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Sample records for accurate chemical analysis

  1. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  2. ACCURATE CHEMICAL MASTER EQUATION SOLUTION USING MULTI-FINITE BUFFERS

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a fundamental framework for studying stochasticity in mesoscopic networks. Because of the multi-scale nature of many networks where reaction rates have large disparity, directly solving dCMEs is intractable due to the exploding size of the state space. It is important to truncate the state space effectively with quantified errors, so accurate solutions can be computed. It is also important to know if all major probabilistic peaks have been computed. Here we introduce the Accurate CME (ACME) algorithm for obtaining direct solutions to dCMEs. With multi-finite buffers for reducing the state space by O(n!), exact steady-state and time-evolving network probability landscapes can be computed. We further describe a theoretical framework of aggregating microstates into a smaller number of macrostates by decomposing a network into independent aggregated birth and death processes, and give an a priori method for rapidly determining steady-state truncation errors. The maximal sizes of the finite buffers for a given error tolerance can also be pre-computed without costly trial solutions of dCMEs. We show exactly computed probability landscapes of three multi-scale networks, namely, a 6-node toggle switch, 11-node phage-lambda epigenetic circuit, and 16-node MAPK cascade network, the latter two with no known solutions. We also show how probabilities of rare events can be computed from first-passage times, another class of unsolved problems challenging for simulation-based techniques due to large separations in time scales. Overall, the ACME method enables accurate and efficient solutions of the dCME for a large class of networks. PMID:27761104

  3. How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

    PubMed

    Grima, Ramon; Thomas, Philipp; Straube, Arthur V

    2011-08-28

    The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order Ω(-3∕2) for reaction systems which do not obey detailed balance and at least accurate to order Ω(-2) for systems obeying detailed balance, where Ω is the characteristic size of the system. Hence, the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order Ω(-1∕2) and variance estimates accurate to order Ω(-3∕2). This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.

  4. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  5. Fast and accurate predictions of covalent bonds in chemical space

    NASA Astrophysics Data System (ADS)

    Chang, K. Y. Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (˜1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H 2+ . Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  6. Fast and accurate predictions of covalent bonds in chemical space.

    PubMed

    Chang, K Y Samuel; Fias, Stijn; Ramakrishnan, Raghunathan; von Lilienfeld, O Anatole

    2016-05-01

    We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated σ bonding to hydrogen, as well as σ and π bonding between main-group elements, occurring in small sets of iso-valence-electronic molecules with elements drawn from second to fourth rows in the p-block of the periodic table. Numerical evidence suggests that first order Taylor expansions of covalent bonding potentials can achieve high accuracy if (i) the alchemical interpolation is vertical (fixed geometry), (ii) it involves elements from the third and fourth rows of the periodic table, and (iii) an optimal reference geometry is used. This leads to near linear changes in the bonding potential, resulting in analytical predictions with chemical accuracy (∼1 kcal/mol). Second order estimates deteriorate the prediction. If initial and final molecules differ not only in composition but also in geometry, all estimates become substantially worse, with second order being slightly more accurate than first order. The independent particle approximation based second order perturbation theory performs poorly when compared to the coupled perturbed or finite difference approach. Taylor series expansions up to fourth order of the potential energy curve of highly symmetric systems indicate a finite radius of convergence, as illustrated for the alchemical stretching of H2 (+). Results are presented for (i) covalent bonds to hydrogen in 12 molecules with 8 valence electrons (CH4, NH3, H2O, HF, SiH4, PH3, H2S, HCl, GeH4, AsH3, H2Se, HBr); (ii) main-group single bonds in 9 molecules with 14 valence electrons (CH3F, CH3Cl, CH3Br, SiH3F, SiH3Cl, SiH3Br, GeH3F, GeH3Cl, GeH3Br); (iii) main-group double bonds in 9 molecules with 12 valence electrons (CH2O, CH2S, CH2Se, SiH2O, SiH2S, SiH2Se, GeH2O, GeH2S, GeH2Se); (iv) main-group triple bonds in 9 molecules with 10 valence electrons (HCN, HCP, HCAs, HSiN, HSi

  7. Line gas sampling system ensures accurate analysis

    SciTech Connect

    Not Available

    1992-06-01

    Tremendous changes in the natural gas business have resulted in new approaches to the way natural gas is measured. Electronic flow measurement has altered the business forever, with developments in instrumentation and a new sensitivity to the importance of proper natural gas sampling techniques. This paper reports that YZ Industries Inc., Snyder, Texas, combined its 40 years of sampling experience with the latest in microprocessor-based technology to develop the KynaPak 2000 series, the first on-line natural gas sampling system that is both compact and extremely accurate. This means the composition of the sampled gas must be representative of the whole and related to flow. If so, relative measurement and sampling techniques are married, gas volumes are accurately accounted for and adjustments to composition can be made.

  8. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    SciTech Connect

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

  9. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  10. Can accurate kinetic laws be created to describe chemical weathering?

    NASA Astrophysics Data System (ADS)

    Schott, Jacques; Oelkers, Eric H.; Bénézeth, Pascale; Goddéris, Yves; François, Louis

    2012-11-01

    Knowledge of the mechanisms and rates of mineral dissolution and growth, especially close to equilibrium, is essential for describing the temporal and spatial evolution of natural processes like weathering and its impact on CO2 budget and climate. The Surface Complexation approach (SC) combined with Transition State Theory (TST) provides an efficient framework for describing mineral dissolution over wide ranges of solution composition, chemical affinity, and temperature. There has been a large debate for several years, however, about the comparative merits of SC/TS versus classical growth theories for describing mineral dissolution and growth at near-to-equilibrium conditions. This study considers recent results obtained in our laboratory on oxides, hydroxides, silicates, and carbonates on near-equilibrium dissolution and growth via the combination of complementary microscopic and macroscopic techniques including hydrothermal atomic force microscopy, hydrogen-electrode concentration cell, mixed flow and batch reactors. Results show that the dissolution and precipitation of hydroxides, kaolinite, and hydromagnesite powders of relatively high BET surface area closely follow SC/TST rate laws with a linear dependence of both dissolution and growth rates on fluid saturation state (Ω) even at very close to equilibrium conditions (|ΔG| < 500 J/mol). This occurs because sufficient reactive sites (e.g. at kink, steps, and edges) are available at the exposed faces for dissolution and/or growth, allowing reactions to proceed via the direct and reversible detachment/attachment of reactants at the surface. In contrast, for magnesite and quartz, which have low surface areas, fewer active sites are available for growth and dissolution. Such minerals exhibit rates dependencies on Ω at near equilibrium conditions ranging from linear to highly non-linear functions of Ω, depending on the treatment of the crystals before the reaction. It follows that the form of the f

  11. Electron Microprobe Analysis Techniques for Accurate Measurements of Apatite

    NASA Astrophysics Data System (ADS)

    Goldoff, B. A.; Webster, J. D.; Harlov, D. E.

    2010-12-01

    Apatite [Ca5(PO4)3(F, Cl, OH)] is a ubiquitous accessory mineral in igneous, metamorphic, and sedimentary rocks. The mineral contains halogens and hydroxyl ions, which can provide important constraints on fugacities of volatile components in fluids and other phases in igneous and metamorphic environments in which apatite has equilibrated. Accurate measurements of these components in apatite are therefore necessary. Analyzing apatite by electron microprobe (EMPA), which is a commonly used geochemical analytical technique, has often been found to be problematic and previous studies have identified sources of error. For example, Stormer et al. (1993) demonstrated that the orientation of an apatite grain relative to the incident electron beam could significantly affect the concentration results. In this study, a variety of alternative EMPA operating conditions for apatite analysis were investigated: a range of electron beam settings, count times, crystal grain orientations, and calibration standards were tested. Twenty synthetic anhydrous apatite samples that span the fluorapatite-chlorapatite solid solution series, and whose halogen concentrations were determined by wet chemistry, were analyzed. Accurate measurements of these samples were obtained with many EMPA techniques. One effective method includes setting a static electron beam to 10-15nA, 15kV, and 10 microns in diameter. Additionally, the apatite sample is oriented with the crystal’s c-axis parallel to the slide surface and the count times are moderate. Importantly, the F and Cl EMPA concentrations are in extremely good agreement with the wet-chemical data. We also present EMPA operating conditions and techniques that are problematic and should be avoided. J.C. Stormer, Jr. et al., Am. Mineral. 78 (1993) 641-648.

  12. Chemical exchange program analysis.

    SciTech Connect

    Waffelaert, Pascale

    2007-09-01

    As part of its EMS, Sandia performs an annual environmental aspects/impacts analysis. The purpose of this analysis is to identify the environmental aspects associated with Sandia's activities, products, and services and the potential environmental impacts associated with those aspects. Division and environmental programs established objectives and targets based on the environmental aspects associated with their operations. In 2007 the most significant aspect identified was Hazardous Materials (Use and Storage). The objective for Hazardous Materials (Use and Storage) was to improve chemical handling, storage, and on-site movement of hazardous materials. One of the targets supporting this objective was to develop an effective chemical exchange program, making a business case for it in FY07, and fully implementing a comprehensive chemical exchange program in FY08. A Chemical Exchange Program (CEP) team was formed to implement this target. The team consists of representatives from the Chemical Information System (CIS), Pollution Prevention (P2), the HWMF, Procurement and the Environmental Management System (EMS). The CEP Team performed benchmarking and conducted a life-cycle analysis of the current management of chemicals at SNL/NM and compared it to Chemical Exchange alternatives. Those alternatives are as follows: (1) Revive the 'Virtual' Chemical Exchange Program; (2) Re-implement a 'Physical' Chemical Exchange Program using a Chemical Information System; and (3) Transition to a Chemical Management Services System. The analysis and benchmarking study shows that the present management of chemicals at SNL/NM is significantly disjointed and a life-cycle or 'Cradle-to-Grave' approach to chemical management is needed. This approach must consider the purchasing and maintenance costs as well as the cost of ultimate disposal of the chemicals and materials. A chemical exchange is needed as a mechanism to re-apply chemicals on site. This will not only reduce the quantity of

  13. A time-accurate implicit method for chemical non-equilibrium flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, Jian-Shun

    1992-01-01

    A new time accurate coupled solution procedure for solving the chemical non-equilibrium Navier-Stokes equations over a wide range of Mach numbers is described. The scheme is shown to be very efficient and robust for flows with velocities ranging from M less than or equal to 10(exp -10) to supersonic speeds.

  14. Chemical process hazards analysis

    SciTech Connect

    1996-02-01

    The Office of Worker Health and Safety (EH-5) under the Assistant Secretary for the Environment, Safety and Health of the US Department (DOE) has published two handbooks for use by DOE contractors managing facilities and processes covered by the Occupational Safety and Health Administration (OSHA) Rule for Process Safety Management of Highly Hazardous Chemicals (29 CFR 1910.119), herein referred to as the PSM Rule. The PSM Rule contains an integrated set of chemical process safety management elements designed to prevent chemical releases that can lead to catastrophic fires, explosions, or toxic exposures. The purpose of the two handbooks, ``Process Safety Management for Highly Hazardous Chemicals`` and ``Chemical Process Hazards Analysis,`` is to facilitate implementation of the provisions of the PSM Rule within the DOE. The purpose of this handbook ``Chemical Process Hazards Analysis,`` is to facilitate, within the DOE, the performance of chemical process hazards analyses (PrHAs) as required under the PSM Rule. It provides basic information for the performance of PrHAs, and should not be considered a complete resource on PrHA methods. Likewise, to determine if a facility is covered by the PSM rule, the reader should refer to the handbook, ``Process Safety Management for Highly Hazardous Chemicals`` (DOE- HDBK-1101-96). Promulgation of the PSM Rule has heightened the awareness of chemical safety management issues within the DOE. This handbook is intended for use by DOE facilities and processes covered by the PSM rule to facilitate contractor implementation of the PrHA element of the PSM Rule. However, contractors whose facilities and processes not covered by the PSM Rule may also use this handbook as a basis for conducting process hazards analyses as part of their good management practices. This handbook explains the minimum requirements for PrHAs outlined in the PSM Rule. Nowhere have requirements been added beyond what is specifically required by the rule.

  15. Chemically accurate energy barriers of small gas molecules moving through hexagonal water rings.

    PubMed

    Hjertenæs, Eirik; Trinh, Thuat T; Koch, Henrik

    2016-07-21

    We present chemically accurate potential energy curves of CH4, CO2 and H2 moving through hexagonal water rings, calculated by CCSD(T)/aug-cc-pVTZ with counterpoise correction. The barriers are extracted from a potential energy surface obtained by allowing the water ring to expand while the gas molecule diffuses through. State-of-the-art XC-functionals are evaluated against the CCSD(T) potential energy surface.

  16. Accurate hydrogen depth profiling by reflection elastic recoil detection analysis

    SciTech Connect

    Verda, R. D.; Tesmer, Joseph R.; Nastasi, Michael Anthony,; Bower, R. W.

    2001-01-01

    A technique to convert reflection elastic recoil detection analysis spectra to depth profiles, the channel-depth conversion, was introduced by Verda, et al [1]. But the channel-depth conversion does not correct for energy spread, the unwanted broadening in the energy of the spectra, which can lead to errors in depth profiling. A work in progress introduces a technique that corrects for energy spread in elastic recoil detection analysis spectra, the energy spread correction [2]. Together, the energy spread correction and the channel-depth conversion comprise an accurate and convenient hydrogen depth profiling method.

  17. Computational Chemical Imaging for Cardiovascular Pathology: Chemical Microscopic Imaging Accurately Determines Cardiac Transplant Rejection

    PubMed Central

    Tiwari, Saumya; Reddy, Vijaya B.; Bhargava, Rohit; Raman, Jaishankar

    2015-01-01

    Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures. PMID:25932912

  18. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space.

    PubMed

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O Anatole; Müller, Klaus-Robert; Tkatchenko, Alexandre

    2015-06-18

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  19. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    SciTech Connect

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

  20. Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

    DOE PAGES

    Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; von Lilienfeld, O. Anatole; Müller, Klaus -Robert; Tkatchenko, Alexandre

    2015-06-04

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstratemore » prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.« less

  1. Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space

    PubMed Central

    2015-01-01

    Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the “holy grail” of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies. PMID:26113956

  2. Chemical and Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bulluck, J. W.; Rushing, R. A.; Thornton, C. P.

    1996-01-01

    Work has included significant research in several areas aimed at further clarification of the aging and chemical failure mechanism of thermoplastics (PVDF or Tefzel) for pipes. Among the areas investigated were the crystallinity changes associated with both the Coflon and Tefzel after various simulated environmental exposures using X-Ray diffraction analysis. We have found that significant changes in polymer crystallinity levels occur as a function of the exposures. These crystallinity changes may have important consequences on the fracture, fatigue, tensile, and chemical resistance of the materials. We have also noted changes in the molecular weight distribution of the Coflon material using a dual detector Gel Permeation Analysis. Again these changes may result in variation in the mechanical and chemical properties in the material. We conducted numerous analytical studies with methods including X-Ray Diffraction, Gel Permeation Chromatography, Fourier Transform Infrared Spectroscopy, Thermogravimetric Analysis, and Differential Scanning Calorimetry. We investigated a number of aged samples of both Tefzel and Coflon that were forwarded from MERL. Pressurized tests were performed in a modified Fluid G, which we will call G2. In this case the ethylene diamine concentration was increased to 3 percent in methanol. Coflon pipe sections and powdered Coflon were exposed in pressure cells at 1700 psi at three separate test temperatures, 70 C, 110 C, and 130 C. The primary purpose of the pressure tests in Fluid G2 was to further elucidate the aging mechanism of PVDF degradation.

  3. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  4. Chemical and Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bulluck, J. W.; Rushing, R. A.

    1997-01-01

    Work during the past three years has included significant research in several areas aimed at further clarification of the aging and chemical failure mechanism of thermoplastics (PVDF or Tefzel) for pipes. Among the areas investigated were the crystallinity changes associated with both the Coflon and Tefzel after various simulated environmental exposures using X-Ray diffraction analysis. We have found that significant changes in polymer crystallinity levels occur as a function of the exposures. These crystallinity changes may have important consequences on the fracture, fatigue, tensile, and chemical resistance of the materials. We have also noted changes in the molecular weight distribution and the increased crosslinking of the Coflon material using Gel Permeation Chromatographic Analysis. Again these changes may result in variations in the mechanical and chemical properties in the material. We conducted numerous analytical studies with methods including X-ray Diffraction, Gel Permeation Chromatography, Fourier Transform Infrared Spectroscopy, and Differential Scanning Calorimetry. We investigated a plethora of aged samples of both Tefzel and Coflon that were forwarded from MERL. Pressurized tests were performed on powdered PVDF in a modified Fluid A, which we will call A-2. In this case the ethylene diamine concentration was increased to 3 percent in methanol. Coflon pipe sections and powdered Coflon were exposed in pressure cells at 1700 psi at three separate test temperatures.

  5. Chemical and Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bulluck, J. W.; Rushing, R. A.

    1994-01-01

    Thermal decomposition activation energies have been determined using two methods of Thermogravimetric Analysis (TGA), with good correlation being obtained between the two techniques. Initial heating curves indicated a two-component system for Coflon (i.e. polymer plus placticizer) but a single component system for Tefzel. Two widely differing activation energies were for Coflon supported this view, 15 kcl/mol being associated with plasticizer, and 40 kcal/mol with polymer degradation. With Tefzel, values were 40-45 kcal/mol, the former perhaps being associated with a low molecular weight fraction. Appropriate acceleration factors have been determined. Thermomechanical Analysis (TMA) has shown considerable dimensional change during temperature cycles. For unaged pipe sections heating to 100 C and then holding the temperature resulted in a stable thickness increase of 2%, whereas the Coflon thickness decreased continuously, reaching -4% in 2.7 weeks. Previously strained tensile bars of Tefzel expanded on cooling during TMA. SEM performed on H2S-aged Coflon samples showed significant changes in both physical and chemical nature. The first may have resulted from explosive decompression after part of the aging process. Chemically extensive dehydrofluorination was indicated, and sulfur was present as a result of the aging. These observations indicate that chemical attack of PVDF can occur in some circumstances.

  6. State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation

    PubMed Central

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-01-01

    The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEG), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of 1) the birth and death model, 2) the single gene expression model, 3) the genetic toggle switch model, and 4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate out theories. Overall, the novel state space

  7. State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation.

    PubMed

    Cao, Youfang; Terebus, Anna; Liang, Jie

    2016-04-01

    The discrete chemical master equation (dCME) provides a general framework for studying stochasticity in mesoscopic reaction networks. Since its direct solution rapidly becomes intractable due to the increasing size of the state space, truncation of the state space is necessary for solving most dCMEs. It is therefore important to assess the consequences of state space truncations so errors can be quantified and minimized. Here we describe a novel method for state space truncation. By partitioning a reaction network into multiple molecular equivalence groups (MEGs), we truncate the state space by limiting the total molecular copy numbers in each MEG. We further describe a theoretical framework for analysis of the truncation error in the steady-state probability landscape using reflecting boundaries. By aggregating the state space based on the usage of a MEG and constructing an aggregated Markov process, we show that the truncation error of a MEG can be asymptotically bounded by the probability of states on the reflecting boundary of the MEG. Furthermore, truncating states of an arbitrary MEG will not undermine the estimated error of truncating any other MEGs. We then provide an overall error estimate for networks with multiple MEGs. To rapidly determine the appropriate size of an arbitrary MEG, we also introduce an a priori method to estimate the upper bound of its truncation error. This a priori estimate can be rapidly computed from reaction rates of the network, without the need of costly trial solutions of the dCME. As examples, we show results of applying our methods to the four stochastic networks of (1) the birth and death model, (2) the single gene expression model, (3) the genetic toggle switch model, and (4) the phage lambda bistable epigenetic switch model. We demonstrate how truncation errors and steady-state probability landscapes can be computed using different sizes of the MEG(s) and how the results validate our theories. Overall, the novel state space

  8. Unconditionally stable, second-order accurate schemes for solid state phase transformations driven by mechano-chemical spinodal decomposition

    DOE PAGES

    Sagiyama, Koki; Rudraraju, Shiva; Garikipati, Krishna

    2016-09-13

    Here, we consider solid state phase transformations that are caused by free energy densities with domains of non-convexity in strain-composition space; we refer to the non-convex domains as mechano-chemical spinodals. The non-convexity with respect to composition and strain causes segregation into phases with different crystal structures. We work on an existing model that couples the classical Cahn-Hilliard model with Toupin’s theory of gradient elasticity at finite strains. Both systems are represented by fourth-order, nonlinear, partial differential equations. The goal of this work is to develop unconditionally stable, second-order accurate time-integration schemes, motivated by the need to carry out large scalemore » computations of dynamically evolving microstructures in three dimensions. We also introduce reduced formulations naturally derived from these proposed schemes for faster computations that are still second-order accurate. Although our method is developed and analyzed here for a specific class of mechano-chemical problems, one can readily apply the same method to develop unconditionally stable, second-order accurate schemes for any problems for which free energy density functions are multivariate polynomials of solution components and component gradients. Apart from an analysis and construction of methods, we present a suite of numerical results that demonstrate the schemes in action.« less

  9. Unconditionally stable, second-order accurate schemes for solid state phase transformations driven by mechano-chemical spinodal decomposition

    NASA Astrophysics Data System (ADS)

    Sagiyama, K.; Rudraraju, S.; Garikipati, K.

    2016-11-01

    We consider solid state phase transformations that are caused by free energy densities with domains of non-convexity in strain-composition space; we refer to the non-convex domains as mechano-chemical spinodals. The non-convexity with respect to composition and strain causes segregation into phases with different crystal structures. We work on an existing model that couples the classical Cahn-Hilliard model with Toupin's theory of gradient elasticity at finite strains. Both systems are represented by fourth-order, nonlinear, partial differential equations. The goal of this work is to develop unconditionally stable, second-order accurate time-integration schemes, motivated by the need to carry out large scale computations of dynamically evolving microstructures in three dimensions. We also introduce reduced formulations naturally derived from these proposed schemes for faster computations that are still second-order accurate. Although our method is developed and analyzed here for a specific class of mechano-chemical problems, one can readily apply the same method to develop unconditionally stable, second-order accurate schemes for any problems for which free energy density functions are multivariate polynomials of solution components and component gradients. Apart from an analysis and construction of methods, we present a suite of numerical results that demonstrate the schemes in action.

  10. A novel automated image analysis method for accurate adipocyte quantification

    PubMed Central

    Osman, Osman S; Selway, Joanne L; Kępczyńska, Małgorzata A; Stocker, Claire J; O’Dowd, Jacqueline F; Cawthorne, Michael A; Arch, Jonathan RS; Jassim, Sabah; Langlands, Kenneth

    2013-01-01

    Increased adipocyte size and number are associated with many of the adverse effects observed in metabolic disease states. While methods to quantify such changes in the adipocyte are of scientific and clinical interest, manual methods to determine adipocyte size are both laborious and intractable to large scale investigations. Moreover, existing computational methods are not fully automated. We, therefore, developed a novel automatic method to provide accurate measurements of the cross-sectional area of adipocytes in histological sections, allowing rapid high-throughput quantification of fat cell size and number. Photomicrographs of H&E-stained paraffin sections of murine gonadal adipose were transformed using standard image processing/analysis algorithms to reduce background and enhance edge-detection. This allowed the isolation of individual adipocytes from which their area could be calculated. Performance was compared with manual measurements made from the same images, in which adipocyte area was calculated from estimates of the major and minor axes of individual adipocytes. Both methods identified an increase in mean adipocyte size in a murine model of obesity, with good concordance, although the calculation used to identify cell area from manual measurements was found to consistently over-estimate cell size. Here we report an accurate method to determine adipocyte area in histological sections that provides a considerable time saving over manual methods. PMID:23991362

  11. Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips

    PubMed Central

    Ding, Huijiang; Sadeghi, Saman; Shah, Gaurav J.; Chen, Supin; Keng, Pei Yuin; Kim, Chang-Jin “CJ”; van Dam, R. Michael

    2015-01-01

    Digital microfluidic chips provide a new platform for manipulating chemicals for multi-step chemical synthesis or assays at the microscale. The organic solvents and reagents needed for these applications are often volatile, sensitive to contamination, and wetting, i.e. have contact angles of < 90° even on the highly hydrophobic surfaces (e.g., Teflon® or Cytop®) typically used on digital microfluidic chips. Furthermore, often the applications dictate that the processes are performed in a gas environment, not allowing the use of a filler liquid (e.g., oil). These properties pose challenges for delivering controlled volumes of liquid to the chip. An automated, simple, accurate and reliable method of delivering reagents from sealed, off-chip reservoirs is presented here. This platform overcomes the issues of evaporative losses of volatile solvents, cross-contamination, and flooding of the chip by combining a syringe pump, a simple on-chip liquid detector and a robust interface design. The impedance-based liquid detection requires only minimal added hardware to provide a feedback signal to ensure accurate volumes of volatile solvents are introduced to the chip, independent of time delays between dispensing operations. On-demand dispensing of multiple droplets of acetonitrile, a frequently used but difficult to handle solvent due to its wetting properties and volatility, was demonstrated and used to synthesize the positron emission tomography (PET) probe [18F]FDG reliably. PMID:22825699

  12. Accurate dispensing of volatile reagents on demand for chemical reactions in EWOD chips.

    PubMed

    Ding, Huijiang; Sadeghi, Saman; Shah, Gaurav J; Chen, Supin; Keng, Pei Yuin; Kim, Chang-Jin C J; van Dam, R Michael

    2012-09-21

    Digital microfluidic chips provide a new platform for manipulating chemicals for multi-step chemical synthesis or assays at the microscale. The organic solvents and reagents needed for these applications are often volatile, sensitive to contamination, and wetting, i.e. have contact angles of <90° even on the highly hydrophobic surfaces (e.g., Teflon® or Cytop®) typically used on digital microfluidic chips. Furthermore, often the applications dictate that the processes are performed in a gas environment, not allowing the use of a filler liquid (e.g., oil). These properties pose challenges for delivering controlled volumes of liquid to the chip. An automated, simple, accurate and reliable method of delivering reagents from sealed, off-chip reservoirs is presented here. This platform overcomes the issues of evaporative losses of volatile solvents, cross-contamination, and flooding of the chip by combining a syringe pump, a simple on-chip liquid detector and a robust interface design. The impedance-based liquid detection requires only minimal added hardware to provide a feedback signal to ensure accurate volumes of volatile solvents are introduced to the chip, independent of time delays between dispensing operations. On-demand dispensing of multiple droplets of acetonitrile, a frequently used but difficult to handle solvent due to its wetting properties and volatility, was demonstrated and used to synthesize the positron emission tomography (PET) probe [(18)F]FDG reliably.

  13. In-Situ Planetary Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Kounaves, S. P.; Buehler, M. G.; Grannan, S. M.; Hecht, M. H.; Kuhlman, K. R.

