimura, Go; Ueda, Takeshi

    2017-03-01

    A post hoc analysis of interim results from PREVAIL, a Phase III, double-blind, placebo-controlled trial of men with metastatic castration-resistant prostate cancer, demonstrated that the treatment effects, safety and pharmacokinetics of enzalutamide in Japanese patients were generally consistent with those of the overall population. A recent longer term analysis of PREVAIL demonstrated continued benefit of enzalutamide treatment over placebo. Here, we report results from a post hoc analysis of Japanese patients enrolled in PREVAIL at the prespecified number of deaths for the final analysis. In Japanese patients, enzalutamide reduced the risk of death by 35% (hazard ratio, 0.65; 95% confidence interval, 0.28-1.51) and the risk of investigator-assessed radiographic progression or death by 60% (hazard ratio, 0.40; 95% confidence interval, 0.18-0.90). These results show that treatment effects and safety in Japanese patients in the final analysis of PREVAIL continued to be generally consistent with those of the overall population. © The Author 2016. Published by Oxford University Press.

  5. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    Science.gov (United States)

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  6. Cost-Effectiveness of Percutaneous Closure of the Left Atrial Appendage in Atrial Fibrillation Based on Results from PROTECT AF vs. PREVAIL

    Science.gov (United States)

    Freeman, James V.; Hutton, David W.; Barnes, Geoffrey D.; Zhu, Ruo P.; Owens, Douglas K.; Garber, Alan M.; Go, Alan S.; Hlatky, Mark A.; Heidenreich, Paul A.; Wang, Paul J.; Al-Ahmad, Amin; Turakhia, Mintu P.

    2016-01-01

    Background Randomized trials of left atrial appendage (LAA) closure with the Watchman device have shown varying results, and its cost-effectiveness compared to anticoagulation has not been evaluated using all available contemporary trial data. Methods and Results We used a Markov decision model to estimate lifetime quality-adjusted survival, costs, and cost-effectiveness of LAA closure with Watchman, compared directly with warfarin and indirectly with dabigatran, using data from the long-term (mean 3.8 year) follow-up of PROTECT AF and PREVAIL randomized trials. Using data from PROTECT AF, the incremental cost-effectiveness ratios (ICER) compared to warfarin and dabigatran were $20,486 and $23,422 per quality adjusted life year (QALY), respectively. Using data from PREVAIL, LAA closure was dominated by warfarin and dabigatran, meaning that it was less effective (8.44, 8.54, and 8.59 QALYs, respectively) and more costly. At a willingness-to-pay-threshold of $50,000 per QALY, LAA closure was cost-effective 90% and 9% of the time under PROTECT AF and PREVAIL assumptions, respectively. These results were sensitive to the rates of ischemic stroke and intracranial hemorrhage for LAA closure and medical anticoagulation. Conclusions Using data from the PROTECT AF trial, LAA closure with the Watchman device was cost-effective; using PREVAIL trial data, Watchman was more costly and less effective than warfarin and dabigatran. PROTECT AF enrolled more patients and has substantially longer follow-up time, allowing greater statistical certainty with the cost-effectiveness results. However, longer term trial results and post-marketing surveillance of major adverse events will be vital to determining the value of the Watchman in clinical practice. PMID:27307517

  7. El suicidio: Una conducta antisocial que prevalece/Suicide: An antisocial behavior that prevails

    Directory of Open Access Journals (Sweden)

    Omar Alejandro De León Palomo

    2012-01-01

    Full Text Available The suicide has existed throughout history and has prevailed as a behavior that was contrary to the rules of the society in terms of preservation of life itself; the objective of this research was to make emphasis on the nature of antisocial behavior of this behavior and show its prevalence in the years 2006 to 2010 in Mexico and Tamaulipas, as well as from 1999 to 2008 in Reynosa, Tamaulipas. For which the data were obtained from the National Institute of Statistics and Geography to the country and the State and the books of the register of deaths by cause violent of the Regional Unit of Expert Services of the Attorney General of Justice, which has its headquarters in Reynosa; developed a theoretical framework on the impact of the conduct in society and the means to prevent it, The data obtained we revealed the continued presence of this conduct year-on-year, 23.554 cases appearing in Mexico and 819 in Tamaulipas in the period from 2006 to 2010; in Reynosa, Tamaulipas were presented 278 suicides in the period 1999 to 2008. The results show us a conduct stable in numbers, but without excessive overflows that prevails year-on-year, suicide, and the attempt of the same should be viewed as a social problem and not detract from the importance that it deserves a conduct of these dimensions, that is no more than a reflection of the situation in which are the means of social control toward the preservation of life itself.

  8. Bioelectrocatalytic dechlorination of trichloroacetic acid at gel-immobilized hemoglobin on multiwalled carbon nanotubes modified graphite electrode: Kinetic modeling and reaction pathways

    International Nuclear Information System (INIS)

    Liu, Qi; Yu, Jianming; Xu, Yinghua; Wang, Jiade; Ying, Le; Song, Xinxin; Zhou, Gendi; Chen, Jianmeng

    2013-01-01

    Highlights: ► The electrons transfer from enzyme in the electrode to COCs was the key step. ► The average current efficiency was influenced by pH and temperature of the systems. ► The most favourable degradation conditions for TCA were found to be pH 3 and 310 K. ► The activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation. ► Bioelectrocatalytic mechanism of TCA was verified by kinetic expressions. -- Abstract: In bioelectrochemically reductive dechlorination of chlorinated organic compounds (COCs), the electrons transfer from enzyme in the electrode to COCs was the key step, which determined the average current efficiency (CE) and was influenced by the pH and temperature of the systems. In this work, the effect of temperature (288–318 K) and pH (2–11) of the electrolyte on decholrination of trichloroacetic acid (TCA) was investigated in the sodium alginate/hemoglobin-multiwalled carbon nanotubes-graphite composite electrode (Hb/SA–MWCNT–GE). The results showed that the most favourable degradation conditions for TCA by Hb/SA–MWCNT–GE were found to be pH 3 and 310 K. By varying the pH of the systems, it was found that a proton accompanied with an electron transfer between the electrode and heme Fe(III)/Fe(II) of Hb during the reaction. Additionally, the activation energy of 26.2 kJ mol −1 was also calculated by the Arrhenius equation for the reaction. The total mass balance of the reactant and the products was in the range of 97–105% during the bioelectrochemically reductive reaction. The CE only decreased from 87% to 83% when the Hb/SA–MWCNT–GE was used 5 times. Based on the intermediates detected, a pathway was proposed for TCA degradation in which it underwent dechlorination process. The main degradation mechanism described by a parallel reaction rather than by a sequential reaction for dechlorination of TCA in Hb/SA–MWCNT–GE system was proposed. These data provided relevant information about the

  9. The Role of Psychological Stress Reactions in the Longitudinal Relation Between Workplace Bullying and Turnover.

    Science.gov (United States)

    Nabe-Nielsen, Kirsten; Grynderup, Matias Brødsgaard; Conway, Paul Maurice; Clausen, Thomas; Bonde, Jens Peter; Garde, Anne Helene; Hogh, Annie; Kaerlev, Linda; Török, Eszter; Hansen, Åse Marie

    2017-07-01

    To investigate the association between workplace bullying and change of job/unemployment, and to investigate whether psychological stress reactions constitute a potential pathway linking workplace bullying and change of job/unemployment. We used questionnaire data on workplace bullying and psychological stress reactions and register data on change of job/unemployment. We applied a multiple pathway approach to estimate the proportion of the association between workplace bullying and subsequent change of job/unemployment that was potentially mediated by psychological stress reactions. Workplace bullying was associated with risk of change of job (odds ratio [OR] = 1.35; 95% confidence interval [CI]: 1.06-1.72; 24% potentially mediated by psychological stress reactions) and unemployment (OR = 4.90; 95% CI: 3.18-7.55; 19% potentially mediated by psychological stress reactions). Workplace bullying has important consequences for labor market outcomes. Psychological stress reactions may play a vital role in this process.

  10. Ozonation of norfloxacin and levofloxacin in water: Specific reaction rate constants and defluorination reaction.

    Science.gov (United States)

    Ling, Wencui; Ben, Weiwei; Xu, Ke; Zhang, Yu; Yang, Min; Qiang, Zhimin

    2018-03-01

    The degradation kinetics and mechanism of two typical fluoroquinolones (FQs), norfloxacin (NF) and levofloxacin (LOF), by ozone in water were investigated. Semi-continuous mode and competition kinetics mode experiments were conducted to determine the reaction rate constants of target FQs with ozone and OH, separately. Results indicate that both NF and LOF were highly reactive toward ozone, and the reactivity was strongly impacted by the solution pH. The specific reaction rate constants of the diprotonated, monoprotonated and deprotonated species were determined to be 7.20 × 10 2 , 8.59 × 10 3 , 4.54 × 10 5  M -1  s -1 respectively for NF and 1.30 × 10 3 , 1.40 × 10 4 , 1.33 × 10 6  M -1  s -1 respectively for LOF. The reaction rate constants of target FQs toward OH were measured to be (4.81-7.41) × 10 9  M -1  s -1 in the pH range of 6.3-8.3. Furthermore, NF was selected as a model compound to clarify the degradation pathways, with a particular focus on the defluorination reaction. The significant release of F - ions and the formation of three F-free organic byproducts indicated that defluorination was a prevalent pathway in ozonation of FQs, while six F-containing organic byproducts indicated that ozone also attacked the piperazinyl and quinolone moieties. Escherichia coli growth inhibition tests revealed that ozonation could effectively eliminate the antibacterial activity of target FQ solutions, and the residual antibacterial activity had a negative linear correlation with the released F - concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Tandem Wittig-ene reaction approach to kainic acid

    Digital Repository Service at National Institute of Oceanography (India)

    Majik, M.S.; Parameswaran, P.S.; Tilve, S.G.

    The first example of a tandem Wittig-intramolecular ene reaction approach and its application toward the synthesis of kainic acid is reported. The synthetic pathway involves conversion of prenyl bromide into phosphorane 3, followed by one-pot Wittig...

  12. Pericyclic reactions in an aqueous molecular flask.

    Science.gov (United States)

    Murase, Takashi; Fujita, Makoto

    2010-10-01

    A self-assembled molecular flask with a nanometer-sized restricted cavity offers a new reaction environment that is quite different from the bulk solution. The self-assembled cage accommodates a pair of hydrophobic molecules to perform unusual Diels-Alder reactions and [2+2] photoadditions of otherwise unreactive aromatic molecules. In this cage, for example, the Diels-Alder reaction of naphthalene proceeds smoothly under mild conditions, and aceanthrylene shows reactivity for both [2+2] and [2+4] cycloadditions via the identical ternary host-guest complex. The observed greatly enhanced reactivity stems from the increased local concentration and pre-organization of the substrate pair within the cage, which reduces the entropic cost and switches the reaction profile from a bimolecular to a pseudo-intramolecular reaction pathway. The reinforced orientation and arrangement of substrate pairs specify regio- and stereo-selectivities of the subsequent reactions in the cavity. Chiral auxiliaries outside the cage create the inner chiral environment and induce asymmetric reactions inside the cage (up to 50% ee). © 2010 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  13. A summary of genomic data relating to E. coli organized by metabolic pathways: An initial version

    Energy Technology Data Exchange (ETDEWEB)

    Price, M.; Raju, M.; Taylor, R.

    1993-01-01

    This report summarizes the reactions that occur in some of the principal metabolic pathways of E. coli. These pathways have been encoded as objects in GenoBase, an integrated database under development at Argonne National Laboratory in collaboration with researchers at the National Institutes of Health and at Harvard University. The report lists the substrates, products, enzymes, and cofactors for each pathway as a whole, followed by a detailed description of each reaction in the pathway. In addition, for each enzyme, the report displays a description and activity as listed in the Enzyme Data Bank, followed by the corresponding Swiss Protein Data Bank entries. Separate summary lines are included for each of the E. coli genes associated with each enzyme.

  14. Farmers prevailing perception profiles regarding GM crops: A classification proposal.

    Science.gov (United States)

    Almeida, Carla; Massarani, Luisa

    2018-04-01

    Genetically modified organisms have been at the centre of a major public controversy, involving different interests and actors. While much attention has been devoted to consumer views on genetically modified food, there have been few attempts to understand the perceptions of genetically modified technology among farmers. By investigating perceptions of genetically modified organisms among Brazilian farmers, we intend to contribute towards filling this gap and thereby add the views of this stakeholder group to the genetically modified debate. A comparative analysis of our data and data from other studies indicate there is a complex variety of views on genetically modified organisms among farmers. Despite this diversity, we found variations in such views occur within limited parameters, concerned principally with expectations or concrete experiences regarding the advantages of genetically modified crops, perceptions of risks associated with them, and ethical questions they raise. We then propose a classification of prevailing profiles to represent the spectrum of perceptions of genetically modified organisms among farmers.

  15. Benzene destruction in claus process by sulfur dioxide: A reaction kinetics study

    KAUST Repository

    Sinha, Sourab; Raj, Abhijeet Dhayal; Alshoaibi, Ahmed S.; Alhassan, Saeed M.; Chung, Suk-Ho

    2014-01-01

    interactions. The mechanism begins with SO2 addition to phenyl radical after overcoming an energy barrier of 6.4 kJ/mol. This addition reaction is highly exothermic, where a reaction energy of 182 kJ/mol is released. The most favorable pathway involves O-S bond

  16. Formation of iodo-trihalomethanes, iodo-acetic acids, and iodo-acetamides during chloramination of iodide-containing waters: Factors influencing formation and reaction pathways

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Shaogang [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China); Guangxi Colleges and Universities Key Laboratory of Food Safety and Pharmaceutical Analytical Chemistry, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi (China); Li, Zhenlin [Guangxi Colleges and Universities Key Laboratory of Food Safety and Pharmaceutical Analytical Chemistry, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning, 530006, Guangxi (China); Dong, Huiyu [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China); Goodman, Bernard A. [College of Physical Science and Engineering, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 520004, Guangxi (China); Qiang, Zhimin, E-mail: qiangz@rcees.ac.cn [Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085 (China)

    2017-01-05

    This study investigated systematically the factors influencing the formation of iodinated disinfection by-products (I-DBPs) during chloramination of I{sup −}-containing waters, including reaction time, NH{sub 2}Cl dose, I{sup −} concentration, pH, natural organic matter (NOM) concentration, Br{sup −}/I{sup −} molar ratio, and water matrix. Among the I-DBPs detected, iodoform (CHI{sub 3}), iodoacetic acid (IAA), diiodoacetic acid (DIAA), triiodoacetic acid (TIAA), and diiodoacetamide (DIAcAm) were the major species produced from reactions between reactive iodine species (HOI/I{sub 2}) and NOM. A kinetic model involving the reactions of NH{sub 2}Cl auto-decomposition, iodine species transformation and NOM consumption was developed, which could well describe NH{sub 2}Cl decay and HOI/I{sub 2} evolution. Higher concentrations of CHI{sub 3}, IAA, DIAA, TIAA, and DIAcAm were observed in chloramination than in chlorination, whereas IO{sub 3}{sup −} was only formed significantly in chlorination. Maximum formation of I-DBPs occurred at pH 8.0, but acidic conditions favored the formation of iodinated haloacetic acids and DIAcAm. Increasing Br{sup −}/I{sup −} molar ratio from 1 to 10 did not increase the total amount of I-DBPs, but produced more bromine-substituting species. In addition, chloramination of 18 model compounds indicated that low-SUVA{sub 254} (specific ultraviolet absorbance at 254 nm) NOM generally favored the formation of I-DBPs compared to high-SUVA{sub 254} NOM. Finally, potential pathways for I-DBPs formation from chloramination of NOM were proposed.

  17. Cost-Effectiveness of Percutaneous Closure of the Left Atrial Appendage in Atrial Fibrillation Based on Results From PROTECT AF Versus PREVAIL.

    Science.gov (United States)

    Freeman, James V; Hutton, David W; Barnes, Geoffrey D; Zhu, Ruo P; Owens, Douglas K; Garber, Alan M; Go, Alan S; Hlatky, Mark A; Heidenreich, Paul A; Wang, Paul J; Al-Ahmad, Amin; Turakhia, Mintu P

    2016-06-01

    Randomized trials of left atrial appendage (LAA) closure with the Watchman device have shown varying results, and its cost effectiveness compared with anticoagulation has not been evaluated using all available contemporary trial data. We used a Markov decision model to estimate lifetime quality-adjusted survival, costs, and cost effectiveness of LAA closure with Watchman, compared directly with warfarin and indirectly with dabigatran, using data from the long-term (mean 3.8 year) follow-up of Percutaneous Closure of the Left Atrial Appendage Versus Warfarin Therapy for Prevention of Stroke in Patients With Atrial Fibrillation (PROTECT AF) and Prospective Randomized Evaluation of the Watchman LAA Closure Device in Patients With Atrial Fibrillation (PREVAIL) randomized trials. Using data from PROTECT AF, the incremental cost-effectiveness ratios compared with warfarin and dabigatran were $20 486 and $23 422 per quality-adjusted life year, respectively. Using data from PREVAIL, LAA closure was dominated by warfarin and dabigatran, meaning that it was less effective (8.44, 8.54, and 8.59 quality-adjusted life years, respectively) and more costly. At a willingness-to-pay threshold of $50 000 per quality-adjusted life year, LAA closure was cost effective 90% and 9% of the time under PROTECT AF and PREVAIL assumptions, respectively. These results were sensitive to the rates of ischemic stroke and intracranial hemorrhage for LAA closure and medical anticoagulation. Using data from the PROTECT AF trial, LAA closure with the Watchman device was cost effective; using PREVAIL trial data, Watchman was more costly and less effective than warfarin and dabigatran. PROTECT AF enrolled more patients and has substantially longer follow-up time, allowing greater statistical certainty with the cost-effectiveness results. However, longer-term trial results and postmarketing surveillance of major adverse events will be vital to determining the value of the Watchman in clinical

  18. Oxidation of nonylphenol and octylphenol by manganese dioxide: Kinetics and pathways

    International Nuclear Information System (INIS)

    Lu, Zhijiang; Gan, Jay

    2013-01-01

    Due to their potent estrogenicity and ubiquitous occurrence, non-ionic surfactant metabolites nonylphenol (NP) and octylphenol (OP) are of significant concern. Abiotic chemical oxidation by naturally abundant metal oxides may be an important route of their environmental attenuation, but is poorly understood. We investigated the reaction kinetics and pathways of NP and OP with MnO 2 . At pH 5.5 and 100 mg/L δ-MnO 2 , 92, 84 and 76% of 4-n-NP, 4-tert-OP and technical nonylphenol (tNP) was transformed in 90 min, respectively. A further experiment using a Mn-containing soil and Mn-removed soil confirmed that soil MnO 2 caused NP removal. Multiple reaction products, including hydroquinone, hydroxylated products, dimers and trimers were identified through fragmentation analysis by GC–MS/MS and UPLC–MS/MS, allowing the construction of tentative pathways. This study suggested that abiotic oxidation by MnO 2 may contribute to the dissipation of tNP, 4-n-NP, 4-tert-OP and their analogues in the natural environment. Highlights: •The oxidation of nonylphenol and octylphenol by manganese dioxide was efficient and pH dependent. •The importance of soil MnO 2 was further confirmed by experiment using Mn-containing soil. •The reaction in environment is substantially slower than with synthetic MnO 2 . •The oxidation was inhibited by metal ions and enhanced by humic acids. •Reaction pathway is proposed based on reaction intermediates identified. -- Naturally occurring MnO 2 may contribute significantly to the attenuation of nonylphenol and octylphenol in soil, water and sediment

  19. Hydrogen/Chlorine exchange reactions of gaseous carbanions.

    Science.gov (United States)

    Chen, Hao; Cooks, R Graham; Meurer, Eduardo C; Eberlin, Marcos N

    2005-12-01

    Gas-phase reactions of three typical carbanions CH(2)NO(2)(-), CH(2)CN(-), and CH(2)S(O)CH(3)(-) with the chloromethanes CH(2)Cl(2), CHCl(3), and CCl(4), examined by tandem mass spectrometry, show a novel hydrogen/chlorine exchange reaction. For example, reaction between the nitromethyl anion CH(2)NO(2)(-) and carbon tetrachloride CCl(4) forms the ion CHClNO(2)(-). The suggested reaction mechanism involves nucleophilic attack by CH(2)NO(2)(-) at the chlorine of CCl(4) followed by proton transfer within the resulting complex [CH(2)ClNO(2) + CCl(3)(-)] to form CHClNO(2)(-) and CHCl(3). Two other carbanions CH(2)CN(-) and CH(2)S(O)CH(3)(-) also undergo the novel hydrogen/chlorine exchange reactions with CCl(4) but to a much smaller extent, their higher nucleophilicities favoring competitive nucleophilic attack reactions. Proton abstraction is the exclusive pathway in the reactions of these carbanions with CHCl(3). While CH(2)CN(-) and CH(2)S(O)CH(3)(-) promote mainly proton abstraction and nucleophilic displacement in reactions with CH(2)Cl(2), CH(2)NO(2)(-) does not react.

  20. Structural parameter identifiability analysis for dynamic reaction networks

    DEFF Research Database (Denmark)

    Davidescu, Florin Paul; Jørgensen, Sten Bay

    2008-01-01

    method based on Lie derivatives. The proposed systematic two phase methodology is illustrated on a mass action based model for an enzymatically catalyzed reaction pathway network where only a limited set of variables is measured. The methodology clearly pinpoints the structurally identifiable parameters...... where for a given set of measured variables it is desirable to investigate which parameters may be estimated prior to spending computational effort on the actual estimation. This contribution addresses the structural parameter identifiability problem for the typical case of reaction network models....... The proposed analysis is performed in two phases. The first phase determines the structurally identifiable reaction rates based on reaction network stoichiometry. The second phase assesses the structural parameter identifiability of the specific kinetic rate expressions using a generating series expansion...

  1. CO2 Reduction Catalyzed by Nitrogenase: Pathways to Formate, Carbon Monoxide, and Methane.

    Science.gov (United States)

    Khadka, Nimesh; Dean, Dennis R; Smith, Dayle; Hoffman, Brian M; Raugei, Simone; Seefeldt, Lance C

    2016-09-06

    The reduction of N2 to NH3 by Mo-dependent nitrogenase at its active-site metal cluster FeMo-cofactor utilizes reductive elimination of Fe-bound hydrides with obligatory loss of H2 to activate the enzyme for binding/reduction of N2. Earlier work showed that wild-type nitrogenase and a nitrogenase with amino acid substitutions in the MoFe protein near FeMo-cofactor can catalytically reduce CO2 by two or eight electrons/protons to carbon monoxide (CO) and methane (CH4) at low rates. Here, it is demonstrated that nitrogenase preferentially reduces CO2 by two electrons/protons to formate (HCOO(-)) at rates >10 times higher than rates of CO2 reduction to CO and CH4. Quantum mechanical calculations on the doubly reduced FeMo-cofactor with a Fe-bound hydride and S-bound proton (E2(2H) state) favor a direct reaction of CO2 with the hydride ("direct hydride transfer" reaction pathway), with facile hydride transfer to CO2 yielding formate. In contrast, a significant barrier is observed for reaction of Fe-bound CO2 with the hydride ("associative" reaction pathway), which leads to CO and CH4. Remarkably, in the direct hydride transfer pathway, the Fe-H behaves as a hydridic hydrogen, whereas in the associative pathway it acts as a protic hydrogen. MoFe proteins with amino acid substitutions near FeMo-cofactor (α-70(Val→Ala), α-195(His→Gln)) are found to significantly alter the distribution of products between formate and CO/CH4.

  2. Chemical reactions confined within carbon nanotubes.

    Science.gov (United States)

    Miners, Scott A; Rance, Graham A; Khlobystov, Andrei N

    2016-08-22

    In this critical review, we survey the wide range of chemical reactions that have been confined within carbon nanotubes, particularly emphasising how the pairwise interactions between the catalysts, reactants, transition states and products of a particular molecular transformation with the host nanotube can be used to control the yields and distributions of products of chemical reactions. We demonstrate that nanoscale confinement within carbon nanotubes enables the control of catalyst activity, morphology and stability, influences the local concentration of reactants and products thus affecting equilibria, rates and selectivity, pre-arranges the reactants for desired reactions and alters the relative stability of isomeric products. We critically evaluate the relative advantages and disadvantages of the confinement of chemical reactions inside carbon nanotubes from a chemical perspective and describe how further developments in the controlled synthesis of carbon nanotubes and the incorporation of multifunctionality are essential for the development of this ever-expanding field, ultimately leading to the effective control of the pathways of chemical reactions through the rational design of multi-functional carbon nanoreactors.

  3. A board game to assist pharmacy students in learning metabolic pathways.

    Science.gov (United States)

    Rose, Tyler M

    2011-11-10

    To develop and evaluate a board game designed to increase students' enjoyment of learning metabolic pathways; their familiarity with pathway reactions, intermediates, and regulation; and, their understanding of how pathways relate to one another and to selected biological conditions. The board game, entitled Race to Glucose, was created as a team activity for first-year pharmacy students in the biochemistry curriculum. A majority of respondents agreed that the game was helpful for learning regulation, intermediates, and interpathway relationships but not for learning reactions, formation of energetic molecules, or relationships, to biological conditions. There was a significant increase in students' scores on game-related examination questions (68.8% pretest vs. 81.3% posttest), but the improvement was no greater than that for examination questions not related to the game (12.5% vs. 10.9%). First-year pharmacy students considered Race to Glucose to be an enjoyable and helpful tool for learning intermediates, regulation, and interpathway relationships.

  4. Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution.

    Science.gov (United States)

    Takenaka, Norio; Kitamura, Yukichi; Nagaoka, Masataka

    2016-03-03

    In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

  5. Enzalutamide in Men with Chemotherapy-naive Metastatic Castration-resistant Prostate Cancer: Extended Analysis of the Phase 3 PREVAIL Study

    NARCIS (Netherlands)

    Beer, T.M.; Armstrong, A.J.; Rathkopf, D.; Loriot, Y.; Sternberg, C.N.; Higano, C.S.; Iversen, P.; Evans, C.P.; Kim, C.S.; Kimura, G.; Miller, K.; Saad, F.; Bjartell, A.S.; Borre, M.; Mulders, P.; Tammela, T.L.; Parli, T.; Sari, S.; Os, S. van; Theeuwes, A.; Tombal, B.

    2017-01-01

    Enzalutamide significantly improved radiographic progression-free survival (rPFS) and overall survival (OS) among men with chemotherapy-naive metastatic castration-resistant prostate cancer at the prespecified interim analysis of PREVAIL, a phase 3, double-blind, randomized study. We evaluated the

  6. The Role of Psychological Stress Reactions in the Longitudinal Relation Between Workplace Bullying and Turnover

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Kirsten; Grynderup, Matias Brødsgaard; Conway, Paul Maurice

    2017-01-01

    OBJECTIVES: To investigate the association between workplace bullying and change of job/unemployment, and to investigate whether psychological stress reactions constitute a potential pathway linking workplace bullying and change of job/unemployment. METHODS: We used questionnaire data on workplace...... bullying and psychological stress reactions and register data on change of job/unemployment. We applied a multiple pathway approach to estimate the proportion of the association between workplace bullying and subsequent change of job/unemployment that was potentially mediated by psychological stress...... reactions. RESULTS: Workplace bullying was associated with risk of change of job (odds ratio [OR] = 1.35; 95% confidence interval [CI]: 1.06-1.72; 24% potentially mediated by psychological stress reactions) and unemployment (OR = 4.90; 95% CI: 3.18-7.55; 19% potentially mediated by psychological stress...

  7. Two-component multistep direct reactions: A microscopic approach

    International Nuclear Information System (INIS)

    Koning, A.J.; Chadwick, M.B.

    1998-03-01

    The authors present two principal advances in multistep direct theory: (1) A two-component formulation of multistep direct reactions, where neutron and proton excitations are explicitly accounted for in the evolution of the reaction, for all orders of scattering. While this may at first seem to be a formidable task, especially for multistep processes where the many possible reaction pathways becomes large in a two-component formalism, the authors show that this is not so -- a rather simple generalization of the FKK convolution expression 1 automatically generates these pathways. Such considerations are particularly relevant when simultaneously analyzing both neutron and proton emission spectra, which is always important since these processes represent competing decay channels. (2) A new, and fully microscopic, method for calculating MSD cross sections which does not make use of particle-hole state densities but instead directly calculates cross sections for all possible particle-hole excitations (again including an exact book-keeping of the neutron/proton type of the particle and hole at all stages of the reaction) determined from a simple non-interacting shell model. This is in contrast to all previous numerical approaches which sample only a small number of such states to estimate the DWBA strength, and utilize simple analytical formulae for the partial state density, based on the equidistant spacing model. The new approach has been applied, along with theories for multistep compound, compound, and collective reactions, to analyze experimental emission spectra for a range of targets and energies. The authors show that the theory correctly accounts for double-differential nucleon spectra

  8. Aspartate aminotransferase: the kinetic barriers facing the covalent intermediates on the reaction pathway

    International Nuclear Information System (INIS)

    Kirsch, J.F.; Julin, D.A.; McLeish, M.; Wiesinger, H.

    1986-01-01

    The intermediates, aldimine (A), quinonoid (Q) and ketimine (K), along the transaminase reaction coordinate were probed by isotope transfer and solvent exchange kinetics. Less than 0.003% of 3 H is transferred from C/sub α/[ 3 H]-aspartate to pyridoxamine phosphate in the cytoplasmic aspartate aminotransferase (cAATase) reaction implying either that Q does not exist as a kinetically competent intermediate or that there is a rapid exchange of isotope with solvent. The ratio of the rate constants for C/sub α/ hydrogen exchange vs keto acid product formation (k/sub exge//k/sub prod/) are 2.5 and 0.5 for the reactions of cAATase with C/sub α/ [ 2 H]-aspartate and mitochondrial (m) AATase with C/sub α/[ 2 H]-glutamate respectively. The latter reaction was also probed from the α-keto-glutarate side with carbonyl 0-18 enriched keto acid. This experiment gave k/sub exge//k/sub prod/ = 1.0 for oxygen-18 exchange in α-ketoglutarate versus amino acid formation. The two exchange experiments with mAATase are interpreted in terms of a model in which the rate constant for diffusion of water from the active site is comparable with those for product forming steps

  9. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

    Science.gov (United States)

    Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

    2014-10-14

    The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a

  10. A controlled vocabulary for pathway entities and events.

    Science.gov (United States)

    Jupe, Steve; Jassal, Bijay; Williams, Mark; Wu, Guanming

    2014-01-01

    Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is accessible via a website, available as downloads in standard reusable formats and via Representational State Transfer (REST)-ful and Simple Object Access Protocol (SOAP) application programming interfaces (APIs). We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve. The CV could be reapplied in any situation where names are used for pathway entities and events. Adoption of this CV would significantly improve naming consistency and readability, with consequent benefits for searching and data mining within and between databases. Database URL: http://www.reactome.org. © The Author(s) 2014. Published by Oxford University Press.