    2000-01-01

    Both, the search for evidence of life on Mars and the assessment of the Martian environment in respect to its compatibility with human explorers, will require the ability to measure and understand the aqueous chemistry of the Martian regolith. Direct in-situ chemical analysis is the only method by which chemical biosignatures can be reliably recognized and the toxicity of the regolith accurately assessed. Qualitative and quantitative determination of the aqueous ionic constituents and their concentrations is critical in developing kinetic and thermodynamic models that can be used to accurately predict the potential of the past or present Martian geochemical environment to have either generated or still sustain life. In-situ chemical characterization could provide evidence as to whether the chemical composition of the regolith or evaporates in suspected ancient water bodies have been biologically influenced.

  14. Chemical and Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bulluck, J. W.; Rushing, R. A.

    1995-01-01

    During the past six months we have conducted significant research in several domains in order to clarify and understanding the aging and chemical failure mechanism of thermoplastics (PVDF or Tefzel) for pipes. We organized numerous analytical studies with methods including Fourier Transform Infrared Spectroscopy, Dynamic Mechanical Analysis, Differential Scanning Calorimetry, and Stress Relaxation experiments. In addition we have reanalyzed previous thermogravimetric data concerning the rate of deplasticization of Coflon pipe. We investigated a number of aged samples of both Tefzel and Coflon that were forwarded from MERL. We conducted stress relaxation experiments of Coflon pipe at several temperatures and determined an activation energy. We also examined the dynamic mechanical response PVDF during deplasticization and during methanol plasticization. We performed numerous DSC analyses to research the changing crystalline morphology. We have noted significant changes in crystallinity upon aging for both PVDF and Tefzel. Little variation in elemental composition was noted for many of the aged Coflon and Tefzel samples tested.

  15. Chemical Sensing in Process Analysis.

    ERIC Educational Resources Information Center

    Hirschfeld, T.; And Others

    1984-01-01

    Discusses: (1) rationale for chemical sensors in process analysis; (2) existing types of process chemical sensors; (3) sensor limitations, considering lessons of chemometrics; (4) trends in process control sensors; and (5) future prospects. (JN)

  16. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems. PMID:26651397

  17. A time-accurate implicit method for chemically reacting flows at all Mach numbers

    NASA Technical Reports Server (NTRS)

    Withington, J. P.; Yang, V.; Shuen, J. S.

    1991-01-01

    The objective of this work is to develop a unified solution algorithm capable of treating time-accurate chemically reacting flows at all Mach numbers, ranging from molecular diffusion velocities to supersonic speeds. A rescaled pressure term is used in the momentum equation to circumvent the singular behavior of pressure at low Mach numbers. A dual time-stepping integration procedure is established. The system eigenvalues become well behaved and have the same order of magnitude, even in the very low Mach number regime. The computational efficiency for moderate and high speed flow is competitive with the conventional density-based scheme. The capabilities of the algorithm are demonstrated by applying it to selected model problems including nozzle flows and flame dynamics.

  18. A time-accurate algorithm for chemical non-equilibrium viscous flows at all speeds

    NASA Technical Reports Server (NTRS)

    Shuen, J.-S.; Chen, K.-H.; Choi, Y.

    1992-01-01

    A time-accurate, coupled solution procedure is described for the chemical nonequilibrium Navier-Stokes equations over a wide range of Mach numbers. This method employs the strong conservation form of the governing equations, but uses primitive variables as unknowns. Real gas properties and equilibrium chemistry are considered. Numerical tests include steady convergent-divergent nozzle flows with air dissociation/recombination chemistry, dump combustor flows with n-pentane-air chemistry, nonreacting flow in a model double annular combustor, and nonreacting unsteady driven cavity flows. Numerical results for both the steady and unsteady flows demonstrate the efficiency and robustness of the present algorithm for Mach numbers ranging from the incompressible limit to supersonic speeds.

  19. Toward an Accurate Estimate of the Exfoliation Energy of Black Phosphorus: A Periodic Quantum Chemical Approach.

    PubMed

    Sansone, Giuseppe; Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Karttunen, Antti

    2016-01-01

    The black phosphorus (black-P) crystal is formed of covalently bound layers of phosphorene stacked together by weak van der Waals interactions. An experimental measurement of the exfoliation energy of black-P is not available presently, making theoretical studies the most important source of information for the optimization of phosphorene production. Here, we provide an accurate estimate of the exfoliation energy of black-P on the basis of multilevel quantum chemical calculations, which include the periodic local Møller-Plesset perturbation theory of second order, augmented by higher-order corrections, which are evaluated with finite clusters mimicking the crystal. Very similar results are also obtained by density functional theory with the D3-version of Grimme's empirical dispersion correction. Our estimate of the exfoliation energy for black-P of -151 meV/atom is substantially larger than that of graphite, suggesting the need for different strategies to generate isolated layers for these two systems.

  20. Chemically Accurate Simulation of a Polyatomic Molecule-Metal Surface Reaction

    PubMed Central

    2016-01-01

    Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking measurements with chemical accuracy (4.2 kJ/mol ≈ 1 kcal/mol). The need for only semilocal exchange makes our scheme computationally tractable for dissociation on transition metals. PMID:27284787

  1. Progress toward accurate high spatial resolution actinide analysis by EPMA

    NASA Astrophysics Data System (ADS)

    Jercinovic, M. J.; Allaz, J. M.; Williams, M. L.

    2010-12-01

    High precision, high spatial resolution EPMA of actinides is a significant issue for geochronology, resource geochemistry, and studies involving the nuclear fuel cycle. Particular interest focuses on understanding of the behavior of Th and U in the growth and breakdown reactions relevant to actinide-bearing phases (monazite, zircon, thorite, allanite, etc.), and geochemical fractionation processes involving Th and U in fluid interactions. Unfortunately, the measurement of minor and trace concentrations of U in the presence of major concentrations of Th and/or REEs is particularly problematic, especially in complexly zoned phases with large compositional variation on the micro or nanoscale - spatial resolutions now accessible with modern instruments. Sub-micron, high precision compositional analysis of minor components is feasible in very high Z phases where scattering is limited at lower kV (15kV or less) and where the beam diameter can be kept below 400nm at high current (e.g. 200-500nA). High collection efficiency spectrometers and high performance electron optics in EPMA now allow the use of lower overvoltage through an exceptional range in beam current, facilitating higher spatial resolution quantitative analysis. The U LIII edge at 17.2 kV precludes L-series analysis at low kV (high spatial resolution), requiring careful measurements of the actinide M series. Also, U-La detection (wavelength = 0.9A) requires the use of LiF (220) or (420), not generally available on most instruments. Strong peak overlaps of Th on U make highly accurate interference correction mandatory, with problems compounded by the ThMIV and ThMV absorption edges affecting peak, background, and interference calibration measurements (especially the interference of the Th M line family on UMb). Complex REE bearing phases such as monazite, zircon, and allanite have particularly complex interference issues due to multiple peak and background overlaps from elements present in the activation

  2. TOXICOGENOMIC STUDY OF TRIAZOLE FUNGICIDES AND PERFLUOROALKYL ACIDS IN RAT LIVERS ACCURATELY CATEGORIZES CHEMICALS AND IDENTIFIES MECHANISMS OF TOXICITY

    EPA Science Inventory

    Toxicogenomic analysis of five environmental chemicals was performed to investigate the ability of genomics to predict toxicity, categorize chemicals, and elucidate mechanisms of toxicity. Three triazole antifungals (myclobutanil, propiconazole, and triadimefon) and two perfluori...

  3. An accurate and self-consistent chemical abundance catalogue for the APOGEE/Kepler sample

    NASA Astrophysics Data System (ADS)

    Hawkins, K.; Masseron, T.; Jofré, P.; Gilmore, G.; Elsworth, Y.; Hekker, S.

    2016-10-01

    Context. The APOGEE survey has obtained high-resolution infrared spectra of more than 100 000 stars. Deriving chemical abundances patterns of these stars is paramount to piecing together the structure of the Milky Way. While the derived chemical abundances have been shown to be precise for most stars, some calibration problems have been reported, in particular for more metal-poor stars. Aims: In this paper, we aim to (1) re-determine the chemical abundances of the APOGEE+Kepler stellar sample (APOKASC) with an independent procedure, line list and line selection, and high-quality surface gravity information from asteroseismology; and (2) extend the abundance catalogue by including abundances that are not currently reported in the most recent APOGEE release (DR12). Methods: We fixed the Teff and log g to those determined using spectrophotometric and asteroseismic techniques, respectively. We made use of the Brussels Automatic Stellar Parameter (BACCHUS) code to derive the metallicity and broadening parameters for the APOKASC sample. In addition, we derived differential abundances with respect to Arcturus. Results: We have validated the BACCHUS code on APOGEE data using several well-known stars, and stars from open and globular clusters. We also provide the abundances of C, N, O, Mg, Ca, Si, Ti, S, Al, Na, Ni, Mn, Fe, K, and V for every star and line, and show the impact of line selection on the final abundances. Improvements have been made for some elements (e.g. Ti, Si, V). Additionally, we measure new abundance ratios not found in the current APOGEE release including P, Cu, Rb, and Yb, which are only upper limits at this time, as well as Co and Cr which are promising. Conclusions: In this paper, we present an independent analysis of the APOKASC sample and provide abundances of up to 21 elements. This catalogue can be used not only to study chemical abundance patterns of the Galaxy but also to train data driven spectral approaches which can improve the abundance

  4. Chemical substructure analysis in toxicology

    SciTech Connect

    Beauchamp, R.O. Jr.

    1990-12-31

    A preliminary examination of chemical-substructure analysis (CSA) demonstrates the effective use of the Chemical Abstracts compound connectivity file in conjunction with the bibliographic file for relating chemical structures to biological activity. The importance of considering the role of metabolic intermediates under a variety of conditions is illustrated, suggesting structures that should be examined that may exhibit potential activity. This CSA technique, which utilizes existing large files accessible with online personal computers, is recommended for use as another tool in examining chemicals in drugs. 2 refs., 4 figs.

  5. Laser Chemical Analysis.

    ERIC Educational Resources Information Center

    Zare, Richard N.

    1984-01-01

    Reviews applications of laser methods to analytical problems, selecting examples from multiphoton ionization and fluorescence analysis. Indicates that laser methodologies promise to improve dramatically the detection of trace substances embedded in "real" matrices, giving the analyst a most powerful means for determining the composition of…

  6. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  7. New insights for accurate chemically specific measurements of slow diffusing molecules.

    PubMed

    Hou, Jianbo; Madsen, Louis A

    2013-02-01

    Investigating the myriad features of molecular transport in materials yields fundamental information for understanding processes such as ion conduction, chemical reactions, and phase transitions. Molecular transport especially impacts the performance of ion-containing liquids and polymeric materials when used as electrolytes and separation media, with applications encompassing battery electrolytes, reverse-osmosis membranes, mechanical transducers, and fuel cells. Nuclear magnetic resonance (NMR) provides a unique probe of molecular translations by allowing measurement of all mobile species via spectral selectivity, access to a broad range of transport coefficients, probing of any material direction, and investigation of variable lengthscales in a material, thus, tying morphology to transport. Here, we present new concepts to test for and guarantee robust diffusion measurements. We first employ a standard pulsed-field-gradient (PFG) calibration protocol using (2)H(2)O and obtain expected results, but we observe crippling artifacts when measuring (1)H-glycerol diffusion with the same experimental parameters. A mathematical analysis of (2)H(2)O and glycerol signals in the presence of PFG transients show tight agreement with experimental observations. These analyses lead to our principal findings that (1) negligible artifacts observed with low gyromagnetic ratio (γ) nuclei may become dominant when observing high γ nuclei, and (2) reducing the sample dimension along the gradient direction predictably reduces non-ideal behaviors of NMR signals. We further provide a useful quantitative strategy for error minimization when measuring diffusing species slower than the one used for gradient calibration. PMID:23406112

  8. New insights for accurate chemically specific measurements of slow diffusing molecules

    NASA Astrophysics Data System (ADS)

    Hou, Jianbo; Madsen, Louis A.

    2013-02-01

    Investigating the myriad features of molecular transport in materials yields fundamental information for understanding processes such as ion conduction, chemical reactions, and phase transitions. Molecular transport especially impacts the performance of ion-containing liquids and polymeric materials when used as electrolytes and separation media, with applications encompassing battery electrolytes, reverse-osmosis membranes, mechanical transducers, and fuel cells. Nuclear magnetic resonance (NMR) provides a unique probe of molecular translations by allowing measurement of all mobile species via spectral selectivity, access to a broad range of transport coefficients, probing of any material direction, and investigation of variable lengthscales in a material, thus, tying morphology to transport. Here, we present new concepts to test for and guarantee robust diffusion measurements. We first employ a standard pulsed-field-gradient (PFG) calibration protocol using 2H2O and obtain expected results, but we observe crippling artifacts when measuring 1H-glycerol diffusion with the same experimental parameters. A mathematical analysis of 2H2O and glycerol signals in the presence of PFG transients show tight agreement with experimental observations. These analyses lead to our principal findings that (1) negligible artifacts observed with low gyromagnetic ratio (γ) nuclei may become dominant when observing high γ nuclei, and (2) reducing the sample dimension along the gradient direction predictably reduces non-ideal behaviors of NMR signals. We further provide a useful quantitative strategy for error minimization when measuring diffusing species slower than the one used for gradient calibration.

  9. Improvements in Accurate GPS Positioning Using Time Series Analysis

    NASA Astrophysics Data System (ADS)

    Koyama, Yuichiro; Tanaka, Toshiyuki

    Although the Global Positioning System (GPS) is used widely in car navigation systems, cell phones, surveying, and other areas, several issues still exist. We focus on the continuous data received in public use of GPS, and propose a new positioning algorithm that uses time series analysis. By fitting an autoregressive model to the time series model of the pseudorange, we propose an appropriate state-space model. We apply the Kalman filter to the state-space model and use the pseudorange estimated by the filter in our positioning calculations. The results of the authors' positioning experiment show that the accuracy of the proposed method is much better than that of the standard method. In addition, as we can obtain valid values estimated by time series analysis using the state-space model, the proposed state-space model can be applied to several other fields.

  10. Accurate feature detection and estimation using nonlinear and multiresolution analysis

    NASA Astrophysics Data System (ADS)

    Rudin, Leonid; Osher, Stanley

    1994-11-01

    A program for feature detection and estimation using nonlinear and multiscale analysis was completed. The state-of-the-art edge detection was combined with multiscale restoration (as suggested by the first author) and robust results in the presence of noise were obtained. Successful applications to numerous images of interest to DOD were made. Also, a new market in the criminal justice field was developed, based in part, on this work.

  11. Reduction procedures for accurate analysis of MSX surveillance experiment data

    NASA Technical Reports Server (NTRS)

    Gaposchkin, E. Mike; Lane, Mark T.; Abbot, Rick I.

    1994-01-01

    Technical challenges of the Midcourse Space Experiment (MSX) science instruments require careful characterization and calibration of these sensors for analysis of surveillance experiment data. Procedures for reduction of Resident Space Object (RSO) detections will be presented which include refinement and calibration of the metric and radiometric (and photometric) data and calculation of a precise MSX ephemeris. Examples will be given which support the reduction, and these are taken from ground-test data similar in characteristics to the MSX sensors and from the IRAS satellite RSO detections. Examples to demonstrate the calculation of a precise ephemeris will be provided from satellites in similar orbits which are equipped with S-band transponders.

  12. Chemical dependency in women. Meeting the challenges of accurate diagnosis and effective treatment.

    PubMed Central

    Unger, K B

    1988-01-01

    Women dependent on alcohol or prescribed or nonprescribed psychoactive drugs present special diagnostic challenges to physicians. Chemical dependency likewise has adverse effects on women who are nonusers through the disease of co-dependency. The natural history of chemical dependency in women includes sex-specific differences in presenting signs and symptoms. Collateral medical history may come from a variety of community sources. Diagnoses may also use sex-specific criteria, with simultaneous diagnoses of chemical dependency and co-dependency considered. Images PMID:3074575

  13. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

    PubMed Central

    Weisbrod, Chad R.; Eng, Jimmy K.; Hoopmann, Michael R.; Baker, Tahmina; Bruce, James E.

    2012-01-01

    FT All Reaction Monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum in order to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails due to fragmenting multiple overlapping precursors. The sensitivity, robustness and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides. PMID:22288382

  14. Response to “Accurate Risk-Based Chemical Screening Relies on Robust Exposure Estimates”

    EPA Science Inventory

    This is a correspondence (letter to the editor) with reference to comments by Rudel and Perovich on the article "Integration of Dosimetry, Exposure, and High-Throughput Screening Data in Chemical Toxicity Assessment". Article Reference: SI # 238882

  15. Active contour approach for accurate quantitative airway analysis

    NASA Astrophysics Data System (ADS)

    Odry, Benjamin L.; Kiraly, Atilla P.; Slabaugh, Greg G.; Novak, Carol L.; Naidich, David P.; Lerallut, Jean-Francois

    2008-03-01

    Chronic airway disease causes structural changes in the lungs including peribronchial thickening and airway dilatation. Multi-detector computed tomography (CT) yields detailed near-isotropic images of the lungs, and thus the potential to obtain quantitative measurements of lumen diameter and airway wall thickness. Such measurements would allow standardized assessment, and physicians to diagnose and locate airway abnormalities, adapt treatment, and monitor progress over time. However, due to the sheer number of airways per patient, systematic analysis is infeasible in routine clinical practice without automation. We have developed an automated and real-time method based on active contours to estimate both airway lumen and wall dimensions; the method does not require manual contour initialization but only a starting point on the targeted airway. While the lumen contour segmentation is purely region-based, the estimation of the outer diameter considers the inner wall segmentation as well as local intensity variation, in order anticipate the presence of nearby arteries and exclude them. These properties make the method more robust than the Full-Width Half Maximum (FWHM) approach. Results are demonstrated on a phantom dataset with known dimensions and on a human dataset where the automated measurements are compared against two human operators. The average error on the phantom measurements was 0.10mm and 0.14mm for inner and outer diameters, showing sub-voxel accuracy. Similarly, the mean variation from the average manual measurement was 0.14mm and 0.18mm for inner and outer diameters respectively.

  16. Small pores in soils: Is the physico-chemical environment accurately reflected in biogeochemical models ?

    NASA Astrophysics Data System (ADS)

    Weber, Tobias K. D.; Riedel, Thomas

    2015-04-01

    Free water is a prerequesite to chemical reactions and biological activity in earth's upper crust essential to life. The void volume between the solid compounds provides space for water, air, and organisms that thrive on the consumption of minerals and organic matter thereby regulating soil carbon turnover. However, not all water in the pore space in soils and sediments is in its liquid state. This is a result of the adhesive forces which reduce the water activity in small pores and charged mineral surfaces. This water has a lower tendency to react chemically in solution as this additional binding energy lowers its activity. In this work, we estimated the amount of soil pore water that is thermodynamically different from a simple aqueous solution. The quantity of soil pore water with properties different to liquid water was found to systematically increase with increasing clay content. The significance of this is that the grain size and surface area apparently affects the thermodynamic state of water. This implies that current methods to determine the amount of water content, traditionally determined from bulk density or gravimetric water content after drying at 105°C overestimates the amount of free water in a soil especially at higher clay content. Our findings have consequences for biogeochemical processes in soils, e.g. nutrients may be contained in water which is not free which could enhance preservation. From water activity measurements on a set of various soils with 0 to 100 wt-% clay, we can show that 5 to 130 mg H2O per g of soil can generally be considered as unsuitable for microbial respiration. These results may therefore provide a unifying explanation for the grain size dependency of organic matter preservation in sedimentary environments and call for a revised view on the biogeochemical environment in soils and sediments. This could allow a different type of process oriented modelling.

  17. Chemical Analysis of Single Cells

    NASA Astrophysics Data System (ADS)

    Borland, Laura M.; Kottegoda, Sumith; Phillips, K. Scott; Allbritton, Nancy L.

    2008-07-01

    Chemical analysis of single cells requires methods for quickly and quantitatively detecting a diverse array of analytes from extremely small volumes (femtoliters to nanoliters) with very high sensitivity and selectivity. Microelectrophoretic separations, using both traditional capillary electrophoresis and emerging microfluidic methods, are well suited for handling the unique size of single cells and limited numbers of intracellular molecules. Numerous analytes, ranging from small molecules such as amino acids and neurotransmitters to large proteins and subcellular organelles, have been quantified in single cells using microelectrophoretic separation techniques. Microseparation techniques, coupled to varying detection schemes including absorbance and fluorescence detection, electrochemical detection, and mass spectrometry, have allowed researchers to examine a number of processes inside single cells. This review also touches on a promising direction in single cell cytometry: the development of microfluidics for integrated cellular manipulation, chemical processing, and separation of cellular contents.

  18. Gas phase chemical detection with an integrated chemical analysis system

    SciTech Connect

    CASALNUOVO,STEPHEN A.; FRYE-MASON,GREGORY CHARLES; KOTTENSTETTE,RICHARD; HELLER,EDWIN J.; MATZKE,CAROLYN M.; LEWIS,PATRICK R.; MANGINELL,RONALD P.; BACA,ALBERT G.; HIETALA,VINCENT M.

    2000-04-12

    Microfabrication technology has been applied to the development of a miniature, multi-channel gas phase chemical laboratory that provides fast response, small size, and enhanced versatility and chemical discrimination. Each analysis channel includes a sample preconcentrator followed by a gas chromatographic separator and a chemically selective surface acoustic wave detector array to achieve high sensitivity and selectivity. The performance of the components, individually and collectively, is described.

  19. Gas Phase Chemical Detection with an Integrated Chemical Analysis System

    SciTech Connect

    Baca, Albert G.; Casalnuovo, Stephen A.; Frye-Mason, Gregory C.; Heller, Edwin J.; Hietala, Susan L.; Hietala, Vincent M.; Kottenstette, Richard J.; Lewis, Patrick R.; Manginell, Ronald P.; Matzke, Carloyn M.; Reno, John L.; Sasaki, Darryl Y.; Schubert, W. Kent

    1999-07-08

    Microfabrication technology has been applied to the development of a miniature, multi-channel gas phase chemical laboratory that provides fast response, small size, and enhanced versatility and chemical discrimination. Each analysis channel includes a sample concentrator followed by a gas chromatographic separator and a chemically selective surface acoustic wave detector array to achieve high sensitivity and selectivity. The performance of the components, individually and collectively, is described. The design and performance of novel micromachined acoustic wave devices, with the potential for improved chemical sensitivity, are also described.

  20. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State 17O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds

    PubMed Central

    Rorick, Amber; Michael, Matthew A.; Yang, Liu; Zhang, Yong

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is of 1455 ppm, a major part of the reported 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  1. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-01

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  2. An accurate, convective energy equation based automated meshing technique for analysis of blood vessels and tissues.

    PubMed

    White, J A; Dutton, A W; Schmidt, J A; Roemer, R B

    2000-01-01

    An automated three-element meshing method for generating finite element based models for the accurate thermal analysis of blood vessels imbedded in tissue has been developed and evaluated. The meshing method places eight noded hexahedral elements inside the vessels where advective flows exist, and four noded tetrahedral elements in the surrounding tissue. The higher order hexahedrals are used where advective flow fields occur, since high accuracy is required and effective upwinding algorithms exist. Tetrahedral elements are placed in the remaining tissue region, since they are computationally more efficient and existing automatic tetrahedral mesh generators can be used. Five noded pyramid elements connect the hexahedrals and tetrahedrals. A convective energy equation (CEE) based finite element algorithm solves for the temperature distributions in the flowing blood, while a finite element formulation of a generalized conduction equation is used in the surrounding tissue. Use of the CEE allows accurate solutions to be obtained without the necessity of assuming ad hoc values for heat transfer coefficients. Comparisons of the predictions of the three-element model to analytical solutions show that the three-element model accurately simulates temperature fields. Energy balance checks show that the three-element model has small, acceptable errors. In summary, this method provides an accurate, automatic finite element gridding procedure for thermal analysis of irregularly shaped tissue regions that contain important blood vessels. At present, the models so generated are relatively large (in order to obtain accurate results) and are, thus, best used for providing accurate reference values for checking other approximate formulations to complicated, conjugated blood heat transfer problems.

  3. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  4. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    SciTech Connect

    Nakhleh, Luay

    2014-03-12

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

  5. Gravitational waves from compact binaries inspiralling along post-Newtonian accurate eccentric orbits: Data analysis implications

    SciTech Connect

    Tessmer, Manuel; Gopakumar, Achamveedu

    2008-10-15

    Compact binaries inspiralling along eccentric orbits are plausible gravitational-wave (GW) sources for the ground-based laser interferometers. We explore the losses in the event rates incurred when searching for GWs from compact binaries inspiralling along post-Newtonian accurate eccentric orbits with certain obvious nonoptimal search templates. For the present analysis, GW signals having 2.5 post-Newtonian (PN) accurate orbital evolution are modeled following the phasing formalism, presented by T. Damour, A. Gopakumar, and B. R. Iyer [Phys. Rev. D 70, 064028 (2004)]. We demonstrate that the search templates that model in a gauge-invariant manner GWs from compact binaries inspiralling under quadrupolar radiation reaction along 2PN accurate circular orbits are very efficient in capturing our somewhat realistic GW signals. However, three types of search templates based on the adiabatic, complete adiabatic, and gauge-dependent complete nonadiabatic approximants, detailed in P. Ajith, B. R. Iyer, C. A. K. Robinson, and B. S. Sathyaprakash, Phys. Rev. D 71, 044029 (2005), relevant for the circular inspiral under the quadrupolar radiation reaction were found to be inefficient in capturing the above-mentioned eccentric signal. We conclude that further investigations will be required to probe the ability of various types of PN accurate circular templates, employed to analyze the LIGO/VIRGO data, to capture GWs from compact binaries having tiny orbital eccentricities.

  6. Gravitational waves from compact binaries inspiralling along post-Newtonian accurate eccentric orbits: Data analysis implications

    NASA Astrophysics Data System (ADS)

    Tessmer, Manuel; Gopakumar, Achamveedu

    2008-10-01

    Compact binaries inspiralling along eccentric orbits are plausible gravitational-wave (GW) sources for the ground-based laser interferometers. We explore the losses in the event rates incurred when searching for GWs from compact binaries inspiralling along post-Newtonian accurate eccentric orbits with certain obvious nonoptimal search templates. For the present analysis, GW signals having 2.5 post-Newtonian (PN) accurate orbital evolution are modeled following the phasing formalism, presented by T. Damour, A. Gopakumar, and B. R. Iyer [Phys. Rev. D 70, 064028 (2004)PRVDAQ0556-282110.1103/PhysRevD.70.064028]. We demonstrate that the search templates that model in a gauge-invariant manner GWs from compact binaries inspiralling under quadrupolar radiation reaction along 2PN accurate circular orbits are very efficient in capturing our somewhat realistic GW signals. However, three types of search templates based on the adiabatic, complete adiabatic, and gauge-dependent complete nonadiabatic approximants, detailed in P. Ajith, B. R. Iyer, C. A. K. Robinson, and B. S. Sathyaprakash, Phys. Rev. D 71, 044029 (2005)PRVDAQ0556-282110.1103/PhysRevD.71.044029, relevant for the circular inspiral under the quadrupolar radiation reaction were found to be inefficient in capturing the above-mentioned eccentric signal. We conclude that further investigations will be required to probe the ability of various types of PN accurate circular templates, employed to analyze the LIGO/VIRGO data, to capture GWs from compact binaries having tiny orbital eccentricities.