  11. Unconventional exo selectivity in thermal normal-electron-demand Diels-Alder reactions

    Science.gov (United States)

    Ho, Guo-Ming; Huang, Ci-Jhang; Li, Elise Yu-Tzu; Hsu, Sheng-Kai; Wu, Ti; Zulueta, Medel Manuel L.; Wu, Kevin Binchia; Hung, Shang-Cheng

    2016-10-01

    The Diels-Alder reaction is a useful tool for generating functionalized chiral molecules through the concerted cycloaddition of dienes and dienophiles leading to six-membered rings. Traditionally, the selective predictions of the products rely heavily on consideration of the secondary orbital interactions that stabilize the endo pathway. However, there remain some basic examples defying this notion and produce the exo-isomer as major product. Here we systematically evaluated of the structural features driving exo selectivity in thermal normal-electron-demand Diels-Alder reactions. Substitution at the Cβ position and the size and electronegativity of the electron-withdrawing group of the dienophile are contributing factors. Experimental and computational studies both point toward the steric and electrostatic forces between the substituents in both the diene and the dienophile that increase the likelihood of the exo pathway. For these substrates, the dominance of the endo pathway is reduced by transition state distortions and poor structural alignments of the reacting partners. We also noted the tilt of the dienophile with respect to the diene causing steric strain on the functionalities at the more advanced bond forming carbon-carbon position of the endo transition state. Insights into such factors may benefit synthetic planning and asserting control over this important named reaction.

  12. Reaction chemistry in rechargeable Li-O2 batteries.

    Science.gov (United States)

    Lim, Hee-Dae; Lee, Byungju; Bae, Youngjoon; Park, Hyeokjun; Ko, Youngmin; Kim, Haegyeom; Kim, Jinsoo; Kang, Kisuk

    2017-05-22

    The seemingly simple reaction of Li-O 2 batteries involving lithium and oxygen makes this chemistry attractive for high-energy-density storage systems; however, achieving this reaction in practical rechargeable Li-O 2 batteries has proven difficult. The reaction paths leading to the final Li 2 O 2 discharge products can be greatly affected by the operating conditions or environment, which often results in major side reactions. Recent research findings have begun to reveal how the reaction paths may be affected by the surrounding conditions and to uncover the factors contributing to the difficulty in achieving the reactions of lithium and oxygen. This progress report describes the current state of understanding of the electrode reaction mechanisms in Li-O 2 batteries; the factors that affect reaction pathways; and the effect of cell components such as solvents, salts, additives, and catalysts on the discharge product and its decomposition during charging. This comprehensive review of the recent progress in understanding the reaction chemistry of the Li-O 2 system will serve as guidelines for future research and aid in the development of reliable high-energy-density rechargeable Li-O 2 batteries.

  13. The Pathway for Oxygen: Tutorial Modelling on Oxygen Transport from Air to Mitochondrion: The Pathway for Oxygen.

    Science.gov (United States)

    Bassingthwaighte, James B; Raymond, Gary M; Dash, Ranjan K; Beard, Daniel A; Nolan, Margaret

    2016-01-01

    The 'Pathway for Oxygen' is captured in a set of models describing quantitative relationships between fluxes and driving forces for the flux of oxygen from the external air source to the mitochondrial sink at cytochrome oxidase. The intervening processes involve convection, membrane permeation, diffusion of free and heme-bound O2 and enzymatic reactions. While this system's basic elements are simple: ventilation, alveolar gas exchange with blood, circulation of the blood, perfusion of an organ, uptake by tissue, and consumption by chemical reaction, integration of these pieces quickly becomes complex. This complexity led us to construct a tutorial on the ideas and principles; these first PathwayO2 models are simple but quantitative and cover: (1) a 'one-alveolus lung' with airway resistance, lung volume compliance, (2) bidirectional transport of solute gasses like O2 and CO2, (3) gas exchange between alveolar air and lung capillary blood, (4) gas solubility in blood, and circulation of blood through the capillary syncytium and back to the lung, and (5) blood-tissue gas exchange in capillaries. These open-source models are at Physiome.org and provide background for the many respiratory models there.

  14. Directing Reaction Pathways through Controlled Reactant Binding at Pd-TiO2 Interfaces.

    Science.gov (United States)

    Zhang, Jing; Wang, Bingwen; Nikolla, Eranda; Medlin, J Will

    2017-06-01

    Recent efforts to design selective catalysts for multi-step reactions, such as hydrodeoxygenation (HDO), have emphasized the preparation of active sites at the interface between two materials having different properties. However, achieving precise control over interfacial properties, and thus reaction selectivity, has remained a challenge. Here, we encapsulated Pd nanoparticles (NPs) with TiO 2 films of regulated porosity to gain a new level of control over catalyst performance, resulting in essentially 100 % HDO selectivity for two biomass-derived alcohols. This catalyst also showed exceptional reaction specificity in HDO of furfural and m-cresol. In addition to improving HDO activity by maximizing the interfacial contact between the metal and metal oxide sites, encapsulation by the nanoporous oxide film provided a significant selectivity boost by restricting the accessible conformations of aromatics on the surface. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Teaching Biochemical Pathways Using Concept Maps

    Directory of Open Access Journals (Sweden)

    Simon Brown

    2013-08-01

    Full Text Available The interesting paper by Dinarvand and Vaisi-Raygan (1 makes valuable points about a particularly challenging aspect of biochemistry learning and teaching. Their work prompts me to ask two questions and make a comment. First, what do the authors mean by a concept map (CM? A pathway map could be considered a CM, but a CM could cover modes of regulation and kinetics in relation to particular reactions or pathways and there are many other possibilities. Irrespective of this, a CM can get extremely complex if more than a few concepts are involved (2, as can be seen in examples given by Novak (3. This is the fundamental problem of teaching and learning biochemistry (4, which combines the network of pathways, compartmentation, macromol¬ecular structure, regulation, kinetics and some fairly sophisticated chemical concepts.Second, how did the students go about preparing CMs? My experience is that students prefer to use a computer for most tasks, but standard CM software (5 may not be suitable. For example, they often struggle unnec¬essarily to use software to prepare a graphical summary of the structural features of a protein, its precursors and the gene encoding it. This distracts them from the material. My suggestions that pencil and paper might be sufficient are usually met with amazement. Third, as Dinarvand and Vaisi-Raygan (1 make clear, a coherent summary of the metabolism considered in a course in metabolic biochemistry is crucial if students are to appreciate the pathways and their interconn-ection and regulation. For many years I have used an approach in which students collaborate in tutorials to achieve this. The sessions are usually initiated by me drawing the plasma membrane and the mitochondrial membranes on a large board and inviting the students to fill in the blanks (I provide large sheets of paper so that students can make copies. With coaxing, someone volunteers and I explain that the volunteer is not alone because everyone is

  16. Photochemical Reactions of Particulate Organic Matter: Deciphering the Role of Direct and Indirect Processes

    Science.gov (United States)

    Carrasquillo, A. J.; Gelfond, C. E.; Kocar, B. D.

    2016-12-01

    Photochemical reactions of natural organic matter (NOM) represent potentially important pathways for biologically recalcitrant material to be chemically altered in aquatic systems. Irradiation can alter the physical state of organic matter by facilitating the cycling between the particulate (POM) and dissolved (DOM) pools, however, a molecular level understanding of this chemically dynamic system is currently lacking. Photochemical reactions of a target molecule proceed by the direct absorption of a photon, or through reaction with a second photolytically generated species (i.e. the hydroxyl radical, singlet oxygen, excited triplet state NOM, hydrogen peroxide, etc.). Here, we isolate the major direct and indirect photochemical reactions of a lignocellulose-rich POM material (Phragmites australis) to determine their relative importance in changing the the chemical structure of the parent POM, and in the production of DOM. We measured POM molecular structure using a combination of NMR and FTIR for bulk analyses and scanning transmission x-ray microscopy (STXM) for spatially resolved chemistry, while the chemical composition of photo-produced DOM was measured using ultra-high resolution mass spectrometry. Results are discussed in the context of the differences in chemical composition of both NOM pools resulting from the isolated photochemical pathways. All treatments result in an increase in DOM with reaction time, indicating that the larger POM matrix is likely fragmenting into smaller more soluble species. Spectroscopic measurements, on the other hand, point to functionalization reactions which increase the abundance of alcohol, acid, and carbonyl moieties in both carbon pools. This unique dataset provides new insight into how photochemical reactions alter the chemical composition of NOM while highlighting the relative importance of indirect pathways.

  17. Should the host reaction to anisakiasis influence the treatment?: Different clinical presentations in two cases

    Directory of Open Access Journals (Sweden)

    Stefano Pontone

    Full Text Available Gastrointestinal anisakiasis is a parasitic infection occurring in people that consume raw or inadequately cooked fish or squid. It is frequently characterized by severe epigastric pain, nausea and vomiting caused by the penetration of the larvae into the gastric wall. Acute gastric anisakiasis with severe chest discomfort is rarely reported in Italy. On the other hand, gastro-allergic anisakiasis with rash, urticaria and isolated angioedema or anaphylaxis is a clinical entity that has been described only recently. Also, if patients usually develop symptoms within 12 hours after raw seafood ingestion, not always endoscopic exploration can promptly identify the Anisakis larvae. Moreover, some authors consider the prevailing allergic reaction as a natural and effective defense against the parasitic attack. We report two cases of peculiar manifestations of anisakiasis in both acute and chronic forms (severe chest discomfort and anaphylactoid reaction.

  18. Charting an Alternate Pathway to Reaction Orders and Rate Laws in Introductory Chemistry Courses

    Science.gov (United States)

    Rushton, Gregory T.; Criswell, Brett A.; McAllister, Nicole D.; Polizzi, Samuel J.; Moore, Lamesha A.; Pierre, Michelle S.

    2014-01-01

    Reaction kinetics is an axiomatic topic in chemistry that is often addressed as early as the high school course and serves as the foundation for more sophisticated conversations in college-level organic, physical, and biological chemistry courses. Despite the fundamental nature of reaction kinetics, students can struggle with transforming their…

  19. False-positive findings in mammography screening induces short-term distress - breast cancer-specific concern prevails longer

    DEFF Research Database (Denmark)

    Aro, A R; Pilvikki Absetz, S; van Elderen, T M

    2000-01-01

    The aim of this study was to examine psychological distress in a mammography screening process as a consequence of screening after adjusting for background, personality and prescreening distress. Subjects, aged 50 years, were invitees at their first screening. There were three groups; normal find...... perceived breast cancer risk and susceptibility. Distress related to screening and false-positive findings seems to be moderate, but prevailing cancer-specific concerns call for improvements in screening programmes....

  20. Conditions for extinction events in chemical reaction networks with discrete state spaces.

    Science.gov (United States)

    Johnston, Matthew D; Anderson, David F; Craciun, Gheorghe; Brijder, Robert

    2018-05-01

    We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.

  1. Large-eddy simulation of pollutant dispersion from a ground-level area source over urban street canyons with irreversible chemical reactions

    Science.gov (United States)

    Du, T. Z.; Liu, C.-H.; Zhao, Y. B.

    2014-10-01

    In this study, the dispersion of chemically reactive pollutants is calculated by large-eddy simulation (LES) in a neutrally stratified urban canopy layer (UCL) over urban areas. As a pilot attempt, idealized street canyons of unity building-height-to-street-width (aspect) ratio are used. Nitric oxide (NO) is emitted from the ground surface of the first street canyon into the domain doped with ozone (O3). In the absence of ultraviolet radiation, this irreversible chemistry produces nitrogen dioxide (NO2), developing a reactive plume over the rough urban surface. A range of timescales of turbulence and chemistry are utilized to examine the mechanism of turbulent mixing and chemical reactions in the UCL. The Damköhler number (Da) and the reaction rate (r) are analyzed along the vertical direction on the plane normal to the prevailing flow at 10 m after the source. The maximum reaction rate peaks at an elevation where Damköhler number Da is equal or close to unity. Hence, comparable timescales of turbulence and reaction could enhance the chemical reactions in the plume.

  2. Fe(II)/Fe(III)-Catalyzed Intramolecular Didehydro-Diels-Alder Reaction of Styrene-ynes.

    Science.gov (United States)

    Mun, Hyeon Jin; Seong, Eun Young; Ahn, Kwang-Hyun; Kang, Eun Joo

    2018-02-02

    The intramolecular didehydro-Diels-Alder reaction of styrene-ynes was catalyzed by Fe(II) and Fe(III) to produce various naphthalene derivatives under microwave heating conditions. Mechanistic calculations found that the Fe(II) catalyst activates the styrenyl diene in an inverse-electron-demand Diels-Alder reaction, and the consecutive dehydrogenation reaction can be promoted by either Fe(II)-catalyzed direct dehydrogenation or an Fe(III)-catalyzed rearomatization/dehydrogenation pathway.

  3. The Atmospheric Oxidation of Volatile Organic Compounds Through Hydrogen Shift Reactions

    DEFF Research Database (Denmark)

    Knap, Hasse Christian

    a radical is denoted as a H-shift reaction. Quantum chemical calculations were carried out to investigate the potential energy surface of the H-shift reactions and the subsequent decomposition pathways. The transition state theory including the Eckart quantum tunneling correction have been used to calculate...... the reaction rate constants of the H-shift reactions. The autoxidation of volatile organic compounds is an important oxidation mechanism that produces secondary organic aerosols (SOA) and recycles hydroxyl (OH) radicals. The autoxidation cycle produces a second generation peroxy radical (OOQOOH) through...... a series of H-shift reactions and O2 attachments. I have investigated the H-shift reactions in two OOQOOH radicals (hydroperoxy peroxy radicals and hydroperoxy acyl peroxy radicals). The H-shift reaction rate constants have been compared with the bimolecular reaction rate constants of the peroxy radicals...

  4. Machine learning methods for metabolic pathway prediction

    Directory of Open Access Journals (Sweden)

    Karp Peter D

    2010-01-01

    Full Text Available Abstract Background A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism. Results To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways. Conclusions ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations.

  5. Machine learning methods for metabolic pathway prediction

    Science.gov (United States)

    2010-01-01

    Background A key challenge in systems biology is the reconstruction of an organism's metabolic network from its genome sequence. One strategy for addressing this problem is to predict which metabolic pathways, from a reference database of known pathways, are present in the organism, based on the annotated genome of the organism. Results To quantitatively validate methods for pathway prediction, we developed a large "gold standard" dataset of 5,610 pathway instances known to be present or absent in curated metabolic pathway databases for six organisms. We defined a collection of 123 pathway features, whose information content we evaluated with respect to the gold standard. Feature data were used as input to an extensive collection of machine learning (ML) methods, including naïve Bayes, decision trees, and logistic regression, together with feature selection and ensemble methods. We compared the ML methods to the previous PathoLogic algorithm for pathway prediction using the gold standard dataset. We found that ML-based prediction methods can match the performance of the PathoLogic algorithm. PathoLogic achieved an accuracy of 91% and an F-measure of 0.786. The ML-based prediction methods achieved accuracy as high as 91.2% and F-measure as high as 0.787. The ML-based methods output a probability for each predicted pathway, whereas PathoLogic does not, which provides more information to the user and facilitates filtering of predicted pathways. Conclusions ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability. More advanced prediction methods and/or more sophisticated input features may improve the performance of ML methods. However, pathway prediction performance appears to be limited largely by the ability to correctly match enzymes to the reactions they catalyze based on genome annotations. PMID:20064214

  6. Modeling position-specific isotope fractionation of organic micropollutants degradation via different reaction pathways

    DEFF Research Database (Denmark)

    Jin, Biao; Rolle, Massimo

    : dichlorobenzamide (BAM), isoproturon (IPU) and diclofenac (DCF). The model successfully reproduces the multi-element isotope data, and precisely captures the dual element isotope trends, characterizing the different degradation pathways. Besides illustrating the model capability of mechanistic evaluation...

  7. Copper-Catalyzed Oxidative Reaction of β-Keto Sulfones with Alcohols via C-S Bond Cleavage: Reaction Development and Mechanism Study.

    Science.gov (United States)

    Du, Bingnan; Wang, Wenmin; Wang, Yang; Qi, Zhenghang; Tian, Jiaqi; Zhou, Jie; Wang, Xiaochen; Han, Jianlin; Ma, Jing; Pan, Yi

    2018-02-16

    A Cu-catalyzed cascade oxidative radical process of β-keto sulfones with alcohols has been achieved by using oxygen as an oxidant. In this reaction, β-keto sulfones were converted into sulfinate esters under the oxidative conditions via cleavage of C-S bond. Experimental and computational studies demonstrate that a new pathway is involved in this reaction, which proceeds through the formation of the key four-coordinated Cu II intermediate, O-O bond homolysis induced C-S bond cleavage and Cu-catalyzed esterification to form the final products. This reaction provides a new strategy to sulfonate esters and enriches the research content of C-S bond cleavage and transformations. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Quantum Chemical Investigation on Photochemical Reactions of Nonanoic Acids at Air-Water Interface.

    Science.gov (United States)

    Xiao, Pin; Wang, Qian; Fang, Wei-Hai; Cui, Ganglong

    2017-06-08

    Photoinduced chemical reactions of organic compounds at the marine boundary layer have recently attracted significant experimental attention because this kind of photoreactions has been proposed to have substantial impact on local new particle formation and their photoproducts could be a source of secondary organic aerosols. In this work, we have employed first-principles density functional theory method combined with cluster models to systematically explore photochemical reaction pathways of nonanoic acids (NAs) to form volatile saturated and unsaturated C 9 and C 8 aldehydes at air-water interfaces. On the basis of the results, we have found that the formation of C 9 aldehydes is not initiated by intermolecular Norrish type II reaction between two NAs but by intramolecular T 1 C-O bond fission of NA generating acyl and hydroxyl radicals. Subsequently, saturated C 9 aldehydes are formed through hydrogenation reaction of acyl radical by another intact NA. Following two dehydrogenation reactions, unsaturated C 9 aldehydes are generated. In parallel, the pathway to C 8 aldehydes is initiated by T 1 C-C bond fission of NA, which generates octyl and carboxyl radicals; then, an octanol is formed through recombination reaction of octyl with hydroxyl radical. In the following, two dehydrogenation reactions result into an enol intermediate from which saturated C 8 aldehydes are produced via NA-assisted intermolecular hydrogen transfer. Finally, two dehydrogenation reactions generate unsaturated C 8 aldehydes. In these reactions, water and NA molecules are found to play important roles. They significantly reduce relevant reaction barriers. Our work has also explored oxygenation reactions of NA with molecular oxygen and radical-radical dimerization reactions.

  9. The Atmospherically Important Reaction of Hydroxyl Radicals with Methyl Nitrate: A Theoretical Study Involving the Calculation of Reaction Mechanisms, Enthalpies, Activation Energies, and Rate Coefficients.

    Science.gov (United States)

    Ng, Maggie; Mok, Daniel K W; Lee, Edmond P F; Dyke, John M

    2017-09-07

    A theoretical study, involving the calculation of reaction enthalpies, activation energies, mechanisms, and rate coefficients, was made of the reaction of hydroxyl radicals with methyl nitrate, an important process for methyl nitrate removal in the earth's atmosphere. Four reaction channels were considered: formation of H 2 O + CH 2 ONO 2 , CH 3 OOH + NO 2 , CH 3 OH + NO 3 , and CH 3 O + HNO 3 . For all channels, geometry optimization and frequency calculations were performed at the M06-2X/6-31+G** level, while relative energies were improved at the UCCSD(T*)-F12/CBS level. The major channel is found to be the H abstraction channel, to give the products H 2 O + CH 2 ONO 2 . The reaction enthalpy (ΔH 298 K RX ) of this channel is computed as -17.90 kcal mol -1 . Although the other reaction channels are also exothermic, their reaction barriers are high (>24 kcal mol -1 ), and therefore these reactions do not contribute to the overall rate coefficient in the temperature range considered (200-400 K). Pathways via three transition states were identified for the H abstraction channel. Rate coefficients were calculated for these pathways at various levels of variational transition state theory including tunneling. The results obtained are used to distinguish between two sets of experimental rate coefficients, measured in the temperature range of 200-400 K, one of which is approximately an order of magnitude greater than the other. This comparison, as well as the temperature dependence of the computed rate coefficients, shows that the lower experimental values are favored. The implications of the results to atmospheric chemistry are discussed.

  10. Review on the prevailing methods for the prediction of potential rock burst / rock spalling in tunnels

    OpenAIRE

    Panthi, Krishna Kanta

    2017-01-01

    Rock burst / rock spalling is among the prevailing stability challenges, which can be met while tunneling through hard rock mass. Especially, this is very relevant for the mountainous country like Norway where hard rock is dominating and many road, railway and hydropower tunnels have to be aligned deep into the mountain with steep valley slope topography. Tunnels passing beneath deep rock cover (overburden), in general, are subjected to high in-situ stresses. If the rock mass is relatively un...

  11. On the mechanism of photocatalytic reactions with eosin Y

    Directory of Open Access Journals (Sweden)

    Michal Majek

    2014-04-01

    Full Text Available A combined spectroscopic, synthetic, and apparative study has allowed a more detailed mechanistic rationalization of several recently reported eosin Y-catalyzed aromatic substitutions at arenediazonium salts. The operation of rapid acid–base equilibria, direct photolysis pathways, and radical chain reactions has been discussed on the basis of pH, solvent polarity, lamp type, absorption properties, and quantum yields. Determination of the latter proved to be an especially valuable tool for the distinction between radical chain and photocatalytic reactions.

  12. Economic impact of enoxaparin after acute ischemic stroke based on PREVAIL.

    Science.gov (United States)

    Pineo, Graham; Lin, Jay; Stern, Lee; Subrahmanian, Tarun; Annemans, Lieven

    2011-04-01

    The efficacy and safety of low-molecular-weight heparins (LMWHs) versus unfractionated heparin (UFH) has been demonstrated for the prevention of venous thromboembolism (VTE) after acute ischemic stroke. Few data exist regarding the economic impact of LMWHs versus UFH in this population. A decision-analytic model was constructed using clinical information from the Prevention of VTE after Acute Ischemic stroke with LMWH Enoxaparin (PREVAIL) study, and drug costs and mean Centers for Medicare & Medicaid Services event costs. When considering the total cost of events and drugs, enoxaparin was associated with cost-savings of $895 per patient compared with UFH ($2018 vs $2913). Findings were retained within the univariate and multivariate analyses. From a payer perspective, enoxaparin was cost-effective compared with UFH in patients with acute ischemic stroke. The difference was driven by the lower clinical event rates with enoxaparin. Use of enoxaparin may help to reduce the clinical and economic burden of VTE.

  13. Formal modeling of a system of chemical reactions under uncertainty.

    Science.gov (United States)

    Ghosh, Krishnendu; Schlipf, John

    2014-10-01

    We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

  14. Anodic Cyclization Reactions and the Mechanistic Strategies That Enable Optimization.

    Science.gov (United States)

    Feng, Ruozhu; Smith, Jake A; Moeller, Kevin D

    2017-09-19

    Oxidation reactions are powerful tools for synthesis because they allow us to reverse the polarity of electron-rich functional groups, generate highly reactive intermediates, and increase the functionality of molecules. For this reason, oxidation reactions have been and continue to be the subject of intense study. Central to these efforts is the development of mechanism-based strategies that allow us to think about the reactive intermediates that are frequently central to the success of the reactions and the mechanistic pathways that those intermediates trigger. For example, consider oxidative cyclization reactions that are triggered by the removal of an electron from an electron-rich olefin and lead to cyclic products that are functionalized for further elaboration. For these reactions to be successful, the radical cation intermediate must first be generated using conditions that limit its polymerization and then channeled down a productive desired pathway. Following the cyclization, a second oxidation step is necessary for product formation, after which the resulting cation must be quenched in a controlled fashion to avoid undesired elimination reactions. Problems can arise at any one or all of these steps, a fact that frequently complicates reaction optimization and can discourage the development of new transformations. Fortunately, anodic electrochemistry offers an outstanding opportunity to systematically probe the mechanism of oxidative cyclization reactions. The use of electrochemical methods allows for the generation of radical cations under neutral conditions in an environment that helps prevent polymerization of the intermediate. Once the intermediates have been generated, a series of "telltale indicators" can be used to diagnose which step in an oxidative cyclization is problematic for less successful transformation. A set of potential solutions to address each type of problem encountered has been developed. For example, problems with the initial

  15. Understanding alternative fluxes/effluxes through comparative metabolic pathway analysis of phylum actinobacteria using a simplified approach.

    Science.gov (United States)

    Verma, Mansi; Lal, Devi; Saxena, Anjali; Anand, Shailly; Kaur, Jasvinder; Kaur, Jaspreet; Lal, Rup

    2013-12-01

    Actinobacteria are known for their diverse metabolism and physiology. Some are dreadful human pathogens whereas some constitute the natural flora for human gut. Therefore, the understanding of metabolic pathways is a key feature for targeting the pathogenic bacteria without disturbing the symbiotic ones. A big challenge faced today is multiple drug resistance by Mycobacterium and other pathogens that utilize alternative fluxes/effluxes. With the availability of genome sequence, it is now feasible to conduct the comparative in silico analysis. Here we present a simplified approach to compare metabolic pathways so that the species specific enzyme may be traced and engineered for future therapeutics. The analyses of four key carbohydrate metabolic pathways, i.e., glycolysis, pyruvate metabolism, tri carboxylic acid cycle and pentose phosphate pathway suggest the presence of alternative fluxes. It was found that the upper pathway of glycolysis was highly variable in the actinobacterial genomes whereas lower glycolytic pathway was highly conserved. Likewise, pentose phosphate pathway was well conserved in contradiction to TCA cycle, which was found to be incomplete in majority of actinobacteria. The clustering based on presence and absence of genes of these metabolic pathways clearly revealed that members of different genera shared identical pathways and, therefore, provided an easy method to identify the metabolic similarities/differences between pathogenic and symbiotic organisms. The analyses could identify isoenzymes and some key enzymes that were found to be missing in some pathogenic actinobacteria. The present work defines a simple approach to explore the effluxes in four metabolic pathways within the phylum actinobacteria. The analysis clearly reflects that actinobacteria exhibit diverse routes for metabolizing substrates. The pathway comparison can help in finding the enzymes that can be used as drug targets for pathogens without effecting symbiotic organisms

  16. Theoretical study of the decomposition pathways and products of C5- perfluorinated ketone (C5 PFK)

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Yuwei; Wang, Xiaohua, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn; Li, Xi; Yang, Aijun; Wu, Yi; Rong, Mingzhe, E-mail: xhw@mail.xjtu.edu.cn, E-mail: mzrong@mail.xjtu.edu.cn [State Key Laboratory of Electrical Insulation and Power Equipment, Xi’an Jiaotong University, No. 28 XianNing West Road, Xi’an, Shaanxi Province 710049 (China); Han, Guohui; Lu, Yanhui [Pinggao Group Co. Ltd., Pingdingshan, Henan Province 467001 (China)

    2016-08-15

    Due to the high global warming potential (GWP) and increasing environmental concerns, efforts on searching the alternative gases to SF{sub 6}, which is predominantly used as insulating and interrupting medium in high-voltage equipment, have become a hot topic in recent decades. Overcoming the drawbacks of the existing candidate gases, C5- perfluorinated ketone (C5 PFK) was reported as a promising gas with remarkable insulation capacity and the low GWP of approximately 1. Experimental measurements of the dielectric strength of this novel gas and its mixtures have been carried out, but the chemical decomposition pathways and products of C5 PFK during breakdown are still unknown, which are the essential factors in evaluating the electric strength of this gas in high-voltage equipment. Therefore, this paper is devoted to exploring all the possible decomposition pathways and species of C5 PFK by density functional theory (DFT). The structural optimizations, vibrational frequency calculations and energy calculations of the species involved in a considered pathway were carried out with DFT-(U)B3LYP/6-311G(d,p) method. Detailed potential energy surface was then investigated thoroughly by the same method. Lastly, six decomposition pathways of C5 PFK decomposition involving fission reactions and the reactions with a transition states were obtained. Important intermediate products were also determined. Among all the pathways studied, the favorable decomposition reactions of C5 PFK were found, involving C-C bond ruptures producing Ia and Ib in pathway I, followed by subsequent C-C bond ruptures and internal F atom transfers in the decomposition of Ia and Ib presented in pathways II + III and IV + V, respectively. Possible routes were pointed out in pathway III and lead to the decomposition of IIa, which is the main intermediate product found in pathway II of Ia decomposition. We also investigated the decomposition of Ib, which can undergo unimolecular reactions to give the

  17. A barrier-free atomic radical-molecule reaction: N (2D) NO2 (2A1) mechanistic study

    Science.gov (United States)

    Zuo, Ming-Hui; Liu, Hui-Ling; Huang, Xu-Ri; Zhan, Jin-Hui; Sun, Chia-Chung

    The reaction of N (2D) radical with NO2 molecule has been studied theoretically using density functional theory and ab initio quantum chemistry method. Singlet electronic state [N2O2] potential energy surfaces (PES) are calculated at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-311+G(d) + ZPE and G3B3 levels of theory. All the involved transition states for generation of (2NO) and (O2 + N2) lie much lower than the reactants. Thus, the novel reaction N + NO2 can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction.

  18. Influence of management practices on C stabilization pathways in agricultural volcanic ash soils (Canary Islands, Spain)

    Science.gov (United States)

    Hernandez, Zulimar; María Álvarez, Ana; Carral, Pilar; de Figueiredo, Tomas; Almendros, Gonzalo

    2014-05-01

    Although C stabilization mechanisms in agricultural soils are still controversial [1], a series of overlapped pathways has been suggested [2] such as: i) insolubilization of low molecular weight precursors of soil organic matter (SOM) with reactive minerals through physical and chemical bonding, ii) selective accumulation of biosynthetic substances which are recalcitrant because of its inherent chemical composition, and iii) preservation and furter diagenetic transformation of particulate SOM entrapped within resistant microaggregates, where diffusion of soil enzymes is largely hampered. In some environments where carbohydrate and N compounds are not readily biodegraded, e.g., with water saturated micropores, an ill-known C stabilization pathway may involve the formation of Maillard's reaction products [3]. In all cases, these pathways converge in the formation of recalcitrant macromolecular substances, sharing several properties with the humic acid (HA) fraction [4]. In template forests, the selective preservation and further microbial reworking of plant biomass has been identified as a prevailing mechanism in the accumulation of recalcitrant SOM forms [5]. However, in volcanic ash soils with intense organomineral interactions, condensation reactions of low molecular weight precursors with short-range minerals may be the main mechanism [6]. In order to shed some light about the effect of agricultural management on soil C stabilization processes on volcanic ash soils, the chemical composition of HA and some structural proxies of SOM informing on its origin and potential resistance to biodegradation, were examined in 30 soils from Canary Islands (Spain) by visible, infrared (IR) and 13C nuclear magnetic resonance (NMR) spectroscopies, elementary analysis and pyrolytic techniques. The results of multivariate treatments, suggested at least three simultaneous C stabilization biogeochemical trends: i) diagenetic alteration of plant biomacromolecules in soils receiving

  19. Formation pathways of DMSO from DMS-OH in the presence of O(2) and NO(x): A theoretical study.

    Science.gov (United States)

    Ramírez-Anguita, Juan M; González-Lafont, Angels; Lluch, José M

    2009-01-30

    The relative importance of the reaction pathways and thus the product yields in the dimethyl sulfide (DMS) degradation scheme initiated by the hydroxyl (OH) radical has been said to be influenced by the content of nitrogen oxides (NO(x)) in chamber experiments. In this study, ab initio and density functional electronic structure calculations of all the possible reaction pathways corresponding to the reaction process initiated by DMS-OH + oxygen (O(2)), leading to the formation of the dimethyl sulfoxide (DMSO) product in the presence of NO(x) (NO and NO(2)), are carried out for the first time. The results for the different pathways are compared with the objective of inferring their kinetic relevance in the laboratory experiments that measure DMSO formation yields. Our theoretical results clearly show the existence of NO(x)-dependent pathways leading to the formation of DMSO in addition to O(2)-dependent channels. So then, NO(x)-containing conditions would have to modify the relative importance of the addition channel in the DMS oxidation process. (c) 2008 Wiley Periodicals, Inc.

  20. MicroRNA-124-3p expression and its prospective functional pathways in hepatocellular carcinoma: A quantitative polymerase chain reaction, gene expression omnibus and bioinformatics study.

    Science.gov (United States)

    He, Rong-Quan; Yang, Xia; Liang, Liang; Chen, Gang; Ma, Jie

    2018-04-01

    The present study aimed to explore the potential clinical significance of microRNA (miR)-124-3p expression in the hepatocarcinogenesis and development of hepatocellular carcinoma (HCC), as well as the potential target genes of functional HCC pathways. Reverse transcription-quantitative polymerase chain reaction was performed to evaluate the expression of miR-124-3p in 101 HCC and adjacent non-cancerous tissue samples. Additionally, the association between miR-124-3p expression and clinical parameters was also analyzed. Differentially expressed genes identified following miR-124-3p transfection, the prospective target genes predicted in silico and the key genes of HCC obtained from Natural Language Processing (NLP) were integrated to obtain potential target genes of miR-124-3p in HCC. Relevant signaling pathways were assessed with protein-protein interaction (PPI) networks, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Protein Annotation Through Evolutionary Relationships (PANTHER) pathway enrichment analysis. miR-124-3p expression was significantly reduced in HCC tissues compared with expression in adjacent non-cancerous liver tissues. In HCC, miR-124-3p was demonstrated to be associated with clinical stage. The mean survival time of the low miR-124-3p expression group was reduced compared with that of the high expression group. A total of 132 genes overlapped from differentially expressed genes, miR-124-3p predicted target genes and NLP identified genes. PPI network construction revealed a total of 109 nodes and 386 edges, and 20 key genes were identified. The major enriched terms of three GO categories included regulation of cell proliferation, positive regulation of cellular biosynthetic processes, cell leading edge, cytosol and cell projection, protein kinase activity, transcription activator activity and enzyme binding. KEGG analysis revealed pancreatic cancer, prostate cancer and non-small cell lung cancer as the

  1. The chemical basis of DNA damage by the direct pathway of ionizing radiation

    International Nuclear Information System (INIS)

    Sharma, Kiran Kumar K.

    2013-01-01

    Free radicals in living system has been implicated as playing a major role in the etiology of variety of diseases. The mechanism of free radicals in vivo involves predominantly the reaction with the DNA, producing different types of damage to the DNA. These lesions induced to the DNA could lead to mutation and even cell death. Radiolysis techniques, which uses ionizing radiation has proven to be one of the most advanced and excellent tool for studying the free radical reaction mechanisms as it can produce a host of well characterized free radicals. The effects of ionizing radiation on DNA have been studied for many years. Ionizing radiation interacts with DNA in vivo by two pathways, direct and indirect. The indirect accounts for 50-60% while the direct effect accounts for 40-50%. The chemical mechanism of the former reaction arising mainly from the reactive species produced by radiolysis of water has been extensively studied, however with respect to the later pathway, which creates holes and electrons to the DNA molecule using DNA films and crystals is an active area of research as both the pathways plays important roles in DNA damage in vivo particularly in chromosomal DNA which are tightly bound with histones and compartmentalized

  2. Reaction pathway towards formation of cobalt single chain magnets and nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Balaji, G.; Desilva, Rohini M.; Palshin, V. [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States); Desilva, N. [Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803 (United States); Palmer, G. [Department of Biochemistry and Cell Biology, Rice University, MS 140, 6100 Main street, Houston, TX 77251 (United States); Kumar, Challa S.S.R., E-mail: ckumar1@lsu.ed [Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Highway, Baton Rouge, LA 70806 (United States)

    2010-03-15

    With the advent of molecular magnets the quest for suitable high density magnetic storage materials has fuelled further research in this area. Here in this report, we present a detailed mechanistic investigation of thermal decomposition of cyclopentadienyl cobalt [CoCp(CO){sub 2}] precursor where Cp is the cyclopentadienyl moiety. The reaction revealed the formation of cobalt nanoparticles (Co-NPs) through an isolable reaction intermediate characterized as a Single Chain Magnet (SCM), [Co(Cp){sub 2}]{sub 2}CoCl{sub 4} (1). The SQUID magnetic measurements showed the presence of very strong antiferromagnetic interactions between Co{sup 2+} ions. The zero-field cooled (ZFC) and field cooled (FC) magnetization curves branch out below 5 K and there is evidence for frequency dependent complex susceptibility along with a maximum observed around 2.5 K. The optical studies indicated that the Co{sup 2+} d-d transition is influenced by the polarity of the solvents. The cobalt nanoparticles (Co-NPs) were obtained, either directly from 1 or from its precursor. They are spherical in shape with a mean size 15 nm, have fcc crystal structure and were found to be ferromagnetic at room temperature.

  3. Transesterification of Jatropha curcas oil glycerides: Theoretical and experimental studies of biodiesel reaction

    Energy Technology Data Exchange (ETDEWEB)

    Neyda C. Om Tapanes; Donato A. Gomes Aranda; Jose W. de Mesquita Carneiro; Octavio A. Ceva Antunes [Universidade Federal do Rio de Janeiro, Rio de Janeiro (Brazil). Laboratorio GREENTEC

    2008-08-15

    Vegetal oil, also known as triglycerides, is a mixture of fatty acid triesters of glycerol. In the triglycerides alkyl chains of Jatropha curcas oil, predominate the palmitic, oleic and linoleic fatty acids. The process usually used to convert these triglycerides to biodiesel is called transesterification. The overall process is a sequence of three equivalent, consecutive and reversible reactions, in which di- and monoglycerides are formed as intermediates. Semi-empirical AM1 molecular orbital calculations were used to investigate the reaction pathways of base-catalyzed transesterification of glycerides of palmitic, oleic and linoleic acid. The most probable pathway and the rate determining-step of the reactions were estimated from the molecular orbital calculations. Our results suggest the formation of only one tetrahedral intermediate, which in a subsequent step rearranges to form the products. The rate determining-step is the break of this tetrahedral intermediate. 27 refs., 6 figs., 4 tabs.

  4. Diversion of the melanin synthetic pathway by dopamine product scavengers: A quantum chemical modeling of the reaction mechanisms

    Directory of Open Access Journals (Sweden)

    T. B. Demissie

    2017-01-01

    Full Text Available We report the stability and reactivity of the oxidation products as well as L-cysteine and N-acetylcysteine adducts of dopamine studied using quantum chemical calculations. The overall reactions studied were subdivided into four reaction channels. The first reaction channel is the oxidation of dopamine to form dopaminoquinone. The second reaction channel leads to melanin formation through subsequent reactions. The third and fourth reaction channels are reactions leading to the formation of dopaminoquinone adducts which are aimed to divert the synthesis of melanin. The results indicate that L-cysteine and N-acetylcysteine undergo chemical reactions mainly at C5 position of dopaminoquinone. The analyses of the thermodynamic energies indicate that L-cysteine and N-acetylcysteine covalently bind to dopaminoquinone by competing with the internal cyclization reaction of dopaminoquinone which leads to the synthesis of melanin. The analysis of the results, based on the reaction free energies, is also supported by the investigation of the natural bond orbitals of the reactants and products.

  5. Familiar units prevail over statistical cues in word segmentation.

    Science.gov (United States)

    Poulin-Charronnat, Bénédicte; Perruchet, Pierre; Tillmann, Barbara; Peereman, Ronald

    2017-09-01

    In language acquisition research, the prevailing position is that listeners exploit statistical cues, in particular transitional probabilities between syllables, to discover words of a language. However, other cues are also involved in word discovery. Assessing the weight learners give to these different cues leads to a better understanding of the processes underlying speech segmentation. The present study evaluated whether adult learners preferentially used known units or statistical cues for segmenting continuous speech. Before the exposure phase, participants were familiarized with part-words of a three-word artificial language. This design allowed the dissociation of the influence of statistical cues and familiar units, with statistical cues favoring word segmentation and familiar units favoring (nonoptimal) part-word segmentation. In Experiment 1, performance in a two-alternative forced choice (2AFC) task between words and part-words revealed part-word segmentation (even though part-words were less cohesive in terms of transitional probabilities and less frequent than words). By contrast, an unfamiliarized group exhibited word segmentation, as usually observed in standard conditions. Experiment 2 used a syllable-detection task to remove the likely contamination of performance by memory and strategy effects in the 2AFC task. Overall, the results suggest that familiar units overrode statistical cues, ultimately questioning the need for computation mechanisms of transitional probabilities (TPs) in natural language speech segmentation.

  6. Kinetic and mechanisms of methanimine reactions with singlet and triplet molecular oxygen: Substituent and catalyst effects

    Science.gov (United States)

    Asgharzadeh, Somaie; Vahedpour, Morteza

    2018-06-01

    Methanimine reaction with O2 on singlet and triplet potential energy surfaces are investigated using B3PW91, M06-2X, MP2 and CCSD(T) methods. Thermodynamic and kinetic parameters are calculated at M06-2X method. The most favorable channel involves H-abstraction of CH2NH+O2 to the formation of HCN + H2O2 products via low level energy barrier. The catalytic effect of water molecule on HCN + H2O2 products pathway are investigated. Result shows that contribution of water molecule using complex formation with methanimine can decreases barrier energy of transition state and the reaction rate increases. Also, substituent effect of fluorine atom as deactivating group are investigated on the main reaction pathway.

  7. SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis

    Science.gov (United States)

    Ohashi, Masao; Liu, Fang; Hai, Yang; Chen, Mengbin; Tang, Man-Cheng; Yang, Zhongyue; Sato, Michio; Watanabe, Kenji; Houk, K. N.; Tang, Yi

    2017-09-01

    Pericyclic reactions—which proceed in a concerted fashion through a cyclic transition state—are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-L-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme ‘toolboxes’. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.

  8. Reaction of phosphorus ylides with carbonyl compounds in supercritical carbon dioxide

    International Nuclear Information System (INIS)

    Jeong, Kyung Il; Kim, Hak Do; Shim, Jae Jin; Ra, Choon Sup

    2004-01-01

    The condensation reaction of (benzylene)triphenylphosphoranes with carbonyl compounds in supercritical carbon dioxide was examined. Reactions of (benzylene)phosphoranes (ca. 1 mmol) with several benzaldehydes in a supercritical carbon dioxide (80 .deg. C, 2,000 psi) containing THF entrainer (5%) in a 24 mL reactor proceed smoothly to yield olefination products in fairly good to excellent yields but slower, compared to reactions in a conventional THF solvent. Generally, phosphoranes that are not substituted with a nitro group show more (Z)-selective reactions with aromatic aldehydes under scCO 2 condition than in THF. The reaction of (benzylene)triphenylphosphosphoranes with 4-t-butylcyclohexanone gave the corresponding olefin compounds with a low conversion under both the supercritical carbon dioxide and the organic THF solvent. Our preliminary study showed the Wittig reaction carries out smoothly in supercritical carbon dioxide medium and also a possible tunability of this reaction pathway by adding a entrainer. The results would be useful for devising a novel process for the environmentally friendly Wittig reaction

  9. A thermodynamic solution model for calcium carbonate: Towards an understanding of multi-equilibria precipitation pathways

    OpenAIRE

    Donnet, Marcel; Bowen, Paul; Lemaître, Jacques

    2009-01-01

    Thermodynamic solubility calculations are normally only related to thermodynamic equilibria in solution. In this paper, we extend the use of such solubility calculations to help elucidate possible precipitation reaction pathways during the entire reaction. We also estimate the interfacial energy of particles using only solubility data by a modification of Mersmann’s approach. We have carried this out by considering precipitation reactions as a succession of small quasi-equilibrium states. Thu...

  10. Measuring protection of aromatic wine thiols from oxidation by competitive reactions vs wine preservatives with ortho-quinones.

    Science.gov (United States)

    Nikolantonaki, Maria; Magiatis, Prokopios; Waterhouse, Andrew L

    2014-11-15

    Quinones are central intermediates in wine oxidation that can degrade the quality of wine by reactions with varietal thiols, such as 3-sulfanylhexanol, decreasing desirable aroma. Protection by wine preservatives (sulphur dioxide, glutathione, ascorbic acid and model tannin, phloroglucinol) was assessed by competitive sacrificial reactions with 4-methyl-1,2-benzoquinone, quantifying products and ratios by HPLC-UV-MS. Regioselectivity was assessed by product isolation and identification by NMR spectroscopy. Nucleophilic addition reactions compete with two electron reduction of quinones by sulphur dioxide or ascorbic acid, and both routes serve as effective quenching pathways, but minor secondary products from coupled redox reactions between the products and reactants are also observed. The wine preservatives were all highly reactive and thus all very protective against 3-sulfanylhexanol loss to the quinone, but showed only additive antioxidant effects. Confirmation of these reaction rates and pathways in wine is needed to assess the actual protective action of each tested preservative. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Three Rate-Constant Kinetic Model for Permanganate Reactions Autocatalyzed by Colloidal Manganese Dioxide: The Oxidation of L-Phenylalanine.

    Science.gov (United States)

    Perez-Benito, Joaquin F; Ferrando, Jordi

    2014-12-26

    The reduction of permanganate ion to MnO(2)-Mn(2)O(3) soluble colloidal mixed oxide by l-phenylalanine in aqueous phosphate-buffered neutral solutions has been followed by a spectrophotometric method, monitoring the decay of permanganate ion at 525 nm and the formation of the colloidal oxide at 420 nm. The reaction is autocatalyzed by the manganese product, and three rate constants have been required to fit the experimental absorbance-time kinetic data. The reaction shows base catalysis, and the values of the activation parameters at different pHs have been determined. A mechanism including both the nonautocatalytic and the autocatalytic reaction pathways, and in agreement with the available experimental data, has been proposed. Some key features of this mechanism are the following: (i) of the two predominant forms of the amino acid, the anionic form exhibits a stronger reducing power than the zwitterionic form; (ii) the nonautocatalytic reaction pathway starts with the transfer of the hydrogen atom in the α position of the amino acid to permanganate ion; and (iii) the autocatalytic reaction pathway involves the reduction of Mn(IV) to Mn(II) by the amino acid and the posterior reoxidation of Mn(II) to Mn(IV) by permanganate ion.

  12. Formation of phosphonates and pyrophosphates in the reactions of ...

    Indian Academy of Sciences (India)

    Bu-4-Me-C6H2O)2P(O)]2O (8) could be isolated, although the reaction mixture showed several other compounds in the phosphorus NMR. A possible pathway for the formation of phosphonate salts is proposed. The X-ray crystal structures of 4, ...

  13. Vibrio Phage KVP40 Encodes a Functional NAD+ Salvage Pathway.

    Science.gov (United States)

    Lee, Jae Yun; Li, Zhiqun; Miller, Eric S

    2017-05-01

    The genome of T4-type Vibrio bacteriophage KVP40 has five genes predicted to encode proteins of pyridine nucleotide metabolism, of which two, nadV and natV , would suffice for an NAD + salvage pathway. NadV is an apparent nicotinamide phosphoribosyltransferase (NAmPRTase), and NatV is an apparent bifunctional nicotinamide mononucleotide adenylyltransferase (NMNATase) and nicotinamide-adenine dinucleotide pyrophosphatase (Nudix hydrolase). Genes encoding the predicted salvage pathway were cloned and expressed in Escherichia coli , the proteins were purified, and their enzymatic properties were examined. KVP40 NadV NAmPRTase is active in vitro , and a clone complements a Salmonella mutant defective in both the bacterial de novo and salvage pathways. Similar to other NAmPRTases, the KVP40 enzyme displayed ATPase activity indicative of energy coupling in the reaction mechanism. The NatV NMNATase activity was measured in a coupled reaction system demonstrating NAD + biosynthesis from nicotinamide, phosphoribosyl pyrophosphate, and ATP. The NatV Nudix hydrolase domain was also shown to be active, with preferred substrates of ADP-ribose, NAD + , and NADH. Expression analysis using reverse transcription-quantitative PCR (qRT-PCR) and enzyme assays of infected Vibrio parahaemolyticus cells demonstrated nadV and natV transcription during the early and delayed-early periods of infection when other KVP40 genes of nucleotide precursor metabolism are expressed. The distribution and phylogeny of NadV and NatV proteins among several large double-stranded DNA (dsDNA) myophages, and also those from some very large siphophages, suggest broad relevance of pyridine nucleotide scavenging in virus-infected cells. NAD + biosynthesis presents another important metabolic resource control point by large, rapidly replicating dsDNA bacteriophages. IMPORTANCE T4-type bacteriophages enhance DNA precursor synthesis through reductive reactions that use NADH/NADPH as the electron donor and NAD

  14. Population causes and consequences of leading chronic diseases: a comparative analysis of prevailing explanations.

    Science.gov (United States)

    Stuckler, David

    2008-06-01

    The mortality numbers and rates of chronic disease are rising faster in developing than in developed countries. This article compares prevailing explanations of population chronic disease trends with theoretical and empirical models of population chronic disease epidemiology and assesses some economic consequences of the growth of chronic diseases in developing countries based on the experiences of developed countries. Four decades of male mortality rates of cardiovascular and chronic noncommunicable diseases were regressed on changes in and levels of country income per capita, market integration, foreign direct investment, urbanization rates, and population aging in fifty-six countries for which comparative data were available. Neoclassical economic growth models were used to estimate the effect of the mortality rates of chronic noncommunicable diseases on economic growth in high-income OECD countries. Processes of economic growth, market integration, foreign direct investment, and urbanization were significant determinants of long-term changes in mortality rates of heart disease and chronic noncommunicable disease, and the observed relationships with these social and economic factors were roughly three times stronger than the relationships with the population's aging. In low-income countries, higher levels of country income per capita, population urbanization, foreign direct investment, and market integration were associated with greater mortality rates of heart disease and chronic noncommunicable disease, less increased or sometimes reduced rates in middle-income countries, and decreased rates in high-income countries. Each 10 percent increase in the working-age mortality rates of chronic noncommunicable disease decreased economic growth rates by close to a half percent. Macrosocial and macroeconomic forces are major determinants of population rises in chronic disease mortality, and some prevailing demographic explanations, such as population aging, are

  15. The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

    Science.gov (United States)

    Igamberdiev, Abir U; Kleczkowski, Leszek A

    2018-01-01

    Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

  16. Photogeochemical reactions of manganese under anoxic conditions

    Science.gov (United States)

    Liu, W.; Yee, N.; Piotrowiak, P.; Falkowski, P. G.

    2017-12-01

    Photogeochemistry describes reactions involving light and naturally occurring chemical species. These reactions often involve a photo-induced electron transfer that does not occur in the absence of light. Although photogeochemical reactions have been known for decades, they are often ignored in geochemical models. In particular, reactions caused by UV radiation during an ozone free early Earth could have influenced the available oxidation states of manganese. Manganese is one of the most abundant transition metals in the crust and is important in both biology and geology. For example, the presence of manganese (VI) oxides in the geologic record has been used as a proxy for oxygenic photosynthesis; however, we suggest that the high oxidation state of Mn can be produced abiotically by photochemical reactions. Aqueous solutions of manganese (II) as well as suspensions of rhodochrosite (MnCO3) were irradiated under anoxic condition using a 450 W mercury lamp and custom built quartz reaction vessels. The photoreaction of the homogeneous solution of Mn(II) produced H2 gas and akhtenskite (ɛ-MnO2) as the solid product . This product is different than the previously identified birnessite. The irradiation of rhodochrosite suspensions also produced H2 gas and resulted in both a spectral shift as well as morphology changes of the mineral particles in the SEM images. These reactions offer alternative, abiotic pathways for the formation of manganese oxides.

  17. Pathway Distiller - multisource biological pathway consolidation.

    Science.gov (United States)

    Doderer, Mark S; Anguiano, Zachry; Suresh, Uthra; Dashnamoorthy, Ravi; Bishop, Alexander J R; Chen, Yidong

    2012-01-01

    One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort has been made to collect curated biological pathways into publicly accessible databases. When combining disparate databases, highly related or redundant pathways exist, making their consolidation into pathway concepts essential. This will facilitate unbiased, comprehensive yet streamlined analysis of experiments that result in large gene sets. After gene set enrichment finds representative pathways for large gene sets, pathways are consolidated into representative pathway concepts. Three complementary, but different methods of pathway consolidation are explored. Enrichment Consolidation combines the set of the pathways enriched for the signature gene list through iterative combining of enriched pathways with other pathways with similar signature gene sets; Weighted Consolidation utilizes a Protein-Protein Interaction network based gene-weighting approach that finds clusters of both enriched and non-enriched pathways limited to the experiments' resultant gene list; and finally the de novo Consolidation method uses several measurements of pathway similarity, that finds static pathway clusters independent of any given experiment. We demonstrate that the three consolidation methods provide unified yet different functional insights of a resultant gene set derived from a genome-wide profiling experiment. Results from the methods are presented, demonstrating their applications in biological studies and comparing with a pathway web-based framework that also combines several pathway databases. Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow

  18. Using Physical Organic Chemistry To Shape the Course of Electrochemical Reactions.

    Science.gov (United States)

    Moeller, Kevin D

    2018-05-09

    While organic electrochemistry can look quite different to a chemist not familiar with the technique, the reactions are at their core organic reactions. As such, they are developed and optimized using the same physical organic chemistry principles employed during the development of any other organic reaction. Certainly, the electron transfer that triggers the reactions can require a consideration of new "wrinkles" to those principles, but those considerations are typically minimal relative to the more traditional approaches needed to manipulate the pathways available to the reactive intermediates formed downstream of that electron transfer. In this review, three very different synthetic challenges-the generation and trapping of radical cations, the development of site-selective reactions on microelectrode arrays, and the optimization of current in a paired electrolysis-are used to illustrate this point.

  19. Reaction mechanism for the free-edge oxidation of soot by O 2

    KAUST Repository

    Raj, Abhijeet

    2012-11-01

    The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

  20. Reaction mechanism for the free-edge oxidation of soot by O 2

    KAUST Repository

    Raj, Abhijeet; da Silva, Gabriel; Chung, Suk-Ho

    2012-01-01

    The reaction pathways for the oxidation by O 2 of polycyclic aromatic hydrocarbons present in soot particles are investigated using density functional theory at B3LYP/6-311++G(d,p) level of theory. For this, pyrene radical (4-pyrenyl) is chosen as the model molecule, as most soot models present in the literature employ the reactions involving the conversion of 4-pyrenyl to 4-phenanthryl by O 2 and OH to account for soot oxidation. Several routes for the formation of CO and CO 2 are proposed. The addition of O 2 on a radical site to form a peroxyl radical is found to be barrierless and exothermic with reaction energy of 188kJ/mol. For the oxidation reaction to proceed further, three pathways are suggested, each of which involve the activation energies of 104, 167 and 115kJ/mol relative to the peroxyl radical. The effect of the presence of H atom on a carbon atom neighboring the radical site on the energetics of carbon oxidation is assessed. Those intermediate species formed during oxidation with seven-membered rings or with a phenolic group are found to be highly stable. The rate constants evaluated using transition state theory in the temperature range of 300-3000K for the reactions involved in the mechanism are provided. © 2012 The Combustion Institute.

  1. CO2 as an Oxidant for High Temperature Reactions

    Directory of Open Access Journals (Sweden)

    Sibudjing eKawi

    2015-03-01

    Full Text Available This paper presents a review on the developments in catalyst technology for the reactions utilizing CO2 for high temperature applications. These include dehydrogenation of alkanes to olefins, the dehydrogenation of ethylbenzene to styrene and finally CO2 reforming of hydrocarbon feedstock (i.e. methane and alcohols. Aspects on the various reaction pathways are also highlighted. The literature on the role of promoters and catalyst development is critically evaluated. Most of the reactions discussed in this review are exploited in industries and related to on-going processes, thus providing extensive data from literature. However some reactions, such as CO2 reforming of ethanol and glycerol which have not reached industrial scale are also reviewed owing to their great potential in terms of sustainability which are essential as energy for the future. This review further illustrates the building-up of knowledge which shows the role of support and catalysts for each reaction and the underlying linkage between certain catalysts which can be adapted for the multiple CO2-related reactions.

  2. Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway.

    Science.gov (United States)

    Ries, Marco I; Ali, Hazrat; Lankhorst, Peter P; Hankemeier, Thomas; Bovenberg, Roel A L; Driessen, Arnold J M; Vreeken, Rob J

    2013-12-27

    Metabolic profiling and structural elucidation of novel secondary metabolites obtained from derived deletion strains of the filamentous fungus Penicillium chrysogenum were used to reassign various previously ascribed synthetase genes of the roquefortine/meleagrin pathway to their corresponding products. Next to the structural characterization of roquefortine F and neoxaline, which are for the first time reported for P. chrysogenum, we identified the novel metabolite roquefortine L, including its degradation products, harboring remarkable chemical structures. Their biosynthesis is discussed, questioning the exclusive role of glandicoline A as key intermediate in the pathway. The results reveal that further enzymes of this pathway are rather unspecific and catalyze more than one reaction, leading to excessive branching in the pathway with meleagrin and neoxaline as end products of two branches.

  3. PSFC: a Pathway Signal Flow Calculator App for Cytoscape [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Lilit Nersisyan

    2017-04-01

    Full Text Available Cell signaling pathways are sequences of biochemical reactions that propagate an input signal, such as a hormone binding to a cell-surface receptor, into the cell to trigger a reactive process. Assessment of pathway activities is crucial for determining which pathways play roles in disease versus normal conditions. To date various pathway flow/perturbation assessment tools are available, however they are constrained to specific algorithms and specific data types. There are no accepted standards for evaluation of pathway activities or simulation of flow propagation events in pathways, and the results of different software are difficult to compare. Here we present Pathway Signal Flow Calculator (PSFC, a Cytoscape app for calculation of a pathway signal flow based on the pathway topology and node input data. The app provides a rich framework for customization of different signal flow algorithms to allow users to apply various approaches within a single computational framework.

  4. Hi-Jack: a novel computational framework for pathway-based inference of host–pathogen interactions

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2015-03-09

    Motivation: Pathogens infect their host and hijack the host machinery to produce more progeny pathogens. Obligate intracellular pathogens, in particular, require resources of the host to replicate. Therefore, infections by these pathogens lead to alterations in the metabolism of the host, shifting in favor of pathogen protein production. Some computational identification of mechanisms of host-pathogen interactions have been proposed, but it seems the problem has yet to be approached from the metabolite-hijacking angle. Results: We propose a novel computational framework, Hi-Jack, for inferring pathway-based interactions between a host and a pathogen that relies on the idea of metabolite hijacking. Hi-Jack searches metabolic network data from hosts and pathogens, and identifies candidate reactions where hijacking occurs. A novel scoring function ranks candidate hijacked reactions and identifies pathways in the host that interact with pathways in the pathogen, as well as the associated frequent hijacked metabolites. We also describe host-pathogen interaction principles that can be used in the future for subsequent studies. Our case study on Mycobacterium tuberculosis (Mtb) revealed pathways in human-e.g. carbohydrate metabolism, lipids metabolism and pathways related to amino acids metabolism-that are likely to be hijacked by the pathogen. In addition, we report interesting potential pathway interconnections between human and Mtb such as linkage of human fatty acid biosynthesis with Mtb biosynthesis of unsaturated fatty acids, or linkage of human pentose phosphate pathway with lipopolysaccharide biosynthesis in Mtb. © The Author 2015. Published by Oxford University Press. All rights reserved.

  5. First direct comparison of clinical outcomes between European and Asian cohorts in transcatheter aortic valve implantation: the Massy study group vs. the PREVAIL JAPAN trial.

    Science.gov (United States)

    Watanabe, Yusuke; Hayashida, Kentaro; Takayama, Morimasa; Mitsudo, Kazuaki; Nanto, Shinsuke; Takanashi, Shuichiro; Komiya, Tatsuhiko; Kuratani, Toru; Tobaru, Tetsuya; Goto, Tsuyoshi; Lefèvre, Thierry; Sawa, Yoshiki; Morice, Marie-Claude

    2015-02-01

    The efficacy and safety of transcatheter aortic valve implantation (TAVI) in Asian populations were unknown. The purpose of this study was to compare directly the clinical outcomes of the first Japanese trial and a European single-center experience after TAVI. Between April 2010 and October 2011, 64 patients were included in the PREVAIL JAPAN multicenter trial which was set up to evaluate the safety and efficacy of the Edwards SAPIEN XT™ (Edwards Lifesciences, Irvine, CA, USA) in high-risk Japanese patients with severe aortic stenosis. Between March 2010 and January 2012, 237 consecutive patients treated with TAVI using the Edwards SAPIEN XT™ prosthesis at Institut Cardiovasculaire Paris Sud were prospectively included in the Massy cohort. We compared the clinical outcomes of these two cohorts. Patients were of similar age (83.4±6.6 years vs. 84.5±6.1 years, p=0.25), but logistic EuroSCORE was higher in the Massy cohort (20.2±11.7% vs. 15.6±8.0%, pPREVAIL JAPAN cohort (1.41±0.14m(2) vs. 1.72±0.18m(2); pPREVAIL JAPAN cohort (12.7±11.4mmHg vs. 10.1±3.6mmHg, p=0.01), but satisfactory improvement in 6-month functional status was obtained in both cohorts (76.5% vs. 77.2%, p=0.91). Clinical outcomes after TAVI in the patients included in the PREVAIL JAPAN trial were acceptable and as safe as that of a single-center European cohort. Copyright © 2014 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

  6. Impacts of Four SO2 Oxidation Pathways on Wintertime Sulfate Concentrations

    Science.gov (United States)

    Sarwar, G.; Fahey, K.; Zhang, Y.; Kang, D.; Mathur, R.; Xing, J.; Wei, C.; Cheng, Y.

    2017-12-01

    Air quality models tend to under-estimate winter-time sulfate concentrations compared to observed data. Such under-estimations are particularly acute in China where very high concentrations of sulfate have been measured. Sulfate is produced by oxidation of sulfur dioxide (SO2) in gas-phase by hydroxyl radical and in aqueous-phase by hydrogen peroxide, ozone, etc. and most air quality models employ such typical reactions. Several additional SO2 oxidation pathways have recently been proposed. Heterogeneous reaction on dust has been suggested to be an important sink for SO2. Oxidation of SO2 on fine particles in presence of nitrogen dioxide (NO2) and ammonia (NH3) at high relative humidity has been implicated for sulfate formation in Chinese haze and London fog. Reactive nitrogen chemistry in aerosol water has also been suggested to produce winter-time sulfate in China. Specifically, high aerosol water can trap SO2 which can be subsequently oxidized by NO2 to form sulfate. Aqueous-phase (in-cloud) oxidation of SO2 by NO2 can also produce sulfate. Here, we use the hemispheric Community Multiscale Air Quality (CMAQ) modeling system to examine the potential impacts of these SO2 oxidation pathways on sulfate formation. We use anthropogenic emissions from the Emissions Database for Global Atmospheric Research and biogenic emissions from Global Emissions InitiAtive. We performed simulations without and with these SO2 oxidation pathways for October-December of 2014 using meteorological fields obtained from the Weather Research and Forecasting model. The standard CMAQ model contains one gas-phase chemical reaction and five aqueous-phase chemical reactions for SO2 oxidation. We implement four additional SO2 oxidation pathways into the CMAQ model. Our preliminary results suggest that the dust chemistry enhances mean sulfate over parts of China and Middle-East, the in-cloud SO2 oxidation by NO2 enhances sulfate over parts of western Europe, oxidation of SO2 by NO2 and NH3 on

  7. Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation.