  7. Spectroscopic chemical analysis methods and apparatus

    NASA Technical Reports Server (NTRS)

    Hug, William F. (Inventor); Reid, Ray D. (Inventor)

    2010-01-01

    Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted simultaneously with native fluorescence spectroscopy to provide high levels of sensitivity and specificity in the same instrument.

  8. Spectroscopic chemical analysis methods and apparatus

    NASA Technical Reports Server (NTRS)

    Hug, William F. (Inventor); Reid, Ray D. (Inventor)

    2009-01-01

    Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted simultaneously with native fluorescence spectroscopy to provide high levels of sensitivity and specificity in the same instrument.

  9. Accurate near-field calculation in the rigorous coupled-wave analysis method

    NASA Astrophysics Data System (ADS)

    Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.

    2015-12-01

    The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.

  10. Chemical abundance analysis of 19 barium stars

    NASA Astrophysics Data System (ADS)

    Yang, Guo-Chao; Liang, Yan-Chun; Spite, Monique; Chen, Yu-Qin; Zhao, Gang; Zhang, Bo; Liu, Guo-Qing; Liu, Yu-Juan; Liu, Nian; Deng, Li-Cai; Spite, Francois; Hill, Vanessa; Zhang, Cai-Xia

    2016-01-01

    We aim at deriving accurate atmospheric parameters and chemical abundances of 19 barium (Ba) stars, including both strong and mild Ba stars, based on the high signal-to-noise ratio and high resolution Echelle spectra obtained from the 2.16 m telescope at Xinglong station of National Astronomical Observatories, Chinese Academy of Sciences. The chemical abundances of the sample stars were obtained from an LTE, plane-parallel and line-blanketed atmospheric model by inputting the atmospheric parameters (effective temperatures Teff, surface gravities log g, metallicity [Fe/H] and microturbulence velocity ξt) and equivalent widths of stellar absorption lines. These samples of Ba stars are giants as indicated by atmospheric parameters, metallicities and kinematic analysis about UVW velocity. Chemical abundances of 17 elements were obtained for these Ba stars. Their Na, Al, α- and iron-peak elements (O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni) are similar to the solar abundances. Our samples of Ba stars show obvious overabundances of neutron-capture (n-capture) process elements relative to the Sun. Their median abundances of [Ba/Fe], [La/Fe] and [Eu/Fe] are 0.54, 0.65 and 0.40, respectively. The Y I and Zr I abundances are lower than Ba, La and Eu, but higher than the α- and iron-peak elements for the strong Ba stars and similar to the iron-peak elements for the mild stars. There exists a positive correlation between Ba intensity and [Ba/Fe]. For the n-capture elements (Y, Zr, Ba, La), there is an anti-correlation between their [X/Fe] and [Fe/H]. We identify nine of our sample stars as strong Ba stars with [Ba/Fe] >0.6 where seven of them have Ba intensity Ba=2-5, one has Ba=1.5 and another one has Ba=1.0. The remaining ten stars are classified as mild Ba stars with 0.17<[Ba/Fe] <0.54.

  11. Accurate and noninvasive embryos screening during in vitro fertilization (IVF) assisted by Raman analysis of embryos culture medium Accurate and noninvasive embryos screening during IVF

    NASA Astrophysics Data System (ADS)

    Shen, A. G.; Peng, J.; Zhao, Q. H.; Su, L.; Wang, X. H.; Hu, J. M.; Yang, J.

    2012-04-01

    In combination with morphological evaluation tests, we employ Raman spectroscopy to select higher potential reproductive embryos during in vitro fertilization (IVF) based on chemical composition of embryos culture medium. In this study, 57 Raman spectra are acquired from both higher and lower quality embryos culture medium (ECM) from 10 patients which have been preliminarily confirmed by clinical assay. Data are fit by using a linear combination model of least squares method in which 12 basis spectra represent the chemical features of ECM. The final fitting coefficients provide insight into the chemical compositions of culture medium samples and are subsequently used as criterion to evaluate the quality of embryos. The relative fitting coefficients ratios of sodium pyruvate/albumin and phenylalanine/albumin seem act as key roles in the embryo screening, attaining 85.7% accuracy in comparison with clinical pregnancy. The good results demonstrate that Raman spectroscopy therefore is an important candidate for an accurate and noninvasive screening of higher quality embryos, which potentially decrease the time-consuming clinical trials during IVF.

  12. Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis.

    PubMed Central

    Sieracki, M E; Reichenbach, S E; Webb, K L

    1989-01-01

    The accurate measurement of bacterial and protistan cell biomass is necessary for understanding their population and trophic dynamics in nature. Direct measurement of fluorescently stained cells is often the method of choice. The tedium of making such measurements visually on the large numbers of cells required has prompted the use of automatic image analysis for this purpose. Accurate measurements by image analysis require an accurate, reliable method of segmenting the image, that is, distinguishing the brightly fluorescing cells from a dark background. This is commonly done by visually choosing a threshold intensity value which most closely coincides with the outline of the cells as perceived by the operator. Ideally, an automated method based on the cell image characteristics should be used. Since the optical nature of edges in images of light-emitting, microscopic fluorescent objects is different from that of images generated by transmitted or reflected light, it seemed that automatic segmentation of such images may require special considerations. We tested nine automated threshold selection methods using standard fluorescent microspheres ranging in size and fluorescence intensity and fluorochrome-stained samples of cells from cultures of cyanobacteria, flagellates, and ciliates. The methods included several variations based on the maximum intensity gradient of the sphere profile (first derivative), the minimum in the second derivative of the sphere profile, the minimum of the image histogram, and the midpoint intensity. Our results indicated that thresholds determined visually and by first-derivative methods tended to overestimate the threshold, causing an underestimation of microsphere size. The method based on the minimum of the second derivative of the profile yielded the most accurate area estimates for spheres of different sizes and brightnesses and for four of the five cell types tested. A simple model of the optical properties of fluorescing objects and

  13. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.

    PubMed

    Mackie, David M; Jahnke, Justin P; Benyamin, Marcus S; Sumner, James J

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users' purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells.

  14. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples

    PubMed Central

    Mackie, David M.; Jahnke, Justin P.; Benyamin, Marcus S.; Sumner, James J.

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users’ purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells. PMID:26977411

  15. Accurate analysis of blood vessel sizes and stenotic lesions using stereoscopic DSA system.

    PubMed

    Fencil, L E; Doi, K; Hoffman, K R

    1988-01-01

    We have developed a technique to determine accurately the magnification factor and three-dimensional orientation of a vessel segment from a stereoscopic pair of digital subtraction angiograms (DSA). Our DSA system includes a stereoscopic x-ray tube with a 25-mm focal spot shift. The magnification and orientation of a selected vessel segment are determined from the distance and direction of the focal spot shift and the stereoscopic discrepancy in image positions for that segment. Our results indicate that the accuracies of determining the magnification and orientation are less than 1% and approximately 5 degrees, respectively. After the magnification and orientation are determined accurately, an iterative deconvolution technique for the measurement of vessel image size is applied to the selected vessel segment. This iterative deconvolution technique provides the best estimate of vessel image size by taking into account the unsharpness of the digital system. With this technique, the vessel image size can be determined to an accuracy of approximately 1.0 mm, which corresponds to one third the pixel size of our DSA system. Information derived from stereoscopic analysis and iterative deconvolution thus allows accurate calculation of actual vascular dimensions from DSA images.

  16. Nonlinear Aeroelastic Analysis Using a Time-Accurate Navier-Stokes Equations Solver

    NASA Technical Reports Server (NTRS)

    Kuruvila, Geojoe; Bartels, Robert E.; Hong, Moeljo S.; Bhatia, G.

    2007-01-01

    A method to simulate limit cycle oscillation (LCO) due to control surface freeplay using a modified CFL3D, a time-accurate Navier-Stokes computational fluid dynamics (CFD) analysis code with structural modeling capability, is presented. This approach can be used to analyze aeroelastic response of aircraft with structural behavior characterized by nonlinearity in the force verses displacement curve. A limited validation of the method, using very low Mach number experimental data for a three-degrees-of-freedom (pitch/plunge/flap deflection) airfoil model with flap freeplay, is also presented.

  17. Nature and Analysis of Chemical Species.

    ERIC Educational Resources Information Center

    Shuman, Mark S.; Fogleman, Wavell W.

    1978-01-01

    Presents a literature review of the nature and analysis of chemical species in water, covering publications of 1976-77. This review is concerned with inorganics, and it covers: (1) electrochemical analysis; (2) spectroscopy; (3) neutron activation, radiochemical analysis, and isotope dilution. A list of 262 references is also presented. (HM)

  18. Accurate Characterization of the Peptide Linkage in the Gas Phase: A Joint Quantum-Chemical and Rotational Spectroscopy Study of the Glycine Dipeptide Analogue.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Largo, Laura; Peña, Isabel; Cabezas, Carlos; Alonso, José Luis

    2014-02-01

    Accurate structures of aminoacids in the gas phase have been obtained by joint microwave and quantum-chemical investigations. However, the structure and conformational behavior of α-aminoacids once incorporated into peptide chains are completely different and have not yet been characterized with the same accuracy. To fill this gap, we present here an accurate characterization of the simplest dipeptide analogue (N-acetyl-glycinamide) involving peptidic bonds. State-of-the-art quantum-chemical computations are complemented by a comprehensive study of the rotational spectrum using a combination of Fourier transform microwave spectroscopy with laser ablation. The coexistence of the C7 and C5 conformers has been proved and energetically as well as spectroscopically characterized. This joint theoretical-experimental investigation demonstrated the feasibility of obtaining accurate structures for flexible small biomolecules, thus paving the route to the elucidation of the inherent behavior of peptides.

  19. Accurate and precise measurement of selenium by instrumental neutron activation analysis.

    PubMed

    Kim, In Jung; Watson, Russell P; Lindstrom, Richard M

    2011-05-01

    An accurate and precise measurement of selenium in Standard Reference Material (SRM) 3149, a primary calibration standard for the quantitative determination of selenium, has been accomplished by instrumental neutron activation analysis (INAA) in order to resolve a question arising during the certification process of the standard. Each limiting factor of the uncertainty in the activation analysis, including the sample preparation, irradiation, and γ-ray spectrometry steps, has been carefully monitored to minimize the uncertainty in the determined mass fraction. Neutron and γ-ray self-shielding within the elemental selenium INAA standards contributed most significantly to the uncertainty of the measurement. An empirical model compensating for neutron self-shielding and reducing the self-shielding uncertainty was successfully applied to these selenium standards. The mass fraction of selenium in the new lot of SRM 3149 was determined with a relative standard uncertainty of 0.6%.

  20. Chemical Analysis of the Fornax Dwarf Galaxy

    NASA Astrophysics Data System (ADS)

    Letarte, Bruno

    2007-03-01

    This thesis is entitled “Chemical Analysis of the Fornax Dwarf Galaxy”, and it’s main goal is to determine what are the chemical elements present in the stars of this galaxy in order to try and understand it’s evolution. Galaxies are not “static” objects, they move, form stars and can interact with other galaxies. Studying the stars composing a galaxy can in principle, inform us about its past. Some stars can be as old as the galaxy itself, some can be much younger and we can use this information to study how the stellar spectra have varied with time over the entire history of star formation in this galaxy. Dwarf galaxies are in principle the most simple and straightforward type of galaxy and their study can be used to test numerous theories of the formation and evolution of stars and galaxies in a range of environments. Dwarf spheroidal galaxies are small, roughly spherical galaxies that are typically found in the vicinity of larger galaxies, such as the Milky Way. They typically do not have any ongoing star formation, nor do they appear to have any gas associated to them. The abundance ratios of different elements in individual stars with a range of ages provide a detailed insight into the various chemical enrichment processes (e.g., supernovae, stellar winds) which in turn improves our understanding of the global processes of formation and evolution of a galaxy as a whole. An important aspect of this thesis is the pipeline developed to analyse a large number of stellar spectra (~100) in a consistent and statistically robust manner, using tools that are typically used on spectra with twice the resolution and larger wavelength coverage. This required bringing together several complex tasks, including accurate stellar atmospheric models, atomic data for the absorption lines, codes of line formation, EW measurements and signal extraction methods, all of which need to be properly included and treated in order to obtain accurate results. The pipeline

  1. Chemical considerations in severe accident analysis

    SciTech Connect

    Malinauskas, A.P.; Kress, T.S.

    1988-01-01

    The Reactor Safety Study presented the first systematic attempt to include fission product physicochemical effects in the determination of expected consequences of hypothetical nuclear reactor power plant accidents. At the time, however, the data base was sparse, and the treatment of fission product behavior was not entirely consistent or accurate. Considerable research has since been performed to identify and understand chemical phenomena that can occur in the course of a nuclear reactor accident, and how these phenomena affect fission product behavior. In this report, the current status of our understanding of the chemistry of fission products in severe core damage accidents is summarized and contrasted with that of the Reactor Safety Study.

  2. Accurate palm vein recognition based on wavelet scattering and spectral regression kernel discriminant analysis

    NASA Astrophysics Data System (ADS)

    Elnasir, Selma; Shamsuddin, Siti Mariyam; Farokhi, Sajad

    2015-01-01

    Palm vein recognition (PVR) is a promising new biometric that has been applied successfully as a method of access control by many organizations, which has even further potential in the field of forensics. The palm vein pattern has highly discriminative features that are difficult to forge because of its subcutaneous position in the palm. Despite considerable progress and a few practical issues, providing accurate palm vein readings has remained an unsolved issue in biometrics. We propose a robust and more accurate PVR method based on the combination of wavelet scattering (WS) with spectral regression kernel discriminant analysis (SRKDA). As the dimension of WS generated features is quite large, SRKDA is required to reduce the extracted features to enhance the discrimination. The results based on two public databases-PolyU Hyper Spectral Palmprint public database and PolyU Multi Spectral Palmprint-show the high performance of the proposed scheme in comparison with state-of-the-art methods. The proposed approach scored a 99.44% identification rate and a 99.90% verification rate [equal error rate (EER)=0.1%] for the hyperspectral database and a 99.97% identification rate and a 99.98% verification rate (EER=0.019%) for the multispectral database.

  3. Accurate determination of protein methionine oxidation by stable isotope labeling and LC-MS analysis.

    PubMed

    Liu, Hongcheng; Ponniah, Gomathinayagam; Neill, Alyssa; Patel, Rekha; Andrien, Bruce

    2013-12-17

    Methionine (Met) oxidation is a major modification of proteins, which converts Met to Met sulfoxide as the common product. It is challenging to determine the level of Met sulfoxide, because it can be generated during sample preparation and analysis as an artifact. To determine the level of Met sulfoxide in proteins accurately, an isotope labeling and LC-MS peptide mapping method was developed. Met residues in proteins were fully oxidized using hydrogen peroxide enriched with (18)O atoms before sample preparation. Therefore, it was impossible to generate Met sulfoxide as an artifact during sample preparation. The molecular weight difference of 2 Da between Met sulfoxide with the (16)O atom and Met sulfoxide with the (18)O atom was used to differentiate and calculate the level of Met sulfoxide in the sample originally. Using a recombinant monoclonal antibody as a model protein, much lower levels of Met sulfoxide were detected for the two susceptible Met residues with this new method compared to a typical peptide mapping procedure. The results demonstrated efficient elimination of the analytical artifact during LC-MS peptide mapping for the measurement of Met sulfoxide. This method can thus be used when accurate determination of the level of Met sulfoxide is critical.

  4. Fast and accurate sensitivity analysis of IMPT treatment plans using Polynomial Chaos Expansion

    NASA Astrophysics Data System (ADS)

    Perkó, Zoltán; van der Voort, Sebastian R.; van de Water, Steven; Hartman, Charlotte M. H.; Hoogeman, Mischa; Lathouwers, Danny

    2016-06-01

    The highly conformal planned dose distribution achievable in intensity modulated proton therapy (IMPT) can severely be compromised by uncertainties in patient setup and proton range. While several robust optimization approaches have been presented to address this issue, appropriate methods to accurately estimate the robustness of treatment plans are still lacking. To fill this gap we present Polynomial Chaos Expansion (PCE) techniques which are easily applicable and create a meta-model of the dose engine by approximating the dose in every voxel with multidimensional polynomials. This Polynomial Chaos (PC) model can be built in an automated fashion relatively cheaply and subsequently it can be used to perform comprehensive robustness analysis. We adapted PC to provide among others the expected dose, the dose variance, accurate probability distribution of dose-volume histogram (DVH) metrics (e.g. minimum tumor or maximum organ dose), exact bandwidths of DVHs, and to separate the effects of random and systematic errors. We present the outcome of our verification experiments based on 6 head-and-neck (HN) patients, and exemplify the usefulness of PCE by comparing a robust and a non-robust treatment plan for a selected HN case. The results suggest that PCE is highly valuable for both research and clinical applications.

  5. Techniques for Accurate Sizing of Gold Nanoparticles Using Dynamic Light Scattering with Particular Application to Chemical and Biological Sensing Based on Aggregate Formation.

    PubMed

    Zheng, Tianyu; Bott, Steven; Huo, Qun

    2016-08-24

    Gold nanoparticles (AuNPs) have found broad applications in chemical and biological sensing, catalysis, biomolecular imaging, in vitro diagnostics, cancer therapy, and many other areas. Dynamic light scattering (DLS) is an analytical tool used routinely for nanoparticle size measurement and analysis. Due to its relatively low cost and ease of operation in comparison to other more sophisticated techniques, DLS is the primary choice of instrumentation for analyzing the size and size distribution of nanoparticle suspensions. However, many DLS users are unfamiliar with the principles behind the DLS measurement and are unware of some of the intrinsic limitations as well as the unique capabilities of this technique. The lack of sufficient understanding of DLS often leads to inappropriate experimental design and misinterpretation of the data. In this study, we performed DLS analyses on a series of citrate-stabilized AuNPs with diameters ranging from 10 to 100 nm. Our study shows that the measured hydrodynamic diameters of the AuNPs can vary significantly with concentration and incident laser power. The scattered light intensity of the AuNPs has a nearly sixth order power law increase with diameter, and the enormous scattered light intensity of AuNPs with diameters around or exceeding 80 nm causes a substantial multiple scattering effect in conventional DLS instruments. The effect leads to significant errors in the reported average hydrodynamic diameter of the AuNPs when the measurements are analyzed in the conventional way, without accounting for the multiple scattering. We present here some useful methods to obtain the accurate hydrodynamic size of the AuNPs using DLS. We also demonstrate and explain an extremely powerful aspect of DLS-its exceptional sensitivity in detecting gold nanoparticle aggregate formation, and the use of this unique capability for chemical and biological sensing applications. PMID:27472008

  6. Chemical Analysis Of Beryllium Shells

    SciTech Connect

    Gunther, J; Cook, R

    2005-11-17

    There is a need to understand the level of high-Z impurities in Beryllium shells prepared by sputter coating. The Ignition Point Design Requirements state the following: ''Except for allowed ingredients, as listed in the ablator composition entries, the ablator material in all layers shall contain sufficiently low impurity levels that the sum over all impurities of atom fraction*Z{sup 2} shall be less than or equal to 0.2''. This is a tight specification that requires careful materials analysis. Early in the first quarter of FY06, we undertook a study of Be shell impurities via ICP-MS{sup 2} and determined that the impurity levels in the sputtered shells are very close to the specification.

  7. Apparatus for use in rapid and accurate controlled-potential coulometric analysis

    DOEpatents

    Frazzini, Thomas L.; Holland, Michael K.; Pietri, Charles E.; Weiss, Jon R.

    1981-01-01

    An apparatus for controlled-potential coulometric analysis of a solution includes a cell to contain the solution to be analyzed and a plurality of electrodes to contact the solution in the cell. Means are provided to stir the solution and to control the atmosphere above it. A potentiostat connected to the electrodes controls potential differences among the electrodes. An electronic circuit connected to the potentiostat provides analog-to-digital conversion and displays a precise count of charge transfer during a desired chemical process. This count provides a measure of the amount of an unknown substance in the solution.

  8. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

    2001-01-01

    A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

  9. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

    PubMed Central

    Lipton, Mary S.; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim; Hixson, Kim K.; Kostandarithes, Heather; Masselon, Christophe; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Stritmatter, Eric; Tolić, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical. PMID:12177431

  10. Spectroscopic chemical analysis methods and apparatus

    NASA Technical Reports Server (NTRS)

    Hug, William F. (Inventor); Reid, Ray D. (Inventor); Bhartia, Rohit (Inventor)

    2013-01-01

    Spectroscopic chemical analysis methods and apparatus are disclosed which employ deep ultraviolet (e.g. in the 200 nm to 300 nm spectral range) electron beam pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor light emitting devices, and hollow cathode metal ion lasers to perform non-contact, non-invasive detection of unknown chemical analytes. These deep ultraviolet sources enable dramatic size, weight and power consumption reductions of chemical analysis instruments. Chemical analysis instruments employed in some embodiments include capillary and gel plane electrophoresis, capillary electrochromatography, high performance liquid chromatography, flow cytometry, flow cells for liquids and aerosols, and surface detection instruments. In some embodiments, Raman spectroscopic detection methods and apparatus use ultra-narrow-band angle tuning filters, acousto-optic tuning filters, and temperature tuned filters to enable ultra-miniature analyzers for chemical identification. In some embodiments Raman analysis is conducted along with photoluminescence spectroscopy (i.e. fluorescence and/or phosphorescence spectroscopy) to provide high levels of sensitivity and specificity in the same instrument.

  11. Toward Sensitive and Accurate Analysis of Antibody Biotherapeutics by Liquid Chromatography Coupled with Mass Spectrometry

    PubMed Central

    An, Bo; Zhang, Ming

    2014-01-01

    Remarkable methodological advances in the past decade have expanded the application of liquid chromatography coupled with mass spectrometry (LC/MS) analysis of biotherapeutics. Currently, LC/MS represents a promising alternative or supplement to the traditional ligand binding assay (LBA) in the pharmacokinetic, pharmacodynamic, and toxicokinetic studies of protein drugs, owing to the rapid and cost-effective method development, high specificity and reproducibility, low sample consumption, the capacity of analyzing multiple targets in one analysis, and the fact that a validated method can be readily adapted across various matrices and species. While promising, technical challenges associated with sensitivity, sample preparation, method development, and quantitative accuracy need to be addressed to enable full utilization of LC/MS. This article introduces the rationale and technical challenges of LC/MS techniques in biotherapeutics analysis and summarizes recently developed strategies to alleviate these challenges. Applications of LC/MS techniques on quantification and characterization of antibody biotherapeutics are also discussed. We speculate that despite the highly attractive features of LC/MS, it will not fully replace traditional assays such as LBA in the foreseeable future; instead, the forthcoming trend is likely the conjunction of biochemical techniques with versatile LC/MS approaches to achieve accurate, sensitive, and unbiased characterization of biotherapeutics in highly complex pharmaceutical/biologic matrices. Such combinations will constitute powerful tools to tackle the challenges posed by the rapidly growing needs for biotherapeutics development. PMID:25185260

  12. Quantitation and accurate mass analysis of pesticides in vegetables by LC/TOF-MS.

    PubMed

    Ferrer, Imma; Thurman, E Michael; Fernández-Alba, Amadeo R

    2005-05-01

    A quantitative method consisting of solvent extraction followed by liquid chromatography/time-of-flight mass spectrometry (LC/TOF-MS) analysis was developed for the identification and quantitation of three chloronicotinyl pesticides (imidacloprid, acetamiprid, thiacloprid) commonly used on salad vegetables. Accurate mass measurements within 3 ppm error were obtained for all the pesticides studied in various vegetable matrixes (cucumber, tomato, lettuce, pepper), which allowed an unequivocal identification of the target pesticides. Calibration curves covering 2 orders of magnitude were linear over the concentration range studied, thus showing the quantitative ability of TOF-MS as a monitoring tool for pesticides in vegetables. Matrix effects were also evaluated using matrix-matched standards showing no significant interferences between matrixes and clean extracts. Intraday reproducibility was 2-3% relative standard deviation (RSD) and interday values were 5% RSD. The precision (standard deviation) of the mass measurements was evaluated and it was less than 0.23 mDa between days. Detection limits of the chloronicotinyl insecticides in salad vegetables ranged from 0.002 to 0.01 mg/kg. These concentrations are equal to or better than the EU directives for controlled pesticides in vegetables showing that LC/TOF-MS analysis is a powerful tool for identification of pesticides in vegetables. Robustness and applicability of the method was validated for the analysis of market vegetable samples. Concentrations found in these samples were in the range of 0.02-0.17 mg/kg of vegetable. PMID:15859598

  13. Accurate abundance analysis of late-type stars: advances in atomic physics

    NASA Astrophysics Data System (ADS)

    Barklem, Paul S.

    2016-05-01

    The measurement of stellar properties such as chemical compositions, masses and ages, through stellar spectra, is a fundamental problem in astrophysics. Progress in the understanding, calculation and measurement of atomic properties and processes relevant to the high-accuracy analysis of F-, G-, and K-type stellar spectra is reviewed, with particular emphasis on abundance analysis. This includes fundamental atomic data such as energy levels, wavelengths, and transition probabilities, as well as processes of photoionisation, collisional broadening and inelastic collisions. A recurring theme throughout the review is the interplay between theoretical atomic physics, laboratory measurements, and astrophysical modelling, all of which contribute to our understanding of atoms and atomic processes, as well as to modelling stellar spectra.

  14. Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

    PubMed Central

    Gusenleitner, Daniel; Auerbach, Scott S.; Melia, Tisha; Gómez, Harold F.; Sherr, David H.; Monti, Stefano

    2014-01-01

    Background Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. Results In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. Conclusion Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure. PMID:25058030

  15. A Global Approach to Accurate and Automatic Quantitative Analysis of NMR Spectra by Complex Least-Squares Curve Fitting

    NASA Astrophysics Data System (ADS)

    Martin, Y. L.

    The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species

  16. Probabilistic Exposure Analysis for Chemical Risk Characterization

    PubMed Central

    Bogen, Kenneth T.; Cullen, Alison C.; Frey, H. Christopher; Price, Paul S.

    2009-01-01

    This paper summarizes the state of the science of probabilistic exposure assessment (PEA) as applied to chemical risk characterization. Current probabilistic risk analysis methods applied to PEA are reviewed. PEA within the context of risk-based decision making is discussed, including probabilistic treatment of related uncertainty, interindividual heterogeneity, and other sources of variability. Key examples of recent experience gained in assessing human exposures to chemicals in the environment, and other applications to chemical risk characterization and assessment, are presented. It is concluded that, although improvements continue to be made, existing methods suffice for effective application of PEA to support quantitative analyses of the risk of chemically induced toxicity that play an increasing role in key decision-making objectives involving health protection, triage, civil justice, and criminal justice. Different types of information required to apply PEA to these different decision contexts are identified, and specific PEA methods are highlighted that are best suited to exposure assessment in these separate contexts. PMID:19223660

  17. Quantum chemical approach for condensed-phase thermochemistry (III): Accurate evaluation of proton hydration energy and standard hydrogen electrode potential

    NASA Astrophysics Data System (ADS)

    Ishikawa, Atsushi; Nakai, Hiromi

    2016-04-01

    Gibbs free energy of hydration of a proton and standard hydrogen electrode potential were evaluated using high-level quantum chemical calculations. The solvent effect was included using the cluster-continuum model, which treated short-range effects by quantum chemical calculations of proton-water complexes, and the long-range effects by a conductor-like polarizable continuum model. The harmonic solvation model (HSM) was employed to estimate enthalpy and entropy contributions due to nuclear motions of the clusters by including the cavity-cluster interactions. Compared to the commonly used ideal gas model, HSM treatment significantly improved the contribution of entropy, showing a systematic convergence toward the experimental data.

  18. Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

    PubMed

    Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

    2012-12-01

    Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance.

  19. Accurate measurement of bromine contents in plastic samples by instrumental neutron activation analysis.

    PubMed

    Kim, I J; Lee, K S; Hwang, E; Min, H S; Yim, Y H

    2013-03-26

    Accurate measurements of bromine contents in plastic samples were made by the direct comparator instrumental neutron activation analysis (INAA). Individual factors affecting the measurements were comprehensively evaluated and compensated, including the volatility loss of bromine from standard comparators, the background bromine level in the filter papers used for preparation of the standard comparators, nuclear interference, γ-ray spectral interference and the variance among replicates of the samples. Uncertainty contributions from those factors were thoroughly evaluated and included in the uncertainty budgeting of the INAA measurement. (81)Br was chosen as the target isotope, and the INAA measurements for bromine were experimentally confirmed to exhibit good linearity within a bromine content range of 10-170 μg. The established method has been applied to the analysis of eight plastic samples: four commercially available certified reference materials (CRMs) of polyethylene and polystyrene and four acrylonitrile butadiene styrene (ABS) samples prepared as the candidate reference materials (KRISS CRM 113-01-012, -013, -014 and -015). The bromine contents of the samples were calculated at three different γ-ray energies and compared, showing good agreement. The results of the four CRMs also showed good consistency with their certified values within the stated uncertainties. Finally, the bromine contents of the ABS samples were determined with expanded uncertainties (at a 95% level of confidence) between 2.5% and 5% in a bromine content range of 25-900 mg kg(-1).

  20. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    PubMed

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data. PMID:24420979

  1. An accurate skull stripping method based on simplex meshes and histogram analysis for magnetic resonance images.

    PubMed

    Galdames, Francisco J; Jaillet, Fabrice; Perez, Claudio A

    2012-01-01

    Skull stripping methods are designed to eliminate the non-brain tissue in magnetic resonance (MR) brain images. Removal of non-brain tissues is a fundamental step in enabling the processing of brain MR images. The aim of this study is to develop an automatic accurate skull stripping method based on deformable models and histogram analysis. A rough-segmentation step is used to find the optimal starting point for the deformation and is based on thresholds and morphological operators. Thresholds are computed using comparisons with an atlas, and modeling by Gaussians. The deformable model is based on a simplex mesh and its deformation is controlled by the image local gray levels and the information obtained on the gray level modeling of the rough-segmentation. Our Simplex Mesh and Histogram Analysis Skull Stripping (SMHASS) method was tested on the following international databases commonly used in scientific articles: BrainWeb, Internet Brain Segmentation Repository (IBSR), and Segmentation Validation Engine (SVE). A comparison was performed against three of the best skull stripping methods previously published: Brain Extraction Tool (BET), Brain Surface Extractor (BSE), and Hybrid Watershed Algorithm (HWA). Performance was measured using the Jaccard index (J) and Dice coefficient (κ). Our method showed the best performance and differences were statistically significant (p<0.05): J=0.904 and κ=0.950 on BrainWeb; J=0.905 and κ=0.950 on IBSR; J=0.946 and κ=0.972 on SVE.

  2. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  3. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    PubMed

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data.

  4. Accurate measurement of bromine contents in plastic samples by instrumental neutron activation analysis.

    PubMed

    Kim, I J; Lee, K S; Hwang, E; Min, H S; Yim, Y H

    2013-03-26

    Accurate measurements of bromine contents in plastic samples were made by the direct comparator instrumental neutron activation analysis (INAA). Individual factors affecting the measurements were comprehensively evaluated and compensated, including the volatility loss of bromine from standard comparators, the background bromine level in the filter papers used for preparation of the standard comparators, nuclear interference, γ-ray spectral interference and the variance among replicates of the samples. Uncertainty contributions from those factors were thoroughly evaluated and included in the uncertainty budgeting of the INAA measurement. (81)Br was chosen as the target isotope, and the INAA measurements for bromine were experimentally confirmed to exhibit good linearity within a bromine content range of 10-170 μg. The established method has been applied to the analysis of eight plastic samples: four commercially available certified reference materials (CRMs) of polyethylene and polystyrene and four acrylonitrile butadiene styrene (ABS) samples prepared as the candidate reference materials (KRISS CRM 113-01-012, -013, -014 and -015). The bromine contents of the samples were calculated at three different γ-ray energies and compared, showing good agreement. The results of the four CRMs also showed good consistency with their certified values within the stated uncertainties. Finally, the bromine contents of the ABS samples were determined with expanded uncertainties (at a 95% level of confidence) between 2.5% and 5% in a bromine content range of 25-900 mg kg(-1). PMID:23498117

  5. Droplet microfluidics in (bio)chemical analysis.

    PubMed

    Basova, Evgenia Yu; Foret, Frantisek

    2015-01-01

    Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation. It can improve not only the analysis scale, possibility for sensitivity improvement, and reduced consumption of chemical and biological reagents, but also the speed of performing a variety of unit operations. At present, microfluidic platforms can reproducibly generate monodisperse droplet populations at kHz or higher rates with droplet sizes suitable for high-throughput experiments, single-cell detection or even single molecule analysis. In addition to being used as microreactors with volume in the micro- to femtoliter range, droplet based systems have also been used to directly synthesize particles and encapsulate biological entities for biomedicine and biotechnology applications. This minireview summarizes various droplet microfluidics operations and applications for (bio)chemical assays described in the literature during the past few years.

  6. Chemical analysis of some standard carbonate rocks

    USGS Publications Warehouse

    Galle, O.K.

    1969-01-01

    Twenty limestone, dolomite and limestone-dolomite blends were analyzed. The samples, which are available from the G. Fredrick Smith Chemical Company of Columbus, Ohio, were issued with an analysis certificate listing values for SiO2, Fe2O3, CaO and MgO. Additional analyses are reported and results compared with certificate values. ?? 1969.

  7. 40 CFR 761.253 - Chemical analysis.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Chemical analysis. 761.253 Section 761.253 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT... Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.253...

  8. 40 CFR 761.253 - Chemical analysis.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Chemical analysis. 761.253 Section 761.253 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT... Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.253...

  9. 40 CFR 761.253 - Chemical analysis.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Chemical analysis. 761.253 Section 761.253 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT... Sample Sites, Collecting Surface Samples, and Analyzing Standard PCB Wipe Samples § 761.253...

  10. Microfabricated Gas Phase Chemical Analysis Systems

    SciTech Connect

    Casalnuovo, Stephen A.; Frye-Mason, Gregory C; Heller, Edwin J.; Hietala, Vincent M.; Kottenstette, Richard J.; Lewis, Patrick R.; Manginell, Ronald P.; Matzke, Carolyn M.; Wong, C. Channy

    1999-08-02

    A portable, autonomous, hand-held chemical laboratory ({mu}ChemLab{trademark}) is being developed for trace detection (ppb) of chemical warfare (CW) agents and explosives in real-world environments containing high concentrations of interfering compounds. Microfabrication is utilized to provide miniature, low-power components that are characterized by rapid, sensitive and selective response. Sensitivity and selectivity are enhanced using two parallel analysis channels, each containing the sequential connection of a front-end sample collector/concentrator, a gas chromatographic (GC) separator, and a surface acoustic wave (SAW) detector. Component design and fabrication and system performance are described.

  11. Electron spectroscopy for chemical analysis: Sample analysis

    NASA Technical Reports Server (NTRS)

    Carter, W. B.

    1989-01-01

    Exposure conditions in atomic oxygen (ESCA) was performed on an SSL-100/206 Small Spot Spectrometer. All data were taken with the use of a low voltage electron flood gun and a charge neutralization screen to minimize charging effects on the data. The X-ray spot size and electron flood gun voltage used are recorded on the individual spectra as are the instrumental resolutions. Two types of spectra were obtained for each specimen: (1) general surveys, and (2) high resolution spectra. The two types of data reduction performed are: (1) semiquantitative compositional analysis, and (2) peak fitting. The materials analyzed are: (1) kapton 4, 5, and 6, (2) HDPE 19, 20, and 21, and (3) PVDF 4, 5, and 6.

  12. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms

    PubMed Central

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F.

    2016-01-01

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7–76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment. PMID:27645567

  13. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    SciTech Connect

    Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

    2015-03-15

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  14. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms.

    PubMed

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F

    2016-09-20

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7-76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment.

  15. Accurate mass tag retention time database for urine proteome analysis by chromatography--mass spectrometry.

    PubMed

    Agron, I A; Avtonomov, D M; Kononikhin, A S; Popov, I A; Moshkovskii, S A; Nikolaev, E N

    2010-05-01

    Information about peptides and proteins in urine can be used to search for biomarkers of early stages of various diseases. The main technology currently used for identification of peptides and proteins is tandem mass spectrometry, in which peptides are identified by mass spectra of their fragmentation products. However, the presence of the fragmentation stage decreases sensitivity of analysis and increases its duration. We have developed a method for identification of human urinary proteins and peptides. This method based on the accurate mass and time tag (AMT) method does not use tandem mass spectrometry. The database of AMT tags containing more than 1381 AMT tags of peptides has been constructed. The software for database filling with AMT tags, normalizing the chromatograms, database application for identification of proteins and peptides, and their quantitative estimation has been developed. The new procedures for peptide identification by tandem mass spectra and the AMT tag database are proposed. The paper also lists novel proteins that have been identified in human urine for the first time. PMID:20632944

  16. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms.

    PubMed

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F

    2016-01-01

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7-76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment. PMID:27645567

  17. Development and experimental verification of a finite element method for accurate analysis of a surface acoustic wave device

    NASA Astrophysics Data System (ADS)

    Mohibul Kabir, K. M.; Matthews, Glenn I.; Sabri, Ylias M.; Russo, Salvy P.; Ippolito, Samuel J.; Bhargava, Suresh K.

    2016-03-01

    Accurate analysis of surface acoustic wave (SAW) devices is highly important due to their use in ever-growing applications in electronics, telecommunication and chemical sensing. In this study, a novel approach for analyzing the SAW devices was developed based on a series of two-dimensional finite element method (FEM) simulations, which has been experimentally verified. It was found that the frequency response of the two SAW device structures, each having slightly different bandwidth and center lobe characteristics, can be successfully obtained utilizing the current density of the electrodes via FEM simulations. The two SAW structures were based on XY Lithium Niobate (LiNbO3) substrates and had two and four electrode finger pairs in both of their interdigital transducers, respectively. Later, SAW devices were fabricated in accordance with the simulated models and their measured frequency responses were found to correlate well with the obtained simulations results. The results indicated that better match between calculated and measured frequency response can be obtained when one of the input electrode finger pairs was set at zero volts and all the current density components were taken into account when calculating the frequency response of the simulated SAW device structures.

  18. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for (Exo-)Planetary Retrieval Models

    NASA Astrophysics Data System (ADS)

    Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.

    2015-12-01

    Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work

  19. Accurate means of detecting and characterizing abnormal patterns of ventricular activation by phase image analysis

    SciTech Connect

    Botvinick, E.H.; Frais, M.A.; Shosa, D.W.; O'Connell, J.W.; Pacheco-Alvarez, J.A.; Scheinman, M.; Hattner, R.S.; Morady, F.; Faulkner, D.B.

    1982-08-01

    The ability of scintigraphic phase image analysis to characterize patterns of abnormal ventricular activation was investigated. The pattern of phase distribution and sequential phase changes over both right and left ventricular regions of interest were evaluated in 16 patients with normal electrical activation and wall motion and compared with those in 8 patients with an artificial pacemaker and 4 patients with sinus rhythm with the Wolff-Parkinson-White syndrome and delta waves. Normally, the site of earliest phase angle was seen at the base of the interventricular septum, with sequential change affecting the body of the septum and the cardiac apex and then spreading laterally to involve the body of both ventricles. The site of earliest phase angle was located at the apex of the right ventricle in seven patients with a right ventricular endocardial pacemaker and on the lateral left ventricular wall in one patient with a left ventricular epicardial pacemaker. In each case the site corresponded exactly to the position of the pacing electrode as seen on posteroanterior and left lateral chest X-ray films, and sequential phase changes spread from the initial focus to affect both ventricles. In each of the patients with the Wolff-Parkinson-White syndrome, the site of earliest ventricular phase angle was located, and it corresponded exactly to the site of the bypass tract as determined by endocardial mapping. In this way, four bypass pathways, two posterior left paraseptal, one left lateral and one right lateral, were correctly localized scintigraphically. On the basis of the sequence of mechanical contraction, phase image analysis provides an accurate noninvasive method of detecting abnormal foci of ventricular activation.

  20. Methods for applying accurate digital PCR analysis on low copy DNA samples.

    PubMed

    Whale, Alexandra S; Cowen, Simon; Foy, Carole A; Huggett, Jim F

    2013-01-01

    Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA.

  1. Unifying Approach to Analytical Chemistry and Chemical Analysis: Problem-Oriented Role of Chemical Analysis.

    ERIC Educational Resources Information Center

    Pardue, Harry L.; Woo, Jannie

    1984-01-01

    Proposes an approach to teaching analytical chemistry and chemical analysis in which a problem to be resolved is the focus of a course. Indicates that this problem-oriented approach is intended to complement detailed discussions of fundamental and applied aspects of chemical determinations and not replace such discussions. (JN)

  2. Identification and quantitative analysis of chemical compounds based on multiscale linear fitting of terahertz spectra

    NASA Astrophysics Data System (ADS)

    Qiao, Lingbo; Wang, Yingxin; Zhao, Ziran; Chen, Zhiqiang

    2014-07-01

    Terahertz (THz) time-domain spectroscopy is considered as an attractive tool for the analysis of chemical composition. The traditional methods for identification and quantitative analysis of chemical compounds by THz spectroscopy are all based on full-spectrum data. However, intrinsic features of the THz spectrum only lie in absorption peaks due to existence of disturbances, such as unexpected components, scattering effects, and barrier materials. We propose a strategy that utilizes Lorentzian parameters of THz absorption peaks, extracted by a multiscale linear fitting method, for both identification of pure chemicals and quantitative analysis of mixtures. The multiscale linear fitting method can automatically remove background content and accurately determine Lorentzian parameters of the absorption peaks. The high recognition rate for 16 pure chemical compounds and the accurate predicted concentrations for theophylline-lactose mixtures demonstrate the practicability of our approach.

  3. Highly Accurate Quantum-Chemical Calculations for the Interstellar Molecules C_3 and l-C_3H^+

    NASA Astrophysics Data System (ADS)

    Botschwina, Peter; Schröder, Benjamin; Stein, Christopher; Sebald, Peter; Oswald, Rainer

    2014-06-01

    Composite potential energy surfaces with coupled-cluster contributions up to CCSDTQP were constructed for C_3 and l-C_3H^+ and used in the calculation of spectroscopic properties. The use of very large AO basis sets and the consideration of higher-order correlation beyond CCSD(T) is of utmost importance for C_3 in order to arrive at quantitative spectroscopic data. The first detection of l-C_3H^+ in the interstellar medium was reported by Pety et al., who attributed 9 radio lines observed in the horsehead photodissociation region to that species. That assignment was questioned by the recent theoretical work of Huang et al. However, our more accurate calculations are well in support of the original assignment. The calculated ground-state rotational constant is B_0 = 11248 MHz, only 0.03% off from the radio astronomical value of 11244.9512±0.0015 MHz. The ratio of centrifugal distortion constants D_0(exp.)/D_e(theor.) of 1.8 is quite large, but reasonable in comparison with C_3O and C_3. J. Pety, P. Gratier, V. Guzmán, E. Roueff, M. Gerin et al., Astron. Astrophys. 2012, A68, 1-8. X. Huang, R. C. Fortenberry, T. J. Lee, Astrophys. J. Lett. 2013, 768:L25, 1-5. P. Botschwina, R. Oswald, J. Chem. Phys. 2008, 129, 044305

  4. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    PubMed

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  5. Chemical analysis of Panax quinquefolius (North American ginseng): A review.

    PubMed

    Wang, Yaping; Choi, Hyung-Kyoon; Brinckmann, Josef A; Jiang, Xue; Huang, Linfang

    2015-12-24

    Panax quinquefolius (PQ) is one of the best-selling natural health products due to its proposed beneficial anti-aging, anti-cancer, anti-stress, anti-fatigue, and anxiolytic effects. In recent years, the quality of PQ has received considerable attention. Sensitive and accurate methods for qualitative and quantitative analyses of chemical constituents are necessary for the comprehensive quality control to ensure the safety and efficacy of PQ. This article reviews recent progress in the chemical analysis of PQ and its preparations. Numerous analytical techniques, including spectroscopy, thin-layer chromatography (TLC), gas chromatography (GC), high-performance liquid chromatography (HPLC), liquid chromatography/mass spectrometry (LC/MS), high-speed centrifugal partition chromatography (HSCPC), high-performance counter-current chromatography (HPCCC), nuclear magnetic resonance spectroscopy (NMR), and immunoassay, are described. Among these techniques, HPLC coupled with mass spectrometry (MS) is the most promising method for quality control. The challenges encountered in the chemical analysis of PQ are also briefly discussed, and the remaining questions regarding the quality control of PQ that require further investigation are highlighted.

  6. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  7. Updated Chemical Kinetics and Sensitivity Analysis Code

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan

    2005-01-01

    An updated version of the General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code has become available. A prior version of LSENS was described in "Program Helps to Determine Chemical-Reaction Mechanisms" (LEW-15758), NASA Tech Briefs, Vol. 19, No. 5 (May 1995), page 66. To recapitulate: LSENS solves complex, homogeneous, gas-phase, chemical-kinetics problems (e.g., combustion of fuels) that are represented by sets of many coupled, nonlinear, first-order ordinary differential equations. LSENS has been designed for flexibility, convenience, and computational efficiency. The present version of LSENS incorporates mathematical models for (1) a static system; (2) steady, one-dimensional inviscid flow; (3) reaction behind an incident shock wave, including boundary layer correction; (4) a perfectly stirred reactor; and (5) a perfectly stirred reactor followed by a plug-flow reactor. In addition, LSENS can compute equilibrium properties for the following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. For static and one-dimensional-flow problems, including those behind an incident shock wave and following a perfectly stirred reactor calculation, LSENS can compute sensitivity coefficients of dependent variables and their derivatives, with respect to the initial values of dependent variables and/or the rate-coefficient parameters of the chemical reactions.

  8. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. However, th...

  9. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize phytochemicals in plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. New methods a...

  10. Collision-induced fragmentation accurate mass spectrometric analysis methods to rapidly characterize plant extracts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid advances in analytical chromatography equipment have made the reliable and reproducible measurement of a wide range of plant chemical components possible. Full chemical characterization of a given plant material is possible with the new mass spectrometers currently available. For phytochem...

  11. Accurate Free Vibration Analysis of the Completely Free Rectangular Mindlin Plate

    NASA Astrophysics Data System (ADS)

    Gorman, D. J.; Ding, Wei

    1996-01-01

    The superposition method is exploited to obtain accurate solutions for the natural frequencies and mode shapes of the completely free Mindlin plate. Computed eigenvalues are tabulated for a number of plate aspect and thickness ratios. Steps taken to avoid computational instability are described. Difficulties associated with choosing mode shape functions, particularly when free edges are involved, have always hindered researchers utilizing the Rayleigh-Ritz method. Such difficulties are obviated here. To the authors' knowledge, this represents the first accurate comprehensive solution to this important plate vibration problem.

  12. Simple optical computing device for chemical analysis

    NASA Astrophysics Data System (ADS)

    Soyemi, Olusola O.; Zhang, Lixia; Eastwood, DeLyle; Li, Hongli; Gemperline, Paul J.; Myrick, Michael L.

    2001-05-01

    Multivariate Optical Computing (MOC) devices have the potential of greatly simplifying as well as reducing the cost of applying the mathematics of multivariate regression to problems of chemical analysis in the real world. These devices utilize special optical interference coatings known as multivariate optical elements (MOEs) that are encoded with pre-determined spectroscopic patterns to selectively quantify a chemical species of interest in the presence of other interfering species. A T-format prototype of the first optical computing device is presented utilizing a multilayer MOE consisting of alternating layers of two metal oxide films (Nb2O5 and SiO2) on a BK-7 glass substrate. The device was tested by using it to quantify copper uroporphyrin in a quaternary mixture consisting of uroporphyrin (freebase), tin uroporphyrin, nickel uroporphyrin, and copper uroporphyrin. A standard error of prediction (SEP) of 0.86(mu) M was obtained for copper uroporphyrin.

  13. LSENS - GENERAL CHEMICAL KINETICS AND SENSITIVITY ANALYSIS CODE

    NASA Technical Reports Server (NTRS)

    Bittker, D. A.

    1994-01-01

    LSENS has been developed for solving complex, homogeneous, gas-phase, chemical kinetics problems. The motivation for the development of this program is the continuing interest in developing detailed chemical reaction mechanisms for complex reactions such as the combustion of fuels and pollutant formation and destruction. A reaction mechanism is the set of all elementary chemical reactions that are required to describe the process of interest. Mathematical descriptions of chemical kinetics problems constitute sets of coupled, nonlinear, first-order ordinary differential equations (ODEs). The number of ODEs can be very large because of the numerous chemical species involved in the reaction mechanism. Further complicating the situation are the many simultaneous reactions needed to describe the chemical kinetics of practical fuels. For example, the mechanism describing the oxidation of the simplest hydrocarbon fuel, methane, involves over 25 species participating in nearly 100 elementary reaction steps. Validating a chemical reaction mechanism requires repetitive solutions of the governing ODEs for a variety of reaction conditions. Analytical solutions to the systems of ODEs describing chemistry are not possible, except for the simplest cases, which are of little or no practical value. Consequently, there is a need for fast and reliable numerical solution techniques for chemical kinetics problems. In addition to solving the ODEs describing chemical kinetics, it is often necessary to know what effects variations in either initial condition values or chemical reaction mechanism parameters have on the solution. Such a need arises in the development of reaction mechanisms from experimental data. The rate coefficients are often not known with great precision and in general, the experimental data are not sufficiently detailed to accurately estimate the rate coefficient parameters. The development of a reaction mechanism is facilitated by a systematic sensitivity analysis

  14. High resolution Physio-chemical Tissue Analysis: Towards Non-invasive In Vivo Biopsy

    PubMed Central

    Xu, Guan; Meng, Zhuo-xian; Lin, Jian-die; Deng, Cheri X.; Carson, Paul L.; Fowlkes, J. Brian; Tao, Chao; Liu, Xiaojun; Wang, Xueding

    2016-01-01

    Conventional gold standard histopathologic diagnosis requires information of both high resolution structural and chemical changes in tissue. Providing optical information at ultrasonic resolution, photoacoustic (PA) technique could provide highly sensitive and highly accurate tissue characterization noninvasively in the authentic in vivo environment, offering a replacement for histopathology. A two-dimensional (2D) physio-chemical spectrogram (PCS) combining micrometer to centimeter morphology and chemical composition simultaneously can be generated for each biological sample with PA measurements at multiple optical wavelengths. This spectrogram presents a unique 2D “physio-chemical signature” for any specific type of tissue. Comprehensive analysis of PCS, termed PA physio-chemical analysis (PAPCA), can lead to very rich diagnostic information, including the contents of all relevant molecular and chemical components along with their corresponding histological microfeatures, comparable to those accessible by conventional histology. PAPCA could contribute to the diagnosis of many diseases involving diffusive patterns such as fatty liver. PMID:26842459

  15. High resolution Physio-chemical Tissue Analysis: Towards Non-invasive In Vivo Biopsy

    NASA Astrophysics Data System (ADS)

    Xu, Guan; Meng, Zhuo-Xian; Lin, Jian-Die; Deng, Cheri X.; Carson, Paul L.; Fowlkes, J. Brian; Tao, Chao; Liu, Xiaojun; Wang, Xueding

    2016-02-01

    Conventional gold standard histopathologic diagnosis requires information of both high resolution structural and chemical changes in tissue. Providing optical information at ultrasonic resolution, photoacoustic (PA) technique could provide highly sensitive and highly accurate tissue characterization noninvasively in the authentic in vivo environment, offering a replacement for histopathology. A two-dimensional (2D) physio-chemical spectrogram (PCS) combining micrometer to centimeter morphology and chemical composition simultaneously can be generated for each biological sample with PA measurements at multiple optical wavelengths. This spectrogram presents a unique 2D “physio-chemical signature” for any specific type of tissue. Comprehensive analysis of PCS, termed PA physio-chemical analysis (PAPCA), can lead to very rich diagnostic information, including the contents of all relevant molecular and chemical components along with their corresponding histological microfeatures, comparable to those accessible by conventional histology. PAPCA could contribute to the diagnosis of many diseases involving diffusive patterns such as fatty liver.

  16. VALIDATION GUIDELINES FOR LABORATORIES PERFORMING FORENSIC ANALYSIS OF CHEMICAL TERRORISM

    EPA Science Inventory

    The Scientific Working Group on Forensic Analysis of Chemical Terrorism (SWGFACT) has developed the following guidelines for laboratories engaged in the forensic analysis of chemical evidence associated with terrorism. This document provides a baseline framework and guidance for...

  17. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration.