    Science.gov (United States)

    Minakata, Daisuke; Crittenden, John

    2011-04-15

    The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.

  8. Mechanochemical Association Reaction of Interfacial Molecules Driven by Shear.

    Science.gov (United States)

    Khajeh, Arash; He, Xin; Yeon, Jejoon; Kim, Seong H; Martini, Ashlie

    2018-05-29

    Shear-driven chemical reaction mechanisms are poorly understood because the relevant reactions are often hidden between two solid surfaces moving in relative motion. Here, this phenomenon is explored by characterizing shear-induced polymerization reactions that occur during vapor phase lubrication of α-pinene between sliding hydroxylated and dehydroxylated silica surfaces, complemented by reactive molecular dynamics simulations. The results suggest that oxidative chemisorption of the α-pinene molecules at reactive surface sites, which transfers oxygen atoms from the surface to the adsorbate molecule, is the critical activation step. Such activation takes place more readily on the dehydroxylated surface. During this activation, the most strained part of the α-pinene molecules undergoes a partial distortion from its equilibrium geometry, which appears to be related to the critical activation volume for mechanical activation. Once α-pinene molecules are activated, association reactions occur between the newly attached oxygen and one of the carbon atoms in another molecule, forming ether bonds. These findings have general implications for mechanochemistry because they reveal that shear-driven reactions may occur through reaction pathways very different from their thermally induced counterparts and specifically the critical role of molecular distortion in such reactions.

  9. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals

    DEFF Research Database (Denmark)

    Chen, Xiulai; Gao, Cong; Guo, Liang

    2018-01-01

    , and pathway optimization at the systems level, offers a conceptual and technological framework to exploit potential pathways, modify existing pathways and create new pathways for the optimal production of desired chemicals. Here, we summarize recent progress of DCEO biotechnology and examples of its......Chemical synthesis is a well established route for producing many chemicals on a large scale, but some drawbacks still exist in this process, such as unstable intermediates, multistep reactions, complex process control, etc. Biobased production provides an attractive alternative to these challenges......, but how to make cells into efficient factories is challenging. As a key enabling technology to develop efficient cell factories, design-construction-evaluation-optimization (DCEO) biotechnology, which incorporates the concepts and techniques of pathway design, pathway construction, pathway evaluation...

  10. Benzene destruction in claus process by sulfur dioxide: A reaction kinetics study

    KAUST Repository

    Sinha, Sourab

    2014-07-02

    Benzene, toluene and xylene (BTX) are present as contaminants in the H 2S gas stream entering a Claus furnace. The exhaust gases from the furnace enter catalytic units, where BTX form soot particles. These particles clog and deactivate the catalysts. A solution to this problem is BTX oxidation before the gases enter catalyst beds. This work presents a theoretical investigation on benzene oxidation by SO2. Density functional theory is used to develop a detailed mechanism for phenyl radical -SO2 interactions. The mechanism begins with SO2 addition to phenyl radical after overcoming an energy barrier of 6.4 kJ/mol. This addition reaction is highly exothermic, where a reaction energy of 182 kJ/mol is released. The most favorable pathway involves O-S bond breakage, leading to the release of SO. A remarkable similarity between the pathways for phenyl radical oxidation by O2 and its oxidation by SO2 is observed. The reaction rate constants are also evaluated to facilitate process simulations. © 2014 American Chemical Society.

  11. Flux analysis of central metabolic pathways in Geobactermetallireducens during reduction of solubleFe(III)-NTA

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yinjie J.; Chakraborty, Romy; Garcia-Martin, Hector; Chu,Jeannie; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

    We analyzed the carbon fluxes in the central metabolism ofGeobacter metallireducens strain GS-15 using 13C isotopomer modeling.Acetate labeled in the 1st or 2nd position was the sole carbon source,and Fe-NTA was the sole terminal electron acceptor. The measured labeledacetate uptake rate was 21 mmol/gdw/h in the exponential growth phase.The resulting isotope labeling pattern of amino acids allowed an accuratedetermination of the in vivo global metabolic reaction rates (fluxes)through the central metabolic pathways using a computational isotopomermodel. The tracer experiments showed that G. metallireducens containedcomplete biosynthesis pathways for essential metabolism, and this strainmight also have an unusual isoleucine biosynthesis route (usingacetyl-CoA and pyruvate as the precursors). The model indicated that over90 percent of the acetate was completely oxidized to CO2 via a completetricarboxylic acid (TCA) cycle while reducing iron. Pyruvate carboxylaseand phosphoenolpyruvate carboxykinase were present under theseconditions, but enzymes in the glyoxylate shunt and malic enzyme wereabsent. Gluconeogenesis and the pentose phosphate pathway were mainlyemployed for biosynthesis and accounted for less than 3 percent of totalcarbon consumption. The model also indicated surprisingly highreversibility in the reaction between oxoglutarate and succinate. Thisstep operates close to the thermodynamic equilibrium possibly becausesuccinate is synthesized via a transferase reaction, and the conversionof oxoglutarate to succinate is a rate limiting step for carbonmetabolism. These findings enable a better understanding of therelationship between genome annotation and extant metabolic pathways inG. metallireducens.

  12. Transformation of aminopyrine in the presence of free available chlorine: Kinetics, products, and reaction pathways.

    Science.gov (United States)

    Cai, Mei-Quan; Feng, Li; Zhang, Li-Qiu

    2017-03-01

    Aminopyrine (AMP) has been frequently detected in the aquatic environment. In this study, the transformation mechanism of AMP by free available chlorine (FAC) oxidation was investigated. The results showed that FAC reacted with AMP rapidly, and a 74% elimination was achieved for 1.30 μM AMP after 2 min at 14.08 μM FAC dose. AMP chlorination was strongly pH-dependent, and its reaction included second- and third-order kinetic processes. Three active FAC species, including chlorine monoxide (Cl 2 O), molecular chlorine (Cl 2 ), and hypochlorous acid (HOCl), were observed to contribute to AMP degradation. The intrinsic rate constants of each FAC species with neutral (AMP 0 ) and cation (AMP + ) species were obtained by kinetic fitting. Cl 2 O exhibited the highest reactivity with AMP 0 (k AMP0, Cl2O  = (4.33 ± 1.4) × 10 9  M -1 s -1 ). In addition, Cl 2 showed high reactivity (10 6 -10 7  M -1 s -1 ) in the presence of chloride, compared with HOCl (k AMP+, HOCl  = (5.73 ± 0.23) × 10 2  M -1 s -1 , k AMP0, HOCl  = (9.68 ± 0.96) × 10 2  M -1 s -1 ). At pH 6.15 and 14.08 μM FAC dose without chloride addition, the contribution of Cl 2 O reached to the maximum (33.3%), but in the whole pH range, HOCl was the main contributor (>66.6%) for AMP degradation. The significance of Cl 2 was noticeable in water containing chloride. Moreover, 11 transformation products were identified, and the main transformation pathways included pyrazole ring breakage, hydroxylation, dehydrogenation, and halogenation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. SVOC exposure indoors: fresh look at dermal pathways.

    Science.gov (United States)

    Weschler, C J; Nazaroff, W W

    2012-10-01

    This paper critically examines indoor exposure to semivolatile organic compounds (SVOCs) via dermal pathways. First, it demonstrates that--in central tendency--an SVOC's abundance on indoor surfaces and in handwipes can be predicted reasonably well from gas-phase concentrations, assuming that thermodynamic equilibrium prevails. Then, equations are developed, based upon idealized mass-transport considerations, to estimate transdermal penetration of an SVOC either from its concentration in skin-surface lipids or its concentration in air. Kinetic constraints limit air-to-skin transport in the case of SVOCs that strongly sorb to skin-surface lipids. Air-to-skin transdermal uptake is estimated to be comparable to or larger than inhalation intake for many SVOCs of current or potential interest indoors, including butylated hydroxytoluene, chlordane, chlorpyrifos, diethyl phthalate, Galaxolide, geranyl acetone, nicotine (in free-base form), PCB28, PCB52, Phantolide, Texanol and Tonalide. Although air-to-skin transdermal uptake is anticipated to be slow for bisphenol A, we find that transdermal permeation may nevertheless be substantial following its transfer to skin via contact with contaminated surfaces. The paper concludes with explorations of the influence of particles and dust on dermal exposure, the role of clothing and bedding as transport vectors, and the potential significance of hair follicles as transport shunts through the epidermis. Human exposure to indoor pollutants can occur through dietary and nondietary ingestion, inhalation, and dermal absorption. Many factors influence the relative importance of these pathways, including physical and chemical properties of the pollutants. This paper argues that exposure to indoor semivolatile organic compounds (SVOCs) through the dermal pathway has often been underestimated. Transdermal permeation of SVOCs can be substantially greater than is commonly assumed. Transport of SVOCs from the air to and through the skin is

  14. Hydronium-Ion-Catalyzed Elimination Pathways of Substituted Cyclohexanols in Zeolite H-ZSM5

    Energy Technology Data Exchange (ETDEWEB)

    Hintermeier, Peter H. [Department; Eckstein, Sebastian [Department; Mei, Donghai [Institute; Olarte, Mariefel V. [Institute; Camaioni, Donald M. [Institute; Baráth, Eszter [Department; Lercher, Johannes A. [Department; Institute

    2017-10-02

    Hydronium ions in the pores of zeolite H-ZSM5 show high catalytic activity in the elimination of water from cyclohexanol in aqueous phase. Substitution induces subtle changes in rates and reaction pathways, which are concluded to be related to steric effects. Exploring the reaction pathways of 2-, 3-, and 4-methylcyclohexanol (2-McyOH, 3-McyOH, and 4-McyOH), 2- and 4-ethylcyclohexanol (2-EcyOH and 4-EcyOH), 2-n-propylcyclohexanol (2-PcyOH), and cyclohexanol (CyOH) it is shown that the E2 character increases with closer positioning of the alkyl and hydroxyl groups. Thus, 4-McyOH dehydration proceeds via an E1-type elimination, while cis-2-McyOH preferentially reacts via an E2 pathway. The entropy of activation decreased with increasing alkyl chain length (ca. 20 J mol-1 K-1 per CH2 unit) for 2-substituted alcohols, which is concluded to result from constraints influencing the configurational entropy of the transition states.

  15. Formation of N-nitrosodimethylamine (NDMA) from reaction of monochloramine: a new disinfection by-product.

    Science.gov (United States)

    Choi, Junghoon; Valentine, Richard L

    2002-02-01

    Studies have been conducted specifically to investigate the hypothesis that N-nitrosodimethylamine (NDMA) can be produced by reactions involving monochloramine. Experiments were conducted using dimethylamine (DMA) as a model precursor. NDMA was formed from the reaction between DMA and monochloramine indicating that it should be considered a potential disinfection by-product. The formation of NDMA increased with increased monochloramine concentration and showed maximum in yield when DMA was varied at fixed monochloramine concentrations. The mass spectra of the NDMA formed from DMA and 15N isotope labeled monochloramine (15NH2Cl) showed that the source of one of the nitrogen atoms in the nitroso group in NDMA was from monochloramine. Addition of 0.05 and 0.5 mM of preformed monochloramine to a secondarily treated wastewater at pH 7.2 also resulted in the formation of 3.6 and 111 ng/L of NDMA, respectively, showing that this is indeed an environmentally relevant NDMA formation pathway. The proposed NDMA formation mechanism consists of (i) the formation of 1,1-dimethylhydrazine (UDMH) intermediate from the reaction of DMA with monochloramine followed by, (ii) the oxidation of UDMH by monochloramine to NDMA, and (iii) the reversible chlorine transfer reaction between monochloramine and DMA which is parallel to (i). We conclude that reactions involving monochloramine in addition to classical nitrosation reactions are potentially important pathways for NDMA formation.

  16. The Prevailing Weather and Traffic Conditions in the Evaluation of a Future ECA in the Mediterranean Sea. A view into the Western Mediterranean

    Directory of Open Access Journals (Sweden)

    Marcella Castells i Sanabra

    2014-03-01

    Full Text Available Appendix III of MARPOL's Annex VI sets out the criteria and procedures for designating an emission control area (ECA.These criteria includes: a clear delineation of the proposed ECA; types of emissions proposed for control, land and sea areas at risk; emission quantification and impact assessment; prevailing weather conditions; data and quality on marine traffic; land based measures concurrent with the ECA adoption and the relative costs of reducing emissions from ships. This paper analyses the climate parameter together with traffic conditions: prevailing weather conditions as a parameter to be kept in mind for the adoption of a future ECA in the Mediterranean Sea. Preliminary results would show how marine emissions coming from existing traffic will impact the sea and land ecology in the Mediterranean area.

  17. Density functional theory study on water-gas-shift reaction over molybdenum disulfide

    DEFF Research Database (Denmark)

    Shi, X. R.; Wang, Shengguang; Hu, J.

    2009-01-01

    . The pathway for water-gas-shift reaction on both terminations has been carefully studied where the most favorable reaction path precedes the redox mechanism, namely the reaction takes place as follows: CO + H2O --> CO + OH + H --> CO + O + 2H --> CO2 + H-2. The most likely reaction candidates for the formate......Density functional theory calculations have been carried out to investigate the adsorption of reaction intermediates appearing during water-gas-shift reaction at the sulfur covered MoS2 (1 0 0)surfaces, Mo-termination with 37.5% S coverage and S-termination with 50% S coverage using periodic slabs...... species HCOO formation is the surface CO2 reaction with H as a side reaction of CO2 desorption on S-termination with 50% S coverage. The formed HCOO species will react further with adsorbed hydrogen yielding H2COO followed by breaking its C-O bond to form the surface CH2O and O species....

  18. Pressure Dependent Product Formation in the Photochemically Initiated Allyl + Allyl Reaction

    Directory of Open Access Journals (Sweden)

    Thomas Zeuch

    2013-11-01

    Full Text Available Photochemically driven reactions involving unsaturated radicals produce a thick global layer of organic haze on Titan, Saturn’s largest moon. The allyl radical self-reaction is an example for this type of chemistry and was examined at room temperature from an experimental and kinetic modelling perspective. The experiments were performed in a static reactor with a volume of 5 L under wall free conditions. The allyl radicals were produced from laser flash photolysis of three different precursors allyl bromide (C3H5Br, allyl chloride (C3H5Cl, and 1,5-hexadiene (CH2CH(CH22CHCH2 at 193 nm. Stable products were identified by their characteristic vibrational modes and quantified using FTIR spectroscopy. In addition to the (re- combination pathway C3H5+C3H5 → C6H10 we found at low pressures around 1 mbar the highest final product yields for allene and propene for the precursor C3H5Br. A kinetic analysis indicates that the end product formation is influenced by specific reaction kinetics of photochemically activated allyl radicals. Above 10 mbar the (re- combination pathway becomes dominant. These findings exemplify the specificities of reaction kinetics involving chemically activated species, which for certain conditions cannot be simply deduced from combustion kinetics or atmospheric chemistry on Earth.

  19. Direct vs. indirect pathway of hepatic glycogen synthesis as a function of glucose infusion rate

    International Nuclear Information System (INIS)

    Bagby, G.J.; Lang, C.H.; Johnson, J.L.; Blakesly, H.L.; Spitzer, J.J.

    1986-01-01

    This study was initiated to determine the influence of the rate of exogenous glucose administration on liver glycogen synthesis by the direct (glucose uptake and incorporation into glycogen) vs the indirect pathway (glucose degradation to 3-carbon intermediates, e.g., lactate, prior to incorporation into glycogen). Catheterized rats were fasted 2 days prior to receiving a 3 hr infusion of glucose at rates of 0 to 230 μmol/min/kg containing tracer [6- 3 H]- and [U- 14 C]-glucose. Plasma glucose (r = 0.80), insulin (r = 0.90) and lactate (r = 0.84) were correlated with glucose infusion rate. The rate of liver glycogen deposition (0.46 +/- 0.03 μmol/min/g) did not differ between a glucose infusion rate of 20 and 230 μmol/min/kg. At the lowest and highest glucose infusion rates hepatic glycogenesis accounted for 87 +/- 6 and 9 +/- 1% of the total glucose load, respectively. The percent contribution of the direct pathways to glycogen deposition ([ 3 H] specific activity in hepatic glycogen/[ 3 H] specific activity in plasma glucose) increased from 16 +/- 3 to 83 +/- 5% from lowest to highest glucose infusion rates (prevailing plasma glucose concentrations: 9 +/- 1 and 21 +/- 2 mM, respectively). The results indicate that the relative contribution of the direct and indirect pathways of glucogen synthesis are dependent upon the glucose load or plasma glucose concentration

  20. Organosulfate Formation through the Heterogeneous Reaction of Sulfur Dioxide with Unsaturated Compounds

    Science.gov (United States)

    George, C.; Passananti, M.; Kong, L.; Shang, J.; Perrier, S.; Jianmin, C.; Donaldson, D. J.

    2016-12-01

    The atmospheric formation of organosulfur derivatives through reaction with SO2 is generally mediated by oxidants such as O3, OH; recently we have proposed a direct reaction between SO2 and unsaturated compounds as another possible pathway for organosulfate formation in the troposphere. For the first time it was shown recently that a heterogeneous reaction between SO2 and oleic acid (OA; an unsaturated fatty acid) takes place and leads efficiently to the formation of organosulfur products. Here, we demonstrate that this reaction proceeds on various unsaturated compounds, and may therefore have a general environmental impact. We used different experimental strategies i.e., a coated flow tube (CFT), an aerosol flow tube (AFT) and a DRIFT (diffuse reflectance infrared Fourier transform) cell. The reaction products were analyzed by means of liquid chromatography coupled to a high resolution mass spectrometer (LC-HR-MS). We report indeed that SO2 reacts with large variety of C=C unsaturations and that even in the presence of ozone, SO2 reacts with OA leading to organosulfur products. A strong enhancement in product formation is observed under actinic illumination, increases the atmospheric significance of this chemical pathway. This is probably due to the chromophoric nature of the SO2 adduct with C=C bonds, and means that the contribution of this direct addition of SO2 could be in excess of 5%. The detection in atmospheric aerosols of organosulfur compounds with the same chemical formulae as the products identified here seems to confirm the importance of this reaction in the atmosphere.

  1. Enzymology and Evolution of the Pyruvate Pathway to 2-Oxobutyrate in Methanocaldococcus jannaschii▿

    OpenAIRE

    Drevland, Randy M.; Waheed, Abdul; Graham, David E.

    2007-01-01

    The archaeon Methanocaldococcus jannaschii uses three different 2-oxoacid elongation pathways, which extend the chain length of precursors in leucine, isoleucine, and coenzyme B biosyntheses. In each of these pathways an aconitase-type hydrolyase catalyzes an hydroxyacid isomerization reaction. The genome sequence of M. jannaschii encodes two homologs of each large and small subunit that forms the hydrolyase, but the genes are not cotranscribed. The genes are more similar to each other than t...

  2. Theoretical study of the oxidation mechanisms of naphthalene initiated by hydroxyl radicals: the OH-addition pathway.

    Science.gov (United States)

    Shiroudi, Abolfazl; Deleuze, Michael S; Canneaux, Sébastien

    2014-07-03

    The oxidation mechanisms of naphthalene by OH radicals under inert (He) conditions have been studied using density functional theory along with various exchange-correlation functionals. Comparison has been made with benchmark CBS-QB3 theoretical results. Kinetic rate constants were correspondingly estimated by means of transition state theory and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Comparison with experiment confirms that, on the OH-addition reaction pathway leading to 1-naphthol, the first bimolecular reaction step has an effective negative activation energy around -1.5 kcal mol(-1), whereas this step is characterized by an activation energy around 1 kcal mol(-1) on the OH-addition reaction pathway leading to 2-naphthol. Effective rate constants have been calculated according to a steady state analysis upon a two-step model reaction mechanism. In line with experiment, the correspondingly obtained branching ratios indicate that, at temperatures lower than 410 K, the most abundant product resulting from the oxidation of naphthalene by OH radicals must be 1-naphthol. The regioselectivity of the OH(•)-addition onto naphthalene decreases with increasing temperatures and decreasing pressures. Because of slightly positive or even negative activation energies, the RRKM calculations demonstrate that the transition state approximation breaks down at ambient pressure (1 bar) for the first bimolecular reaction steps. Overwhelmingly high pressures, larger than 10(5) bar, would be required for restoring to some extent (within ∼5% accuracy) the validity of this approximation for all the reaction channels that are involved in the OH-addition pathway. Analysis of the computed structures, bond orders, and free energy profiles demonstrate that all reaction steps involved in the oxidation of naphthalene by OH radicals satisfy Leffler-Hammond's principle. Nucleus independent chemical shift indices and natural bond orbital analysis also show that the computed

  3. Curation and Computational Design of Bioenergy-Related Metabolic Pathways

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Peter D. [SRI International, Menlo Park, CA (United States)

    2014-09-12

    . The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.

  4. Reaction of phosphorus ylides with carbonyl compounds in supercritical carbon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kyung Il; Kim, Hak Do; Shim, Jae Jin; Ra, Choon Sup [Yeungnam Univ., Gyongsan (Korea, Republic of)

    2004-02-15

    The condensation reaction of (benzylene)triphenylphosphoranes with carbonyl compounds in supercritical carbon dioxide was examined. Reactions of (benzylene)phosphoranes (ca. 1 mmol) with several benzaldehydes in a supercritical carbon dioxide (80 .deg. C, 2,000 psi) containing THF entrainer (5%) in a 24 mL reactor proceed smoothly to yield olefination products in fairly good to excellent yields but slower, compared to reactions in a conventional THF solvent. Generally, phosphoranes that are not substituted with a nitro group show more (Z)-selective reactions with aromatic aldehydes under scCO{sub 2} condition than in THF. The reaction of (benzylene)triphenylphosphosphoranes with 4-t-butylcyclohexanone gave the corresponding olefin compounds with a low conversion under both the supercritical carbon dioxide and the organic THF solvent. Our preliminary study showed the Wittig reaction carries out smoothly in supercritical carbon dioxide medium and also a possible tunability of this reaction pathway by adding a entrainer. The results would be useful for devising a novel process for the environmentally friendly Wittig reaction.

  5. SABIO-RK: A data warehouse for biochemical reactions and their kinetics

    Directory of Open Access Journals (Sweden)

    Krebs Olga

    2007-03-01

    Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

  6. Penicillin Hydrolysis: A Kinetic Study of a Multistep, Multiproduct Reaction.

    Science.gov (United States)

    McCarrick, Thomas A.; McLafferty, Fred W.

    1984-01-01

    Background, procedures used, and typical results are provided for an experiment in which students carry out the necessary measurements on the acid-catalysis of penicillin in two hours. By applying kinetic theory to the data obtained, the reaction pathways for the hydrolysis of potassium benzyl penicillin are elucidated. (JN)

  7. Engineering the spatial organization of metabolic pathways

    DEFF Research Database (Denmark)

    Albertsen, Line; Maury, Jerome; Bach, Lars Stougaard

    One of the goals of metabolic engineering is to optimize the production of valuable metabolites in cell factories. In this context, modulating the gene expression and activity of enzymes are tools that have been extensively used. Another approach that is gaining interest is the engineering...... of the spatial organization of biosynthetic pathways. Several natural systems for ensuring optimal spatial arrangement of biosynthetic enzymes exist. Sequentially acting enzymes can for example be positioned in close proximity by attachment to cellular structures, up-concentration in membrane enclosed organelles...... or assembly into large complexes. The vision is that by positioning sequentially acting enzymes in close proximity, the cell can accelerate reaction rates and thereby prevent loss of intermediates through diffusion, degradation or competing pathways. The production of valuable metabolites in cell factories...

  8. Complete active space second order perturbation theory (CASPT2) study of N({sup 2}D) + H{sub 2}O reaction paths on D{sub 1} and D{sub 0} potential energy surfaces: Direct and roaming pathways

    Energy Technology Data Exchange (ETDEWEB)

    Isegawa, Miho; Liu, Fengyi [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Kyoto 606-8103 (Japan); Maeda, Satoshi [Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan); Morokuma, Keiji, E-mail: morokuma@fukui.kyoto-u.ac.jp [Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Kyoto 606-8103 (Japan); Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)

    2014-10-21

    We report reaction paths starting from N({sup 2}D) + H{sub 2}O for doublet spin states, D{sub 0} and D{sub 1}. The potential energy surfaces are explored in an automated fashion using the global reaction route mapping strategy. The critical points and reaction paths have been fully optimized at the complete active space second order perturbation theory level taking all valence electrons in the active space. In addition to direct dissociation pathways that would be dominant, three roaming processes, two roaming dissociation, and one roaming isomerization: (1) H{sub 2}ON → H–O(H)N → H–HON → NO({sup 2}Π) + H{sub 2}, (2) cis-HNOH → HNO–H → H–HNO → NO + H{sub 2}, (3) H{sub 2}NO → H–HNO → HNO–H → trans-HNOH, are confirmed on the D{sub 0} surface.

  9. Responses of Synechocystis sp. PCC 6803 to heterologous biosynthetic pathways

    DEFF Research Database (Denmark)

    Vavitsas, Konstantinos; Rue, Emil Østergaard; Stefánsdóttir, Lára Kristín

    2017-01-01

    BACKGROUND: There are an increasing number of studies regarding genetic manipulation of cyanobacteria to produce commercially interesting compounds. The majority of these works study the expression and optimization of a selected heterologous pathway, largely ignoring the wholeness and complexity...... different compounds, the cyanogenic glucoside dhurrin and the diterpenoid 13R-manoyl oxide in Synechocystis PCC 6803. We used genome-scale metabolic modelling to study fluxes in individual reactions and pathways, and we determined the concentrations of key metabolites, such as amino acids, carotenoids...

  10. Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Domratcheva, Tatiana; Shahi, Abdul Rehaman Moughal

    2012-01-01

    of cryptochrome must arise from the photoactivation reaction occurring in the protein: exposure to blue light results in electron transfer to a flavin pigment co-factor, leading to formation of an electron spin-entangled pair of radicals. Theoretical and experimental studies established long ago that such radical...... pairs, indeed, can act as a magnetic compass. The photo-reaction pathway in cryptochrome is not fully resolved yet. We employ ab initio quantum chemistry and classical all-atom MD simulations for Arabidopsis thaliana cryptochrome to determine how the radical pair is formed, becomes stabilized through...

  11. The olefin metathesis reaction: reorganization and cyclization of organic compounds

    International Nuclear Information System (INIS)

    Frederico, Daniel; Brocksom, Ursula; Brocksom, Timothy John

    2005-01-01

    The olefin metathesis reaction allows the exchange of complex alkyl units between two olefins, with the formation of a new olefinic link and a sub-product olefin usually ethylene. This reaction has found extensive application in the last ten years with the development of the Grubbs and Schrock catalysts, in total synthesis of complex organic molecules, as opposed to the very important use in the petrochemical industry with relatively simple molecules. This review intends to trace a historical and mechanistic pathway from industry to academy, before illustrating the more recent advances. (author)

  12. Desaturation reactions catalyzed by soluble methane monooxygenase.

    Science.gov (United States)

    Jin, Y; Lipscomb, J D

    2001-09-01

    Soluble methane monooxygenase (MMO) is shown to be capable of catalyzing desaturation reactions in addition to the usual hydroxylation and epoxidation reactions. Dehydrogenated products are generated from MMO-catalyzed oxidation of certain substrates including ethylbenzene and cyclohexadienes. In the reaction of ethylbenzene, desaturation of ethyl C-H occurred along with the conventional hydroxvlations of ethyl and phenyl C-Hs. As a result, styrene is formed together with ethylphenols and phenylethanols. Similarly, when 1,3- and 1,4-cyclohexadienes were used as substrates, benzene was detected as a product in addition to the corresponding alcohols and epoxides. In all cases, reaction conditions were found to significantly affect the distribution among the different products. This new activity of MMO is postulated to be associated with the chemical properties of the substrates rather than fundamental changes in the nature of the oxygen and C-H activation chemistries. The formation of the desaturated products is rationalized by formation of a substrate cationic intermediate, possibly via a radical precursor. The cationic species is then proposed to partition between recombination (alcohol formation) and elimination (alkene production) pathways. This novel function of MMO indicates close mechanistic kinship between the hydroxylation and desaturation reactions catalyzed by the nonheme diiron clusters.

  13. lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.

    Directory of Open Access Journals (Sweden)

    Meric Ataman

    2017-07-01

    Full Text Available In the post-genomic era, Genome-scale metabolic networks (GEMs have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional roles to implement a specific biological process or structural complex, such as glycolysis and TCA cycle. Subsystem/pathway definition is also employed to delineate the biosynthetic routes that produce biomass building blocks. In databases, such as MetaCyc and SEED, these representations are composed of linear routes from precursors to target biomass building blocks. However, this approach cannot capture the nested, complex nature of GEMs. Here we implemented an algorithm, lumpGEM, which generates biosynthetic subnetworks composed of reactions that can synthesize a target metabolite from a set of defined core precursor metabolites. lumpGEM captures balanced subnetworks, which account for the fate of all metabolites along the synthesis routes, thus encapsulating reactions from various subsystems/pathways to balance these metabolites in the metabolic network. Moreover, lumpGEM collapses these subnetworks into elementally balanced lumped reactions that specify the cost of all precursor metabolites and cofactors. It also generates alternative subnetworks and lumped reactions for the same metabolite, accounting for the flexibility of organisms. lumpGEM is applicable to any GEM and any target metabolite defined in the network. Lumped reactions generated by lumpGEM can be also used to generate properly balanced reduced core metabolic models.

  14. Oxidation of Tris (2-chloroethyl) phosphate in aqueous solution by UV-activated peroxymonosulfate: Kinetics, water matrix effects, degradation products and reaction pathways.