    PubMed

    Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y

    2000-01-01

    Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688

  18. Revisit to three-dimensional percolation theory: Accurate analysis for highly stretchable conductive composite materials

    PubMed Central

    Kim, Sangwoo; Choi, Seongdae; Oh, Eunho; Byun, Junghwan; Kim, Hyunjong; Lee, Byeongmoon; Lee, Seunghwan; Hong, Yongtaek

    2016-01-01

    A percolation theory based on variation of conductive filler fraction has been widely used to explain the behavior of conductive composite materials under both small and large deformation conditions. However, it typically fails in properly analyzing the materials under the large deformation since the assumption may not be valid in such a case. Therefore, we proposed a new three-dimensional percolation theory by considering three key factors: nonlinear elasticity, precisely measured strain-dependent Poisson’s ratio, and strain-dependent percolation threshold. Digital image correlation (DIC) method was used to determine actual Poisson’s ratios at various strain levels, which were used to accurately estimate variation of conductive filler volume fraction under deformation. We also adopted strain-dependent percolation threshold caused by the filler re-location with deformation. When three key factors were considered, electrical performance change was accurately analyzed for composite materials with both isotropic and anisotropic mechanical properties. PMID:27694856

  19. An Accurate Scene Segmentation Method Based on Graph Analysis Using Object Matching and Audio Feature

    NASA Astrophysics Data System (ADS)

    Yamamoto, Makoto; Haseyama, Miki

    A method for accurate scene segmentation using two kinds of directed graph obtained by object matching and audio features is proposed. Generally, in audiovisual materials, such as broadcast programs and movies, there are repeated appearances of similar shots that include frames of the same background, object or place, and such shots are included in a single scene. Many scene segmentation methods based on this idea have been proposed; however, since they use color information as visual features, they cannot provide accurate scene segmentation results if the color features change in different shots for which frames include the same object due to camera operations such as zooming and panning. In order to solve this problem, scene segmentation by the proposed method is realized by using two novel approaches. In the first approach, object matching is performed between two frames that are each included in different shots. By using these matching results, repeated appearances of shots for which frames include the same object can be successfully found and represented as a directed graph. The proposed method also generates another directed graph that represents the repeated appearances of shots with similar audio features in the second approach. By combined use of these two directed graphs, degradation of scene segmentation accuracy, which results from using only one kind of graph, can be avoided in the proposed method and thereby accurate scene segmentation can be realized. Experimental results performed by applying the proposed method to actual broadcast programs are shown to verify the effectiveness of the proposed method.

  20. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    SciTech Connect

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Anderson, Kevin K.; Daly, Don S.; Smith, Richard D.

    2005-08-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/- 5 ppm and 1 ppm) and NET value (no constraint, +/- 0.05 and 0.01 on a 0-1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LCMS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate easurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/- 1 ppm and elution time easurements within +/- 0.01 NET.

  1. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  2. Systems analysis of past, present, and future chemical terrorism scenarios.

    SciTech Connect

    Hoette, Trisha Marie

    2012-03-01

    Throughout history, as new chemical threats arose, strategies for the defense against chemical attacks have also evolved. As a part of an Early Career Laboratory Directed Research and Development project, a systems analysis of past, present, and future chemical terrorism scenarios was performed to understand how the chemical threats and attack strategies change over time. For the analysis, the difficulty in executing chemical attack was evaluated within a framework of three major scenario elements. First, historical examples of chemical terrorism were examined to determine how the use of chemical threats, versus other weapons, contributed to the successful execution of the attack. Using the same framework, the future of chemical terrorism was assessed with respect to the impact of globalization and new technologies. Finally, the efficacy of the current defenses against contemporary chemical terrorism was considered briefly. The results of this analysis justify the need for continued diligence in chemical defense.

  3. Accurate electronic and chemical properties of 3d transition metal oxides using a calculated linear response U and a DFT + U(V) method

    SciTech Connect

    Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy

    2015-04-14

    We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.

  4. Analysis of hydraulic fracturing flowback and produced waters using accurate mass: identification of ethoxylated surfactants.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Blotevogel, Jens; Borch, Thomas

    2014-10-01

    Two series of ethylene oxide (EO) surfactants, polyethylene glycols (PEGs from EO3 to EO33) and linear alkyl ethoxylates (LAEs C-9 to C-15 with EO3-EO28), were identified in hydraulic fracturing flowback and produced water using a new application of the Kendrick mass defect and liquid chromatography/quadrupole-time-of-flight mass spectrometry. The Kendrick mass defect differentiates the proton, ammonium, and sodium adducts in both singly and doubly charged forms. A structural model of adduct formation is presented, and binding constants are calculated, which is based on a spherical cagelike conformation, where the central cation (NH4(+) or Na(+)) is coordinated with ether oxygens. A major purpose of the study was the identification of the ethylene oxide (EO) surfactants and the construction of a database with accurate masses and retention times in order to unravel the mass spectral complexity of surfactant mixtures used in hydraulic fracturing fluids. For example, over 500 accurate mass assignments are made in a few seconds of computer time, which then is used as a fingerprint chromatogram of the water samples. This technique is applied to a series of flowback and produced water samples to illustrate the usefulness of ethoxylate "fingerprinting", in a first application to monitor water quality that results from fluids used in hydraulic fracturing. PMID:25164376

  5. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear-Layer. Part 2

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Lockard, David P.

    2002-01-01

    Unsteady computational simulations of a multi-element, high-lift configuration are performed. Emphasis is placed on accurate spatiotemporal resolution of the free shear layer in the slat-cove region. The excessive dissipative effects of the turbulence model, so prevalent in previous simulations, are circumvented by switching off the turbulence-production term in the slat cove region. The justifications and physical arguments for taking such a step are explained in detail. The removal of this excess damping allows the shear layer to amplify large-scale structures, to achieve a proper non-linear saturation state, and to permit vortex merging. The large-scale disturbances are self-excited, and unlike our prior fully turbulent simulations, no external forcing of the shear layer is required. To obtain the farfield acoustics, the Ffowcs Williams and Hawkings equation is evaluated numerically using the simulated time-accurate flow data. The present comparison between the computed and measured farfield acoustic spectra shows much better agreement for the amplitude and frequency content than past calculations. The effect of the angle-of-attack on the slat's flow features radiated acoustic field are also simulated presented.

  6. SALI chemical analysis of provided samples

    NASA Technical Reports Server (NTRS)

    Becker, Christopher H.

    1993-01-01

    SRI has completed the chemical analysis of all the samples supplied by NASA. The final batch of four samples consisted of: one inch diameter MgF2 mirror, control 1200-ID-FL3; one inch diameter neat resin, PMR-15, AO171-IV-55, half exposed and half unexposed; one inch diameter chromic acid anodized, EOIM-3 120-47 aluminum disc; and AO-exposed and unexposed samples of fullerene extract material in powdered form, pressed into In foil for analysis. Chemical analyses of the surfaces were performed by the surface analysis by laser ionization (SALI) method. The analyses emphasize surface contamination or general organic composition. SALI uses nonselective photoionization of sputtered or desorbed atoms and molecules above but close (approximately one mm) to the surface, followed by time-of-flight (TOF) mass spectrometry. In these studies, we used laser-induced desorption by 5-ns pulse-width 355-nm light (10-100 mJ/sq cm) and single-photon ionization (SPI) by coherent 118-nm radiation (at approximately 5 x 10(exp 5) W/sq cm). SPI was chosen primarily for its ability to obtain molecular information, whereas multiphoton ionization (not used in the present studies) is intended primarily for elemental and small molecule information. In addition to these four samples, the Au mirror (EOIM-3 200-11, sample four) was depth profiled again. Argon ion sputtering was used together with photoionization with intense 355-nm radiation (35-ps pulsewidths). Depth profiles are similar to those reported earlier, showing reproducibility. No chromium was found in the sample above noise level; its presence could at most be at the trace level. Somewhat more Ni appears to be present in the Au layer in the unexposed side, indicating thermal diffusion without chemical enhancement. The result of the presence of oxygen is apparently to tie-up/draw out the Ni as an oxide at the surface. The exposed region has a brownish tint appearance to the naked eye.

  7. Transient analysis of a chemical synaptic transmission.

    PubMed

    Melkonian, D S

    1993-01-01

    The statistical dynamics of an impulse induced quanta turnover is studied by means of a nonstationary stochastic model--double barrier synapse--resulting from a previously developed mathematical theory of chemical synaptic transmission. An essential aspect of nonstationarities of the model is that the interpool quanta transfers follow binomial distribution at impulse arrival time, while in the absence of stimulation they obey Yule-Furry statistics. Under a variety of conditions, corresponding to those in actual experiments, the transient behaviour of the model is simulated and analysed in detail. As a result, the quantitative description of immediate and delayed components of synaptic action is introduced. If simulations of quantal fluctuations are performed numerically, then for the treatment of dynamic regularities, besides numerical procedures, an analytical method of envelopes is developed. It is supported by the theorems which reduce behaviour of the double-barrier synapse to the super-position of simpler solutions for single-barrier systems. With short-term facilitation quantitative analysis and simulations, the synaptic resonance phenomenon is theoretically predicted: different resonant frequencies are found at different levels of facilitation. The importance of this phenomenon treated as a clue to the information processing capabilities of a chemical synapse is discussed. PMID:8097407

  8. Energy analysis of thermal, chemical, and metallurgical processes

    SciTech Connect

    Szargut, J.; Morris, D.R.; Steward, F.R.

    1988-01-01

    This book consists of the following chapters: The exergy concept and exergy losses; Calculation of exergy; Physical and chemical exergy of typical substances; Exergy analysis of typical thermal and chemical processes; Cumulative exergy consumption and cumulative degree of perfection; Reduction of external exergy losses; Exergy analysis of major thermal and chemical processes; Thermoeconomic applications of exergy; and Ecological applications of exergy.

  9. Ecological food web analysis for chemical risk assessment.

    PubMed

    Preziosi, Damian V; Pastorok, Robert A

    2008-12-01

    Food web analysis can be a critical component of ecological risk assessment, yet it has received relatively little attention among risk assessors. Food web data are currently used in modeling bioaccumulation of toxic chemicals and, to a limited extent, in the determination of the ecological significance of risks. Achieving more realism in ecological risk assessments requires new analysis tools and models that incorporate accurate information on key receptors in a food web paradigm. Application of food web analysis in risk assessments demands consideration of: 1) different kinds of food webs; 2) definition of trophic guilds; 3) variation in food webs with habitat, space, and time; and 4) issues for basic sampling design and collection of dietary data. The different kinds of food webs include connectance webs, materials flow webs, and functional (or interaction) webs. These three kinds of webs play different roles throughout various phases of an ecological risk assessment, but risk assessors have failed to distinguish among web types. When modeling food webs, choices must be made regarding the level of complexity for the web, assignment of species to trophic guilds, selection of representative species for guilds, use of average diets, the characterization of variation among individuals or guild members within a web, and the spatial and temporal scales/dynamics of webs. Integrating exposure and effects data in ecological models for risk assessment of toxic chemicals relies on coupling food web analysis with bioaccumulation models (e.g., Gobas-type models for fish and their food webs), wildlife exposure models, dose-response models, and population dynamics models. PMID:18703218

  10. Black tea: chemical analysis and stability.

    PubMed

    Li, Shiming; Lo, Chih-Yu; Pan, Min-Hsiung; Lai, Ching-Shu; Ho, Chi-Tang

    2013-01-01

    Tea is the most popular flavored and functional drink worldwide. The nutritional value of tea is mostly from the tea polyphenols that are reported to possess a broad spectrum of biological activities, including anti-oxidant properties, reduction of various cancers, inhibition of inflammation, and protective effects against diabetes, hyperlipidemia and obesity. Tea polyphenols include catechins and gallic acid in green and white teas, and theaflavins and thearubigins as well as other catechin polymers in black and oolong teas. Accurate analysis of black tea polyphenols plays a significant role in the identification of black tea contents, quality control of commercial tea beverages and extracts, differentiation of various contents of theaflavins and catechins and correlations of black tea identity and quality with biological activity, and most importantly, the establishment of the relationship between quantitative tea polyphenol content and its efficacy in animal or human studies. Global research in tea polyphenols has generated much in vitro and in vivo data rationally correlating tea polyphenols with their preventive and therapeutic properties in human diseases such as cancer, and metabolic and cardiovascular diseases etc. Based on these scientific findings, numerous tea products have been developed including flavored tea drinks, tea-based functional drinks, tea extracts and concentrates, and dietary supplements and food ingredients, demonstrating the broad applications of tea and its extracts, particularly in the field of functional food.

  11. The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

    NASA Astrophysics Data System (ADS)

    López-Sanjuan, C.; Cenarro, A. J.; Varela, J.; Viironen, K.; Molino, A.; Benítez, N.; Arnalte-Mur, P.; Ascaso, B.; Díaz-García, L. A.; Fernández-Soto, A.; Jiménez-Teja, Y.; Márquez, I.; Masegosa, J.; Moles, M.; Pović, M.; Aguerri, J. A. L.; Alfaro, E.; Aparicio-Villegas, T.; Broadhurst, T.; Cabrera-Caño, J.; Castander, F. J.; Cepa, J.; Cerviño, M.; Cristóbal-Hornillos, D.; Del Olmo, A.; González Delgado, R. M.; Husillos, C.; Infante, L.; Martínez, V. J.; Perea, J.; Prada, F.; Quintana, J. M.

    2015-04-01

    Aims: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. Methods: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections. We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. Results: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20-1.1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2.7 ± 0.5) than for red galaxies (n = 1.3 ± 0.4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nmred = 0.57 ± 0.05 for red galaxies and Nmblue = 0.26 ± 0.02 for blue galaxies. Conclusions: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (CSIC).The catalogues, probabilities, and figures of the ALHAMBRA close pairs detected in Sect. 5.1 are available at http://https://cloud.iaa.csic.es/alhambra/catalogues/ClosePairs

  12. TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology

    PubMed Central

    Hong, Dongwan; Park, Sung-Soo; Ju, Young Seok; Kim, Sheehyun; Shin, Jong-Yeon; Kim, Sujung; Yu, Saet-Byeol; Lee, Won-Chul; Lee, Seungbok; Park, Hansoo; Kim, Jong-Il; Seo, Jeong-Sun

    2011-01-01

    High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research. PMID:21051338

  13. Guided resonances on lithium niobate for extremely small electric field detection investigated by accurate sensitivity analysis.

    PubMed

    Qiu, Wentao; Ndao, Abdoulaye; Lu, Huihui; Bernal, Maria-Pilar; Baida, Fadi Issam

    2016-09-01

    We present a theoretical study of guided resonances (GR) on a thin film lithium niobate rectangular lattice photonic crystal by band diagram calculations and 3D Finite Difference Time Domain (FDTD) transmission investigations which cover a broad range of parameters. A photonic crystal with an active zone as small as 13μm×13μm×0.7μm can be easily designed to obtain a resonance Q value in the order of 1000. These resonances are then employed in electric field (E-field) sensing applications exploiting the electro optic (EO) effect of lithium niobate. A local field factor that is calculated locally for each FDTD cell is proposed to accurately estimate the sensitivity of GR based E-field sensor. The local field factor allows well agreement between simulations and reported experimental data therefore providing a valuable method in optimizing the GR structure to obtain high sensitivities. When these resonances are associated with sub-picometer optical spectrum analyzer and high field enhancement antenna design, an E-field probe with a sensitivity of 50 μV/m could be achieved. The results of our simulations could be also exploited in other EO based applications such as EEG (Electroencephalography) or ECG (Electrocardiography) probe and E-field frequency detector with an 'invisible' probe to the field being detected etc. PMID:27607627

  14. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

    PubMed Central

    Wang, Yi; Lu, James; Yu, Jin; Gibbs, Richard A.; Yu, Fuli

    2013-01-01

    Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical modeling of sequencing data; (2) variance ratio scoring, a variance-based statistic that discovers polymorphic loci with high sensitivity and specificity; and (3) BAM-specific binomial mixture modeling (BBMM), a clustering algorithm that generates robust genotype likelihoods from heterogeneous sequencing data. Last, we develop an imputation engine that refines raw genotype likelihoods to produce high-quality phased genotypes/haplotypes. Designed for large population studies, SNPTools' input/output (I/O) and storage aware design leads to improved computing performance on large sequencing data sets. We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray. PMID:23296920

  15. Accurate reliability analysis method for quantum-dot cellular automata circuits

    NASA Astrophysics Data System (ADS)

    Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo

    2015-10-01

    Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.

  16. Mechanical Analysis and Hierarchies of Multi-digit Synergies during Accurate Object Rotation

    PubMed Central

    Zhang, Wei; Olafsdottir, Halla B.; Zatsiorsky, Vladimir M.; Latash, Mark L.

    2009-01-01

    We studied the mechanical variables (the grip force and the total moment of force) and multi-digit synergies at two levels (the virtual finger-thumb level, VF-TH, and the individual finger level, IMRL) of a hypothetical control hierarchy during accurate rotation of a hand-held instrumented handle. Synergies were defined as co-varied changes in elemental variables (forces and moments of force) that stabilize the output at a particular level. Indices of multi-digit synergies showed higher values at the hierarchically higher level (VF-TH) for both normal and tangential forces. The moment of force was stabilized at both hierarchical levels during the steady-state phases but not during the movement. The results support the principles of superposition and of mechanical advantage. They also support an earlier hypothesis on an inherent trade-off between synergies at the two hierarchical levels, although the controller showed more subtle and versatile synergic control than the one hypothesized earlier. PMID:19799165

  17. Collection and chemical analysis of lichens for biomonitoring. Book chapter

    SciTech Connect

    Jackson, L.L.; Ford, J.; Schwartzman, D.

    1991-01-01

    The chapter discusses the interrelated aspects of biomonitoring using chemical analysis of lichens. Many unique aspects of study objectives, study design (including design tasks, considerations, and sampling schemes), sample collection, sample preparation, and sample analysis that are required for a successful biomonitoring program using chemical analysis are emphasized. The advantages and disadvantages of common analytical methods suitable for chemical analysis of lichens are briefly discussed. Aspects of a quality assurance program and final contract reports are highlighted. In addition, some examples of studies using chemical analysis of lichens are discussed.

  18. Spectroscopic Chemical Analysis Methods and Apparatus

    NASA Technical Reports Server (NTRS)

    Hug, William F.; Reid, Ray D.

    2012-01-01

    This invention relates to non-contact spectroscopic methods and apparatus for performing chemical analysis and the ideal wavelengths and sources needed for this analysis. It employs deep ultraviolet (200- to 300-nm spectral range) electron-beam-pumped wide bandgap semiconductor lasers, incoherent wide bandgap semiconductor lightemitting devices, and hollow cathode metal ion lasers. Three achieved goals for this innovation are to reduce the size (under 20 L), reduce the weight [under 100 lb (.45 kg)], and reduce the power consumption (under 100 W). This method can be used in microscope or macroscope to provide measurement of Raman and/or native fluorescence emission spectra either by point-by-point measurement, or by global imaging of emissions within specific ultraviolet spectral bands. In other embodiments, the method can be used in analytical instruments such as capillary electrophoresis, capillary electro-chromatography, high-performance liquid chromatography, flow cytometry, and related instruments for detection and identification of unknown analytes using a combination of native fluorescence and/or Raman spectroscopic methods. This design provides an electron-beampumped semiconductor radiation-producing method, or source, that can emit at a wavelength (or wavelengths) below 300 nm, e.g. in the deep ultraviolet between about 200 and 300 nm, and more preferably less than 260 nm. In some variations, the method is to produce incoherent radiation, while in other implementations it produces laser radiation. In some variations, this object is achieved by using an AlGaN emission medium, while in other implementations a diamond emission medium may be used. This instrument irradiates a sample with deep UV radiation, and then uses an improved filter for separating wavelengths to be detected. This provides a multi-stage analysis of the sample. To avoid the difficulties related to producing deep UV semiconductor sources, a pumping approach has been developed that uses

  19. A Nanoengineered Conductometric Device for Accurate Analysis of Elemental Mercury Vapor.

    PubMed

    Griffin, Matthew J; Kabir, K M Mohibul; Coyle, Victoria E; Kandjani, Ahmad Esmaielzadeh; Sabri, Ylias M; Ippolito, Samuel J; Bhargava, Suresh K

    2016-02-01

    We developed a novel conductometric device with nanostructured gold (Au) sensitive layer which showed high-performance for elemental mercury (Hg(0)) vapor detection under simulated conditions that resemble harsh industrial environments. That is, the Hg(0) vapor sensing performance of the developed sensor was investigated under different operating temperatures (30-130 °C) and working conditions (i.e., humid) as well as in the presence of various interfering gas species, including ammonia (NH3), hydrogen sulfide (H2S), nitric oxide (NO), carbon mono-oxide (CO), carbon dioxide (CO2), sulfur dioxide (SO2), hydrogen (H2), methane (CH4), and volatile organic compounds (VOCs) such as ethylmercaptan (EM), acetaldehyde (MeCHO) and methyl ethyl ketone (MEK) among others. The results indicate that the introduction of Au nanostructures (referred to as nanospikes) on the sensor's surface enhanced the sensitivity toward Hg(0) vapor by up-to 450%. The newly developed sensor exhibited a limit of detection (LoD) (∼35 μg/m(3)), repeatability (∼94%), desorption efficiency (100%) and selectivity (∼93%) when exposed to different concentrations of Hg(0) vapor (0.5 to 9.1 mg/m(3)) and interfering gas species at a chosen operating temperature of 105 °C. Furthermore, the sensor was also found to show 91% average selectivity when exposed toward harsher industrial gases such as NO, CO, CO2, and SO2 along with same concentrations of Hg(0) vapor in similar operating conditions. In fact, this is the first time a conductometric sensor is shown to have high selectivity toward Hg(0) vapor even in the presence of H2S. Overall results indicate that the developed sensor has immense potential to be used as accurate online Hg(0) vapor monitoring technology within industrial processes.

  20. Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach

    SciTech Connect

    Zimmer, Jennifer S.; Monroe, Matthew E.; Qian, Weijun; Smith, Richard D.

    2006-01-20

    Proteomics, and the larger field of systems biology, have recently demonstrated utility in both the understanding of cellular processes on the molecular level and the identification of potential biomarkers of various disease states. The large amount of data generated by utilizing high mass accuracy mass spectrometry for high-throughput proteomics analyses presents a challenge in data processing, analysis and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics analysis and the accompanying data processing tools that have been developed in order to interpret and display the large volumes of data produced.

  1. Can Raters with Reduced Job Descriptive Information Provide Accurate Position Analysis Questionnaire (PAQ) Ratings?

    ERIC Educational Resources Information Center

    Friedman, Lee; Harvey, Robert J.

    1986-01-01

    Job-naive raters provided with job descriptive information made Position Analysis Questionnaire (PAQ) ratings which were validated against ratings of job analysts who were also job content experts. None of the reduced job descriptive information conditions enabled job-naive raters to obtain either acceptable levels of convergent validity with…

  2. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  3. Solid rocket booster internal flow analysis by highly accurate adaptive computational methods

    NASA Technical Reports Server (NTRS)

    Huang, C. Y.; Tworzydlo, W.; Oden, J. T.; Bass, J. M.; Cullen, C.; Vadaketh, S.

    1991-01-01

    The primary objective of this project was to develop an adaptive finite element flow solver for simulating internal flows in the solid rocket booster. Described here is a unique flow simulator code for analyzing highly complex flow phenomena in the solid rocket booster. New methodologies and features incorporated into this analysis tool are described.

  4. Morphometric analysis of Russian Plain's small lakes on the base of accurate digital bathymetric models

    NASA Astrophysics Data System (ADS)

    Naumenko, Mikhail; Guzivaty, Vadim; Sapelko, Tatiana

    2016-04-01

    Lake morphometry refers to physical factors (shape, size, structure, etc) that determine the lake depression. Morphology has a great influence on lake ecological characteristics especially on water thermal conditions and mixing depth. Depth analyses, including sediment measurement at various depths, volumes of strata and shoreline characteristics are often critical to the investigation of biological, chemical and physical properties of fresh waters as well as theoretical retention time. Management techniques such as loading capacity for effluents and selective removal of undesirable components of the biota are also dependent on detailed knowledge of the morphometry and flow characteristics. During the recent years a lake bathymetric surveys were carried out by using echo sounder with a high bottom depth resolution and GPS coordinate determination. Few digital bathymetric models have been created with 10*10 m spatial grid for some small lakes of Russian Plain which the areas not exceed 1-2 sq. km. The statistical characteristics of the depth and slopes distribution of these lakes calculated on an equidistant grid. It will provide the level-surface-volume variations of small lakes and reservoirs, calculated through combination of various satellite images. We discuss the methodological aspects of creating of morphometric models of depths and slopes of small lakes as well as the advantages of digital models over traditional methods.

  5. Chemical Discrimination of Cortex Phellodendri amurensis and Cortex Phellodendri chinensis by Multivariate Analysis Approach

    PubMed Central

    Sun, Hui; Wang, Huiyu; Zhang, Aihua; Yan, Guangli; Han, Ying; Li, Yuan; Wu, Xiuhong; Meng, Xiangcai; Wang, Xijun

    2016-01-01

    Background: As herbal medicines have an important position in health care systems worldwide, their current assessment, and quality control are a major bottleneck. Cortex Phellodendri chinensis (CPC) and Cortex Phellodendri amurensis (CPA) are widely used in China, however, how to identify species of CPA and CPC has become urgent. Materials and Methods: In this study, multivariate analysis approach was performed to the investigation of chemical discrimination of CPA and CPC. Results: Principal component analysis showed that two herbs could be separated clearly. The chemical markers such as berberine, palmatine, phellodendrine, magnoflorine, obacunone, and obaculactone were identified through the orthogonal partial least squared discriminant analysis, and were identified tentatively by the accurate mass of quadruple-time-of-flight mass spectrometry. A total of 29 components can be used as the chemical markers for discrimination of CPA and CPC. Of them, phellodenrine is significantly higher in CPC than that of CPA, whereas obacunone and obaculactone are significantly higher in CPA than that of CPC. Conclusion: The present study proves that multivariate analysis approach based chemical analysis greatly contributes to the investigation of CPA and CPC, and showed that the identified chemical markers as a whole should be used to discriminate the two herbal medicines, and simultaneously the results also provided chemical information for their quality assessment. SUMMARY Multivariate analysis approach was performed to the investigate the herbal medicineThe chemical markers were identified through multivariate analysis approachA total of 29 components can be used as the chemical markers. UPLC-Q/TOF-MS-based multivariate analysis method for the herbal medicine samples Abbreviations used: CPC: Cortex Phellodendri chinensis, CPA: Cortex Phellodendri amurensis, PCA: Principal component analysis, OPLS-DA: Orthogonal partial least squares discriminant analysis, BPI: Base peaks ion

  6. The calculation of accurate 17O hyperfine coupling constants in the hydroxyl radical: A difficult problem for current quantum chemical methods

    NASA Astrophysics Data System (ADS)

    Wetmore, Stacey D.; Eriksson, Leif A.; Boyd, Russell J.

    1998-12-01

    The hyperfine coupling constants (HFCCs) in the hydroxyl radical are investigated through comparison of results obtained from a variety of quantum chemical methods. The couplings obtained from the multi-reference configuration interaction (MRCI) wave function, built upon the restricted open-shell Hartree-Fock (ROHF) reference determinant, are investigated in terms of the basis set, the configuration selection energy threshold, and the size of the reference space. Overall results which converge to the experimental couplings are obtained for hydrogen, but not for oxygen. In particular, the MRCI method shows no improvement over density functional theory (the B3LYP functional), for the calculation of Aiso(17O). On the other hand, results in excellent agreement with experiment are obtained through the use of the quadratic configuration interaction (QCISD) method based on the unrestricted HF (UHF) reference determinant with the identical basis sets. Examination of UHF and ROHF based coupled-cluster methods, CCSD and CCSD(T), indicates that once a high enough level of electron correlation is included, the oxygen HFCC is independent of the form of the reference determinant. Unlike the ROHF-CCSD method, which yields reliable results once the effects of triple excitations have been taken into account, the MRCI wave function cannot easily be adjusted to account for the inadequacies of the ROHF reference determinant in order to accurately predict 17O HFCCs.