    Science.gov (United States)

    Xu, Xinxin; Chen, Jing; Qu, Ruijuan; Wang, Zunyao

    2017-10-01

    The feasibility of UV-activated peroxymonosulfate (PMS) technology for the degradation of Tris (2-chloroethyl) phosphate (TCEP) in an aqueous solution was investigated in this study. The conditions of [PMS] 0 : [TCEP] 0  = 20:1, T = 25 ± 2 °C and pH = 5.5 ± 0.5 cause a 94.6% removal of TCEP (1 mg L -1 ) after 30 min of Hg lamp irradiation. The effects of operating parameters (the oxidant doses, pH and presence of typical cations (Fe 3+ , Cu 2+ , Ni 2+ , NH 4 + ), anions (Cl - , HCO 3 - , NO 3 - , HPO 4 2- ) and humic acid (HA)) were evaluated. It was found that an increase of the PMS dose and the presence of Fe 3+ could accelerate the reaction, while the anions and HA inhibited the reaction. Meanwhile, TCEP removal in various water matrices was compared, and the order for TCEP removal was as follows: ultrapure water > tap water > synthetic water > secondary clarifier effluent > Jiuxiang river water. Twenty-two oxidation products were identified using an electrospray time-of-flight mass spectrometer, and the degradation pathways mainly involved radicals' addition and CO bond cleavage. Furthermore, ECOSAR analysis revealed that the intermediate products during the TCEP oxidation process were generally not harmful to three typical aquatic species. Hence, UV/PMS can be used as an efficient technology to treat TCEP-containing water and wastewaters. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. A Density Functional Theory Study on the Reaction Mechanism of Terpinolene with O{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hahkjoon [Duksung Women' s University, Seoul (Korea, Republic of)

    2016-02-15

    The energies of chemical species involved in the early stage of the reaction of terpinolene with ozone were calculated to understand the oxidation mechanism of terpinolene with atmospheric O{sub 2} and NO determined experimentally. All the quantum calculations for geometry optimization and frequency calculations in this study were carried out using B3LYP with the 6-31G(d,p) basis (Gaussian 03 software package). In conclusion, quantum chemical calculations were performed to obtain the relative energies and energy barriers for the early stage of the reaction pathways of terpinolene with ozone. The branching ratio for pathways 3 and 4 determined experimentally is in qualitative agreement with the current calculations. The results of these calculations are important for assessing the relative stabilities of the intermediates in the reaction of terpinolene with ozone although detailed RRKM calculations are still needed to fully understand the branching ratios of the final products.

  16. Radiation therapy and late reactions in normal tissues

    International Nuclear Information System (INIS)

    Aoyama, Takashi; Kuroda, Yasumasa

    1998-01-01

    Recent developments in cancer therapy have made us increasingly aware that the quality of life of a patient is as valuable as other benefits received from therapy. This awareness leads to an emphasis on organ and/or function preservation in the course of therapy. In line with this new thinking, greater consideration is placed on radiation therapy as an appropriate modality of cancer therapy. Possible complications in normal tissues, especially those of late reaction type after the therapy must be overcome. This review, therefore, focuses on recent progress of studies on mechanisms of the complications of the late reaction type. An observation of a clinical case concerning a late reaction of spinal cord (radiation myelopathy) and surveys of experimental studies on the mechanisms of late reactions (including radiation pneumonitis and lung fibrosis, and radiation response of vascular endothelial cells) provide a hypothesis that apoptosis through the pathway starting with radiation-induced sphingomyelin hydrolysis may play an important role in causing a variety of late reactions. This insight is based on the fact that radiation also activates protein kinase C which appears to block apoptosis. The mechanisms of late reactions, therefore, may involve a balance between radiation-induced apoptotic death and its down regulation by suppressor mechanisms through protein kinase C. (author)

  17. The Photoconversion of Phytochrome Includes an Unproductive Shunt Reaction Pathway.

    Science.gov (United States)

    Buhrke, David; Kuhlmann, Uwe; Michael, Norbert; Hildebrandt, Peter

    2018-03-05

    Phytochromes are modular bimodal photoswitches that control gene expression for morphogenetic processes in plants. These functions are triggered by photoinduced conversions between the inactive and active states of the photosensory module, denoted as Pr and Pfr, respectively. In the present time-resolved resonance Raman spectroscopic study of bacterial representatives of this photoreceptor family, we demonstrate that these phototransformations do not represent linear processes but include a branching reaction back to the initial state, prior to (de)activation of the output module. Thus, only a fraction of the photoreceptors undergoing the phototransformations can initiate the downstream signaling process, consistent with phytochrome's function as a sensor for more durable changes of light conditions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Direct single-molecule dynamic detection of chemical reactions.

    Science.gov (United States)

    Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng

    2018-02-01

    Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

  19. Macrocyclic bis-thioureas catalyze stereospecific glycosylation reactions.

    Science.gov (United States)

    Park, Yongho; Harper, Kaid C; Kuhl, Nadine; Kwan, Eugene E; Liu, Richard Y; Jacobsen, Eric N

    2017-01-13

    Carbohydrates are involved in nearly all aspects of biochemistry, but their complex chemical structures present long-standing practical challenges to their synthesis. In particular, stereochemical outcomes in glycosylation reactions are highly dependent on the steric and electronic properties of coupling partners; thus, carbohydrate synthesis is not easily predictable. Here we report the discovery of a macrocyclic bis-thiourea derivative that catalyzes stereospecific invertive substitution pathways of glycosyl chlorides. The utility of the catalyst is demonstrated in the synthesis of trans-1,2-, cis-1,2-, and 2-deoxy-β-glycosides. Mechanistic studies are consistent with a cooperative mechanism in which an electrophile and a nucleophile are simultaneously activated to effect a stereospecific substitution reaction. Copyright © 2017, American Association for the Advancement of Science.

  20. Age and size at maturity: a quantitative review of diet-induced reaction norms in insects.

    Science.gov (United States)

    Teder, Tiit; Vellau, Helen; Tammaru, Toomas

    2014-11-01

    Optimality models predict that diet-induced bivariate reaction norms for age and size at maturity can have diverse shapes, with the slope varying from negative to positive. To evaluate these predictions, we perform a quantitative review of relevant data, using a literature-derived database of body sizes and development times for over 200 insect species. We show that bivariate reaction norms with a negative slope prevail in nearly all taxonomic and ecological categories of insects as well as in some other ectotherm taxa with comparable life histories (arachnids and amphibians). In insects, positive slopes are largely limited to species, which feed on discrete resource items, parasitoids in particular. By contrast, with virtually no meaningful exceptions, herbivorous and predatory insects display reaction norms with a negative slope. This is consistent with the idea that predictable resource depletion, a scenario selecting for positively sloped reaction norms, is not frequent for these insects. Another source of such selection-a positive correlation between resource levels and juvenile mortality rates-should similarly be rare among insects. Positive slopes can also be predicted by models which integrate life-history evolution and population dynamics. As bottom-up regulation is not common in most insect groups, such models may not be most appropriate for insects. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  1. Propan-1-ol Oxidation Reaction on Au/TiO2 Catalysts

    African Journals Online (AJOL)

    MBI

    2014-11-27

    Nov 27, 2014 ... a decomposition pathway, producing CO2 and H2O. However, the presence of gold ... complete oxidation reaction of propan-1-ol on the catalysts. Keywords: Gold Catalysis ... flowed at a rate of 30 mL min-1. Propan- o-l was.

  2. Chemical equilibrium and reaction modeling of arsenic and selenium in soils

    Science.gov (United States)

    The chemical processes and soil factors that affect the concentrations of As and Se in soil solution were discussed. Both elements occur in two redox states differing in toxicity and reactivity. Methylation and volatilization reactions occur in soils and can act as detoxification pathways. Precip...

  3. CO{sub 2} as an Oxidant for High-Temperature Reactions

    Energy Technology Data Exchange (ETDEWEB)

    Kawi, Sibudjing, E-mail: chekawis@nus.edu.sg; Kathiraser, Yasotha [Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore (Singapore)

    2015-03-18

    This paper presents a review on the developments in catalyst technology for the reactions utilizing CO{sub 2} for high-temperature applications. These include dehydrogenation of alkanes to olefins, the dehydrogenation of ethylbenzene to styrene, and finally CO{sub 2} reforming of hydrocarbon feedstock (i.e., methane) and alcohols. Aspects on the various reaction pathways are also highlighted. The literature on the role of promoters and catalyst development is critically evaluated. Most of the reactions discussed in this review are exploited in industries and related to on-going processes, thus providing extensive data from literature. However, some reactions, such as CO{sub 2} reforming of ethanol and glycerol, which have not reached industrial scale, are also reviewed owing to their great potential in terms of sustainability, which is essential as energy for the future. This review further illustrates the building-up of knowledge that shows the role of support and catalysts for each reaction and the underlying linkage between certain catalysts, which can be adapted for the multiple CO{sub 2}-related reactions.

  4. Kinetics of ion/molecule reactions in Xe++acteone system

    International Nuclear Information System (INIS)

    Vinogradov, P.S.; Misharin, A.S.

    2002-01-01

    A reaction of Xe+ ion with acetone and subsequent transformations of the product ions at a buffer gas pressure (He) of 1.1 Torr were studied by the flow reactor technique mass spectrometry. A kinetic scheme describing the evolution of the ionic composition has been determined. The rate constants of the key reactions involved in the scheme have been evaluated. A channel of the production of acetone cation in A state in a charge transfer reaction was observed. A production of slowly reacting isomer of the acetone cation in secondary reactions was detected. Its product in the reaction with acetone is the 'nonprotonated dimer'. The kinetics of the production of ternary ions - ( CH 3 CO + CH 3 COCH 3 )(m/e=101), CH 3 COCH 3 H + (m/e=59) as well as the production of ions of the fourth generation ( CH 3 CO + (CH 3 COCH 3 ) 2 ) (m/e=159) and (CH 3 COCH 3 ) 2 H + was observed. CH 3 CO + ion (m/e=43) was found as the main reaction product. The main pathways scheme of ionic transformations is shown. (nevyjel)

  5. Pathways to diagnosis: a qualitative study of the experiences and emotional reactions of parents of children diagnosed with type 1 diabetes.

    Science.gov (United States)

    Rankin, David; Harden, Jeni; Waugh, Norman; Noyes, Kathryn; Barnard, Katharine D; Stephen, John; Robertson, Kenneth J; Bath, Louise; Robertson, Linda; Lawton, Julia

    2014-12-01

    The aim of this study was to explore from parents' perspectives the circumstances and events which led to their child being diagnosed with type 1 diabetes (T1D). The objective was to understand reasons for delays in seeking treatment and parents' emotional reactions to diagnosis so others can be better informed and supported in future. In-depth interviews with 54 parents of children (aged ≤12 yr) with T1D were conducted. Data analysis used an inductive, thematic approach. Parents described a 'prompt' and a 'delayed' pathway to their child being diagnosed. Parents who considered the diagnosis to be 'prompt' reported how they, or other people, had recognized their child had developed symptoms of T1D which resulted in a rapid presentation to health care professionals. In contrast, parents who perceived their child's diagnosis to be 'delayed' did not recognize signs of T1D and attributed their child's deteriorating health to other conditions, being out of routines and/or their stage of development. These parents often only sought medical help when symptoms became extreme. All parents were distressed by their child's diagnosis; however, parents in the 'delayed' pathway expressed unresolved feelings of guilt, particularly when their child was diagnosed with diabetic ketoacidosis. Parents' and other people's knowledge about T1D can affect the duration between onset of their child's symptoms and diagnosis. Campaigns to raise awareness should ensure that parents are made aware of symptoms and that T1D can develop during childhood. Health care professionals could discuss with parents the events preceding their child's diagnosis to better determine their emotional support needs. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  6. Pathways for the OH + Br2 → HOBr + Br and HOBr + Br → HBr + BrO Reactions.

    Science.gov (United States)

    Wang, Hongyan; Qiu, Yudong; Schaefer, Henry F

    2016-02-11

    The OH radical reaction with Br2 and the subsequent reaction HOBr + Br are of exceptional importance to atmospheric chemistry and environmental chemistry. The entrance complex, transition state, and exit complex for both reactions have been determined using the coupled-cluster method with single, double, and perturbative triple excitations CCSD(T) with correlation consistent basis sets up to size cc-pV5Z and cc-pV5Z-PP. Coupled cluster effects with full triples (CCSDT) and full quadruples (CCSDTQ) are explicitly investigated. Scalar relativistic effects, spin-orbit coupling, and zero-point vibrational energy corrections are evaluated. The results from the all-electron basis sets are compared with those from the effective core potential (ECP) pseudopotential (PP) basis sets. The results are consistent. The OH + Br2 reaction is predicted to be exothermic 4.1 ± 0.5 kcal/mol, compared to experiment, 3.9 ± 0.2 kcal/mol. The entrance complex HO···BrBr is bound by 2.2 ± 0.2 kcal/mol. The transition state lies similarly well below the reactants OH + Br2. The exit complex HOBr···Br is bound by 2.7 ± 0.6 kcal/mol relative to separated HOBr + Br. The endothermicity of the reaction HOBr + Br → HBr + BrO is 9.6 ± 0.7 kcal/mol, compared with experiment 8.7 ± 0.3 kcal/mol. For the more important reverse (exothermic) HBr + BrO reaction, the entrance complex BrO···HBr is bound by 1.8 ± 0.6 kcal/mol. The barrier for the HBr + BrO reaction is 6.8 ± 0.9 kcal/mol. The exit complex (Br···HOBr) for the HBr + BrO reaction is bound by 1.9 ± 0.2 kcal/mol with respect to the products HOBr + Br.

  7. Evaluation of operational numerical weather predictions in relation to the prevailing synoptic conditions

    Science.gov (United States)

    Pytharoulis, Ioannis; Tegoulias, Ioannis; Karacostas, Theodore; Kotsopoulos, Stylianos; Kartsios, Stergios; Bampzelis, Dimitrios

    2015-04-01

    The Thessaly plain, which is located in central Greece, has a vital role in the financial life of the country, because of its significant agricultural production. The aim of DAPHNE project (http://www.daphne-meteo.gr) is to tackle the problem of drought in this area by means of Weather Modification in convective clouds. This problem is reinforced by the increase of population and the water demand for irrigation, especially during the warm period of the year. The nonhydrostatic Weather Research and Forecasting model (WRF), is utilized for research and operational purposes of DAPHNE project. The WRF output fields are employed by the partners in order to provide high-resolution meteorological guidance and plan the project's operations. The model domains cover: i) Europe, the Mediterranean sea and northern Africa, ii) Greece and iii) the wider region of Thessaly (at selected periods), at horizontal grid-spacings of 15km, 5km and 1km, respectively, using 2-way telescoping nesting. The aim of this research work is to investigate the model performance in relation to the prevailing upper-air synoptic circulation. The statistical evaluation of the high-resolution operational forecasts of near-surface and upper air fields is performed at a selected period of the operational phase of the project using surface observations, gridded fields and weather radar data. The verification is based on gridded, point and object oriented techniques. The 10 upper-air circulation types, which describe the prevailing conditions over Greece, are employed in the synoptic classification. This methodology allows the identification of model errors that occur and/or are maximized at specific synoptic conditions and may otherwise be obscured in aggregate statistics. Preliminary analysis indicates that the largest errors are associated with cyclonic conditions. Acknowledgments This research work of Daphne project (11SYN_8_1088) is co-funded by the European Union (European Regional Development Fund

  8. Understanding organometallic reaction mechanisms and catalysis experimental and computational tools computational and experimental tools

    CERN Document Server

    Ananikov, Valentin P

    2014-01-01

    Exploring and highlighting the new horizons in the studies of reaction mechanisms that open joint application of experimental studies and theoretical calculations is the goal of this book. The latest insights and developments in the mechanistic studies of organometallic reactions and catalytic processes are presented and reviewed. The book adopts a unique approach, exemplifying how to use experiments, spectroscopy measurements, and computational methods to reveal reaction pathways and molecular structures of catalysts, rather than concentrating solely on one discipline. The result is a deeper

  9. The nucleus accumbens 5-HTR₄-CART pathway ties anorexia to hyperactivity.

    Science.gov (United States)

    Jean, A; Laurent, L; Bockaert, J; Charnay, Y; Dusticier, N; Nieoullon, A; Barrot, M; Neve, R; Compan, V

    2012-12-11

    In mental diseases, the brain does not systematically adjust motor activity to feeding. Probably, the most outlined example is the association between hyperactivity and anorexia in Anorexia nervosa. The neural underpinnings of this 'paradox', however, are poorly elucidated. Although anorexia and hyperactivity prevail over self-preservation, both symptoms rarely exist independently, suggesting commonalities in neural pathways, most likely in the reward system. We previously discovered an addictive molecular facet of anorexia, involving production, in the nucleus accumbens (NAc), of the same transcripts stimulated in response to cocaine and amphetamine (CART) upon stimulation of the 5-HT(4) receptors (5-HTR(4)) or MDMA (ecstasy). Here, we tested whether this pathway predisposes not only to anorexia but also to hyperactivity. Following food restriction, mice are expected to overeat. However, selecting hyperactive and addiction-related animal models, we observed that mice lacking 5-HTR(1B) self-imposed food restriction after deprivation and still displayed anorexia and hyperactivity after ecstasy. Decryption of the mechanisms showed a gain-of-function of 5-HTR(4) in the absence of 5-HTR(1B), associated with CART surplus in the NAc and not in other brain areas. NAc-5-HTR(4) overexpression upregulated NAc-CART, provoked anorexia and hyperactivity. NAc-5-HTR(4) knockdown or blockade reduced ecstasy-induced hyperactivity. Finally, NAc-CART knockdown suppressed hyperactivity upon stimulation of the NAc-5-HTR(4). Additionally, inactivating NAc-5-HTR(4) suppressed ecstasy's preference, strengthening the rewarding facet of anorexia. In conclusion, the NAc-5-HTR(4)/CART pathway establishes a 'tight-junction' between anorexia and hyperactivity, suggesting the existence of a primary functional unit susceptible to limit overeating associated with resting following homeostasis rules.

  10. Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

    International Nuclear Information System (INIS)

    Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan, Richard; Hazen, Terry C.; Keasling, Jay D.

    2007-01-01

    Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both GC-MS and Fourier Transform-Ion Cyclotron Resonance mass spectrometry (FT-ICR MS) indicate the lack of oxidatively functional TCA cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80 percent of the lactate was converted to acetate and the reactions involved are the primary route of energy production (NAD(P)H and ATP production). Independent of the TCA cycle, direct cleavage of acetyl-CoA to CO and 5,10-methyl-THF also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports (the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase). These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris, and also demonstrate FT-ICR MS as a powerful tool for isotopomer analysis, overcoming problems in both GC-MS and NMR spectroscopy

  11. Hydronium-Induced Switching between CO2 Electroreduction Pathways.

    Science.gov (United States)

    Seifitokaldani, Ali; Gabardo, Christine M; Burdyny, Thomas; Dinh, Cao-Thang; Edwards, Jonathan P; Kibria, Md Golam; Bushuyev, Oleksandr S; Kelley, Shana O; Sinton, David; Sargent, Edward H

    2018-03-21

    Over a broad range of operating conditions, many CO 2 electroreduction catalysts can maintain selectivity toward certain reduction products, leading to materials and surfaces being categorized according to their products; here we ask, is product selectivity truly a property of the catalyst? Silver is among the best electrocatalysts for CO in aqueous electrolytes, where it reaches near-unity selectivity. We consider the hydrogenations of the oxygen and carbon atoms via the two proton-coupled-electron-transfer processes as chief determinants of product selectivity; and find using density functional theory (DFT) that the hydronium (H 3 O + ) intermediate plays a key role in the first oxygen hydrogenation step and lowers the activation energy barrier for CO formation. When this hydronium influence is removed, the activation energy barrier for oxygen hydrogenation increases significantly, and the barrier for carbon hydrogenation is reduced. These effects make the formate reaction pathway more favorable than CO. Experimentally, we then carry out CO 2 reduction in highly concentrated potassium hydroxide (KOH), limiting the hydronium concentration in the aqueous electrolyte. The product selectivity of a silver catalyst switches from entirely CO under neutral conditions to over 50% formate in the alkaline environment. The simulated and experimentally observed selectivity shift provides new insights into the role of hydronium on CO 2 electroreduction processes and the ability for electrolyte manipulation to directly influence transition state (TS) kinetics, altering favored CO 2 reaction pathways. We argue that selectivity should be considered less of an intrinsic catalyst property, and rather a combined product of the catalyst and reaction environment.

  12. Base-catalyzed tandem Michael/dehydro-Diels-Alder reaction of α,α-dicyanoolefins with electron-deficient 1,3-conjugated enynes: a facile entry to angularly fused polycycles.

    Science.gov (United States)

    Zhang, Mingrui; Zhang, Junliang

    2014-01-07

    Angularly fused carbocyclic frameworks and their heteroatom-substituted analogues exist in many natural products that display a broad and interesting range of biological activities. Preparation of polycyclic products by cycloaddition reactions have been the long-standing hot topic in the synthetic community. Dehydro-Diels-Alder (DDA) reactions are one class of dehydropericyclic reactions that are derived conceptually by systematic removal of hydrogen atom pairs. A base-promoted tandem Michael addition and DDA reaction of α,α-dicyanoolefins with electron-deficient 1,3-conjugated enynes was realized in which a DDA reaction takes place between the arylalkynes and electron-deficient tetrasubstituted olefin. The control experiments support the stepwise anionic reaction pathway rather than the concerted reaction pathway. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Population Causes and Consequences of Leading Chronic Diseases: A Comparative Analysis of Prevailing Explanations

    Science.gov (United States)

    Stuckler, David

    2008-01-01

    Context The mortality numbers and rates of chronic disease are rising faster in developing than in developed countries. This article compares prevailing explanations of population chronic disease trends with theoretical and empirical models of population chronic disease epidemiology and assesses some economic consequences of the growth of chronic diseases in developing countries based on the experiences of developed countries. Methods Four decades of male mortality rates of cardiovascular and chronic noncommunicable diseases were regressed on changes in and levels of country income per capita, market integration, foreign direct investment, urbanization rates, and population aging in fifty-six countries for which comparative data were available. Neoclassical economic growth models were used to estimate the effect of the mortality rates of chronic noncommunicable diseases on economic growth in high-income OECD countries. Findings Processes of economic growth, market integration, foreign direct investment, and urbanization were significant determinants of long-term changes in mortality rates of heart disease and chronic noncommunicable disease, and the observed relationships with these social and economic factors were roughly three times stronger than the relationships with the population's aging. In low-income countries, higher levels of country income per capita, population urbanization, foreign direct investment, and market integration were associated with greater mortality rates of heart disease and chronic noncommunicable disease, less increased or sometimes reduced rates in middle-income countries, and decreased rates in high-income countries. Each 10 percent increase in the working-age mortality rates of chronic noncommunicable disease decreased economic growth rates by close to a half percent. Conclusions Macrosocial and macroeconomic forces are major determinants of population rises in chronic disease mortality, and some prevailing demographic explanations

  14. Birnessite catalysis of the Maillard Reaction: Its significance in natural humification

    Science.gov (United States)

    Jokic, A.; Frenkel, A. I.; Vairavamurthy, M. A.; Huang, P. M.

    Although mineral colloids are known to play a significant role in transforming organic matter in soils and sediments, there still are many gaps in our understanding of the mechanisms of organic-mineral interactions. In this study, we investigated the role of a major oxide-mineral birnessite (a form of Mn(IV) oxide) in catalyzing the condensation reaction between sugars and amino acids, the Maillard reaction, for forming humic substances. The Maillard reaction is perceived to be a major pathway in natural humification. Using a suite of spectroscopic methods (including ESR, XANES, EXAFS and 13C NMR), our results show that Mn(IV) oxide markedly accelerates the Maillard reaction between glucose and glycine at ranges of temperatures and pH typical of natural environments. These results demonstrate the importance of manganese oxide catalysis in the Maillard reaction, and its significance in the natural abiotic formation of humic substances.

  15. Deciphering the Astrocyte Reaction in Alzheimer’s Disease

    Directory of Open Access Journals (Sweden)

    Beatriz G. Perez-Nievas

    2018-04-01

    Full Text Available Reactive astrocytes were identified as a component of senile amyloid plaques in the cortex of Alzheimer’s disease (AD patients several decades ago. However, their role in AD pathophysiology has remained elusive ever since, in part owing to the extrapolation of the literature from primary astrocyte cultures and acute brain injury models to a chronic neurodegenerative scenario. Recent accumulating evidence supports the idea that reactive astrocytes in AD acquire neurotoxic properties, likely due to both a gain of toxic function and a loss of their neurotrophic effects. However, the diversity and complexity of this glial cell is only beginning to be unveiled, anticipating that astrocyte reaction might be heterogeneous as well. Herein we review the evidence from mouse models of AD and human neuropathological studies and attempt to decipher the main conundrums that astrocytes pose to our understanding of AD development and progression. We discuss the morphological features that characterize astrocyte reaction in the AD brain, the consequences of astrocyte reaction for both astrocyte biology and AD pathological hallmarks, and the molecular pathways that have been implicated in this reaction.

  16. Assessing and Modulating Kynurenine Pathway Dynamics in Huntington's Disease: Focus on Kynurenine 3-Monooxygenase.

    Science.gov (United States)

    Sathyasaikumar, Korrapati V; Breda, Carlo; Schwarcz, Robert; Giorgini, Flaviano

    2018-01-01

    The link between disturbances in kynurenine pathway (KP) metabolism and Huntington's disease (HD) pathogenesis has been explored for a number of years. Several novel genetic and pharmacological tools have recently been developed to modulate key regulatory steps in the KP such as the reaction catalyzed by the enzyme kynurenine 3-monooxygenase (KMO). This insight has offered new options for exploring the mechanistic link between this metabolic pathway and HD, and provided novel opportunities for the development of candidate drug-like compounds. Here, we present an overview of the field, focusing on some novel approaches for interrogating the pathway experimentally.

  17. Hedgehog pathway as a potential treatment target in human cholangiocarcinoma.

    Science.gov (United States)

    Riedlinger, Dorothee; Bahra, Marcus; Boas-Knoop, Sabine; Lippert, Steffen; Bradtmöller, Maren; Guse, Katrin; Seehofer, Daniel; Bova, Roberta; Sauer, Igor M; Neuhaus, Peter; Koch, Arend; Kamphues, Carsten

    2014-08-01

    Innovative treatment concepts targeting essential signaling pathways may offer new chances for patients suffering from cholangiocarcinoma (CCC). For that, we performed a systematic molecular genetic analysis concerning the Hedgehog activity in human CCC samples and analyzed the effect of Hh inhibition on CCC cells in vitro and in vivo. Activation of the Hh pathway was analyzed in 50 human CCC samples using quantitative polymerase chain reaction (qPCR). The efficacy of Hh inhibition using cyclopamine and BMS-833923 was evaluated in vitro. In addition, the effect of BMS-833923, alone or in combination with gemcitabine, was analyzed in vivo in a murine subcutaneous xenograft model. Expression analysis revealed a significant activation of the Hh-signaling pathway in nearly 50% of CCCs. Hh inhibition resulted in a significant decrease in cell proliferation of CCC cells. Moreover, a distinct inhibition of tumor growth could be seen as a result of a combined therapy with BMS-833923 and gemcitabine in CCC xenografts. The results of our study suggest that the Hh pathway plays a relevant role at least in a subset of human CCC. Inhibition of this pathway may represent a possible treatment option for CCC patients in which the Hh pathway is activated. © 2014 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

  18. The formation of urea in space. I. Ion-molecule, neutral-neutral, and radical gas-phase reactions

    Science.gov (United States)

    Brigiano, Flavio Siro; Jeanvoine, Yannick; Largo, Antonio; Spezia, Riccardo

    2018-02-01

    Context. Many organic molecules have been observed in the interstellar medium thanks to advances in radioastronomy, and very recently the presence of urea was also suggested. While those molecules were observed, it is not clear what the mechanisms responsible to their formation are. In fact, if gas-phase reactions are responsible, they should occur through barrierless mechanisms (or with very low barriers). In the past, mechanisms for the formation of different organic molecules were studied, providing only in a few cases energetic conditions favorable to a synthesis at very low temperature. A particularly intriguing class of such molecules are those containing one N-C-O peptide bond, which could be a building block for the formation of biological molecules. Urea is a particular case because two nitrogen atoms are linked to the C-O moiety. Thus, motivated also by the recent tentative observation of urea, we have considered the synthetic pathways responsible to its formation. Aims: We have studied the possibility of forming urea in the gas phase via different kinds of bi-molecular reactions: ion-molecule, neutral, and radical. In particular we have focused on the activation energy of these reactions in order to find possible reactants that could be responsible for to barrierless (or very low energy) pathways. Methods: We have used very accurate, highly correlated quantum chemistry calculations to locate and characterize the reaction pathways in terms of minima and transition states connecting reactants to products. Results: Most of the reactions considered have an activation energy that is too high; but the ion-molecule reaction between NH2OHNH2OH2+ and formamide is not too high. These reactants could be responsible not only for the formation of urea but also of isocyanic acid, which is an organic molecule also observed in the interstellar medium.

  19. On the chemistry of ethanol on basic oxides: revising mechanisms and intermediates in the Lebedev and Guerbet reactions.

    Science.gov (United States)

    Chieregato, Alessandro; Velasquez Ochoa, Juliana; Bandinelli, Claudia; Fornasari, Giuseppe; Cavani, Fabrizio; Mella, Massimo

    2015-01-01

    A common way to convert ethanol into chemicals is by upgrading it over oxide catalysts with basic features; this method makes it possible to obtain important chemicals such as 1-butanol (Guerbet reaction) and 1,3-butadiene (Lebedev reaction). Despite their long history in chemistry, the details of the close inter-relationship of these reactions have yet to be discussed properly. Our present study focuses on reactivity tests, in situ diffuse reflectance infrared Fourier transform spectroscopy, MS analysis, and theoretical modeling. We used MgO as a reference catalyst with pure basic features to explore ethanol conversion from its very early stages. Based on the obtained results, we formulate a new mechanistic theory able to explain not only our results but also most of the scientific literature on Lebedev and Guerbet chemistry. This provides a rational description of the intermediates shared by the two reaction pathways as well as an innovative perspective on the catalyst requirements to direct the reaction pathway toward 1-butanol or butadiene. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Reaction trajectory revealed by a joint analysis of protein data bank.

    Science.gov (United States)

    Ren, Zhong

    2013-01-01

    Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article), and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.

  1. Reaction trajectory revealed by a joint analysis of protein data bank.

    Directory of Open Access Journals (Sweden)

    Zhong Ren

    Full Text Available Structural motions along a reaction pathway hold the secret about how a biological macromolecule functions. If each static structure were considered as a snapshot of the protein molecule in action, a large collection of structures would constitute a multidimensional conformational space of an enormous size. Here I present a joint analysis of hundreds of known structures of human hemoglobin in the Protein Data Bank. By applying singular value decomposition to distance matrices of these structures, I demonstrate that this large collection of structural snapshots, derived under a wide range of experimental conditions, arrange orderly along a reaction pathway. The structural motions along this extensive trajectory, including several helical transformations, arrive at a reverse engineered mechanism of the cooperative machinery (Ren, companion article, and shed light on pathological properties of the abnormal homotetrameric hemoglobins from α-thalassemia. This method of meta-analysis provides a general approach to structural dynamics based on static protein structures in this post genomics era.

  2. Construction and completion of flux balance models from pathway databases.

    Science.gov (United States)

    Latendresse, Mario; Krummenacker, Markus; Trupp, Miles; Karp, Peter D

    2012-02-01

    Flux balance analysis (FBA) is a well-known technique for genome-scale modeling of metabolic flux. Typically, an FBA formulation requires the accurate specification of four sets: biochemical reactions, biomass metabolites, nutrients and secreted metabolites. The development of FBA models can be time consuming and tedious because of the difficulty in assembling completely accurate descriptions of these sets, and in identifying errors in the composition of these sets. For example, the presence of a single non-producible metabolite in the biomass will make the entire model infeasible. Other difficulties in FBA modeling are that model distributions, and predicted fluxes, can be cryptic and difficult to understand. We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escherichia coli and Homo sapiens. Pathway Tools with MetaFlux is freely available to academic users, and for a fee to commercial users. Download from: biocyc.org/download.shtml. mario.latendresse@sri.com Supplementary data are available at Bioinformatics online.

  3. Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

    International Nuclear Information System (INIS)

    FitzPatrick, Benjamin L.; Lau, K.-C.; Butler, Laurie J.; Lee, S.-H.; Lin, Jim Jr-Min

    2008-01-01

    These experiments study the preparation of and product channels resulting from OCH 2 CHCH 2 , a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH 2 CHCH 2 radicals; these undergo a facile ring opening to the OCH 2 CHCH 2 radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH 2 CHCH 2 radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C 3 H 4 O (acrolein)+H, C 2 H 4 +HCO (formyl radical), and H 2 CO (formaldehyde)+C 2 H 3 . A small signal from C 2 H 2 O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C 2 H 5 +CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to

  4. Investigation of the O+allyl addition/elimination reaction pathways from the OCH2CHCH2 radical intermediate

    Science.gov (United States)

    Fitzpatrick, Benjamin L.; Lau, Kai-Chung; Butler, Laurie J.; Lee, Shih-Huang; Lin, Jim-Min, Jr.

    2008-08-01

    These experiments study the preparation of and product channels resulting from OCH2CHCH2, a key radical intermediate in the O+allyl bimolecular reaction. The data include velocity map imaging and molecular beam scattering results to probe the photolytic generation of the radical intermediate and the subsequent pathways by which the radicals access the energetically allowed product channels of the bimolecular reaction. The photodissociation of epichlorohydrin at 193.3 nm produces chlorine atoms and c-OCH2CHCH2 radicals; these undergo a facile ring opening to the OCH2CHCH2 radical intermediate. State-selective resonance-enhanced multiphoton ionization (REMPI) detection resolves the velocity distributions of ground and spin-orbit excited state chlorine independently, allowing for a more accurate determination of the internal energy distribution of the nascent radicals. We obtain good agreement detecting the velocity distributions of the Cl atoms with REMPI, vacuum ultraviolet (VUV) photoionization at 13.8 eV, and electron bombardment ionization; all show a bimodal distribution of recoil kinetic energies. The dominant high recoil kinetic energy feature peaks near 33 kcal/mol. To elucidate the product channels resulting from the OCH2CHCH2 radical intermediate, the crossed laser-molecular beam experiment uses VUV photoionization and detects the velocity distribution of the possible products. The data identify the three dominant product channels as C3H4O (acrolein)+H, C2H4+HCO (formyl radical), and H2CO (formaldehyde)+C2H3. A small signal from C2H2O (ketene) product is also detected. The measured velocity distributions and relative signal intensities at m/e=27, 28, and 29 at two photoionization energies show that the most exothermic product channel, C2H5+CO, does not contribute significantly to the product branching. The higher internal energy onset of the acrolein+H product channel is consistent with the relative barriers en route to each of these product channels

  5. A mechanochemical study of the effects of compression on a Diels-Alder reaction

    Science.gov (United States)

    Jha, Sanjiv K.; Brown, Katie; Todde, Guido; Subramanian, Gopinath

    2016-08-01

    We examine the effects of compressive external forces on the mechanisms of the parent Diels-Alder (DA) reaction between butadiene and ethylene. Reaction pathways and transition states were calculated using the nudged elastic band method within a mechanochemical framework at the CASSCF(6,6)/6-31G**, as well as the B3LYP/6-311++G** levels of theory. Our results suggest that compressive hydrostatic pressure lowers the energy barrier for the parent DA reaction while suppressing the undesirable side reaction, thereby leading to a direct increase in the yield of cyclohexene. Compressive pressure also increases the exothermicity of the parent DA reaction, which would lead to increased temperatures in a reaction vessel and thereby indirectly increase the yield of cyclohexene. Our estimates indicate that the compression used in our study corresponds to a range of 68 MPa-1410 MPa.

  6. FindPath: a Matlab solution for in silico design of synthetic metabolic pathways.

    Science.gov (United States)

    Vieira, Gilles; Carnicer, Marc; Portais, Jean-Charles; Heux, Stéphanie

    2014-10-15

    Several methods and computational tools have been developed to design novel metabolic pathways. A major challenge is evaluating the metabolic efficiency of the designed pathways in the host organism. Here we present FindPath, a unified system to predict and rank possible pathways according to their metabolic efficiency in the cellular system. This tool uses a chemical reaction database to generate possible metabolic pathways and exploits constraint-based models (CBMs) to identify the most efficient synthetic pathway to achieve the desired metabolic function in a given host microorganism. FindPath can be used with common tools for CBM manipulation and uses the standard SBML format for both input and output files. http://metasys.insa-toulouse.fr/software/findpath/. heux@insa-toulouse.fr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Bonding pathways of high-pressure chemical transformations

    International Nuclear Information System (INIS)

    Hu Anguang; Zhang Fan

    2013-01-01

    A three-stage bonding pathway towards high-pressure chemical transformations from molecular precursors or intermediate states has been identified by first-principles simulations. With the evolution of principal stress tensor components in the response of chemical bonding to compressive loading, the three stages can be defined as the van der Waals bonding destruction, a bond breaking and forming reaction, and equilibrium of new bonds. The three-stage bonding pathway leads to the establishment of a fundamental principle of chemical bonding under compression. It reveals that during high-pressure chemical transformation, electrons moving away from functional groups follow anti-addition, collision-free paths to form new bonds in counteracting the local stress confinement. In applying this principle, a large number of molecular precursors were identified for high-pressure chemical transformations, resulting in new materials. (fast track communication)

  8. Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry

    Directory of Open Access Journals (Sweden)

    Tariq eSiddique

    2014-03-01

    Full Text Available Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management of oil sands tailings ponds in northern Alberta, Canada. We have observed that microorganisms indigenous to the tailings ponds accelerate consolidation of mature fine tailings (MFT during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry to indirectly increase consolidation of MFT. Here, we describe Pathway II comprising significant, direct and complementary biogeochemical reactions with MFT mineral surfaces. An anaerobic microbial community comprising Bacteria (predominantly Clostridiales, Synergistaceae and Desulfobulbaceae and Archaea (Methanolinea/Methanoregula and Methanosaeta transformed FeIII minerals in MFT to amorphous FeII minerals during methanogenic metabolism of an added organic substrate. Synchrotron analyses suggested that ferrihydrite (5Fe2O3. 9H2O and goethite (α-FeOOH were the dominant FeIII minerals in MFT. The formation of amorphous iron sulfide (FeS and possibly green rust entrapped and masked electronegative clay surfaces in amended MFT. Both Pathways I and II reduced the surface charge potential (repulsive forces of the clay particles in MFT, which aided aggregation of clays and formation of networks of pores, as visualized using cryo-scanning electron microscopy. These reactions facilitated the egress of porewater from MFT and increased consolidation of tailings solids. These results have large-scale implications for management and reclamation of oil sands tailings ponds, a burgeoning environmental issue for the public and government regulators.

  9. Microbially-accelerated consolidation of oil sands tailings. Pathway II: solid phase biogeochemistry.

    Science.gov (United States)

    Siddique, Tariq; Kuznetsov, Petr; Kuznetsova, Alsu; Li, Carmen; Young, Rozlyn; Arocena, Joselito M; Foght, Julia M

    2014-01-01

    Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management of oil sands tailings ponds in northern Alberta, Canada. We have observed that microorganisms indigenous to the tailings ponds accelerate consolidation of mature fine tailings (MFT) during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry to indirectly increase consolidation of MFT. Here, we describe Pathway II comprising significant, direct and complementary biogeochemical reactions with MFT mineral surfaces. An anaerobic microbial community comprising Bacteria (predominantly Clostridiales, Synergistaceae, and Desulfobulbaceae) and Archaea (Methanolinea/Methanoregula and Methanosaeta) transformed Fe(III) minerals in MFT to amorphous Fe(II) minerals during methanogenic metabolism of an added organic substrate. Synchrotron analyses suggested that ferrihydrite (5Fe2O3. 9H2O) and goethite (α-FeOOH) were the dominant Fe(III) minerals in MFT. The formation of amorphous iron sulfide (FeS) and possibly green rust entrapped and masked electronegative clay surfaces in amended MFT. Both Pathways I and II reduced the surface charge potential (repulsive forces) of the clay particles in MFT, which aided aggregation of clays and formation of networks of pores, as visualized using cryo-scanning electron microscopy (SEM). These reactions facilitated the egress of porewater from MFT and increased consolidation of tailings solids. These results have large-scale implications for management and reclamation of oil sands tailings ponds, a burgeoning environmental issue for the public and government regulators.

  10. Chemical reaction networks as a model to describe UVC- and radiolytically-induced reactions of simple compounds.

    Science.gov (United States)

    Dondi, Daniele; Merli, Daniele; Albini, Angelo; Zeffiro, Alberto; Serpone, Nick

    2012-05-01

    When a chemical system is submitted to high energy sources (UV, ionizing radiation, plasma sparks, etc.), as is expected to be the case of prebiotic chemistry studies, a plethora of reactive intermediates could form. If oxygen is present in excess, carbon dioxide and water are the major products. More interesting is the case of reducing conditions where synthetic pathways are also possible. This article examines the theoretical modeling of such systems with random-generated chemical networks. Four types of random-generated chemical networks were considered that originated from a combination of two connection topologies (viz., Poisson and scale-free) with reversible and irreversible chemical reactions. The results were analyzed taking into account the number of the most abundant products required for reaching 50% of the total number of moles of compounds at equilibrium, as this may be related to an actual problem of complex mixture analysis. The model accounts for multi-component reaction systems with no a priori knowledge of reacting species and the intermediates involved if system components are sufficiently interconnected. The approach taken is relevant to an earlier study on reactions that may have occurred in prebiotic systems where only a few compounds were detected. A validation of the model was attained on the basis of results of UVC and radiolytic reactions of prebiotic mixtures of low molecular weight compounds likely present on the primeval Earth.

  11. A Reaction Database for Small Molecule Pharmaceutical Processes Integrated with Process Information

    Directory of Open Access Journals (Sweden)

    Emmanouil Papadakis

    2017-10-01

    Full Text Available This article describes the development of a reaction database with the objective to collect data for multiphase reactions involved in small molecule pharmaceutical processes with a search engine to retrieve necessary data in investigations of reaction-separation schemes, such as the role of organic solvents in reaction performance improvement. The focus of this reaction database is to provide a data rich environment with process information available to assist during the early stage synthesis of pharmaceutical products. The database is structured in terms of reaction classification of reaction types; compounds participating in the reaction; use of organic solvents and their function; information for single step and multistep reactions; target products; reaction conditions and reaction data. Information for reactor scale-up together with information for the separation and other relevant information for each reaction and reference are also available in the database. Additionally, the retrieved information obtained from the database can be evaluated in terms of sustainability using well-known “green” metrics published in the scientific literature. The application of the database is illustrated through the synthesis of ibuprofen, for which data on different reaction pathways have been retrieved from the database and compared using “green” chemistry metrics.

  12. Influence of prevailing disturbances on soil biology and biochemistry of montane habitats at Nanda Devi Biosphere Reserve, India during wet and dry seasons

    DEFF Research Database (Denmark)

    Singh, S.K.; Singh, Anoop; Rai, J.P.N.

    2011-01-01

    The impact of prevailing disturbances in montane habitats of Nanda Devi Biosphere Reserve (NDBR) was studied on soil microbial population, biomass, soil respiration and enzyme activities during wet and dry seasons. The physico-chemical characteristics of soils exhibited conspicuous variation in t...

  13. Structure Sensitivity in Pt Nanoparticle Catalysts for Hydrogenation of 1,3-Butadiene: In Situ Study of Reaction Intermediates Using SFG Vibrational Spectroscopy

    KAUST Repository

    Michalak, William D.

    2013-01-31

    The product selectivity during 1,3-butadiene hydrogenation on monodisperse, colloidally synthesized, Pt nanoparticles was studied under reaction conditions with kinetic measurements and in situ sum frequency generation (SFG) vibrational spectroscopy. SFG was performed with the capping ligands intact in order to maintain nanoparticle size by reduced sintering. Four products are formed at 75 C: 1-butene, cis-2-butene, trans-2-butene, and n-butane. Ensembles of Pt nanoparticles with average diameters of 0.9 and 1.8 nm exhibit a ∼30% and ∼20% increase in the full hydrogenation products, respectively, as compared to Pt nanoparticles with average diameters of 4.6 and 6.7 nm. Methyl and methylene vibrational stretches of reaction intermediates observed under working conditions using SFG were used to correlate the stable reaction intermediates with the product distribution. Kinetic and SFG results correlate with previous DFT predictions for two parallel reaction pathways of 1,3-butadiene hydrogenation. Hydrogenation of 1,3-butadiene can initiate with H-addition at internal or terminal carbons leading to the formation of 1-buten-4-yl radical (metallocycle) and 2-buten-1-yl radical intermediates, respectively. Small (0.9 and 1.8 nm) nanoparticles exhibited vibrational resonances originating from both intermediates, while the large (4.6 and 6.7 nm) particles exhibited vibrational resonances originating predominately from the 2-buten-1-yl radical. This suggests each reaction pathway competes for partial and full hydrogenation and the nanoparticle size affects the kinetic preference for the two pathways. The reaction pathway through the metallocycle intermediate on the small nanoparticles is likely due to the presence of low-coordinated sites. © 2012 American Chemical Society.

  14. Bridge mediated two-electron transfer reactions: Analysis of stepwise and concerted pathways

    International Nuclear Information System (INIS)

    Petrov, E.G.; May, V.

    2004-01-01

    A theory of nonadiabatic donor (D)-acceptor (A) two-electron transfer (TET) mediated by a single regular bridge (B) is developed. The presence of different intermediate two-electron states connecting the reactant state D -- BA with the product state DBA -- results in complex multiexponential kinetics. The conditions are discussed at which a reduction to two-exponential as well as single-exponential kinetics becomes possible. For the latter case the rate K TET is calculated, which describes the bridge-mediated reaction as an effective two-electron D-A transfer. In the limit of small populations of the intermediate TET states D - B - A, DB -- A, D - BA - , and DB - A - , K TET is obtained as a sum of the rates K TET (step) and K TET (sup) . The first rate describes stepwise TET originated by transitions of a single electron. It starts at D -- BA and reaches DBA -- via the intermediate state D - BA - . These transitions cover contributions from sequential as well as superexchange reactions all including reduced bridge states. In contrast, a specific two-electron superexchange mechanism from D -- BA to DBA -- defines K TET (sup) . An analytic dependence of K TET (step) and K TET (sup) on the number of bridging units is presented and different regimes of D-A TET are studied

  15. Computational Chemical Synthesis Analysis and Pathway Design

    Directory of Open Access Journals (Sweden)

    Fan Feng

    2018-06-01

    Full Text Available With the idea of retrosynthetic analysis, which was raised in the 1960s, chemical synthesis analysis and pathway design have been transformed from a complex problem to a regular process of structural simplification. This review aims to summarize the developments of computer-assisted synthetic analysis and design in recent years, and how machine-learning algorithms contributed to them. LHASA system started the pioneering work of designing semi-empirical reaction modes in computers, with its following rule-based and network-searching work not only expanding the databases, but also building new approaches to indicating reaction rules. Programs like ARChem Route Designer replaced hand-coded reaction modes with automatically-extracted rules, and programs like Chematica changed traditional designing into network searching. Afterward, with the help of machine learning, two-step models which combine reaction rules and statistical methods became the main stream. Recently, fully data-driven learning methods using deep neural networks which even do not require any prior knowledge, were applied into this field. Up to now, however, these methods still cannot replace experienced human organic chemists due to their relatively low accuracies. Future new algorithms with the aid of powerful computational hardware will make this topic promising and with good prospects.

  16. Graph-representation of oxidative folding pathways

    Directory of Open Access Journals (Sweden)

    Kaján László

    2005-01-01

    Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

  17. Heterogeneous reactions of ozone with methoxyphenols, in presence and absence of light

    Science.gov (United States)

    Net, Sopheak; Alvarez, Elena Gómez; Gligorovski, Sasho; Wortham, Henri

    2011-06-01

    In this work, we investigated the heterogeneous reactions between gaseous ozone and seven particulate methoxyphenols, biomass tracers. The ozonolysis of silica particles coated with vanillin, vanillic acid, syringaldehyde, syringic acid, acetovanillone, acetonsyringone and coniferyl alcohol was studied successively and was carried out both in total darkness and under illumination with simulated solar light at 297 K. The condensed-phase products which emerged in such heterogeneous reactions were analyzed by gas chromatography-mass spectrometry (GC/MS). No reaction product was detected during the ozonolysis of vanillic acid, syringic acid, acetovanillone and acetosyringone under our experimental conditions. The main tranformation of pathway vanillin and syringaldehyde was the conversion of an aldehyde group to a carboxylic fonction. Thus, syringic acid and vanillic acid were respectively the main oxidation products of syringaldehyde and vanillin. The oxidation of coniferyl alcohol was relatively fast and the total degradation was observed after 16 h of ozone exposure. Five oxidation products: glycolic acid, oxalic acid, vanillin, vanillic acid and 3,4-dihydroxybenzoic acid, were identified and confirmed by their corresponding standards. It is interesting to note that 3,4-dihydroxybenzoic acid was detected only in the experiment performed under combined ozone and light exposure of the particles coated with coniferyl alcohol. Vanillin and vanillic acid also absorb light in the tropospheric actinic window and therefore they can be photochemically active which in turn can induce further modifications of the aerosol particles. A mechanistic pathway was proposed in order to elucidate the ozonolysis reaction of coniferyl alcohol and to explain the identified reaction products.

  18. Additional chain-branching pathways in the low-temperature oxidation of branched alkanes

    KAUST Repository

    Wang, Zhandong

    2015-12-31

    Chain-branching reactions represent a general motif in chemistry, encountered in atmospheric chemistry, combustion, polymerization, and photochemistry; the nature and amount of radicals generated by chain-branching are decisive for the reaction progress, its energy signature, and the time towards its completion. In this study, experimental evidence for two new types of chain-branching reactions is presented, based upon detection of highly oxidized multifunctional molecules (HOM) formed during the gas-phase low-temperature oxidation of a branched alkane under conditions relevant to combustion. The oxidation of 2,5-dimethylhexane (DMH) in a jet-stirred reactor (JSR) was studied using synchrotron vacuum ultra-violet photoionization molecular beam mass spectrometry (SVUV-PI-MBMS). Specifically, species with four and five oxygen atoms were probed, having molecular formulas of C8H14O4 (e.g., diketo-hydroperoxide/keto-hydroperoxy cyclic ether) and C8H16O5 (e.g., keto-dihydroperoxide/dihydroperoxy cyclic ether), respectively. The formation of C8H16O5 species involves alternative isomerization of OOQOOH radicals via intramolecular H-atom migration, followed by third O2 addition, intramolecular isomerization, and OH release; C8H14O4 species are proposed to result from subsequent reactions of C8H16O5 species. The mechanistic pathways involving these species are related to those proposed as a source of low-volatility highly oxygenated species in Earth\\'s troposphere. At the higher temperatures relevant to auto-ignition, they can result in a net increase of hydroxyl radical production, so these are additional radical chain-branching pathways for ignition. The results presented herein extend the conceptual basis of reaction mechanisms used to predict the reaction behavior of ignition, and have implications on atmospheric gas-phase chemistry and the oxidative stability of organic substances. © 2015 The Combustion Institute.

  19. The OH-initiated atmospheric oxidation of divinyl sulfoxide: A theoretical investigation on the reaction mechanism

    Science.gov (United States)

    Zhang, Weichao; Zhang, Dongju

    2012-08-01

    The potential energy surfaces for the OH + divinyl sulfoxide reaction in the presence of O2/NO are theoretically characterized at the CCSD(T)/6-311+G(d,p)//BH&HLYP/6-311++G(d,p)+ZPE level of theory. Various possible pathways including the direct hydrogen abstraction channels and the addition-elimination channels are considered. The calculations show that the exclusive feasible entrance channel is the formation of adduct CH2(OH)CHS(O)CHdbnd CH2 (IM1) in the initial reaction pathways. In the atmosphere, the newly formed adduct IM1 can further react with O2/NO to form the dominant products HCHO + C(O)HS(O)CHdbnd CH2 (P9). The calculated results confirm the experimental studies.

  20. Reaction-induced fracturing during olivine serpentinization: A mechanistic investigation at the interface scale

    NARCIS (Netherlands)

    Plümper, O.; Røyne, A.; Malthe-Sørenssen, A.; King, H. E.; Jamtveit, B.

    Serpentinization of the Earth's impermeable upper mantle is one of the most fundamental metamorphic hydration reactions. It governs lithospheric weakening, geochemical subduction zone input and possibly even the formation of life-essential building blocks. Serpentinization relies on fluid pathway

  1. PathwayAccess: CellDesigner plugins for pathway databases.

    Science.gov (United States)

    Van Hemert, John L; Dickerson, Julie A

    2010-09-15

    CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

  2. Activation pathways taking place at molecular copper precatalysts for the oxygen evolution reaction

    NARCIS (Netherlands)

    van der Ham, C.J.M.; Işık, F.; Verhoeven, T.W.G.M.; Niemantsverdriet, J.W.; Hetterscheid, D.G.H.

    2017-01-01

    The activation processes of [CuII(bdmpza)2] in the water oxidation reaction were investigated using cyclic voltammetry and chronoamperometry. Two different paths wherein CuO is formed were distinguished. [CuII(bdmpza)2] can be oxidized at high potentials to form CuO, which was observed by a slight

  3. Chemical Exchange Saturation Transfer in Chemical Reactions: A Mechanistic Tool for NMR Detection and Characterization of Transient Intermediates.

    Science.gov (United States)

    Lokesh, N; Seegerer, Andreas; Hioe, Johnny; Gschwind, Ruth M

    2018-02-07

    The low sensitivity of NMR and transient key intermediates below detection limit are the central problems studying reaction mechanisms by NMR. Sensitivity can be enhanced by hyperpolarization techniques such as dynamic nuclear polarization or the incorporation/interaction of special hyperpolarized molecules. However, all of these techniques require special equipment, are restricted to selective reactions, or undesirably influence the reaction pathways. Here, we apply the chemical exchange saturation transfer (CEST) technique for the first time to NMR detect and characterize previously unobserved transient reaction intermediates in organocatalysis. The higher sensitivity of CEST and chemical equilibria present in the reaction pathway are exploited to access population and kinetics information on low populated intermediates. The potential of the method is demonstrated on the proline-catalyzed enamine formation for unprecedented in situ detection of a DPU stabilized zwitterionic iminium species, the elusive key intermediate between enamine and oxazolidinones. The quantitative analysis of CEST data at 250 K revealed the population ratio of [Z-iminium]/[exo-oxazolidinone] 0.02, relative free energy +8.1 kJ/mol (calculated +7.3 kJ/mol), and free energy barrier of +45.9 kJ/mol (ΔG ⧧ calc. (268 K) = +42.2 kJ/mol) for Z-iminium → exo-oxazolidinone. The findings underpin the iminium ion participation in enamine formation pathway corroborating our earlier theoretical prediction and help in better understanding. The reliability of CEST is validated using 1D EXSY-build-up techniques at low temperature (213 K). The CEST method thus serves as a new tool for mechanistic investigations in organocatalysis to access key information, such as chemical shifts, populations, and reaction kinetics of intermediates below the standard NMR detection limit.

  4. Biochemical research elucidating metabolic pathways in Pneumocystis*

    Directory of Open Access Journals (Sweden)

    Kaneshiro E.S.

    2010-12-01

    Full Text Available Advances in sequencing the Pneumocystis carinii genome have helped identify potential metabolic pathways operative in the organism. Also, data from characterizing the biochemical and physiological nature of these organisms now allow elucidation of metabolic pathways as well as pose new challenges and questions that require additional experiments. These experiments are being performed despite the difficulty in doing experiments directly on this pathogen that has yet to be subcultured indefinitely and produce mass numbers of cells in vitro. This article reviews biochemical approaches that have provided insights into several Pneumocystis metabolic pathways. It focuses on 1 S-adenosyl-L-methionine (AdoMet; SAM, which is a ubiquitous participant in numerous cellular reactions; 2 sterols: focusing on oxidosqualene cyclase that forms lanosterol in P. carinii; SAM:sterol C-24 methyltransferase that adds methyl groups at the C-24 position of the sterol side chain; and sterol 14α-demethylase that removes a methyl group at the C-14 position of the sterol nucleus; and 3 synthesis of ubiquinone homologs, which play a pivotal role in mitochondrial inner membrane and other cellular membrane electron transport.

  5. A potential role of substrate as a base for deprotonation pathway in Rh-catalysed C-H amination of heteroArenes: DFT insights

    KAUST Repository

    Ajitha, Manjaly John

    2016-03-29

    The possibility of direct introduction of a new functionality through C–H bond activation is an attractive strategy in covalent synthesis. Here, we investigated the mechanism of Rh-catalysed C-H amination of the hetero-aryl substrate (2-phenylpyridine) using phenyl azide as nitrogen source by density functional theory (DFT). For the deprotocyclometallation and protodecyclometallation processes of the title reaction, we propose a stepwise base-assisted mechanism (pathway I) instead of previously reported concerted mechanism (pathway II). In the new mechanism proposed here, 2-phenylpyridine acts as a base in the initial deprotonation step (C-H bond cleavage) and transports the proton towards the final protonation step. In fact, the N-H bond of the strong conjugate acid (formed during initial C-H bond cleavage) considered in pathway I (via TS4) is more acidic than the C-H bond of the neutral substrate considered in pathway II (via TS5). The higher activation barrier of TS5 mainly originates from the ring strain of the four membered cyclic transition state. The vital role of base, as disclosed here, can potentially have broader mechanistic implications for the development of reaction conditions of transition metal catalysed reactions.

  6. TRIMOLECULAR REACTIONS OF URANIUM HEXAFLUORIDE WITH WATER

    Energy Technology Data Exchange (ETDEWEB)

    Westbrook, M.; Becnel, J.; Garrison, S.

    2010-02-25

    The hydrolysis reaction of uranium hexafluoride (UF{sub 6}) is a key step in the synthesis of uranium dioxide (UO{sub 2}) powder for nuclear fuels. Mechanisms for the hydrolysis reactions are studied here with density functional theory and the Stuttgart small-core scalar relativistic pseudopotential and associated basis set for uranium. The reaction of a single UF{sub 6} molecule with a water molecule in the gas phase has been previously predicted to proceed over a relatively sizeable barrier of 78.2 kJ {center_dot} mol{sup -1}, indicating this reaction is only feasible at elevated temperatures. Given the observed formation of a second morphology for the UO{sub 2} product coupled with the observations of rapid, spontaneous hydrolysis at ambient conditions, an alternate reaction pathway must exist. In the present work, two trimolecular hydrolysis mechanisms are studied with density functional theory: (1) the reaction between two UF{sub 6} molecules and one water molecule, and (2) the reaction of two water molecules with a single UF{sub 6} molecule. The predicted reaction of two UF{sub 6} molecules with one water molecule displays an interesting 'fluorine-shuttle' mechanism, a significant energy barrier of 69.0 kJ {center_dot} mol{sup -1} to the formation of UF{sub 5}OH, and an enthalpy of reaction ({Delta}H{sub 298}) of +17.9 kJ {center_dot} mol{sup -1}. The reaction of a single UF{sub 6} molecule with two water molecules displays a 'proton-shuttle' mechanism, and is more favorable, having a slightly lower computed energy barrier of 58.9 kJ {center_dot} mol{sup -1} and an exothermic enthalpy of reaction ({Delta}H{sub 298}) of -13.9 kJ {center_dot} mol{sup -1}. The exothermic nature of the overall UF{sub 6} + 2 {center_dot} H{sub 2}O trimolecular reaction and the lowering of the barrier height with respect to the bimolecular reaction are encouraging; however, the sizable energy barrier indicates further study of the UF{sub 6} hydrolysis reaction

  7. Determination of rate constants for the oxygen reduction reaction

    Energy Technology Data Exchange (ETDEWEB)

    Racz, A.; Walter, T.; Stimming, U. [Munich Technical Univ., Garching (Germany). Dept. of Physics

    2008-07-01

    The oxygen reduction reaction (ORR) in fuel cells is a complex and fundamental electrochemical reaction. However, greater insight is needed into this multi-electron reaction in order to develop efficient and innovative catalysts. The rotating ring disc electrode (RRDE) is a useful tool for studying reaction intermediates of the ORR and to better understand the reaction pathway. Carbon materials such as carbon nanofilaments-platelets (CNF-PL) have high electrical conductivity and may be considered for fuel cells. In particular Pt and RuSe{sub x}, deposited on CNF-PL materials could act as efficient catalysts in fuel cells. This study used the RRDE to evaluate the oxygen reduction kinetics of these catalysts in oxygen-saturated, diluted sulphuric acid at room temperature. Kinetic data and hydrogen peroxide formation were determined by depositing a thin-film of the catalyst on the Au disc. The values for the constants k1, k2 and k3 were obtained using diagnostic criteria and expressions to calculate the rate constants of the cathodic oxygen reduction reaction for RuSe on new carbon supports. A potential dependency of the constants k1 and k2 for RuSe{sub x}/CNF-PL was observed. The transition of the Tafel slopes for this catalyst was obtained. 4 refs., 1 fig.

  8. Deciphering Selectivity in Organic Reactions: A Multifaceted Problem.

    Science.gov (United States)

    Balcells, David; Clot, Eric; Eisenstein, Odile; Nova, Ainara; Perrin, Lionel

    2016-05-17

    Computational chemistry has made a sustained contribution to the understanding of chemical reactions. In earlier times, half a century ago, the goal was to distinguish allowed from forbidden reactions (e.g., Woodward-Hoffmann rules), that is, reactions with low or high to very high activation barriers. A great achievement of computational chemistry was also to contribute to the determination of structures with the bonus of proposing a rationalization (e.g., anomeric effect, isolobal analogy, Gillespie valence shell pair electron repulsion rules and counter examples, Wade-Mingos rules for molecular clusters). With the development of new methods and the constant increase in computing power, computational chemists move to more challenging problems, close to the daily concerns of the experimental chemists, in determining the factors that make a reaction both efficient and selective: a key issue in organic synthesis. For this purpose, experimental chemists use advanced synthetic and analytical techniques to which computational chemists added other ways of determining reaction pathways. The transition states and intermediates contributing to the transformation of reactants into the desired and undesired products can now be determined, including their geometries, energies, charges, spin densities, spectroscopy properties, etc. Such studies remain challenging due to the large number of chemical species commonly present in the reactive media whose role may have to be determined. Calculating chemical systems as they are in the experiment is not always possible, bringing its own share of complexity through the large number of atoms and the associated large number of conformers to consider. Modeling the chemical species with smaller systems is an alternative that historically led to artifacts. Another important topic is the choice of the computational method. While DFT is widely used, the vast diversity of functionals available is both an opportunity and a challenge. Though

  9. Nuclear Forensics and Radiochemistry: Reaction Networks

    Energy Technology Data Exchange (ETDEWEB)

    Rundberg, Robert S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-11-22

    In the intense neutron flux of a nuclear explosion the production of isotopes may occur through successive neutron induced reactions. The pathway to these isotopes illustrates both the complexity of the problem and the need for high quality nuclear data. The growth and decay of radioactive isotopes can follow a similarly complex network. The Bateman equation will be described and modified to apply to the transmutation of isotopes in a high flux reactor. A alternative model of growth and decay, the GD code, that can be applied to fission products will also be described.