  7. Accurate RT-qPCR gene expression analysis on cell culture lysates

    PubMed Central

    Van Peer, Gert; Mestdagh, Pieter; Vandesompele, Jo

    2012-01-01

    Gene expression quantification on cultured cells using the reverse transcription quantitative polymerase chain reaction (RT-qPCR) typically involves an RNA purification step that limits sample processing throughput and precludes parallel analysis of large numbers of samples. An approach in which cDNA synthesis is carried out on crude cell lysates instead of on purified RNA samples can offer a fast and straightforward alternative. Here, we evaluate such an approach, benchmarking Ambion's Cells-to-CT kit with the classic workflow of RNA purification and cDNA synthesis, and demonstrate its good accuracy and superior sensitivity. PMID:22355736

  8. Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach

    PubMed Central

    Zimmer, Jennifer S.D.; Monroe, Matthew E.; Qian, Wei-Jun; Smith, Richard D.

    2007-01-01

    Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. PMID:16429408

  9. Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics

    PubMed Central

    Xu, Xiayu; Ding, Wenxiang; Wang, Xuemin; Cao, Ruofan; Zhang, Maiye; Lv, Peilin; Xu, Feng

    2016-01-01

    Retinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries. PMID:27698369

  10. High Resolution Melting Analysis: A Rapid and Accurate Method to Detect CALR Mutations

    PubMed Central

    Moreno, Melania; Torres, Laura; Santana-Lopez, Gonzalo; Rodriguez-Medina, Carlos; Perera, María; Bellosillo, Beatriz; de la Iglesia, Silvia; Molero, Teresa; Gomez-Casares, Maria Teresa

    2014-01-01

    Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations. PMID:25068507

  11. Tritium speciation in nuclear reactor bioshield concrete and its impact on accurate analysis.

    PubMed

    Kim, Dae Ji; E Warwick, Phillip; Croudace, Ian W

    2008-07-15

    Tritium ((3)H) is produced in nuclear reactors via several neutron-induced reactions [(2)H(n, gamma)(3)H, (6)Li(n, alpha)(3)H, (10)B(n, 2alpha)(3)H, (14)N(n, (3)H)(12)C, and ternary fission (fission yield <0.01%)]. Typically, (3)H is present as tritiated water (HTO) and can become adsorbed into structural concrete from the surface inward where it will be held in a weakly bound form. However, a systematic analysis of a sequence of subsamples taken from a reactor bioshield using combustion and liquid scintillation analysis has identified two forms of (3)H, one weakly bound and one strongly bound. The strongly bound tritium, which originates from neutron capture on trace lithium ((6)Li) within mineral phases, requires temperatures in excess of 350 degrees C to achieve quantitative recovery. The weakly bound form of tritium can be liberated at significantly lower temperatures (100 degrees C) as HTO and is associated with dehydration of hydrous mineral components. Without an appreciation that two forms of tritium can exist in reactor bioshields, the (3)H content of samples may be severely underestimated using conventional analytical approaches. These findings exemplify the need to develop robust radioactive waste characterization procedures in support of nuclear decommissioning programs. PMID:18543953

  12. Tritium speciation in nuclear reactor bioshield concrete and its impact on accurate analysis.

    PubMed

    Kim, Dae Ji; E Warwick, Phillip; Croudace, Ian W

    2008-07-15

    Tritium ((3)H) is produced in nuclear reactors via several neutron-induced reactions [(2)H(n, gamma)(3)H, (6)Li(n, alpha)(3)H, (10)B(n, 2alpha)(3)H, (14)N(n, (3)H)(12)C, and ternary fission (fission yield <0.01%)]. Typically, (3)H is present as tritiated water (HTO) and can become adsorbed into structural concrete from the surface inward where it will be held in a weakly bound form. However, a systematic analysis of a sequence of subsamples taken from a reactor bioshield using combustion and liquid scintillation analysis has identified two forms of (3)H, one weakly bound and one strongly bound. The strongly bound tritium, which originates from neutron capture on trace lithium ((6)Li) within mineral phases, requires temperatures in excess of 350 degrees C to achieve quantitative recovery. The weakly bound form of tritium can be liberated at significantly lower temperatures (100 degrees C) as HTO and is associated with dehydration of hydrous mineral components. Without an appreciation that two forms of tritium can exist in reactor bioshields, the (3)H content of samples may be severely underestimated using conventional analytical approaches. These findings exemplify the need to develop robust radioactive waste characterization procedures in support of nuclear decommissioning programs.

  13. Automated system for fast and accurate analysis of SF6 injected in the surface ocean.

    PubMed

    Koo, Chul-Min; Lee, Kitack; Kim, Miok; Kim, Dae-Ok

    2005-11-01

    This paper describes an automated sampling and analysis system for the shipboard measurement of dissolved sulfur hexafluoride (SF6) in surface marine environments into which SF6 has been deliberately released. This underway system includes a gas chromatograph associated with an electron capture detector, a fast and highly efficient SF6-extraction device, a global positioning system, and a data acquisition system based on Visual Basic 6.0/C 6.0. This work is distinct from previous studies in that it quantifies the efficiency of the SF6-extraction device and its carryover effect and examines the effect of surfactant on the SF6-extraction efficiency. Measurements can be continuously performed on seawater samples taken from a seawater line installed onboard a research vessel. The system runs on an hourly cycle during which one set of four SF6 standards is measured and SF6 derived from the seawater stream is subsequently analyzed for the rest of each 1 h period. This state-of-art system was successfully used to trace a water mass carrying Cochlodinium polykrikoides, which causes harmful algal blooms (HAB) in the coastal waters of southern Korea. The successful application of this analysis system in tracing the HAB-infected water mass suggests that the SF6 detection method described in this paper will improve the quality of the future study of biogeochemical processes in the marine environment. PMID:16294883

  14. Automated system for fast and accurate analysis of SF6 injected in the surface ocean.

    PubMed

    Koo, Chul-Min; Lee, Kitack; Kim, Miok; Kim, Dae-Ok

    2005-11-01

    This paper describes an automated sampling and analysis system for the shipboard measurement of dissolved sulfur hexafluoride (SF6) in surface marine environments into which SF6 has been deliberately released. This underway system includes a gas chromatograph associated with an electron capture detector, a fast and highly efficient SF6-extraction device, a global positioning system, and a data acquisition system based on Visual Basic 6.0/C 6.0. This work is distinct from previous studies in that it quantifies the efficiency of the SF6-extraction device and its carryover effect and examines the effect of surfactant on the SF6-extraction efficiency. Measurements can be continuously performed on seawater samples taken from a seawater line installed onboard a research vessel. The system runs on an hourly cycle during which one set of four SF6 standards is measured and SF6 derived from the seawater stream is subsequently analyzed for the rest of each 1 h period. This state-of-art system was successfully used to trace a water mass carrying Cochlodinium polykrikoides, which causes harmful algal blooms (HAB) in the coastal waters of southern Korea. The successful application of this analysis system in tracing the HAB-infected water mass suggests that the SF6 detection method described in this paper will improve the quality of the future study of biogeochemical processes in the marine environment.

  15. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  16. Simulating Expert Clinical Comprehension: Adapting Latent Semantic Analysis to Accurately Extract Clinical Concepts from Psychiatric Narrative

    PubMed Central

    Cohen, Trevor; Blatter, Brett; Patel, Vimla

    2008-01-01

    Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested. PMID:18455483

  17. Computer-implemented system and method for automated and highly accurate plaque analysis, reporting, and visualization

    NASA Technical Reports Server (NTRS)

    Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)

    2008-01-01

    A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.

  18. Quantum analysis of a bandpass Purcell filter for accurate qubit readout

    NASA Astrophysics Data System (ADS)

    Sete, Eyob A.; Martinis, John M.; Korotkov, Alexander N.

    2015-03-01

    In a circuit QED setup the readout fidelity of a superconducting qubit is partially limited by the qubit relaxation through the resonator into a transmission line, which is also known as the Purcell effect. One way to suppress this effect is to employ a filter, which impedes microwave propagation at the qubit frequency. We present a quantum analysis for the bandpass Purcell filter that was recently realized by E. Jeffrey et al. [1]. Using experimental parameters, we show that the bandpass filter suppresses the qubit relaxation rate by two orders of magnitude while keeping the measurement rate the same. We also show that in the presence of a microwave drive the qubit relaxation rate further decreases with increasing drive strength.

  19. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

    PubMed Central

    2010-01-01

    High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

  20. Wind effect on PV module temperature: Analysis of different techniques for an accurate estimation.

    NASA Astrophysics Data System (ADS)

    Schwingshackl, Clemens; Petitta, Marcello; Ernst Wagner, Jochen; Belluardo, Giorgio; Moser, David; Castelli, Mariapina; Zebisch, Marc; Tetzlaff, Anke

    2013-04-01

    In this abstract a study on the influence of wind to model the PV module temperature is presented. This study is carried out in the framework of the PV-Alps INTERREG project in which the potential of different photovoltaic technologies is analysed for alpine regions. The PV module temperature depends on different parameters, such as ambient temperature, irradiance, wind speed and PV technology [1]. In most models, a very simple approach is used, where the PV module temperature is calculated from NOCT (nominal operating cell temperature), ambient temperature and irradiance alone [2]. In this study the influence of wind speed on the PV module temperature was investigated. First, different approaches suggested by various authors were tested [1], [2], [3], [4], [5]. For our analysis, temperature, irradiance and wind data from a PV test facility at the airport Bolzano (South Tyrol, Italy) from the EURAC Institute of Renewable Energies were used. The PV module temperature was calculated with different models and compared to the measured PV module temperature at the single panels. The best results were achieved with the approach suggested by Skoplaki et al. [1]. Preliminary results indicate that for all PV technologies which were tested (monocrystalline, amorphous, microcrystalline and polycrystalline silicon and cadmium telluride), modelled and measured PV module temperatures show a higher agreement (RMSE about 3-4 K) compared to standard approaches in which wind is not considered. For further investigation the in-situ measured wind velocities were replaced with wind data from numerical weather forecast models (ECMWF, reanalysis fields). Our results show that the PV module temperature calculated with wind data from ECMWF is still in very good agreement with the measured one (R² > 0.9 for all technologies). Compared to the previous analysis, we find comparable mean values and an increasing standard deviation. These results open a promising approach for PV module

  1. Accurate analysis of taurine, anserine, carnosine and free amino acids in a cattle muscle biopsy sample.

    PubMed

    Imanari, Mai; Higuchi, Mikito; Shiba, Nobuya; Watanabe, Akira

    2010-06-01

    We have established an analysis method for some free amino acids (FAAs), as well as taurine (Tau), anserine (Ans) and carnosine (Car), in a fresh biopsy sample from cattle muscle. A series of model biopsy samples, corresponding to the mixtures of lean meat, fat and connective tissue, was prepared and showed high correlation coefficients between the compound concentration and the 3-methylhistidine (3-MeHis) content derived from hydrolysis of the biopsy sample (r = 0.74-0.95, P < 0.01). Interference from blood contamination could not be neglected, because the concentration of some FAAs in blood was comparable to that in muscle. However, it was possible to control the contamination of Tau, Ans, Car, glutamic acid, glutamine, asparatic acid and alanine to less than 5.0% when the blood contamination was controlled to less than 23%.These results suggest the necessity of measuring 3-MeHis as an index of lean meat and hemoglobin as an index of blood contamination when compounds in muscle biopsy samples are evaluated. We have carried out a series of these analyses using one biopsy sample and reveal differences in Tau, Ans, Car and some FAAs in beef muscle after different feeding regimes.

  2. Photo-detachment signal analysis to accurately determine electronegativity, electron temperature, and charged species density

    NASA Astrophysics Data System (ADS)

    Oudini, N.; Sirse, N.; Taccogna, F.; Ellingboe, A. R.; Bendib, A.

    2016-09-01

    Laser pulse induced photo-detachment combined with Langmuir probing has been introduced to diagnose plasma electronegativity. This technique uses a laser pulse to convert negative ions into electron-atom pairs and tracks the change of electron saturation current by a Langmuir probe. The existing model determines plasma electronegativity as the ratio of electron saturation current before and after detachment. However, this model depends on various assumptions and neglects the formation of a potential barrier between the laser channel and surrounding electronegative plasma. In this letter, we present a new analytical model to analyze photo-detachment signals in order to improve the accuracy of electronegativity measurements and extend this technique for measuring electron temperature and charged species density. This analytical model is supported by Particle-In-Cell simulation of electronegative plasma dynamics following laser photo-detachment. The analysis of the signal, detected on a simulated probe, shows that the present analytical model determines electronegativity, electron temperature, and plasma density with a relative error of ˜20%, ˜20%, and ˜50%, respectively, whereas the electronegativity obtained from a previous model is underestimated by an order of magnitude.

  3. A Cost-Benefit and Accurate Method for Assessing Microalbuminuria: Single versus Frequent Urine Analysis

    PubMed Central

    Hemmati, Roholla; Gharipour, Mojgan; Khosravi, Alireza; Jozan, Mahnaz

    2013-01-01

    Background. The purpose of this study was to answer the question whether a single testing for microalbuminuria results in a reliable conclusion leading costs saving. Methods. This current cross-sectional study included a total of 126 consecutive persons. Microalbuminuria was assessed by collection of two fasting random urine specimens on arrival to the clinic as well as one week later in the morning. Results. In overall, 17 out of 126 participants suffered from microalbuminuria that, among them, 12 subjects were also diagnosed as microalbuminuria once assessing this factor with a sensitivity of 70.6%, a specificity of 100%, a PPV of 100%, a NPV of 95.6%, and an accuracy of 96.0%. The measured sensitivity, specificity, PVV, NPV, and accuracy in hypertensive patients were 73.3%, 100%, 100%, 94.8%, and 95.5%, respectively. Also, these rates in nonhypertensive groups were 50.0%, 100%, 100%, 97.3%, and 97.4%, respectively. According to the ROC curve analysis, a single measurement of UACR had a high value for discriminating defected from normal renal function state (c = 0.989). Urinary albumin concentration in a single measurement had also high discriminative value for diagnosis of damaged kidney (c = 0.995). Conclusion. The single testing of both UACR and urine albumin level rather frequent testing leads to high diagnostic sensitivity, specificity, and accuracy as well as high predictive values in total population and also in hypertensive subgroups. PMID:24455207

  4. Borehole flowmeter logging for the accurate design and analysis of tracer tests.

    PubMed

    Basiricò, Stefano; Crosta, Giovanni B; Frattini, Paolo; Villa, Alberto; Godio, Alberto

    2015-04-01

    Tracer tests often give ambiguous interpretations that may be due to the erroneous location of sampling points and/or the lack of flow rate measurements through the sampler. To obtain more reliable tracer test results, we propose a methodology that optimizes the design and analysis of tracer tests in a cross borehole mode by using vertical borehole flow rate measurements. Experiments using this approach, herein defined as the Bh-flow tracer test, have been performed by implementing three sequential steps: (1) single-hole flowmeter test, (2) cross-hole flowmeter test, and (3) tracer test. At the experimental site, core logging, pumping tests, and static water-level measurements were previously carried out to determine stratigraphy, fracture characteristics, and bulk hydraulic conductivity. Single-hole flowmeter testing makes it possible to detect the presence of vertical flows as well as inflow and outflow zones, whereas cross-hole flowmeter testing detects the presence of connections along sets of flow conduits or discontinuities intercepted by boreholes. Finally, the specific pathways and rates of groundwater flow through selected flowpaths are determined by tracer testing. We conclude that the combined use of single and cross-borehole flowmeter tests is fundamental to the formulation of the tracer test strategy and interpretation of the tracer test results. PMID:25417730

  5. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing

    PubMed Central

    Guo, Xiaoge; Lehner, Kevin; O’Connell, Karen; Zhang, Jenny; Dave, Sandeep S.; Jinks-Robertson, Sue

    2015-01-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  6. Accurate fast method with high chemical yield for determination of uranium isotopes (234U, 235U, 238U) in granitic samples using alpha spectroscopy

    NASA Astrophysics Data System (ADS)

    Guirguis, Laila A.; Farag, Nagdy M.; Salim, Adham K.

    2015-03-01

    The present study aims to use the α-spectroscopy at Nuclear Materials Authority (NMA) of Egypt. A radiochemical technique for analysis uranium isotopes was carried out for ten mineralized granitic samples together with the International standards RGU-1 (IAEA) and St4 (NMA). Several steps of sample preparation, radiochemical separation and source preparation were performed before analysis. Uranium was separated from sample matrix with 0.2 M TOPO in cyclohexane as an extracting agent with a chemical yield 98.95% then uranium was purified from lanthanides and actinides present with 0.2 M TOA in xylene as an extracting agent. The pure fraction was electrodeposited on a mirror-polished copper disc from buffer solution (NaHSO4+H2SO4+NH4OH). Rectangle pt-electrode with an anode-cathode distance of 2 cm was used. Current was 900 mA and the electrodeposition time reach up to 120 min. The achieved results show that the chemical yield ranged between 87.9±6.8 and 98±8.6.

  7. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed Central

    Tyson, G. H.; Chen, Y.; Li, C.; Mukherjee, S.; Young, S.; Lam, C.; Folster, J. P.; Whichard, J. M.; McDermott, P. F.

    2015-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  8. CHEMICAL ANALYSIS METHODS FOR ATMOSPHERIC AEROSOL COMPONENTS

    EPA Science Inventory

    This chapter surveys the analytical techniques used to determine the concentrations of aerosol mass and its chemical components. The techniques surveyed include mass, major ions (sulfate, nitrate, ammonium), organic carbon, elemental carbon, and trace elements. As reported in...

  9. Chemical Engineering Data Analysis Made Easy with DataFit

    ERIC Educational Resources Information Center

    Brenner, James R.

    2006-01-01

    The outline for half of a one-credit-hour course in analysis of chemical engineering data is presented, along with a range of typical problems encountered later on in the chemical engineering curriculum that can be used to reinforce the data analysis skills learned in the course. This mini course allows students to be exposed to a variety of ChE…

  10. Forecasting for energy and chemical decision analysis

    SciTech Connect

    Cazalet, E.G.

    1984-08-01

    This paper focuses on uncertainty and bias in forecasts used for major energy and chemical investment decisions. Probability methods for characterizing uncertainty in the forecast are reviewed. Sources of forecasting bias are classified based on the results of relevant psychology research. Examples are drawn from the energy and chemical industry to illustrate the value of explicit characterization of uncertainty and reduction of bias in forecasts.

  11. Isotopic Ratio Outlier Analysis of the S. cerevisiae Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery.

    PubMed

    Qiu, Yunping; Moir, Robyn; Willis, Ian; Beecher, Chris; Tsai, Yu-Hsuan; Garrett, Timothy J; Yost, Richard A; Kurland, Irwin J

    2016-03-01

    Isotopic ratio outlier analysis (IROA) is a (13)C metabolomics profiling method that eliminates sample to sample variance, discriminates against noise and artifacts, and improves identification of compounds, previously done with accurate mass liquid chromatography/mass spectrometry (LC/MS). This is the first report using IROA technology in combination with accurate mass gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), here used to examine the S. cerevisiae metabolome. S. cerevisiae was grown in YNB media, containing randomized 95% (13)C, or 5%(13)C glucose as the single carbon source, in order that the isotopomer pattern of all metabolites would mirror the labeled glucose. When these IROA experiments are combined, the abundance of the heavy isotopologues in the 5%(13)C extracts, or light isotopologues in the 95%(13)C extracts, follows the binomial distribution, showing mirrored peak pairs for the molecular ion. The mass difference between the (12)C monoisotopic and the (13)C monoisotopic equals the number of carbons in the molecules. The IROA-GC/MS protocol developed, using both chemical and electron ionization, extends the information acquired from the isotopic peak patterns for formulas generation. The process that can be formulated as an algorithm, in which the number of carbons, as well as the number of methoximations and silylations are used as search constraints. In electron impact (EI/IROA) spectra, the artifactual peaks are identified and easily removed, which has the potential to generate "clean" EI libraries. The combination of chemical ionization (CI) IROA and EI/IROA affords a metabolite identification procedure that enables the identification of coeluting metabolites, and allowed us to characterize 126 metabolites in the current study. PMID:26820234

  12. Accurate mass fragment library for rapid analysis of pesticides on produce using ambient pressure desorption ionization with high-resolution mass spectrometry.

    PubMed

    Kern, Sara E; Lin, Lora A; Fricke, Frederick L

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]⁺) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]⁺ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]⁺ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli

  13. Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

    2014-08-01

    U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The

  14. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    PubMed

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-06-28

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  15. An accurate retrieval of leaf water content from mid to thermal infrared spectra using continuous wavelet analysis.

    PubMed

    Ullah, Saleem; Skidmore, Andrew K; Naeem, Mohammad; Schlerf, Martin

    2012-10-15

    Leaf water content determines plant health, vitality, photosynthetic efficiency and is an important indicator of drought assessment. The retrieval of leaf water content from the visible to shortwave infrared spectra is well known. Here for the first time, we estimated leaf water content from the mid to thermal infrared (2.5-14.0 μm) spectra, based on continuous wavelet analysis. The dataset comprised 394 spectra from nine plant species, with different water contents achieved through progressive drying. To identify the spectral feature most sensitive to the variations in leaf water content, first the Directional Hemispherical Reflectance (DHR) spectra were transformed into a wavelet power scalogram, and then linear relations were established between the wavelet power scalogram and leaf water content. The six individual wavelet features identified in the mid infrared yielded high correlations with leaf water content (R(2)=0.86 maximum, 0.83 minimum), as well as low RMSE (minimum 8.56%, maximum 9.27%). The combination of four wavelet features produced the most accurate model (R(2)=0.88, RMSE=8.00%). The models were consistent in terms of accuracy estimation for both calibration and validation datasets, indicating that leaf water content can be accurately retrieved from the mid to thermal infrared domain of the electromagnetic radiation.

  16. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    PubMed Central

    Ross, Charles W.; Simonsick, William J.; Bogusky, Michael J.; Celikay, Recep W.; Guare, James P.; Newton, Randall C.

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  17. A Simple and Accurate Analysis of Conductivity Loss in Millimeter-Wave Helical Slow-Wave Structures

    NASA Astrophysics Data System (ADS)

    Datta, S. K.; Kumar, Lalit; Basu, B. N.

    2009-04-01

    Electromagnetic field analysis of a helix slow-wave structure was carried out and a closed form expression was derived for the inductance per unit length of the transmission-line equivalent circuit of the structure, taking into account the actual helix tape dimensions and surface current on the helix over the actual metallic area of the tape. The expression of the inductance per unit length, thus obtained, was used for estimating the increment in the inductance per unit length caused due to penetration of the magnetic flux into the conducting surfaces following Wheeler’s incremental inductance rule, which was subsequently interpreted for the attenuation constant of the propagating structure. The analysis was computationally simple and accurate, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The approach was benchmarked against measurement for two practical structures, and excellent agreement was observed. The analysis was subsequently applied to demonstrate the effects of conductivity on the attenuation constant of a typical broadband millimeter-wave helical slow-wave structure with respect to helix materials and copper plating on the helix, surface finish of the helix, dielectric loading effect and effect of high temperature operation - a comparative study of various such aspects are covered.

  18. Accurate Enumeration of Aspergillus brasiliensis in Hair Color and Mascara by Time-Lapse Shadow Image Analysis.

    PubMed

    Ogawa, Hiroyuki; Matsuoka, Hideaki; Saito, Mikako

    2015-01-01

    The growth of black mold (Aspergillus brasiliensis) in black-colored samples such as hair color and mascara was measured with an automatic count system based on time-lapse shadow image analysis (TSIA). A. brasiliensis suspended in a lecithin and polysorbate (LP) solution of each sample (hair color or mascara) was spread on a potato dextrose agar medium plate containing LP. The background image darkness of the agar plate could be adjusted to attain accurate colony counts. 95 colonies in hair color and 22 colonies in mascara could be automatically determined at 48 h. The accuracy of the colony counts could be confirmed from the timelapse image data. In contrast, conventional visual counting at a specified time could not determine the number of colonies or led to false colony counts.

  19. Theory, Image Simulation, and Data Analysis of Chemical Release Experiments

    NASA Technical Reports Server (NTRS)

    Wescott, Eugene M.

    1994-01-01

    The final phase of Grant NAG6-1 involved analysis of physics of chemical releases in the upper atmosphere and analysis of data obtained on previous NASA sponsored chemical release rocket experiments. Several lines of investigation of past chemical release experiments and computer simulations have been proceeding in parallel. This report summarizes the work performed and the resulting publications. The following topics are addressed: analysis of the 1987 Greenland rocket experiments; calculation of emission rates for barium, strontium, and calcium; the CRIT 1 and 2 experiments (Collisional Ionization Cross Section experiments); image calibration using background stars; rapid ray motions in ionospheric plasma clouds; and the NOONCUSP rocket experiments.

  20. Environmental analysis of the chemical release module. [space shuttle payload

    NASA Technical Reports Server (NTRS)

    Heppner, J. P.; Dubin, M.

    1980-01-01

    The environmental analysis of the Chemical Release Module (a free flying spacecraft deployed from the space shuttle to perform chemical release experiments) is reviewed. Considerations of possible effects of the injectants on human health, ionosphere, weather, ground based optical astronomical observations, and satellite operations are included. It is concluded that no deleterious environmental effects of widespread or long lasting nature are anticipated from chemical releases in the upper atmosphere of the type indicated for the program.

  1. Quantifying chemical reactions by using mixing analysis.

    PubMed

    Jurado, Anna; Vázquez-Suñé, Enric; Carrera, Jesús; Tubau, Isabel; Pujades, Estanislao

    2015-01-01

    This work is motivated by a sound understanding of the chemical processes that affect the organic pollutants in an urban aquifer. We propose an approach to quantify such processes using mixing calculations. The methodology consists of the following steps: (1) identification of the recharge sources (end-members) and selection of the species (conservative and non-conservative) to be used, (2) identification of the chemical processes and (3) evaluation of mixing ratios including the chemical processes. This methodology has been applied in the Besòs River Delta (NE Barcelona, Spain), where the River Besòs is the main aquifer recharge source. A total number of 51 groundwater samples were collected from July 2007 to May 2010 during four field campaigns. Three river end-members were necessary to explain the temporal variability of the River Besòs: one river end-member is from the wet periods (W1) and two are from dry periods (D1 and D2). This methodology has proved to be useful not only to compute the mixing ratios but also to quantify processes such as calcite and magnesite dissolution, aerobic respiration and denitrification undergone at each observation point.

  2. Alpha particle backscattering measurements used for chemical analysis of surfaces

    NASA Technical Reports Server (NTRS)

    Patterson, J. H.

    1967-01-01

    Alpha particle backscattering performs a chemical analysis of surfaces. The apparatus uses a curium source and a semiconductor detector to determine the energy spectrum of the particles. This in turn determines the chemical composition of the surface after calibration to known samples.