  10. Dynamic pathways to mediate reactions buried in thermal fluctuations. I. Time-dependent normal form theory for multidimensional Langevin equation.

    Science.gov (United States)

    Kawai, Shinnosuke; Komatsuzaki, Tamiki

    2009-12-14

    We present a novel theory which enables us to explore the mechanism of reaction selectivity and robust functions in complex systems persisting under thermal fluctuation. The theory constructs a nonlinear coordinate transformation so that the equation of motion for the new reaction coordinate is independent of the other nonreactive coordinates in the presence of thermal fluctuation. In this article we suppose that reacting systems subject to thermal noise are described by a multidimensional Langevin equation without a priori assumption for the form of potential. The reaction coordinate is composed not only of all the coordinates and velocities associated with the system (solute) but also of the random force exerted by the environment (solvent) with friction constants. The sign of the reaction coordinate at any instantaneous moment in the region of a saddle determines the fate of the reaction, i.e., whether the reaction will proceed through to the products or go back to the reactants. By assuming the statistical properties of the random force, one can know a priori a well-defined boundary of the reaction which separates the full position-velocity space in the saddle region into mainly reactive and mainly nonreactive regions even under thermal fluctuation. The analytical expression of the reaction coordinate provides the firm foundation on the mechanism of how and why reaction proceeds in thermal fluctuating environments.

  11. Comparison of Metabolic Pathways in Escherichia coli by Using Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Patricia Ortegon

    2015-01-01

    Full Text Available In order to understand how cellular metabolism has taken its modern form, the conservation and variations between metabolic pathways were evaluated by using a genetic algorithm (GA. The GA approach considered information on the complete metabolism of the bacterium Escherichia coli K-12, as deposited in the KEGG database, and the enzymes belonging to a particular pathway were transformed into enzymatic step sequences by using the breadth-first search algorithm. These sequences represent contiguous enzymes linked to each other, based on their catalytic activities as they are encoded in the Enzyme Commission numbers. In a posterior step, these sequences were compared using a GA in an all-against-all (pairwise comparisons approach. Individual reactions were chosen based on their measure of fitness to act as parents of offspring, which constitute the new generation. The sequences compared were used to construct a similarity matrix (of fitness values that was then considered to be clustered by using a k-medoids algorithm. A total of 34 clusters of conserved reactions were obtained, and their sequences were finally aligned with a multiple-sequence alignment GA optimized to align all the reaction sequences included in each group or cluster. From these comparisons, maps associated with the metabolism of similar compounds also contained similar enzymatic step sequences, reinforcing the Patchwork Model for the evolution of metabolism in E. coli K-12, an observation that can be expanded to other organisms, for which there is metabolism information. Finally, our mapping of these reactions is discussed, with illustrations from a particular case.

  12. Stability and isomerization reactions of phenyl cation C{sub 6}H{sub 5}{sup +} isomers

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Dandan [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yang, Xue [College of Science, Jilin Institute of Chemical Technology, Jilin 132022 (China); Zhang, Xiaomei; Shan, Shimin [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Xu, Haifeng, E-mail: xuhf@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yan, Bing, E-mail: yanbing@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China)

    2016-03-01

    Highlights: • A total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations were obtained at density functional theory. • The stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers were performed. • The structures, frequencies, thermodynamic properties of isomers were summarized. • Ring to ring or chain isomerization pathways were investigated using IRC method. • Result shows reactions contain hydrogen transfer, bond broken and reconstruction. - Abstract: As a key polyatomic molecular cation that plays a pivotal role in growth of the polycyclic aromatic hydrocarbons, phenyl cation C{sub 6}H{sub 5}{sup +} exhibits various isomers and isomerization reactions. Investigation on the structure and stability of the isomers as well as the isomerization is important for better understanding the chemical reactions involving C{sub 6}H{sub 5}{sup +} cations. In this work, we have performed a theoretical study on the stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers at density functional theory B3LYP/6-311G (d, p) level. We have obtained a total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations, most of which are reported for the first time. The geometries, vibrational frequencies, thermodynamic properties and stability of 28 out of 60 isomers have been summarized in detail. Different ring-to-ring and ring-to-chain isomerization pathways, which are connected via 28 transition states, have been investigated using the intrinsic reaction coordinate method. The results show that the isomerization reactions occur via hydrogen migration followed by bond-breaking and reconstruction.

  13. Optimization of the THP-1 activation assay to detect pharmaceuticals with potential to cause immune mediated drug reactions.

    Science.gov (United States)

    Corti, Daniele; Galbiati, Valentina; Gatti, Nicolò; Marinovich, Marina; Galli, Corrado L; Corsini, Emanuela

    2015-10-01

    Despite important impacts of systemic hypersensitivity induced by pharmaceuticals, for such endpoint no reliable preclinical approaches are available. We previously established an in vitro test to identify contact and respiratory allergens based on interleukin-8 (IL-8) production in THP-1 cells. Here, we challenged it for identification of pharmaceuticals associated with systemic hypersensitivity reactions, with the idea that drug sensitizers share common mechanisms of cell activation. Cells were exposed to drugs associated with systemic hypersensitivity reactions (streptozotocin, sulfamethoxazole, neomycin, probenecid, clonidine, procainamide, ofloxacin, methyl salicylate), while metformin was used as negative drug. Differently to chemicals, drugs tested were well tolerated, except clonidine and probenecid, with no signs of cytotoxicity up to 1-2mg/ml. THP-1 activation assay was adjusted, and conditions, that allow identification of all sensitizing drugs tested, were established. Next, using streptozotocin and selective inhibitors of PKC-β and p38 MAPK, two pathways involved in chemical allergen-induced cell activation, we tested the hypothesis that similar pathways were also involved in drug-induced IL-8 production and CD86 upregulation. Results indicated that drugs and chemical allergens share similar activation pathways. Finally, we made a structure-activity hypothesis related to hypersensitivity reactions, trying to individuate structural requisite that can be involved in immune mediated adverse reactions. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Spectroscopy and reactions of vibrationally excited transient molecules

    Energy Technology Data Exchange (ETDEWEB)

    Dai, H.L. [Univ. of Pennsylvania, Philadelphia (United States)

    1993-12-01

    Spectroscopy, energy transfer and reactions of vibrationally excited transient molecules are studied through a combination of laser-based excitation techniques and efficient detection of emission from the energized molecules with frequency and time resolution. Specifically, a Time-resolved Fourier Transform Emission Spectroscopy technique has been developed for detecting dispersed laser-induced fluorescence in the IR, visible and UV regions. The structure and spectroscopy of the excited vibrational levels in the electronic ground state, as well as energy relaxation and reactions induced by specific vibronic excitations of a transient molecule can be characterized from time-resolved dispersed fluorescence in the visible and UV region. IR emissions from highly vibrational excited levels, on the other hand, reveal the pathways and rates of collision induced vibrational energy transfer.

  15. The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Tully, John C. [Yale Univ., New Haven, CT (United States)

    2017-06-10

    Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opens up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.

  16. Structure Sensitivity in Pt Nanoparticle Catalysts for Hydrogenation of 1,3-Butadiene: In Situ Study of Reaction Intermediates Using SFG Vibrational Spectroscopy

    KAUST Repository

    Michalak, William D.; Krier, James M.; Komvopoulos, Kyriakos; Somorjai, Gabor A.

    2013-01-01

    hydrogenation and the nanoparticle size affects the kinetic preference for the two pathways. The reaction pathway through the metallocycle intermediate on the small nanoparticles is likely due to the presence of low-coordinated sites. © 2012 American Chemical

  17. Enzyme chemistry and the evolution of metabolic diversity: the β-ketoadipate pathway

    International Nuclear Information System (INIS)

    Kozarich, J.W.

    1986-01-01

    The two converging catechol and protocatechuate branches of the β-ketoadipate pathway in Pseudomonas putida have long been considered a paradigm of evolutionary divergence of specialized enzymes from a common ancestor. The structural similarities of substrates, products and the enzymes themselves have supported this hypothesis. Employing chemical and 1 H NMR techniques, they have determined the absolute stereochemical courses of the reactions catalyzed by β-carboxymuconate cycloisomerase, muconolactone isomerase, and γ-carboxymuconolactone decarboxylase. Surprisingly, β-carboxymuconate cycloisomerase proceeds via an anti addition while the corresponding muconate cycloisomerase has been shown to catalyze a syn addition. Moreover, the chiral centers generated in the products of both enzymes are of the opposite relative configuration. They believe that the shift in mechanism may reflect basic energetic differences of the two reactions. The stereochemistries of the isomerase and decarboxylase have been established by 1 H NMR using a ricochet analysis. Both reactions proceed via a syn process; the relative configurations of muconolactone and γ-carboxymuconolactone necessitate that the enzymes operate on opposite faces of the common enol-lactone product. These findings suggest that either critical active site changes have occurred in these enzymes to accommodate preferred mechanistic pathways or the evolutionary relationship of the two branches is more remote than previously believed

  18. Reactions of carbonyl compounds with α,β-unsaturated nitriles as a convenient pathway to carbo- and heterocycles

    International Nuclear Information System (INIS)

    Sharanin, Yu A; Goncharenko, M P; Litvinov, Victor P

    1998-01-01

    Published data on the methods for synthesis of carbo- and heterocyclic compounds based on reactions of α,β-unsaturated nitriles with carbonyl compounds and activated phenols are surveyed. It is demonstrated that all these reactions occur via nucleophilic addition of the carbanion generated from a carbonyl compound to the double bond of an unsaturated nitrile (the Michael reaction). The main routes of transformation of the adducts into carbo- and heterocyclic compounds are considered. The methods for regioselective preparation of fused 4H-pyrans or 1,4-dihydropyridines by varying conditions of cyclisation of Michael adducts are discussed. The bibliography includes 249 references.

  19. Degradation of sulfadimethoxine catalyzed by laccase with soybean meal extract as natural mediator: Mechanism and reaction pathway.

    Science.gov (United States)

    Liang, Shangtao; Luo, Qi; Huang, Qingguo

    2017-08-01

    Natural laccase-mediator systems have been well recognized as an eco-friendly and energy-saving approach in environmental remediation, whose further application is however limited by the high cost of natural mediators and relatively long treatment time span. This study evaluated the water extract of soybean meal, a low-cost compound system, in mediating the laccase catalyzed degradation of a model contaminant of emerging concern, sulfadimethoxine (SDM), and demonstrated it as a promising alternative mediator for soil and water remediation. Removal of 73.3% and 65.6% was achieved in 9 h using soybean meal extract (SBE) as the mediating system for laccase-catalyzed degradation of sulfadimethoxine at the concentration of 1 ppm and 10 ppm, respectively. Further degradation of sulfadimethoxine was observed with multiple SBE additions. Using SBE as mediator increased the 9-h removal of SDM at 1 ppm initial concentration by 52.9%, 49.4%, and 36.3% in comparison to the system mediated by 1-Hydroxybenzotriazole (HBT), p-Coumaric acid (COU) and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS), respectively. With the detection of stable coupling products formed with radical scavenger (5,5-Dimethyl-1-pyrroline N-oxide, DMPO), three phenolic compounds (vanillin, apocynin, and daidzein) in SBE were confirmed to serve as mediators for Trametes versicolor laccase. Reaction pathways were proposed based on the results of High Resolution Mass Spectrometry. SO 2 excursion happened during SDM transformation, leading to elimination of antimicrobial activity. Therefore, as a natural, phenol rich, and affordable compound system, the future application of SBE in wastewater and soil remediation is worth exploring. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Pathways and Mechanisms Underlying the Photophysics and Photochemistry of Riboflavin induced cornea crosslinking

    DEFF Research Database (Denmark)

    Breitenbach, Thomas; Ogilby, Peter Remsen

    In this talk, we will describe general pathways involved in the photophysics of a photosensitized process, which can lead to crosslinking due to light excitation of Riboflavin in the cornea. Furthermore, we will elucidate different aspects of reactions that can produce crosslinks, with respect...

  1. Radiographic progression with nonrising PSA in metastatic castration-resistant prostate cancer: post hoc analysis of PREVAIL.

    Science.gov (United States)

    Bryce, A H; Alumkal, J J; Armstrong, A; Higano, C S; Iversen, P; Sternberg, C N; Rathkopf, D; Loriot, Y; de Bono, J; Tombal, B; Abhyankar, S; Lin, P; Krivoshik, A; Phung, D; Beer, T M

    2017-06-01

    Advanced prostate cancer is a phenotypically diverse disease that evolves through multiple clinical courses. PSA level is the most widely used parameter for disease monitoring, but it has well-recognized limitations. Unlike in clinical trials, in practice, clinicians may rely on PSA monitoring alone to determine disease status on therapy. This approach has not been adequately tested. Chemotherapy-naive asymptomatic or mildly symptomatic men (n=872) with metastatic castration-resistant prostate cancer (mCRPC) who were treated with the androgen receptor inhibitor enzalutamide in the PREVAIL study were analyzed post hoc for rising versus nonrising PSA (empirically defined as >1.05 vs ⩽1.05 times the PSA level from 3 months earlier) at the time of radiographic progression. Clinical characteristics and disease outcomes were compared between the rising and nonrising PSA groups. Of 265 PREVAIL patients with radiographic progression and evaluable PSA levels on the enzalutamide arm, nearly one-quarter had a nonrising PSA. Median progression-free survival in this cohort was 8.3 months versus 11.1 months in the rising PSA cohort (hazard ratio 1.68; 95% confidence interval 1.26-2.23); overall survival was similar between the two groups, although less than half of patients in either group were still at risk at 24 months. Baseline clinical characteristics of the two groups were similar. Non-rising PSA at radiographic progression is a common phenomenon in mCRPC patients treated with enzalutamide. As restaging in advanced prostate cancer patients is often guided by increases in PSA levels, our results demonstrate that disease progression on enzalutamide can occur without rising PSA levels. Therefore, a disease monitoring strategy that includes imaging not entirely reliant on serial serum PSA measurement may more accurately identify disease progression.

  2. Effect of Visceral Disease Site on Outcomes in Patients With Metastatic Castration-resistant Prostate Cancer Treated With Enzalutamide in the PREVAIL Trial.

    Science.gov (United States)

    Alumkal, Joshi J; Chowdhury, Simon; Loriot, Yohann; Sternberg, Cora N; de Bono, Johann S; Tombal, Bertrand; Carles, Joan; Flaig, Thomas W; Dorff, Tanya B; Phung, De; Forer, David; Noonberg, Sarah B; Mansbach, Hank; Beer, Tomasz M; Higano, Celestia S

    2017-10-01

    The Multinational Phase 3, Randomized, Double-Blind, Placebo-Controlled Efficacy and Safety Study of Oral MDV3100 in Chemotherapy-Naive Patients With Progressive Metastatic Prostate Cancer Who Have Failed Androgen Deprivation Therapy (PREVAIL) trial was unique as it included patients with visceral disease. This analysis was designed to describe outcomes for the subgroup of men from PREVAIL with specific sites of visceral disease to help clinicians understand how these patients responded to enzalutamide prior to chemotherapy. Prespecified analyses examined the coprimary endpoints of radiographic progression-free survival (rPFS) and overall survival (OS) only. All other efficacy analyses were post hoc. The visceral subgroup was divided into liver or lung subsets. Patients with both liver and lung metastases were included in the liver subset. Of the 1717 patients in PREVAIL, 204 (12%) had visceral metastases at screening (liver only or liver/lung metastases, n = 74; lung only metastases, n = 130). In patients with liver metastases, enzalutamide was associated with an improvement in rPFS (hazard ratio [HR], 0.44; 95% confidence interval [CI], 0.22-0.90) but not OS (HR, 1.04; 95% CI, 0.57-1.87). In patients with lung metastases only, the HR for rPFS (0.14; 95% CI, 0.06-0.36) and the HR for OS (0.59; 95% CI, 0.33-1.06) favored enzalutamide over placebo. Patients with liver metastases had worse outcomes than those with lung metastases, regardless of treatment. Enzalutamide was well tolerated in patients with visceral disease. Enzalutamide is an active first-line treatment option for men with asymptomatic or mildly symptomatic chemotherapy-naive metastatic castration-resistant prostate cancer and visceral disease. Patients with lung-only disease fared better than patients with liver disease, regardless of treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Quantum measurement corrections to CIDNP in photosynthetic reaction centers

    International Nuclear Information System (INIS)

    Kominis, Iannis K

    2013-01-01

    Chemically induced dynamic nuclear polarization is a signature of spin order appearing in many photosynthetic reaction centers. Such polarization, significantly enhanced above thermal equilibrium, is known to result from the nuclear spin sorting inherent in the radical pair mechanism underlying long-lived charge-separated states in photosynthetic reaction centers. We will show here that the recently understood fundamental quantum dynamics of radical-ion-pair reactions open up a new and completely unexpected pathway toward obtaining chemically induced dynamic nuclear polarization signals. The fundamental decoherence mechanism inherent in the recombination process of radical pairs is shown to produce nuclear spin polarizations of the order of 10 4 times (or more) higher than the thermal equilibrium value at the Earth's magnetic field relevant to natural photosynthesis. This opens up the possibility of a fundamentally new exploration of the biological significance of high nuclear polarizations in photosynthesis. (paper)

  4. Fatty acid hydroperoxides pathways in plants. A review.

    Directory of Open Access Journals (Sweden)

    Fauconnier, M. L.

    1997-02-01

    Full Text Available The present paper focusses on the fatty acid hydroperoxides pathways, mainly hydroperoxide lyase and hydroperoxide dehydrase. For each enzyme, the definition, occurrence and subcellular localization is presented. Particular attention is given to reaction mecanisms and to substrate specificity. Physiological roles of reaction products are also discussed.

    El presente artículo se centra en las rutas de los hidroperóxidos de ácidos grasos, principalmente la hidroperóxido liasa y la hidroperóxido dehidrasa. Se presenta para cada enzima, la definición, distribución y localización subcelular. Se da atención particular a los mecanismos de reacción y a la especificidad de sustrato. También se discuten los papeles fisiológicos de los productos de reacción.

  5. Single-Atom Catalyst of Platinum Supported on Titanium Nitride for Selective Electrochemical Reactions.

    Science.gov (United States)

    Yang, Sungeun; Kim, Jiwhan; Tak, Young Joo; Soon, Aloysius; Lee, Hyunjoo

    2016-02-05

    As a catalyst, single-atom platinum may provide an ideal structure for platinum minimization. Herein, a single-atom catalyst of platinum supported on titanium nitride nanoparticles were successfully prepared with the aid of chlorine ligands. Unlike platinum nanoparticles, the single-atom active sites predominantly produced hydrogen peroxide in the electrochemical oxygen reduction with the highest mass activity reported so far. The electrocatalytic oxidation of small organic molecules, such as formic acid and methanol, also exhibited unique selectivity on the single-atom platinum catalyst. A lack of platinum ensemble sites changed the reaction pathway for the oxygen-reduction reaction toward a two-electron pathway and formic acid oxidation toward direct dehydrogenation, and also induced no activity for the methanol oxidation. This work demonstrates that single-atom platinum can be an efficient electrocatalyst with high mass activity and unique selectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Oxidation of β-lactam antibiotics by peracetic acid: Reaction kinetics, product and pathway evaluation.

    Science.gov (United States)

    Zhang, Kejia; Zhou, Xinyan; Du, Penghui; Zhang, Tuqiao; Cai, Meiquan; Sun, Peizhe; Huang, Ching-Hua

    2017-10-15

    Peracetic acid (PAA) is a disinfection oxidant used in many industries including wastewater treatment. β-Lactams, a group of widely prescribed antibiotics, are frequently detected in wastewater effluents and surface waters. The reaction kinetics and transformation of seven β-lactams (cefalexin (CFX), cefadroxil (CFR), cefapirin (CFP), cephalothin (CFT), ampicillin (AMP), amoxicillin (AMX) and penicillin G (PG)) toward PAA were investigated to elucidate the behavior of β-lactams during PAA oxidation processes. The reaction follows second-order kinetics and is much faster at pH 5 and 7 than at pH 9 due to speciation of PAA. Reactivity to PAA follows the order of CFR ∼ CFX > AMP ∼ AMX > CFT ∼ CFP ∼ PG and is related to β-lactam's nucleophilicity. The thioether sulfur of β-lactams is attacked by PAA to generate sulfoxide products. Presence of the phenylglycinyl amino group on β-lactams can significantly influence electron distribution and the highest occupied molecular orbital (HOMO) location and energy in ways that enhance the reactivity to PAA. Reaction rate constants obtained in clean water matrix can be used to accurately model the decay of β-lactams by PAA in surface water matrix and only slightly overestimate the decay in wastewater matrix. Results of this study indicate that the oxidative transformation of β-lactams by PAA can be expected under appropriate wastewater treatment conditions. Copyright © 2017. Published by Elsevier Ltd.

  7. DESHARKY: automatic design of metabolic pathways for optimal cell growth.

    Science.gov (United States)

    Rodrigo, Guillermo; Carrera, Javier; Prather, Kristala Jones; Jaramillo, Alfonso

    2008-11-01

    The biological solution for synthesis or remediation of organic compounds using living organisms, particularly bacteria and yeast, has been promoted because of the cost reduction with respect to the non-living chemical approach. In that way, computational frameworks can profit from the previous knowledge stored in large databases of compounds, enzymes and reactions. In addition, the cell behavior can be studied by modeling the cellular context. We have implemented a Monte Carlo algorithm (DESHARKY) that finds a metabolic pathway from a target compound by exploring a database of enzymatic reactions. DESHARKY outputs a biochemical route to the host metabolism together with its impact in the cellular context by using mathematical models of the cell resources and metabolism. Furthermore, we provide the sequence of amino acids for the enzymes involved in the route closest phylogenetically to the considered organism. We provide examples of designed metabolic pathways with their genetic load characterizations. Here, we have used Escherichia coli as host organism. In addition, our bioinformatic tool can be applied for biodegradation or biosynthesis and its performance scales with the database size. Software, a tutorial and examples are freely available and open source at http://soft.synth-bio.org/desharky.html

  8. Enhanced performance of the methylerythritol phosphate pathway by manipulation of redox reactions relevant to IspC, IspG, and IspH.

    Science.gov (United States)

    Zhou, Jia; Yang, Liyang; Wang, Chonglong; Choi, Eui-Sung; Kim, Seon-Won

    2017-04-20

    The 2C-methyl-D-erythritol 4-phosphate (MEP) pathway is a carbon-efficient route for synthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the building blocks of isoprenoids. However, practical application of a native or recombinant MEP pathway for the mass production of isoprenoids in Escherichia coli has been unsatisfactory. In this study, the entire recombinant MEP pathway was established with plasmids and used for the production of an isoprenoid, protoilludene. E. coli harboring the recombinant MEP pathway plasmid (ME) and a protoilludene synthesis pathway plasmid (AO) produced 10.4mg/L of protoilludene after 48h of culture. To determine the rate-limiting gene on plasmid ME, each constituent gene of the MEP pathway was additionally overexpressed on the plasmid AO. The additional overexpression of IPP isomerase (IDI) enhanced protoilludene production to 67.4mg/L. Overexpression of the Fpr and FldA protein complex, which could mediate electron transfer from NADPH to Fe-S cluster proteins such as IspG and IspH of the MEP pathway, increased protoilludene production to 318.8mg/L. Given that it is required for IspC as well as IspG/H, the MEP pathway has high demand for NADPH. To increase the supply of NADPH, a NADH kinase from Saccharomyces cerevisiae (tPos5p) that converts NADH to NADPH was introduced along with the deletion of a promiscuous NADPH-dependent aldehyde reductase (YjgB) that consumes NADPH. This resulted in a protoilludene production of 512.7mg/L. The results indicate that IDI, Fpr-FldA redox proteins, and NADPH regenerators are key engineering points for boosting the metabolic flux toward a recombinant MEP pathway. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. GAS-PHASE REACTIONS OF POLYCYCLIC AROMATIC HYDROCARBON ANIONS WITH MOLECULES OF INTERSTELLAR RELEVANCE

    International Nuclear Information System (INIS)

    Demarais, Nicholas J.; Yang Zhibo; Martinez, Oscar; Wehres, Nadine; Bierbaum, Veronica M.; Snow, Theodore P.

    2012-01-01

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C 6 H – 5 ), naphthalenide (C 10 H – 7 ), and anthracenide (C 14 H – 9 ) with atomic H, H 2 , and D 2 using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O 2 , CO 2 , N 2 O, C 2 H 2 , CH 3 OH, CH 3 CN, (CH 3 ) 2 CO, CH 3 CHO, CH 3 Cl, and (CH 3 CH 2 ) 2 O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  10. Gas-phase Reactions of Polycyclic Aromatic Hydrocarbon Anions with Molecules of Interstellar Relevance

    Science.gov (United States)

    Demarais, Nicholas J.; Yang, Zhibo; Martinez, Oscar; Wehres, Nadine; Snow, Theodore P.; Bierbaum, Veronica M.

    2012-02-01

    We have studied reactions of small dehydrogenated polycyclic aromatic hydrocarbon anions with neutral species of interstellar relevance. Reaction rate constants are measured at 300 K for the reactions of phenide (C6H- 5), naphthalenide (C10H- 7), and anthracenide (C14H- 9) with atomic H, H2, and D2 using a flowing afterglow-selected ion flow tube instrument. Reaction rate constants of phenide with neutral molecules (CO, O2, CO2, N2O, C2H2, CH3OH, CH3CN, (CH3)2CO, CH3CHO, CH3Cl, and (CH3CH2)2O) are also measured under the same conditions. Experimental measurements are accompanied by ab initio calculations to provide insight into reaction pathways and enthalpies. Our measured reaction rate constants should prove useful in the modeling of astrophysical environments, particularly when applied to dense regions of the interstellar and circumstellar medium.

  11. On the prevailing construction waste recycling practices: a South East Queensland study.

    Science.gov (United States)

    Tam, Vivian W Y; Kotrayothar, Duangthidar; Loo, Yew-Chaye

    2009-03-01

    Waste generated from construction and building demolition work constitutes about 68% of all solid waste generated each year in South East Queensland. Consequently, it has created a serious waste management problem. The State Governments of Victoria and New South Wales have been encouraging the use of recycled materials from construction and related waste; they have also promulgated specifications for their use. In Queensland, however, similar regulations are not anticipated in the near future, which explains the lack of funded research conducted in this important arena. This paper presents an evaluation of the prevailing waste recycling practices in Queensland. Nine sites were visited, including two construction sites, three demolition sites, three recycling plants and one landfill in South East Queensland. The difficulties encountered by the recycling programme operators and their associates at these sites are described and the benefits of recycling construction materials are presented. One of the major barriers is that the local councils disallow the use of recycled materials in new construction work. To help rectify these impediments to recycling, recommendations are given to increase the use of recycled construction waste in South East Queensland.

  12. A Chemical Activation Study of the Unimolecular Reactions of CD3CD2CHCl2 and CHCl2CHCl2 with Analysis of the 1,1-HCl Elimination Pathway.

    Science.gov (United States)

    Larkin, Allie C; Nestler, Matthew J; Smith, Caleb A; Heard, George L; Setser, Donald W; Holmes, Bert E

    2016-10-03

    Chemically activated C2D5CHCl2 molecules were generated with 88 kcal mol-1 of vibrational energy by the recombination of C2D5 and CHCl2 radicals in a room temperature bath gas. The competing 2,1-DCl and 1,1-HCl unimolecular reactions were identified by the observation of the CD3CD=CHCl and CD3CD=CDCl products. The initial CD3CD2C-Cl carbene product from 1,1-HCl elimination rearranges to CD3CD=CDCl under the conditions of the experiments. The experimental rate constants were 2.7 x107 and 0.47 x107 s-1 for 2,1-DCl and 1,1-HCl elimination reactions, respectively, which corresponds to branching fractions of 0.84 and 0.16. The experimental rate constants were compared to calculated statistical rate constants to assign threshold energies of 54 and ≈ 66 kcal mol-1 for the 1,2-DCl and 1,1-HCl reactions, respectively. The statistical rate constants were obtained from models developed from electronic-structure calculations for the molecule and its transition states. The rate constant (5.3 x 107 s-1) for the unimolecular decomposition of CHCl2CHCl2 molecules formed with 82 kcal mol-1 of vibrational energy by the recombination of CHCl2 radicals also is reported. Based upon the magnitude of the calculated rate constant, 1,1-HCl elimination must contribute less than 15% to the reaction; 1,2-HCl elimination is the major reaction and the threshold energy is 59 kcal mol-1. Calculations also were done to analyze previously published rate constants for chemically activated CD2Cl-CHCl2 molecules with 86 kcal mol-1 of energy in order to obtain a better overall description of the nature of the 1,1-HCl pathway for 1,1-dichloroalkanes. The interplay of the threshold energies for the 2,1-HCl and 1,1-HCl reactions and the available energy determines the product branching fractions for individual molecules. The unusual nature of the transition state for 1,1-HCl elimination is discussed.

  13. Study of the peripheral projectile-like fragments from the reaction 129Xe on 27Al, natCu, 139La and 165Ho, at E/A = 50 MeV

    International Nuclear Information System (INIS)

    Garcia-Solis, E.J.; Russ, D.E.; Madani, H.

    1996-01-01

    There are several reaction mechanisms identified for peripheral heavy-ion collisions. For low bombarding energies (E/A ∼ 10 MeV) the predominant reaction channel is the deep-inelastic reaction mechanism. In this process, the projectile and target form a rotating binary system, interchanging nucleons and angular momentum until they separate. At higher bombarding energies (E/A ∼ 50 to 100 MeV) incomplete fusion is thought to be the prevailing reaction channel. In this type of interaction part of the projectile merges with the target during the collision. Finally, for energies greater than 100 MeV/A, the main reaction channel is characterized by the formation of a highly-excited separate fragment (fireball) produced during the overlap between the projectile and the target. The data set studied was from an experiment designed to characterize the projectile-like products of the 27 Al, nat Cu, 139 La, and 165 Ho reactions at E/A = 50 MeV, which was performed at the Michigan State University Super Cyclotron Laboratory (MSU-NSCL). The Maryland Forward Array (MFA), was used to measure projectile-like fragments in coincidence with target-like fragments and light-charge particles in the MSU 4π detector

  14. Skin: Major target organ of allergic reactions to small molecular weight compounds

    International Nuclear Information System (INIS)

    Merk, Hans F.; Baron, Jens M.; Neis, Mark M.; Obrigkeit, Daniela Hoeller; Karlberg, Ann-Therese

    2007-01-01

    Skin is a major target organ for allergic reactions to small molecular weight compounds. Drug allergic reactions may be life-threatening such as in the case of anaphylactic reactions or bullous drug reactions and occur in about 5% of all hospitalized patients. Allergic contact dermatitis has an enormous influence on the social life of the patient because it is the most frequent reason for occupational skin diseases and the treatment and prevention of this disease cost approximately Euro 3 billion per year in Germany. The different proposed pathophysiological pathways leading to a drug eruption are discussed in this paper. All major enzymes which are involved in the metabolism of xenobiotica were shown to be present in skin. Evidence supporting the role of metabolism in the development of drug allergy and allergic contact dermatitis is demonstrated in the example of sulphonamides and fragrances

  15. On the mechanism of photocatalytic reactions with eosin Y

    OpenAIRE

    Majek, Michal; Filace, Fabiana; von Wangelin, Axel Jacobi

    2014-01-01

    Summary A combined spectroscopic, synthetic, and apparative study has allowed a more detailed mechanistic rationalization of several recently reported eosin Y-catalyzed aromatic substitutions at arenediazonium salts. The operation of rapid acid–base equilibria, direct photolysis pathways, and radical chain reactions has been discussed on the basis of pH, solvent polarity, lamp type, absorption properties, and quantum yields. Determination of the latter proved to be an especially valuable tool...

  16. Phenylalanine ammonia lyase catalyzed synthesis of amino acids by an MIO-cofactor independent pathway.

    Science.gov (United States)

    Lovelock, Sarah L; Lloyd, Richard C; Turner, Nicholas J

    2014-04-25

    Phenylalanine ammonia lyases (PALs) belong to a family of 4-methylideneimidazole-5-one (MIO) cofactor dependent enzymes which are responsible for the conversion of L-phenylalanine into trans-cinnamic acid in eukaryotic and prokaryotic organisms. Under conditions of high ammonia concentration, this deamination reaction is reversible and hence there is considerable interest in the development of PALs as biocatalysts for the enantioselective synthesis of non-natural amino acids. Herein the discovery of a previously unobserved competing MIO-independent reaction pathway, which proceeds in a non-stereoselective manner and results in the generation of both L- and D-phenylalanine derivatives, is described. The mechanism of the MIO-independent pathway is explored through isotopic-labeling studies and mutagenesis of key active-site residues. The results obtained are consistent with amino acid deamination occurring by a stepwise E1 cB elimination mechanism. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Biomimicry Promotes the Efficiency of a 10-Step Sequential Enzymatic Reaction on Nanoparticles, Converting Glucose to Lactate.

    Science.gov (United States)

    Mukai, Chinatsu; Gao, Lizeng; Nelson, Jacquelyn L; Lata, James P; Cohen, Roy; Wu, Lauren; Hinchman, Meleana M; Bergkvist, Magnus; Sherwood, Robert W; Zhang, Sheng; Travis, Alexander J

    2017-01-02

    For nanobiotechnology to achieve its potential, complex organic-inorganic systems must grow to utilize the sequential functions of multiple biological components. Critical challenges exist: immobilizing enzymes can block substrate-binding sites or prohibit conformational changes, substrate composition can interfere with activity, and multistep reactions risk diffusion of intermediates. As a result, the most complex tethered reaction reported involves only 3 enzymes. Inspired by the oriented immobilization of glycolytic enzymes on the fibrous sheath of mammalian sperm, here we show a complex reaction of 10 enzymes tethered to nanoparticles. Although individual enzyme efficiency was higher in solution, the efficacy of the 10-step pathway measured by conversion of glucose to lactate was significantly higher when tethered. To our knowledge, this is the most complex organic-inorganic system described, and it shows that tethered, multi-step biological pathways can be reconstituted in hybrid systems to carry out functions such as energy production or delivery of molecular cargo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. A Scholarly Pathway in Quality Improvement and Patient Safety.

    Science.gov (United States)

    Ferguson, Catherine C; Lamb, Geoffrey

    2015-10-01

    There are several challenges to teaching quality improvement (QI) and patient safety material to medical students, as successful programs should combine didactic and experiential teaching methods, integrate the material into the preclinical and clinical years, and tailor the material to the schools' existing curriculum. The authors describe the development, implementation, and assessment of the Quality Improvement and Patient Safety (QuIPS) Scholarly Pathway-a faculty-mentored, three-year experience for students interested in gaining exposure to QI and patient safety concepts at the Medical College of Wisconsin (MCW). The QuIPS pathway capitalized on the existing structure of scholarly pathways for MCW medical students, allowing QI and patient safety to be incorporated into the existing curriculum using didactic and experiential instruction and spanning preclinical and clinical education. Student reaction to the QuIPS pathway has been favorable. Preliminary data demonstrate that student knowledge as measured by the Quality Improvement Knowledge Assessment Tool significantly increased after the first year of implementation. A novel curriculum such as the QuIPS pathway provides an important opportunity to develop and test new assessment tools for curricula in systems-based practice and practice-based learning and improvement. The authors also hope that by bringing together local QI and patient safety experts and stakeholders during the curricular development process, they have laid the groundwork for the creation of a more pervasive curriculum that will reach all MCW students in the future. The model may be generalizable to other U.S. medical schools with scholarly pathways as well.

  19. High-level theoretical characterization of the vinoxy radical (•CH2CHO) + O2 reaction

    Science.gov (United States)

    Weidman, Jared D.; Allen, Ryan T.; Moore, Kevin B.; Schaefer, Henry F.

    2018-05-01

    Numerous processes in atmospheric and combustion chemistry produce the vinoxy radical (•CH2CHO). To understand the fate of this radical and to provide reliable energies needed for kinetic modeling of such processes, we have examined its reaction with O2 using highly reliable theoretical methods. Utilizing the focal point approach, the energetics of this reaction and subsequent reactions were obtained using coupled-cluster theory with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set limit. These extrapolated energies were appended with several corrections including a treatment of full triples and connected quadruple excitations, i.e., CCSDT(Q). In addition, this study models the initial vinoxy radical + O2 reaction for the first time with multireference methods. We predict a barrier for this reaction of approximately 0.4 kcal mol-1. This result agrees with experimental findings but is in disagreement with previous theoretical studies. The vinoxy radical + O2 reaction produces a 2-oxoethylperoxy radical which can undergo a number of unimolecular reactions. Abstraction of a β-hydrogen (a 1,4-hydrogen shift) and dissociation back to reactants are predicted to be competitive to each other due to their similar barriers of 21.2 and 22.3 kcal mol-1, respectively. The minimum-energy β-hydrogen abstraction pathway produces a hydroperoxy radical (QOOH) that eventually decomposes to formaldehyde, CO, and •OH. Two other unimolecular reactions of the peroxy radical are α-hydrogen abstraction (38.7 kcal mol-1 barrier) and HO2• elimination (43.5 kcal mol-1 barrier). These pathways lead to glyoxal + •OH and ketene + HO2• formation, respectively, but they are expected to be uncompetitive due to their high barriers.

  20. Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

    International Nuclear Information System (INIS)

    Kurosaki, Yuzuru; Ho, Tak-San; Rabitz, Herschel

    2014-01-01

    We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O 2 + O asymptote on the ground-state 1 A ′ potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excited electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization

  1. Oxygen diffusion pathways in a cofactor-independent dioxygenase

    Science.gov (United States)

    Di Russo, Natali V.; Condurso, Heather L.; Li, Kunhua; Bruner, Steven D.; Roitberg, Adrian E.

    2015-01-01

    Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O2 diffusion is emerging, where specific channels guide O2 to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O2 reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O2 at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O2 in the absence of cofactors or metals, the way O2 reaches the active site is similar to that reported for other O2-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O2 access that are conserved among very different types of proteins. PMID:26508997

  2. Solid State Pathways towards Molecular Complexity in Space

    Science.gov (United States)

    Linnartz, Harold; Bossa, Jean-Baptiste; Bouwman, Jordy; Cuppen, Herma M.; Cuylle, Steven H.; van Dishoeck, Ewine F.; Fayolle, Edith C.; Fedoseev, Gleb; Fuchs, Guido W.; Ioppolo, Sergio; Isokoski, Karoliina; Lamberts, Thanja; Öberg, Karin I.; Romanzin, Claire; Tenenbaum, Emily; Zhen, Junfeng

    2011-12-01

    It has been a long standing problem in astrochemistry to explain how molecules can form in a highly dilute environment such as the interstellar medium. In the last decennium more and more evidence has been found that the observed mix of small and complex, stable and highly transient species in space is the cumulative result of gas phase and solid state reactions as well as gas-grain interactions. Solid state reactions on icy dust grains are specifically found to play an important role in the formation of the more complex ``organic'' compounds. In order to investigate the underlying physical and chemical processes detailed laboratory based experiments are needed that simulate surface reactions triggered by processes as different as thermal heating, photon (UV) irradiation and particle (atom, cosmic ray, electron) bombardment of interstellar ice analogues. Here, some of the latest research performed in the Sackler Laboratory for Astrophysics in Leiden, the Netherlands is reviewed. The focus is on hydrogenation, i.e., H-atom addition reactions and vacuum ultraviolet irradiation of interstellar ice analogues at astronomically relevant temperatures. It is shown that solid state processes are crucial in the chemical evolution of the interstellar medium, providing pathways towards molecular complexity in space.

  3. Kinetic studies of the yeast His-Asp phosphorelay signaling pathway

    Science.gov (United States)

    Kaserer, Alla O.; Andi, Babak; Cook, Paul F.; West, Ann H.

    2010-01-01

    For both prokaryotic and eukaryotic His-Asp phosphorelay signaling pathways, the rates of protein phosphorylation and dephosphorylation determine the stimulus-to-response time frame. Thus, kinetic studies of phosphoryl group transfer between signaling partners are important for gaining a full understanding of how the system is regulated. In many cases, the phosphotransfer reactions are too fast for rates to be determined by manual experimentation. Rapid quench flow techniques thus provide a powerful method for studying rapid reactions that occur in the millisecond time frame. In this chapter, we describe experimental design and procedures for kinetic characterization of the yeast SLN1-YPD1-SSK1 osmoregulatory phosphorelay system using a rapid quench flow kinetic instrument. PMID:20946842

  4. Natural uranium-series radionuclide inventories in coastal and oceanic waters of the south-western Pacific - insights into trace metal flux and removal pathway analysis

    International Nuclear Information System (INIS)

    Szymczak, R.; Jeffree, R.A.; Peck, G.A.

    2003-01-01

    Participate scavenging of trace metals plays a major role in determining their ecosystem flux and incident dissolved concentrations. Differences in the half-lives and biogeochemical behaviour of natural uranium series radioisotope pairs (eg. 238 U/ 234 Th, 210 Pb/ 210 Po) allow their application as oceanic process tracers. Coincidental measurements of dissolved and particulate trace element concentrations and inventories of radionuclides in the Noumea coral lagoon and adjacent offshore waters were used to quantify water column flux rates and provide insights on removal pathway analysis. Understanding prevailing pathways and respective flux rates of pollutants in specific coastal and oceanic systems will assist to establish the fate and consequence of pollutants and allow sustainable management strategies to be developed. Both natural and pollutant chemical species introduced to the marine environment may either remain benign in solution or undergo physiological uptake by biota, but most often associate with colloids and fine particles, which subsequent undergo aggregation, sedimentation and removal to the sea floor

  5. Status survey on the adverse reactions of CT contrast media

    International Nuclear Information System (INIS)

    Moon, Il Bong; Dong, Kyung Rae; Kim, Kwang Cheol

    2016-01-01

    This study is aimed at suggesting the necessity of critical paths for the adverse reactions of contrast media, and investigating the ways to respond properly at the time of adverse reactions. The question on the size of hospitals in possession of CT equipment indicated that general hospitals accounted for 50% at the highest rate. In terms of job experience, 50% of radiological technologists had more than 10 years of experience, which accounted for the highest rate. It was shown that the average number of radiological technologists in the CT room was 3, that of nurses 0.6 and that of administrative workers and others 0.3 (87.5%) of respondents explained the treatment method of adverse reaction, and 97.5% responded that they were using the manual for the case of adverse reactions. Also, 87.5% of respondents indicated that they had the division of works at the time of adverse reaction, and the yearly average number of cases was 35. The average handling time was shown to be 51 minutes. This Emergency treatment manual and Critical Pathway program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings

  6. Status survey on the adverse reactions of CT contrast media

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Il Bong; Dong, Kyung Rae [Dept. of Radiological Technology, Gwangju Health University, Gwangju (Korea, Republic of); Kim, Kwang Cheol [Social Disaster Management Division, Jeollanamdo Provincial Government, Muan (Korea, Republic of)

    2016-11-15

    This study is aimed at suggesting the necessity of critical paths for the adverse reactions of contrast media, and investigating the ways to respond properly at the time of adverse reactions. The question on the size of hospitals in possession of CT equipment indicated that general hospitals accounted for 50% at the highest rate. In terms of job experience, 50% of radiological technologists had more than 10 years of experience, which accounted for the highest rate. It was shown that the average number of radiological technologists in the CT room was 3, that of nurses 0.6 and that of administrative workers and others 0.3 (87.5%) of respondents explained the treatment method of adverse reaction, and 97.5% responded that they were using the manual for the case of adverse reactions. Also, 87.5% of respondents indicated that they had the division of works at the time of adverse reaction, and the yearly average number of cases was 35. The average handling time was shown to be 51 minutes. This Emergency treatment manual and Critical Pathway program can be used as one of the patient care tools for reducing the adverse reactions to contrast media and increasing the efficiency of care process in CT examination settings.

  7. Voltammetry coupled to mass spectrometry in the presence of isotope {sup 18}O labeled water for the prediction of oxidative transformation pathways of activated aromatic ethers: Acebutolol

    Energy Technology Data Exchange (ETDEWEB)

    Bussy, Ugo; Tea, Illa [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Ferchaud-Roucher, Véronique; Krempf, Michel [Université de Nantes, Plateforme Spectrométrie de Masse, CRNH, SFR Santé F. Bonamy, Institut du Thorax, UMR S1087, IRT-UN, BP 70721, 8 Quai Moncousu, 44007 Nantes cedex 1 (France); Silvestre, Virginie; Galland, Nicolas [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Jacquemin, Denis [LUNAM Université de Nantes, CNRS, Chimie et Interdisciplinarité: Synthèse, Analyse et Modélisation (CEISAM), UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Institut Universitaire de France, 103, Boulevard Saint-Michel, 75005 Cedex 5 France (France); Andresen-Bergström, Moa; Jurva, Ulrik [CVGI iMed DMPK, AstraZeneca R and D Mölndal, Mölndal (Sweden); and others

    2013-01-31

    Highlights: ► Voltammetry coupled to mass spectrometry method as a useful tool for on-line predictions of electrochemical transformations. ► Evidence of the O-dealkoxylation reaction pathway of acebutolol in the presence of labeled water. ► New approach for on line EC-MS applications. -- Abstract: The coupling between an electrochemical cell (EC) and a mass spectrometer (MS) is a useful screening tool (EC-MS) to study the oxidative transformation pathways of various electroactive species. For that purpose, we showed that the EC-MS method, carried out in the presence and absence of isotope {sup 18}O labeled water leads not only to a fast identification of oxidation products but also leads to a fast elucidation of the mechanism pathway reaction. We examined herein the case of the electrochemical hydrolysis of activated aromatic ether. Acebutolol (β-blockers) was selected herein as model of activated aromatic ether, and its electrochemical oxidation was examined in both the presence and absence of isotope {sup 18}O labeled water. To elucidate electrochemical hydrolysis pathway reaction: O-dealkylation or O-dealkoxylation, our approach was used to prove its applicability. The electrochemical oxidation mechanism was then elucidated showing an O-dealkoxylation reaction. In addition, density functional theory (DFT) calculations fully support the experimental conclusions.

  8. The contributions of the cerebellum in sensorimotor control: what are the prevailing opinions which will guide forthcoming studies?

    Science.gov (United States)

    Manto, Mario; Oulad Ben Taib, Nordeyn

    2013-06-01

    Although considerable progress has been made in developing models of cerebellar function in sensorimotor control, the exact nature of the basic operations performed by the cerebellum remain elusive. Several major theories have emerged these last decades. According to the hypothesis of Marr and Albus, the climbing fiber input carries an error signal weakening the strength of a subset of parallel fibers/Purkinje neurons synapses in the cerebellar cortex. Cerebellar circuits would gain the control of movement through trial and error. The hypothesis of internal models emulating movements is currently highly cited. There is a general agreement that (1) the central nervous system has to cope with an intrinsic time delay of sensory feedback related to motor activities and (2) estimations of future motor states are essential to perform fast and accurate movements. According to this second theory, cerebellar dysmetria, one of the cardinal cerebellar deficits, would result from a distorted predictive control. A third popular theory relates to the inverse models that would be stored in the cerebellum. Acquisition of a motor act would require forward models, and the acquisition process itself would generate an inverse model to allow an unconscious coordinated movement. Recently, an international panel of experts from various disciplines discussed the prevailing opinions in a consensus statement and tried to extract their clinical relevance in terms of pathogenesis of the clinical symptoms. Although a consensus is still not reached, the prevailing opinions provide a sound framework to conduct novel studies and try to discover the secrets of cerebellar circuits.

  9. Photodegradation of malachite green under simulated and natural irradiation: Kinetics, products, and pathways

    International Nuclear Information System (INIS)

    Yong, Li; Zhanqi, Gao; Yuefei, Ji; Xiaobin, Hu; Cheng, Sun; Shaogui, Yang; Lianhong, Wang; Qingeng, Wang; Die, Fang

    2015-01-01

    Highlights: • Photofate of malachite green was studied under simulated and natural irradiation. • Favorable conditions for degradation were optimized by the orthogonal array design. • Main ROS for the decomposition were determined by free radical quenchers. • Fifty-three products were determined by LC–MS and GC–MS. • Pathways were proposed with the aid of theoretical calculation. - Abstract: In this work photodegradation rates and pathways of malachite green were studied under simulated and solar irradiation with the goal of assessing the potential of photolysis as a removal mechanism in real aquatic environment. Factors influencing the photodegradation process were investigated, including pH, humic acid, Fe 2+ , Ca 2+ , HCO 3 − , and NO 3 − , of which favorable conditions were optimized by the orthogonal array design under simulated sunlight irradiation in the presence of dissolved oxygen. The degradation processes of malachite green conformed to pseudo first-order kinetics and their degradation rate constants were between 0.0062 and 0.4012 h −1 . Under solar irradiation, the decolorization efficiency of most tests can reach almost 100%, and relatively thorough mineralization could be observed. Forty degradation products were detected by liquid chromatography–mass spectrometry, and thirteen small molecular products were identified by gas chromatography–mass spectrometry. Based on the analyses of the degradation products and calculation of the frontier electron density, the pathways were proposed: decomposition of conjugated structure, N-demethylation reactions, hydroxyl addition reactions, the removal of benzene ring, and the ring-opening reaction. This study has provided a reference, both for photodegradation of malachite green and future safety applications and predictions of decontamination of related triphenylmethane dyes under real conditions

  10. Homogeneous and Heterogeneous Reaction and Transformation of Hg and Trace Metals in Combustion Systems

    Energy Technology Data Exchange (ETDEWEB)

    J. Helble; Clara Smith; David Miller

    2009-08-31

    The overall goal of this project was to produce a working dynamic model to predict the transformation and partitioning of trace metals resulting from combustion of a broad range of fuels. The information provided from this model will be instrumental in efforts to identify fuels and conditions that can be varied to reduce metal emissions. Through the course of this project, it was determined that mercury (Hg) and arsenic (As) would be the focus of the experimental investigation. Experiments were therefore conducted to examine homogeneous and heterogeneous mercury oxidation pathways, and to assess potential interactions between arsenic and calcium. As described in this report, results indicated that the role of SO{sub 2} on Hg oxidation was complex and depended upon overall gas phase chemistry, that iron oxide (hematite) particles contributed directly to heterogeneous Hg oxidation, and that As-Ca interactions occurred through both gas-solid and within-char reaction pathways. Modeling based on this study indicated that, depending upon coal type and fly ash particle size, vaporization-condensation, vaporization-surface reaction, and As-CaO in-char reaction all play a role in arsenic transformations under combustion conditions.

  11. Indistinguishability and identifiability of kinetic models for the MurC reaction in peptidoglycan biosynthesis.

    Science.gov (United States)

    Hattersley, J G; Pérez-Velázquez, J; Chappell, M J; Bearup, D; Roper, D; Dowson, C; Bugg, T; Evans, N D

    2011-11-01

    An important question in Systems Biology is the design of experiments that enable discrimination between two (or more) competing chemical pathway models or biological mechanisms. In this paper analysis is performed between two different models describing the kinetic mechanism of a three-substrate three-product reaction, namely the MurC reaction in the cytoplasmic phase of peptidoglycan biosynthesis. One model involves ordered substrate binding and ordered release of the three products; the competing model also assumes ordered substrate binding, but with fast release of the three products. The two versions are shown to be distinguishable; however, if standard quasi-steady-state assumptions are made distinguishability cannot be determined. Once model structure uniqueness is ensured the experimenter must determine if it is possible to successfully recover rate constant values given the experiment observations, a process known as structural identifiability. Structural identifiability analysis is carried out for both models to determine which of the unknown reaction parameters can be determined uniquely, or otherwise, from the ideal system outputs. This structural analysis forms an integrated step towards the modelling of the full pathway of the cytoplasmic phase of peptidoglycan biosynthesis. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  12. Insights into the mechanisms on chemical reactions: reaction paths for chemical reactions

    International Nuclear Information System (INIS)

    Dunning, T.H. Jr.; Rosen, E.; Eades, R.A.

    1987-01-01

    We report reaction paths for two prototypical chemical reactions: Li + HF, an electron transfer reaction, and OH + H 2 , an abstraction reaction. In the first reaction we consider the connection between the energetic terms in the reaction path Hamiltonian and the electronic changes which occur upon reaction. In the second reaction we consider the treatment of vibrational effects in chemical reactions in the reaction path formalism. 30 refs., 9 figs

  13. Geometric phase and quantum interference in photosynthetic reaction center: Regulation of electron transfer

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Yuming, E-mail: ymsun@ytu.edu.cn; Su, Yuehua; Dai, Zhenhong; Wang, WeiTian

    2016-10-20

    Photosynthesis is driven by electron transfer in reaction centers in which the functional unit is composed of several simple molecules C{sub 2}-symmetrically arranged into two branches. In view of quantum mechanism, both branches are possible pathways traversed by the transferred electron. Due to different evolution of spin state along two pathways in transmembrane electric potential (TEP), quantum state of the transferred electron at the bridged site acquires a geometric phase difference dependent on TEP, the most efficient electron transport takes place in a specific range of TEP beyond which electron transfer is dramatically suppressed. What’s more, reaction center acts like elaborately designed quantum device preparing polarized spin dependent on TEP for the transferred electron to regulate the reduction potential at bridged site. In brief, electron transfer generates the TEP, reversely, TEP modulates the efficiency of electron transfer. This may be an important approach to maintaining an appreciable pH environment in photosynthesis.

  14. Reactions of neopentane and neohexane on platinum/Y-zeolite and platinum/silica catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Foger, K.; Anderson, J.R.

    1978-10-13

    The hydrocracking/hydroisomerization reaction of 20:1 hydrogen/neopentane at 455-625/sup 0/K was studied on platinum-exchanged sodium, calcium, and lanthanum Y zeolites and Aerosil-supported platinum of 1-20 nm average platinum particle size, by analysis of the product distribution, ESCA, and temperature-programed desorption. The results suggested that the reaction occurs only on platinum and that it proceeds by two parallel pathways which have different activation energies and whose relative proportion depends on the particle size. One pathway is the conventionally accepted one on low-index crystallite facets; the other proceeds on single-surface platinum atoms of low coordination (corner or edge atoms) which become more abundant at lower crystallite size. In both cases, the adsorbed intermediate may undergo either isomerization or hydrogenolysis; the selectivity depends on the hydrogen partial pressure and the relative strength of adsorption of hydrogen and neopentane. Neohexane isomerization selectivity on the same catalysts is consistent with a carbonium ion mechanism on a dual-function catalyst.

  15. Mechanistic Insights into the Unique Role of Copper in CO2 Electroreduction Reactions.

    Science.gov (United States)

    Liu, Shan Ping; Zhao, Ming; Gao, Wang; Jiang, Qing

    2017-01-20

    Cu demonstrates a unique capability towards CO 2 electroreduction that can close the anthropogenic carbon cycle; however, its reaction mechanism remains elusive, owing to the obscurity of the solid-liquid interface on Cu surfaces where electrochemical reactions occur. Using a genetic algorithm method in addition to density functional theory, we explicitly identify the configuration of a water bilayer on Cu(2 1 1) and build electrochemical models. These enable us to reveal a mechanistic picture for CO 2 electroreduction, finding the key intermediates CCO* for the C 2 H 4 pathway and CH* for the CH 4 pathway, which rationalize a series of experimental observations. Furthermore, we find that the interplay between the Cu surfaces, carbon monomers, and water network (but not the binding of CO*) essentially determine the unique capability of Cu towards CO 2 electroreduction, proposing a new and effective descriptor for exploiting optimal catalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Attainment of chemical equilibrium in effusive beam sources of the heterogeneous reaction type

    International Nuclear Information System (INIS)

    Hildenbrand, D.L.

    1979-01-01

    Effusive beam sources derived from gas-solid reactions provide a very important pathway for widening the scope of high temperature thermodynamic studies, but the attainment of chemical equilibrium within these sources is problematical. Some of the underlying kinetic factors associated with the use of these sources are discussed. As one might expect, it is important to maximize the ratio of reactive surface area to exit orifice area. Equilibrium seems to be achieved more readily among the products of gas-solid reactions than among reactant and products, as suggested by the quasi-equilibrium model. Some experiences with the use of heterogeneous reaction sources are described, and two definitive tests for the establishment of equilibrium are outlined

  17. Nonequilibrium photochemical reactions induced by lasers. Technical progress report

    International Nuclear Information System (INIS)

    Steinfeld, J.I.

    1978-04-01

    Research has progressed in six principal subject areas of interest to DOE advanced (laser) isotope separation efforts. These are (1) Infrared double resonance spectroscopy of molecules excited by multiple infrared photon absorption, particularly SF 6 and vinyl chloride. (2) Infrared multiphoton excitation of metastable triplet-state molecules, e.g., biacetyl. (3) An Information Theory analysis of multiphoton excitation and collisional deactivation has been carried out. (4) The mechanism of infrared energy deposition and multiphoton-induced reactions in chlorinated ethylene derivatives; and RRKM (statistical) model accounts for all observed behavior of the system, and a deuterium-specific reaction pathway has been identified. (5) Diffusion-enhanced laser isotope separation in N 16 O/N 18 O. (6) A technical evaluation of laser-induced chemistry and isotope separation

  18. Surface Interrogation Scanning Electrochemical Microscopy for a Photoelectrochemical Reaction: Water Oxidation on a Hematite Surface.

    Science.gov (United States)

    Kim, Jae Young; Ahn, Hyun S; Bard, Allen J

    2018-03-06

    To understand the pathway of a photoelectrochemical (PEC) reaction, quantitative knowledge of reaction intermediates is important. We describe here surface interrogation scanning electrochemical microscopy for this purpose (PEC SI-SECM), where a light pulse to a photoactive semiconductor film at a given potential generates intermediates that are then analyzed by a tip generated titrant at known times after the light pulse. The improvements were demonstrated for photoelectrochemical water oxidation (oxygen evolution) reaction on a hematite surface. The density of photoactive sites, proposed to be Fe 4+ species, on a hematite surface was successfully quantified, and the photoelectrochemical water oxidation reaction dynamics were elucidated by time-dependent redox titration experiments. The new configuration of PEC SI-SECM should find expanded usage to understand and investigate more complicated PEC reactions with other materials.

  19. The nucleus accumbens 5-HTR4-CART pathway ties anorexia to hyperactivity

    Science.gov (United States)

    Jean, A; Laurent, L; Bockaert, J; Charnay, Y; Dusticier, N; Nieoullon, A; Barrot, M; Neve, R; Compan, V

    2012-01-01

    In mental diseases, the brain does not systematically adjust motor activity to feeding. Probably, the most outlined example is the association between hyperactivity and anorexia in Anorexia nervosa. The neural underpinnings of this ‘paradox', however, are poorly elucidated. Although anorexia and hyperactivity prevail over self-preservation, both symptoms rarely exist independently, suggesting commonalities in neural pathways, most likely in the reward system. We previously discovered an addictive molecular facet of anorexia, involving production, in the nucleus accumbens (NAc), of the same transcripts stimulated in response to cocaine and amphetamine (CART) upon stimulation of the 5-HT4 receptors (5-HTR4) or MDMA (ecstasy). Here, we tested whether this pathway predisposes not only to anorexia but also to hyperactivity. Following food restriction, mice are expected to overeat. However, selecting hyperactive and addiction-related animal models, we observed that mice lacking 5-HTR1B self-imposed food restriction after deprivation and still displayed anorexia and hyperactivity after ecstasy. Decryption of the mechanisms showed a gain-of-function of 5-HTR4 in the absence of 5-HTR1B, associated with CART surplus in the NAc and not in other brain areas. NAc-5-HTR4 overexpression upregulated NAc-CART, provoked anorexia and hyperactivity. NAc-5-HTR4 knockdown or blockade reduced ecstasy-induced hyperactivity. Finally, NAc-CART knockdown suppressed hyperactivity upon stimulation of the NAc-5-HTR4. Additionally, inactivating NAc-5-HTR4 suppressed ecstasy's preference, strengthening the rewarding facet of anorexia. In conclusion, the NAc-5-HTR4/CART pathway establishes a ‘tight-junction' between anorexia and hyperactivity, suggesting the existence of a primary functional unit susceptible to limit overeating associated with resting following homeostasis rules. PMID:23233022

  20. Actinide complexation kinetics: rate and mechanism of dioxoneptunium (V) reaction with chlorophosphonazo III

    International Nuclear Information System (INIS)

    Fugate, G.; Feil-Jenkins, J.F.; Sullivan, J.C.; Nash, K.L.

    1996-12-01

    Rates of complex formation and dissociation in NpO 2 + - Chlorophosphonazo III (2,7-bis(4-chloro-2-phosphonobenzeneazo)-1,8- dihydroxynapthalene-3,6-disulfonic acid)(CLIII) were investigated by stopped-flow spectrophotometry. Also, limited studies were made of the rates of reaction of La 3+ , Eu 3+ , Dy 3+ , and Fe 3+ with CLIII. Rate determining step in each system is an intramolecular process, the NpO 2 + -CLIII reaction proceeding by a first order approach to equilibrium in the acid range from 0.1 to 1.0 M. Complex formation occurs independent of acidity, while both acid dependent and independent dissociation pathways are observed. Activation parameters for the complex formation reaction are ΔH=46.2±0.3 kJ/m and ΔS=7± J/mK (I=1.0 M); these for the acid dependent and independent dissociation pathways are ΔH=38.8±0.6 kJ/m, ΔS=-96±18 J/mK, ΔH=70.0± kJ/m, and ΔS=17±1 J/mK, respectively. An isokinetic relationship is observed between the activation parameters for CLIII complex formation with NpO 2 + , UO 2 2+ , Th 4+ , and Zr 4+ . Rates of CLIII complex formation reactions for Fe 3+ , Zr 4+ , NpO 2 + , UO 2 2+ , Th 4+ , La 3+ , Eu 3+ , and Dy 3+ correlate with cation radius rather than charge/radius ratio