  3. Chemical properties and methods of analysis of refractory compounds

    NASA Technical Reports Server (NTRS)

    Samsonov, G. V. (Editor); Frantsevich, I. N. (Editor); Yeremenko, V. N. (Editor); Nazarchuk, T. N. (Editor); Popova, O. I. (Editor)

    1978-01-01

    Reactions involving refractory metals and the alloys based on them are discussed. Chemical, electrochemical, photometric, spectrophotometric, and X-ray analysis are among the methods described for analyzing the results of the reactions and for determining the chemical properties of these materials.

  4. Tribology analysis of chemical-mechanical polishing

    NASA Astrophysics Data System (ADS)

    Runnels, Scott R.; Eyman, L. Michael

    1994-06-01

    To better understand the variation of material removal rate on a wafer during chemical-mechanical polishing (CMP), knowledge of the stress distribution on the wafer surface is required. The difference in wafer-surface stress distributions could be considerable depending on whether or not the wafer hydroplanes during polishing. This study analyzes the fluid film between the wafer and pad and demonstrates that hydroplaning is possible for standard CMP processes. The importance of wafer curvature, slurry viscosity, and rotation speed on the thickness of the fluid film is also demonstrated.

  5. Quantitative Chemical Analysis of Single Cells

    NASA Astrophysics Data System (ADS)

    Heien, Michael L.; Ewing, Andrew G.

    Exocytosis, the fusion of intracellular vesicles with the membrane and subsequent release of vesicular contents, is important in intercellular communication. The release event is a rapid process (milliseconds), hence detection of released chemicals requires a detection scheme that is both sensitive and has rapid temporal dynamics. Electrochemistry at carbon-fiber microelectrodes allows time-resolved exocytosis of electroactive catecholamines to be observed at very low levels. When coupled with constant-potential amperometry, the number of molecules released and the kinetics of quantal release can be determined. The rapid response time (milliseconds) of microelectrodes makes them well suited for monitoring the dynamic process of exocytosis.

  6. Chemical Diversity, Origin, and Analysis of Phycotoxins.

    PubMed

    Rasmussen, Silas Anselm; Andersen, Aaron John Christian; Andersen, Nikolaj Gedsted; Nielsen, Kristian Fog; Hansen, Per Juel; Larsen, Thomas Ostenfeld

    2016-03-25

    Microalgae, particularly those from the lineage Dinoflagellata, are very well-known for their ability to produce phycotoxins that may accumulate in the marine food chain and eventually cause poisoning in humans. This includes toxins accumulating in shellfish, such as saxitoxin, okadaic acid, yessotoxins, azaspiracids, brevetoxins, and pinnatoxins. Other toxins, such as ciguatoxins and maitotoxins, accumulate in fish, where, as is the case for the latter compounds, they can be metabolized to even more toxic metabolites. On the other hand, much less is known about the chemical nature of compounds that are toxic to fish, the so-called ichthyotoxins. Despite numerous reports of algal blooms causing massive fish kills worldwide, only a few types of compounds, such as the karlotoxins, have been proven to be true ichthyotoxins. This review will highlight marine microalgae as the source of some of the most complex natural compounds known to mankind, with chemical structures that show no resemblance to what has been characterized from plants, fungi, or bacteria. In addition, it will summarize algal species known to be related to fish-killing blooms, but from which ichthyotoxins are yet to be characterized. PMID:26901085

  7. Accurate Analysis of the Change in Volume, Location, and Shape of Metastatic Cervical Lymph Nodes During Radiotherapy

    SciTech Connect

    Takao, Seishin; Tadano, Shigeru; Taguchi, Hiroshi; Yasuda, Koichi; Onimaru, Rikiya; Ishikawa, Masayori; Bengua, Gerard; Suzuki, Ryusuke; Shirato, Hiroki

    2011-11-01

    Purpose: To establish a method for the accurate acquisition and analysis of the variations in tumor volume, location, and three-dimensional (3D) shape of tumors during radiotherapy in the era of image-guided radiotherapy. Methods and Materials: Finite element models of lymph nodes were developed based on computed tomography (CT) images taken before the start of treatment and every week during the treatment period. A surface geometry map with a volumetric scale was adopted and used for the analysis. Six metastatic cervical lymph nodes, 3.5 to 55.1 cm{sup 3} before treatment, in 6 patients with head and neck carcinomas were analyzed in this study. Three fiducial markers implanted in mouthpieces were used for the fusion of CT images. Changes in the location of the lymph nodes were measured on the basis of these fiducial markers. Results: The surface geometry maps showed convex regions in red and concave regions in blue to ensure that the characteristics of the 3D tumor geometries are simply understood visually. After the irradiation of 66 to 70 Gy in 2 Gy daily doses, the patterns of the colors had not changed significantly, and the maps before and during treatment were strongly correlated (average correlation coefficient was 0.808), suggesting that the tumors shrank uniformly, maintaining the original characteristics of the shapes in all 6 patients. The movement of the gravitational center of the lymph nodes during the treatment period was everywhere less than {+-}5 mm except in 1 patient, in whom the change reached nearly 10 mm. Conclusions: The surface geometry map was useful for an accurate evaluation of the changes in volume and 3D shapes of metastatic lymph nodes. The fusion of the initial and follow-up CT images based on fiducial markers enabled an analysis of changes in the location of the targets. Metastatic cervical lymph nodes in patients were suggested to decrease in size without significant changes in the 3D shape during radiotherapy. The movements of the

  8. Negative chemical ionization gas chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry and automated accurate mass data processing for determination of pesticides in fruit and vegetables.

    PubMed

    Besil, Natalia; Uclés, Samanta; Mezcúa, Milagros; Heinzen, Horacio; Fernández-Alba, Amadeo R

    2015-08-01

    Gas chromatography coupled to high resolution hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS), operating in negative chemical ionization (NCI) mode and combining full scan with MSMS experiments using accurate mass analysis, has been explored for the automated determination of pesticide residues in fruit and vegetables. Seventy compounds were included in this approach where 50 % of them are not approved by the EU legislation. A global 76 % of the analytes could be identified at 1 μg kg(-1). Recovery studies were developed at three concentration levels (1, 5, and 10 μg kg(-1)). Seventy-seven percent of the detected pesticides at the lowest level yielded recoveries within the 70 %-120 % range, whereas 94 % could be quantified at 5 μg kg(-1), and the 100 % were determined at 10 μg kg(-1). Good repeatability, expressed as relative standard deviation (RSD <20 %), was obtained for all compounds. The main drawback of the method was the limited dynamic range that was observed for some analytes that can be overcome either diluting the sample or lowering the injection volume. A home-made database was developed and applied to an automatic accurate mass data processing. Measured mass accuracies of the generated ions were mainly less than 5 ppm for at least one diagnostic ion. When only one ion was obtained in the single-stage NCI-MS, a representative product ion from MSMS experiments was used as identification criterion. A total of 30 real samples were analyzed and 67 % of the samples were positive for 12 different pesticides in the range 1.0-1321.3 μg kg(-1). PMID:25694145

  9. SYSTEMS CHEMICAL ANALYSIS OF PETROLEUM POLLUTANTS

    EPA Science Inventory

    The application of an established mathematical treatment useful for the characterization and identification of petroleum pollutants is described. Using discriminant analysis of relevant infrared spectrophotometric data, 99% of numerous known and unknown oil samples have been corr...

  10. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose. PMID:27410113

  11. Wavelet prism decomposition analysis applied to CARS spectroscopy: a tool for accurate and quantitative extraction of resonant vibrational responses.

    PubMed

    Kan, Yelena; Lensu, Lasse; Hehl, Gregor; Volkmer, Andreas; Vartiainen, Erik M

    2016-05-30

    We propose an approach, based on wavelet prism decomposition analysis, for correcting experimental artefacts in a coherent anti-Stokes Raman scattering (CARS) spectrum. This method allows estimating and eliminating a slowly varying modulation error function in the measured normalized CARS spectrum and yields a corrected CARS line-shape. The main advantage of the approach is that the spectral phase and amplitude corrections are avoided in the retrieved Raman line-shape spectrum, thus significantly simplifying the quantitative reconstruction of the sample's Raman response from a normalized CARS spectrum in the presence of experimental artefacts. Moreover, the approach obviates the need for assumptions about the modulation error distribution and the chemical composition of the specimens under study. The method is quantitatively validated on normalized CARS spectra recorded for equimolar aqueous solutions of D-fructose, D-glucose, and their disaccharide combination sucrose.

  12. Electron Spectroscopy: Applications for Chemical Analysis

    ERIC Educational Resources Information Center

    Heercules, David M.

    2004-01-01

    The development of XPS as an effective method for surface analysis during the period 1964-1977 is presented. The study shows that unlike other surface methods, XPS data can be obtained for both conductors and insulators and a variety of samples can be handled effectively, which is one of the major reasons for the popularity of the technique.

  13. Methods for Chemical Analysis of Fresh Waters.

    ERIC Educational Resources Information Center

    Golterman, H. L.

    This manual, one of a series prepared for the guidance of research workers conducting studies as part of the International Biological Programme, contains recommended methods for the analysis of fresh water. The techniques are grouped in the following major sections: Sample Taking and Storage; Conductivity, pH, Oxidation-Reduction Potential,…

  14. 40 CFR 761.253 - Chemical analysis.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Determining a PCB Concentration for Purposes of Abandonment or Disposal of Natural Gas Pipeline: Selecting... analysis. (a) Extract PCBs from the standard wipe sample collection medium and clean-up the extracted PCBs... SW-846, or a method validated under subpart Q of this part, to analyze these extracts for PCBs....

  15. 40 CFR 761.253 - Chemical analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Determining a PCB Concentration for Purposes of Abandonment or Disposal of Natural Gas Pipeline: Selecting... analysis. (a) Extract PCBs from the standard wipe sample collection medium and clean-up the extracted PCBs... SW-846, or a method validated under subpart Q of this part, to analyze these extracts for PCBs....

  16. Analysis and accurate reconstruction of incomplete data in X-ray differential phase-contrast computed tomography.

    PubMed

    Fu, Jian; Tan, Renbo; Chen, Liyuan

    2014-01-01

    X-ray differential phase-contrast computed tomography (DPC-CT) is a powerful physical and biochemical analysis tool. In practical applications, there are often challenges for DPC-CT due to insufficient data caused by few-view, bad or missing detector channels, or limited scanning angular range. They occur quite frequently because of experimental constraints from imaging hardware, scanning geometry, and the exposure dose delivered to living specimens. In this work, we analyze the influence of incomplete data on DPC-CT image reconstruction. Then, a reconstruction method is developed and investigated for incomplete data DPC-CT. It is based on an algebraic iteration reconstruction technique, which minimizes the image total variation and permits accurate tomographic imaging with less data. This work comprises a numerical study of the method and its experimental verification using a dataset measured at the W2 beamline of the storage ring DORIS III equipped with a Talbot-Lau interferometer. The numerical and experimental results demonstrate that the presented method can handle incomplete data. It will be of interest for a wide range of DPC-CT applications in medicine, biology, and nondestructive testing.

  17. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

    PubMed

    Kapp, Eugene A; Schütz, Frédéric; Connolly, Lisa M; Chakel, John A; Meza, Jose E; Miller, Christine A; Fenyo, David; Eng, Jimmy K; Adkins, Joshua N; Omenn, Gilbert S; Simpson, Richard J

    2005-08-01

    MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X!Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, PeptideProphet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X!Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of "consensus scoring", i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.

  18. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and Specificity analysis.

    SciTech Connect

    Kapp, Eugene; Schutz, Frederick; Connolly, Lisa M.; Chakel, John A.; Meza, Jose E.; Miller, Christine A.; Fenyo, David; Eng, Jimmy K.; Adkins, Joshua N.; Omenn, Gilbert; Simpson, Richard

    2005-08-01

    MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X-Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, Peptide Prophet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X-Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of ''consensus scoring'', i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.

  19. Mathematical analysis and algorithms for efficiently and accurately implementing stochastic simulations of short-term synaptic depression and facilitation.

    PubMed

    McDonnell, Mark D; Mohan, Ashutosh; Stricker, Christian

    2013-01-01

    The release of neurotransmitter vesicles after arrival of a pre-synaptic action potential (AP) at cortical synapses is known to be a stochastic process, as is the availability of vesicles for release. These processes are known to also depend on the recent history of AP arrivals, and this can be described in terms of time-varying probabilities of vesicle release. Mathematical models of such synaptic dynamics frequently are based only on the mean number of vesicles released by each pre-synaptic AP, since if it is assumed there are sufficiently many vesicle sites, then variance is small. However, it has been shown recently that variance across sites can be significant for neuron and network dynamics, and this suggests the potential importance of studying short-term plasticity using simulations that do generate trial-to-trial variability. Therefore, in this paper we study several well-known conceptual models for stochastic availability and release. We state explicitly the random variables that these models describe and propose efficient algorithms for accurately implementing stochastic simulations of these random variables in software or hardware. Our results are complemented by mathematical analysis and statement of pseudo-code algorithms.

  20. Pretest uncertainty analysis for chemical rocket engine tests

    NASA Technical Reports Server (NTRS)

    Davidian, Kenneth J.

    1987-01-01

    A parametric pretest uncertainty analysis has been performed for a chemical rocket engine test at a unique 1000:1 area ratio altitude test facility. Results from the parametric study provide the error limits required in order to maintain a maximum uncertainty of 1 percent on specific impulse. Equations used in the uncertainty analysis are presented.

  1. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli

    PubMed Central

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1α and TUB were the most stable genes for abiotic stresses, whereas EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley. PMID:27746803

  2. Efficient parametric analysis of the chemical master equation through model order reduction

    PubMed Central

    2012-01-01

    Background Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state space dimension of these equations, numerical simulations are computationally expensive. This is a particular problem for analysis tasks requiring repeated simulations for different parameter values. Such tasks are computationally expensive to the point of infeasibility with the chemical master equation. Results In this article, we apply parametric model order reduction techniques in order to construct accurate low-dimensional parametric models of the chemical master equation. These surrogate models can be used in various parametric analysis task such as identifiability analysis, parameter estimation, or sensitivity analysis. As biological examples, we consider two models for gene regulation networks, a bistable switch and a network displaying stochastic oscillations. Conclusions The results show that the parametric model reduction yields efficient models of stochastic biochemical reaction networks, and that these models can be useful for systems biology applications involving parametric analysis problems such as parameter exploration, optimization, estimation or sensitivity analysis. PMID:22748204

  3. A model for evaluating physico-chemical substance properties required by consequence analysis models.

    PubMed

    Nikmo, Juha; Kukkonen, Jaakko; Riikonen, Kari

    2002-04-26

    Modeling systems for analyzing the consequences of chemical emergencies require as input values a number of physico-chemical substance properties, commonly as a function of temperature at atmospheric pressure. This paper presents a mathematical model "CHEMIC", which can be used for evaluating such substance properties, assuming that six basic constant quantities are available (molecular weight, freezing or melting point, normal boiling point, critical temperature, critical pressure and critical volume). The model has been designed to yield reasonably accurate numerical predictions, while at the same time keeping the amount of input data to a minimum. The model is based on molecular theory or thermodynamics, together with empirical corrections. Mostly, model equations are based on the so-called law of corresponding states. The model evaluates substance properties as a function of temperature at atmospheric pressure. These include seven properties commonly required by consequence analysis and heavy gas dispersion modeling systems: vapor pressure, vapor and liquid densities, heat of vaporization, vapor and liquid viscosities and binary diffusion coefficient. The model predictions for vapor pressure, vapor and liquid densities and heat of vaporization have been evaluated by using the Clausius-Clapeyron equation. We have also compared the predictions of the CHEMIC model with those of the DATABANK database (developed by the AEA Technology, UK), which includes detailed semi-empirical correlations. The computer program CHEMIC could be easily introduced into consequence analysis modeling systems in order to extend their performance to address a wider selection of substances.

  4. Meta-Analysis of Mass Balances Examining Chemical Fate during Wastewater Treatment

    PubMed Central

    2008-01-01

    Mass balances are an instructive means for investigating the fate of chemicals during wastewater treatment. In addition to the aqueous-phase removal efficiency (Φ), they can inform on chemical partitioning, transformation, and persistence, as well as on the chemical loading to streams and soils receiving, respectively, treated effluent and digested sewage sludge (biosolids). Release rates computed on a per-capita basis can serve to extrapolate findings to a larger scale. This review examines over a dozen mass balances conducted for various organic wastewater contaminants, including prescription drugs, estrogens, fragrances, antimicrobials, and surfactants of differing sorption potential (hydrophobicity), here expressed as the 1-octanol−water partition coefficient (KOW) and the organic carbon normalized sorption coefficient (KOC). Major challenges to mass balances are the collection of representative samples and accurate quantification of chemicals in sludge. A meta-analysis of peer-reviewed data identified sorption potential as the principal determinant governing chemical persistence in biosolids. Occurrence data for organic wastewater compounds detected in digested sludge followed a simple nonlinear model that required only KOW or KOC as the input and yielded a correlation coefficient of 0.9 in both instances. The model predicted persistence in biosolids for the majority (>50%) of the input load of organic wastewater compounds featuring a log10KOW value of greater than 5.2 (log10KOC > 4.4). In contrast, hydrophobicity had no or only limited value for estimating, respectively, Φ and the overall persistence of a chemical during conventional wastewater treatment. PMID:18800497

  5. Airborne chemistry: acoustic levitation in chemical analysis.

    PubMed

    Santesson, Sabina; Nilsson, Staffan

    2004-04-01

    This review with 60 references describes a unique path to miniaturisation, that is, the use of acoustic levitation in analytical and bioanalytical chemistry applications. Levitation of small volumes of sample by means of a levitation technique can be used as a way to avoid solid walls around the sample, thus circumventing the main problem of miniaturisation, the unfavourable surface-to-volume ratio. Different techniques for sample levitation have been developed and improved. Of the levitation techniques described, acoustic or ultrasonic levitation fulfils all requirements for analytical chemistry applications. This technique has previously been used to study properties of molten materials and the equilibrium shape()and stability of liquid drops. Temperature and mass transfer in levitated drops have also been described, as have crystallisation and microgravity applications. The airborne analytical system described here is equipped with different and exchangeable remote detection systems. The levitated drops are normally in the 100 nL-2 microL volume range and additions to the levitated drop can be made in the pL-volume range. The use of levitated drops in analytical and bioanalytical chemistry offers several benefits. Several remote detection systems are compatible with acoustic levitation, including fluorescence imaging detection, right angle light scattering, Raman spectroscopy, and X-ray diffraction. Applications include liquid/liquid extractions, solvent exchange, analyte enrichment, single-cell analysis, cell-cell communication studies, precipitation screening of proteins to establish nucleation conditions, and crystallisation of proteins and pharmaceuticals. PMID:14762640

  6. Non-targeted screening for contaminants in paper and board food-contact materials using effect-directed analysis and accurate mass spectrometry.

    PubMed

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia; Jensen, Lisbeth Krüger; Granby, Kit; Vinggaard, Anne Marie; Driffield, Malcolm; Højslev Petersen, Jens

    2016-06-01

    Due to large knowledge gaps in chemical composition and toxicological data for substances involved, paper and board food-contact materials (P&B FCM) have been emerging as a FCM type of particular concern for consumer safety. This study describes the development of a step-by-step strategy, including extraction, high-performance liquid chromatography (HPLC) fractionation, tentative identification of relevant substances and in vitro testing of selected tentatively identified substances. As a case study, we used two fractions from a recycled pizza box sample which exhibited aryl hydrocarbon receptor (AhR) activity. These fractions were analysed by gas chromatography (GC) and ultra-HPLC (UHPLC) coupled to quadrupole time-of-flight mass spectrometers (QTOF MS) in order tentatively to identify substances. The elemental composition was determined for peaks above a threshold, and compared with entries in a commercial mass spectral library for GC-MS (GC-EI-QTOF MS) analysis and an in-house built library of accurate masses for substances known to be used in P&B packaging for UHPLC-QTOF analysis. Of 75 tentatively identified substances, 15 were initially selected for further testing in vitro; however, only seven were commercially available and subsequently tested in vitro and quantified. Of these seven, the identities of three pigments found in printing inks were confirmed by UHPLC tandem mass spectrometry (QqQ MS/MS). Two pigments had entries in the database, meaning that a material relevant accurate mass database can provide a fast tentative identification. Pure standards of the seven tentatively identified substances were tested in vitro but could not explain a significant proportion of the AhR-response in the extract. Targeted analyses of dioxins and PCBs, both well-known AhR agonists, was performed. However, the dioxins could explain approximately 3% of the activity observed in the pizza box extract indicating that some very AhR active substance(s) still remain to be

  7. Non-targeted screening for contaminants in paper and board food-contact materials using effect-directed analysis and accurate mass spectrometry.

    PubMed

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia; Jensen, Lisbeth Krüger; Granby, Kit; Vinggaard, Anne Marie; Driffield, Malcolm; Højslev Petersen, Jens

    2016-06-01

    Due to large knowledge gaps in chemical composition and toxicological data for substances involved, paper and board food-contact materials (P&B FCM) have been emerging as a FCM type of particular concern for consumer safety. This study describes the development of a step-by-step strategy, including extraction, high-performance liquid chromatography (HPLC) fractionation, tentative identification of relevant substances and in vitro testing of selected tentatively identified substances. As a case study, we used two fractions from a recycled pizza box sample which exhibited aryl hydrocarbon receptor (AhR) activity. These fractions were analysed by gas chromatography (GC) and ultra-HPLC (UHPLC) coupled to quadrupole time-of-flight mass spectrometers (QTOF MS) in order tentatively to identify substances. The elemental composition was determined for peaks above a threshold, and compared with entries in a commercial mass spectral library for GC-MS (GC-EI-QTOF MS) analysis and an in-house built library of accurate masses for substances known to be used in P&B packaging for UHPLC-QTOF analysis. Of 75 tentatively identified substances, 15 were initially selected for further testing in vitro; however, only seven were commercially available and subsequently tested in vitro and quantified. Of these seven, the identities of three pigments found in printing inks were confirmed by UHPLC tandem mass spectrometry (QqQ MS/MS). Two pigments had entries in the database, meaning that a material relevant accurate mass database can provide a fast tentative identification. Pure standards of the seven tentatively identified substances were tested in vitro but could not explain a significant proportion of the AhR-response in the extract. Targeted analyses of dioxins and PCBs, both well-known AhR agonists, was performed. However, the dioxins could explain approximately 3% of the activity observed in the pizza box extract indicating that some very AhR active substance(s) still remain to be

  8. Appendix C. Collection of Samples for Chemical Agent Analysis

    SciTech Connect

    Koester, C; Thompson, C; Doerr, T; Scripsick, R

    2005-09-23

    This chapter describes procedures for the collection and analysis of samples of various matrices for the purpose of determining the presence of chemical agents in a civilian setting. This appendix is intended to provide the reader with sufficient information to make informed decisions about the sampling and analysis process and to suggest analytical strategies that might be implemented by the scientists performing sampling and analysis. This appendix is not intended to be used as a standard operating procedure to provide detailed instructions as to how trained scientists should handle samples. Chemical agents can be classified by their physical and chemical properties. Table 1 lists the chemical agents considered by this report. In selecting sampling and analysis methods, we have considered procedures proposed by the Organization for Prohibition of Chemical Weapons (OPCW), the U. S. Environmental Protection Agency (EPA), and peer-reviewed scientific literature. EPA analytical methods are good resources describing issues of quality assurance with respect to chain-of-custody, sample handling, and quality control requirements.

  9. Accurate determination of human serum transferrin isoforms: Exploring metal-specific isotope dilution analysis as a quantitative proteomic tool.

    PubMed

    Busto, M Estela del Castillo; Montes-Bayón, Maria; Sanz-Medel, Alfredo

    2006-12-15

    Carbohydrate-deficient transferrin (CDT) measurements are considered a reliable marker for chronic alcohol consumption, and its use is becoming extensive in forensic medicine. However, CDT is not a single molecular entity but refers to a group of sialic acid-deficient transferrin isoforms from mono- to trisialotransferrin. Thus, the development of methods to analyze accurately and precisely individual transferrin isoforms in biological fluids such as serum is of increasing importance. The present work illustrates the use of ICPMS isotope dilution analysis for the quantification of transferrin isoforms once saturated with iron and separated by anion exchange chromatography (Mono Q 5/50) using a mobile phase consisting of a gradient of ammonium acetate (0-250 mM) in 25 mM Tris-acetic acid (pH 6.5). Species-specific and species-unspecific spikes have been explored. In the first part of the study, the use of postcolumn addition of a solution of 200 ng mL(-1) isotopically enriched iron (57Fe, 95%) in 25 mM sodium citrate/citric acid (pH 4) permitted the quantification of individual sialoforms of transferrin (from S2 to S5) in human serum samples of healthy individuals as well as alcoholic patients. Second, the species-specific spike method was performed by synthesizing an isotopically enriched standard of saturated transferrin (saturated with 57Fe). The characterization of the spike was performed by postcolumn reverse isotope dilution analysis (this is, by postcolumn addition of a solution of 200 ng mL(-1) natural iron in sodium citrate/citric acid of pH 4). Also, the stability of the transferrin spike was tested during one week with negligible species transformation. Finally, the enriched transferrin was used to quantify the individual isoforms in the same serum samples obtaining results comparative to those of postcolumn isotope dilution and to those previously published in the literature, demonstrating the suitability of both strategies for quantitative transferrin

  10. Molecular-genetic analysis is essential for accurate classification of renal carcinoma resembling Xp11.2 translocation carcinoma.

    PubMed

    Hayes, Malcolm; Peckova, Kvetoslava; Martinek, Petr; Hora, Milan; Kalusova, Kristyna; Straka, Lubomir; Daum, Ondrej; Kokoskova, Bohuslava; Rotterova, Pavla; Pivovarčikova, Kristyna; Branzovsky, Jindrich; Dubova, Magdalena; Vesela, Pavla; Michal, Michal; Hes, Ondrej

    2015-03-01

    tumours can only be sub-classified accurately by multi-parameter molecular-genetic analysis. PMID:25544614

  11. A review of chemical gradient systems for cell analysis.

    PubMed

    Somaweera, Himali; Ibraguimov, Akif; Pappas, Dimitri

    2016-02-11

    Microfluidic spatial and temporal gradient generators have played an important role in many biological assays such as in the analysis of wound healing, inflammation, and cancer metastasis. Chemical gradient systems can also be applied to other fields such as drug design, chemical synthesis, chemotaxis, etc. Microfluidic systems are particularly amenable to gradient formation, as the length scales used in chips enable fluid processes that cannot be conducted in bulk scale. In this review we discuss new microfluidic devices for gradient generation and applications of those systems in cell analysis.

  12. Evaluating Geographically Weighted Regression Models for Environmental Chemical Risk Analysis

    PubMed Central

    Czarnota, Jenna; Wheeler, David C; Gennings, Chris

    2015-01-01

    In the evaluation of cancer risk related to environmental chemical exposures, the effect of many correlated chemicals on disease is often of interest. The relationship between correlated environmental chemicals and health effects is not always constant across a study area, as exposure levels may change spatially due to various environmental factors. Geographically weighted regression (GWR) has been proposed to model spatially varying effects. However, concerns about collinearity effects, including regression coefficient sign reversal (ie, reversal paradox), may limit the applicability of GWR for environmental chemical risk analysis. A penalized version of GWR, the geographically weighted lasso, has been proposed to remediate the collinearity effects in GWR models. Our focus in this study was on assessing through a simulation study the ability of GWR and GWL to correctly identify spatially varying chemical effects for a mixture of correlated chemicals within a study area. Our results showed that GWR suffered from the reversal paradox, while GWL overpenalized the effects for the chemical most strongly related to the outcome. PMID:25983546

  13. ANALYSIS OF SAMPLES FROM TANK 5F CHEMICAL CLEANING

    SciTech Connect

    Poirier, M.; Fink, S.

    2011-03-07

    The Savannah River Site (SRS) is preparing Tank 5F for closure. The first step in preparing the tank for closure is mechanical sludge removal. Following mechanical sludge removal, SRS performed chemical cleaning with oxalic acid to remove the sludge heel. Personnel are currently assessing the effectiveness of the chemical cleaning. SRS personnel collected liquid samples during chemical cleaning and submitted them to Savannah River National Laboratory (SRNL) for analysis. Following chemical cleaning, they collected a solid sample (also known as 'process sample') and submitted it to SRNL for analysis. The authors analyzed these samples to assess the effectiveness of the chemical cleaning process. The conclusions from this work are: (1) With the exception of iron, the dissolution of sludge components from Tank 5F agreed with results from the actual waste demonstration performed in 2007. The fraction of iron removed from Tank 5F by chemical cleaning was significantly less than the fraction removed in the SRNL demonstrations. The likely cause of this difference is the high pH following the first oxalic acid strike. (2) Most of the sludge mass remaining in the tank is iron and nickel. (3) The remaining sludge contains approximately 26 kg of barium, 37 kg of chromium, and 37 kg of mercury. (4) Most of the radioactivity remaining in the residual material is beta emitters and {sup 90}Sr. (5) The chemical cleaning removed more than {approx} 90% of the uranium isotopes and {sup 137}Cs. (6) The chemical cleaning removed {approx} 70% of the neptunium, {approx} 83% of the {sup 90}Sr, and {approx} 21% of the {sup 60}Co. (7) The chemical cleaning removed less than 10% of the plutonium, americium, and curium isotopes. (8) The chemical cleaning removed more than 90% of the aluminium, calcium, and sodium from the tank. (9) The cleaning operations removed 61% of lithium, 88% of non-radioactive strontium, and 65% of zirconium. The {sup 90}Sr and non-radioactive strontium were measured

  14. Surface chemical composition analysis of heat-treated bamboo

    NASA Astrophysics Data System (ADS)

    Meng, Fan-dan; Yu, Yang-lun; Zhang, Ya-mei; Yu, Wen-ji; Gao, Jian-min

    2016-05-01

    In this study, the effect of heat treatment on the chemical composition of bamboo slivers was studied. The chemical properties of the samples were examined by chemical analysis. Results showed a decrease in the contents of holocellulose and α-cellulose, as well as an increase in the contents of lignin and extractives. Changes in the chemical structure of bamboo components were analyzed by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). FTIR spectroscopy results indicated that hemicellulose contents decrease, whereas lignin contents increase after heat treatment. Ester formation linked to lignin decreased the hygroscopicity of the bamboo samples and consequently improved their dimensional stability and durability. XPS spectroscopy results showed that hemicelluloses and celluloses are relatively more sensitive to the heating process than lignin. As a consequence, hemicellulose and cellulose contents decreased, whereas lignin contents increased during heat treatment. The results obtained in this study provide useful information for the future utilization of heat-treated bamboo.

  15. Micropyrolyzer for chemical analysis of liquid and solid samples

    DOEpatents

    Mowry, Curtis D.; Morgan, Catherine H.; Manginell, Ronald P.; Frye-Mason, Gregory C.

    2006-07-18

    A micropyrolyzer has applications to pyrolysis, heated chemistry, and thermal desorption from liquid or solid samples. The micropyrolyzer can be fabricated from semiconductor materials and metals using standard integrated circuit technologies. The micropyrolyzer enables very small volume samples of less than 3 microliters and high sample heating rates of greater than 20.degree. C. per millisecond. A portable analyzer for the field analysis of liquid and solid samples can be realized when the micropyrolyzer is combined with a chemical preconcentrator, chemical separator, and chemical detector. Such a portable analyzer can be used in a variety of government and industrial applications, such as non-proliferation monitoring, chemical and biological warfare detection, industrial process control, water and air quality monitoring, and industrial hygiene.

  16. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  17. Probing silicon and aluminium chemical environments in silicate and aluminosilicate glasses by solid state NMR spectroscopy and accurate first-principles calculations

    NASA Astrophysics Data System (ADS)

    Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault

    2014-01-01

    Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.

  18. Electron Spectroscopy for Chemical Analysis (ESCA) study of atmospheric particles

    NASA Technical Reports Server (NTRS)

    Dillard, J. G.; Seals, R. D.; Wightman, J. P.

    1979-01-01

    The results of analyses by ESCA (Electron Spectroscopy for Chemical Analysis) on several Nuclepore filters which were exposed during air pollution studies are presented along with correlative measurements by Neutron Activation Analysis and Scanning Electron Microscopy. Samples were exposed during air pollution studies at Norfolk, Virginia and the NASA Kennedy Space Center (KSC). It was demonstrated that with the ESCA technique it was possible to identify the chemical (bonding) state of elements contained in the atmospheric particulate matter collected on Nuclepore filters. Sulfur, nitrogen, mercury, chlorine, alkali, and alkaline earth metal species were identified in the Norfolk samples. ESCA binding energy data for aluminum indicated that three chemically different types of aluminum are present in the launch and background samples from NASA-KSC.

  19. Inferences on active faults at the Southern Alps-Liguria basin junction from accurate analysis of low energy seismicity

    NASA Astrophysics Data System (ADS)

    Turino, Chiara; Scafidi, Davide; Eva, Elena; Solarino, Stefano

    2009-10-01

    Seismotectonic studies concern themselves with understanding the distribution of earthquakes in space, time, size and style. Therefore, the better these parameters are known, the most correct the association of any seismic event with the faulting structure that caused it will result. The use of accurate location methods is especially required when dealing with very complex areas, where several faulting systems or relatively small seismogenic structures exist. In fact, even though routinely determined epicentres are capable of revealing the rough picture of the seismicity, they are not suitable for studies of the fine structure of the causative fault, as their location uncertainties are often larger than the source dimension itself. In this work the probabilistic approach of the "Non Linear Localization" has been used to compute precise locations for earthquakes occurred in the last twenty years nearby the Saorge-Taggia line, a complex fault system situated in Western Liguria, close to the border between Italy and France. Together with the Breil-Sospel-Monaco and the Peille-Laghet faults, this line is responsible for the seismic activity of the area. The seismotectonic study is completed through a local tomographic study and the analysis of the focal mechanisms computed for an enlarged area. The results show that the seismicity associated with this fault system is confined within the first 10 km depth. Many clusters of seismic events are identified along the Saorge-Taggia line. The existence of a not previously mapped branch perpendicular to the Saorge-Taggia line is also recognized. Although its position may suggest it to be the continuation of the Breil-Sospel-Monaco fault system towards NE, our finding would rather suggest no association with the fault. The overall results confirm the complexity of the area; in particular the hypothesis that the Saorge-Taggia system may represent the eastward limit of a subalpine crustal block comprised within the Nice Arc, the

  20. Rethinking the history of artists' pigments through chemical analysis.

    PubMed

    Berrie, Barbara H

    2012-01-01

    Following a brief overview of the history of analysis of artists' pigments, I discuss the illustrative example of lead-tin yellow. Recent advances in our knowledge of artists' use of red lakes, glassy pigments, and metallic pigments in works of cultural heritage, particularly European paintings, as determined from chemical analyses are described. PMID:22708904

  1. Rethinking the History of Artists' Pigments Through Chemical Analysis

    NASA Astrophysics Data System (ADS)

    Berrie, Barbara H.

    2012-07-01

    Following a brief overview of the history of analysis of artists' pigments, I discuss the illustrative example of lead-tin yellow. Recent advances in our knowledge of artists' use of red lakes, glassy pigments, and metallic pigments in works of cultural heritage, particularly European paintings, as determined from chemical analyses are described.

  2. Methods of chemical analysis used to characterize battery materials

    SciTech Connect

    Jensen, K. J.; Streets, W. E.

    1980-05-01

    Procedures are given for the chemical analysis of a variety of materials of interest in battery development and research. These materials include LiCl-KCl eutectic, Li-Al alloys, lithium sulfide, lithium aluminum chloride, calcium sulfide, titanium sulfide, and various sulfides of iron, nickel, copper, and cobalt. 8 tables.

  3. Methods of chemical analysis used to characterize battery materials

    NASA Astrophysics Data System (ADS)

    Jensen, K. J.; Streets, W. E.

    1980-05-01

    Procedures are given for the chemical analysis of a variety of materials of interest in battery development and research. These materials include LiCl-KCl eutectic, Li-Al alloys, lithium sulfide, lithium aluminum chloride, calcium sulfide, titanium sulfide and various sulfides of iron, nickel, copper, and cobalt.

  4. Standardization of Cassia spectabilis with respect to authenticity, assay and chemical constituent analysis.

    PubMed

    Torey, Angeline; Sasidharan, Sreenivasan; Yeng, Chen; Latha, Lachimanan Yoga

    2010-05-01

    Quality control standardizations of the various medicinal plants used in traditional medicine is becoming more important today in view of the commercialization of formulations based on these plants. An attempt at standardization of Cassia spectabilis leaf has been carried out with respect to authenticity, assay and chemical constituent analysis. The authentication involved many parameters, including gross morphology, microscopy of the leaves and functional group analysis by Fourier Transform Infrared (FTIR) spectroscopy. The assay part of standardization involved determination of the minimum inhibitory concentration (MIC) of the extract which could help assess the chemical effects and establish curative values. The MIC of the C. spectabilis leaf extracts was investigated using the Broth Dilution Method. The extracts showed a MIC value of 6.25 mg/mL, independent of the extraction time. The chemical constituent aspect of standardization involves quantification of the main chemical components in C. spectabilis. The GCMS method used for quantification of 2,4-(1H,3H)-pyrimidinedione in the extract was rapid, accurate, precise, linear (R(2) = 0.8685), rugged and robust. Hence this method was suitable for quantification of this component in C. spectabilis. The standardization of C. spectabilis is needed to facilitate marketing of medicinal plants, with a view to promoting the export of valuable Malaysian Traditional Medicinal plants such as C. spectabilis.

  5. Profiling and accurate quantification of Rubus ellagitannins and ellagic acid conjugates using direct UPLC-Q-TOF HDMS and HPLC-DAD analysis.

    PubMed

    Gasperotti, Mattia; Masuero, Domenico; Vrhovsek, Urska; Guella, Graziano; Mattivi, Fulvio

    2010-04-28

    Accurate quantification and structural characterization of ellagitannins and ellagic acid conjugates in food, beverages, and food supplements are essential starting points for studying their effect on human health. However, accuracy is hindered both by the lack of pure standard compounds and by methods that maintain the compounds in their native form, avoiding any chemical modification of the structure. The objective of this work was to develop a new method for the purification, chromatographic separation, and accurate quantification of ellagitannins and ellagic acid conjugates to provide thorough characterization of the diversity in composition of 11 Rubus cultivars grown in Trentino, Italy. As such, two major steps were required: (i) the isolation and purification (with associated detailed structural characterization and determination of their molar extinction coefficients) of sanguiin H-6 and lambertianin C, providing essential data for their use, together with ellagic acid, as external standards, and (ii) the determination of the chemical structure of 20 novel minor ellagitannins and 4 ellagic acid conjugates on the basis of their Q-TOF-HDMS and DAD spectra. This survey of ellagitannins and ellagic acid conjugates provides evidence for the existence of significant differences in the pattern between and within blackberry and raspberry cultivars. To our knowledge, this is the first paper that has combined detailed metabolite profiling with accurate quantification of the main ellagitannins in Rubus using their respective standards.

  6. Global analysis of large-scale chemical and biological experiments

    PubMed Central

    Root, David E; Kelley, Brian P

    2005-01-01

    Research in the life sciences is increasingly dominated by high-throughput data collection methods that benefit from a global approach to data analysis. Recent innovations that facilitate such comprehensive analyses are highlighted. Several developments enable the study of the relationships between newly derived experimental information, such as biological activity in chemical screens or gene expression studies, and prior information, such as physical descriptors for small molecules or functional annotation for genes. The way in which global analyses can be applied to both chemical screens and transcription profiling experiments using a set of common machine learning tools is discussed. PMID:12058610

  7. Component pattern analysis of chemicals using multispectral THz imaging system

    NASA Astrophysics Data System (ADS)

    Kawase, Kodo; Ogawa, Yuichi; Watanabe, Yuki

    2004-04-01

    We have developed a novel basic technology for terahertz (THz) imaging, which allows detection and identification of chemicals by introducing the component spatial pattern analysis. The spatial distributions of the chemicals were obtained from terahertz multispectral transillumination images, using absorption spectra previously measured with a widely tunable THz-wave parametric oscillator. Further we have applied this technique to the detection and identification of illicit drugs concealed in envelopes. The samples we used were methamphetamine and MDMA, two of the most widely consumed illegal drugs in Japan, and aspirin as a reference.

  8. Near-field Optical Imagigng and Chemical Analysis

    NASA Astrophysics Data System (ADS)

    Andres, La Rosa

    1998-03-01

    Identification of molecular structures in complex mixtures represents a major challenge in chemical research today. Microfabricated devices or lab-on-a-chip that perform chemical analysis allows dynamic sampling of picoliter microenvironments and separation. The long-term goals of nanochemistry down to the femtoliter scale involve refinement of the detection limit to single-molecule. Our approach consists in designing a very sensitive near-field optical microscope (NSOM-SIAM) to explore the mesoscopic properties of organic compounds. The validity, sensitivity and unique spatial resolution of this system will be discussed for multiple analyte chemosensing.

  9. Toward Accurate Modelling of Enzymatic Reactions: All Electron Quantum Chemical Analysis combined with QM/MM Calculation of Chorismate Mutase

    SciTech Connect

    Ishida, Toyokazu

    2008-09-17

    To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.

  10. Automating the analytical laboratory via the Chemical Analysis Automation paradigm

    SciTech Connect

    Hollen, R.; Rzeszutko, C.

    1997-10-01

    To address the need for standardization within the analytical chemistry laboratories of the nation, the Chemical Analysis Automation (CAA) program within the US Department of Energy, Office of Science and Technology`s Robotic Technology Development Program is developing laboratory sample analysis systems that will automate the environmental chemical laboratories. The current laboratory automation paradigm consists of islands-of-automation that do not integrate into a system architecture. Thus, today the chemist must perform most aspects of environmental analysis manually using instrumentation that generally cannot communicate with other devices in the laboratory. CAA is working towards a standardized and modular approach to laboratory automation based upon the Standard Analysis Method (SAM) architecture. Each SAM system automates a complete chemical method. The building block of a SAM is known as the Standard Laboratory Module (SLM). The SLM, either hardware or software, automates a subprotocol of an analysis method and can operate as a standalone or as a unit within a SAM. The CAA concept allows the chemist to easily assemble an automated analysis system, from sample extraction through data interpretation, using standardized SLMs without the worry of hardware or software incompatibility or the necessity of generating complicated control programs. A Task Sequence Controller (TSC) software program schedules and monitors the individual tasks to be performed by each SLM configured within a SAM. The chemist interfaces with the operation of the TSC through the Human Computer Interface (HCI), a logical, icon-driven graphical user interface. The CAA paradigm has successfully been applied in automating EPA SW-846 Methods 3541/3620/8081 for the analysis of PCBs in a soil matrix utilizing commercially available equipment in tandem with SLMs constructed by CAA.

  11. Exploring Chemical Analysis, 1st Edition (by Daniel C. Harris)

    NASA Astrophysics Data System (ADS)

    Wright, John C.

    1998-01-01

    W. H. Freeman: New York, 1997. ISBN: 0716730421. $80.00. Daniel Harris's book Quantitative Chemical Analysis is one of the 1000-pound gorillas for introductory analytical chemistry, both because of its dominance in the field and its size and information content. Students find the writing informal, interesting, and clear. Faculty like the completeness of the book and its sound treatment of the subject matter. It contains everything that an introductory analytical course could possibly want. Daniel Harris's recent book, Exploring Chemical Analysis, is a tamed version of the 1000-pound gorilla for nonchemistry majors. Students will find the same informality, interest, and clarity as in the earlier text but they will also find the book a comfortable companion. Faculty will find an abbreviated but excellent treatment of the subject matter. It contains most of the things that an introductory nonmajors analytical course should want.

  12. Bioassay-directed chemical analysis in environmental research

    SciTech Connect

    Schuetzle, D.; Lewtas, J.

    1986-01-01

    The use of short-term bioassay tests in conjunction with analytical measurements, constitute a powerful tool for identifying important environmental contaminants. The authors have coined the terminology bioassay directed chemical analysis to best describe this marriage of analytical chemistry and biology. The objective of this methodology is to identify key compounds in various types of air-pollutant samples. Once that task is completed, studies on metabolism, sources, environmental exposure and atmospheric chemistry can be undertaken. The principles and methodologies for bioassay directed chemical analysis are presented and illustrated in this paper. Most of this work has been directed toward the characterization of ambient air and diesel particulates, which are used as examples in this report to illustrate the analytical logic used for identifying the bio-active components of complex mixtures.

  13. Device for high spatial resolution chemical analysis of a sample and method of high spatial resolution chemical analysis

    DOEpatents

    Van Berkel, Gary J.

    2015-10-06

    A system and method for analyzing a chemical composition of a specimen are described. The system can include at least one pin; a sampling device configured to contact a liquid with a specimen on the at least one pin to form a testing solution; and a stepper mechanism configured to move the at least one pin and the sampling device relative to one another. The system can also include an analytical instrument for determining a chemical composition of the specimen from the testing solution. In particular, the systems and methods described herein enable chemical analysis of specimens, such as tissue, to be evaluated in a manner that the spatial-resolution is limited by the size of the pins used to obtain tissue samples, not the size of the sampling device used to solubilize the samples coupled to the pins.

  14. Electrochemical approaches for chemical and biological analysis on Mars

    NASA Technical Reports Server (NTRS)

    Kounaves, Samuel P.

    2003-01-01

    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  15. Electrochemical approaches for chemical and biological analysis on Mars.

    PubMed

    Kounaves, Samuel P

    2003-02-17

    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  16. Electrochemical approaches for chemical and biological analysis on Mars.

    PubMed

    Kounaves, Samuel P

    2003-02-17

    Obtaining in situ chemical data from planetary bodies such as Mars or Europa can present significant challenges. The one analytical technique that has many of the requisite characteristics to meet such a challenge is electroanalysis. Described here are three electroanalytical devices designed for in situ geochemical and biological analysis on Mars. The Mars Environmental Compatibility Assessment (MECA) was built and flight qualified for the now cancelled NASA Mars 2001 Lander. Part of MECA consisted of four "cells" containing arrays of electrochemical based sensors for measuring the ionic species in soil samples. A next-generation MECA, the Robotic Chemical Analysis Laboratory (RCAL), uses a carousel-type system to allow for greater customization of analytical procedures. A second instrument, proposed as part of the 2007 CryoScout mission, consists of a flow-through inorganic chemical analyzer (MICA). CryoScout is a torpedo-like device designed for subsurface investigation of the stratigraphic climate record embedded in Mars' north polar cap. As the CryoScout melts its way through the ice cap, MICA will collect and analyze the meltwater for a variety of inorganics and chemical parameters. By analyzing the chemistry locked in the layers of dust, salt, and ice, geologists will be able to determine the recent history of climate, water, and atmosphere on Mars and link it to the past. Finally, electroanalysis shows its abilities in the detection of possible microorganism on Mars or elsewhere in the solar system. To identify an unknown microorganism, one that may not even use Earth-type biochemistry, requires a detection scheme which makes minimal assumptions and looks for the most general features. Recent work has demonstrated that the use of an array of electrochemical sensors which monitors the changes in a solution via electrical conductivity, pH, and ion selective electrodes, can be used to detect minute chemical perturbations caused by the growth of bacteria and

  17. Analysis of the stochastic excitability in the flow chemical reactor

    SciTech Connect

    Bashkirtseva, Irina

    2015-11-30

    A dynamic model of the thermochemical process in the flow reactor is considered. We study an influence of the random disturbances on the stationary regime of this model. A phenomenon of noise-induced excitability is demonstrated. For the analysis of this phenomenon, a constructive technique based on the stochastic sensitivity functions and confidence domains is applied. It is shown how elaborated technique can be used for the probabilistic analysis of the generation of mixed-mode stochastic oscillations in the flow chemical reactor.

  18. Meta-analysis of mass balances examining chemical fate during wastewater treatment.

    PubMed

    Heidler, Jochen; Halden, Rolf U

    2008-09-01

    Mass balances are an instructive means for investigating the fate of chemicals during wastewater treatment. In addition to the aqueous-phase removal efficiency (phi), they can inform on chemical partitioning, transformation, and persistence, as well as on the chemical loading to streams and soils receiving, respectively, treated effluent and digested sewage sludge (biosolids). Release rates computed on a per-capita basis can serve to extrapolate findings to a larger scale. This review examines over a dozen mass balances conducted for various organic wastewater contaminants, including prescription drugs, estrogens, fragrances, antimicrobials, and surfactants of differing sorption potential (hydrophobicity), here expressed as the 1-octanol-water partition coefficient (K(OW)) and the organic carbon normalized sorption coefficient (K(OC)). Major challengesto mass balances are the collection of representative samples and accurate quantification of chemicals in sludge. A meta-analysis of peer-reviewed data identified sorption potential as the principal determinant governing chemical persistence in biosolids. Occurrence data for organic wastewater compounds detected in digested sludge followed a simple nonlinear model that required only K(OW) or K(OC) as the input and yielded a correlation coefficient of 0.9 in both instances. The model predicted persistence in biosolids for the majority (> 50%) of the input load of organic wastewater compounds featuring a log10 K(OW) value of greater than 5.2 (log10 K(OC) > 4.4). In contrast, hydrophobicity had no or only limited value for estimating, respectively, phi and the overall persistence of a chemical during conventional wastewater treatment.

  19. Application of Surface Chemical Analysis Tools for Characterization of Nanoparticles

    PubMed Central

    Baer, DR; Gaspar, DJ; Nachimuthu, P; Techane, SD; Castner, DG

    2010-01-01

    The important role that surface chemical analysis methods can and should play in the characterization of nanoparticles is described. The types of information that can be obtained from analysis of nanoparticles using Auger electron spectroscopy (AES); X-ray photoelectron spectroscopy (XPS); time of flight secondary ion mass spectrometry (TOF-SIMS); low energy ion scattering (LEIS); and scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), are briefly summarized. Examples describing the characterization of engineered nanoparticles are provided. Specific analysis considerations and issues associated with using surface analysis methods for the characterization of nanoparticles are discussed and summarized, along with the impact that shape instability, environmentally induced changes, deliberate and accidental coating, etc., have on nanoparticle properties. PMID:20052578

  20. Solution of the surface Euler equations for accurate three-dimensional boundary-layer analysis of aerodynamic configurations

    NASA Technical Reports Server (NTRS)

    Iyer, V.; Harris, J. E.

    1987-01-01

    The three-dimensional boundary-layer equations in the limit as the normal coordinate tends to infinity are called the surface Euler equations. The present paper describes an accurate method for generating edge conditions for three-dimensional boundary-layer codes using these equations. The inviscid pressure distribution is first interpolated to the boundary-layer grid. The surface Euler equations are then solved with this pressure field and a prescribed set of initial and boundary conditions to yield the velocities along the two surface coordinate directions. Results for typical wing and fuselage geometries are presented. The smoothness and accuracy of the edge conditions obtained are found to be superior to the conventional interpolation procedures.

  1. Analysis of continuous oxygen saturation data for accurate representation of retinal exposure to oxygen in the preterm infant.

    PubMed

    Cirelli, Josie; McGregor, Carolyn; Graydon, Brenda; James, Andrew

    2013-01-01

    Maintaining blood oxygen saturation within the intended target range for preterm infants receiving neonatal intensive care is challenging. Supplemental oxygen is believed to lead to increased risk of retinopathy of prematurity and hence managing the level of oxygen within this population is important within their care. Current quality improvement activities use coarse hourly spot readings to measure supplemental oxygen levels as associated with targeted ranges that vary based on gestational age. In this research we use Artemis, a real-time online healthcare analytics platform to ascertain if the collection of second by second data provides a better representation of retinal exposure to oxygen than an infrequent, intermittent spot reading. We show that Artemis is capable of producing more accurate information from the higher frequency data, as it includes all the episodic events in the activity of the hour, which provides a better understanding of oxygen fluctuation ranges which affect the physiological status of the infant.

  2. Analysis of algebraic reconstruction technique for accurate imaging of gas temperature and concentration based on tunable diode laser absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Hui-Hui, Xia; Rui-Feng, Kan; Jian-Guo, Liu; Zhen-Yu, Xu; Ya-Bai, He

    2016-06-01

    An improved algebraic reconstruction technique (ART) combined with tunable diode laser absorption spectroscopy(TDLAS) is presented in this paper for determining two-dimensional (2D) distribution of H2O concentration and temperature in a simulated combustion flame. This work aims to simulate the reconstruction of spectroscopic measurements by a multi-view parallel-beam scanning geometry and analyze the effects of projection rays on reconstruction accuracy. It finally proves that reconstruction quality dramatically increases with the number of projection rays increasing until more than 180 for 20 × 20 grid, and after that point, the number of projection rays has little influence on reconstruction accuracy. It is clear that the temperature reconstruction results are more accurate than the water vapor concentration obtained by the traditional concentration calculation method. In the present study an innovative way to reduce the error of concentration reconstruction and improve the reconstruction quality greatly is also proposed, and the capability of this new method is evaluated by using appropriate assessment parameters. By using this new approach, not only the concentration reconstruction accuracy is greatly improved, but also a suitable parallel-beam arrangement is put forward for high reconstruction accuracy and simplicity of experimental validation. Finally, a bimodal structure of the combustion region is assumed to demonstrate the robustness and universality of the proposed method. Numerical investigation indicates that the proposed TDLAS tomographic algorithm is capable of detecting accurate temperature and concentration profiles. This feasible formula for reconstruction research is expected to resolve several key issues in practical combustion devices. Project supported by the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 61205151), the National Key Scientific Instrument and Equipment Development Project of China (Grant

  3. Analysis of algebraic reconstruction technique for accurate imaging of gas temperature and concentration based on tunable diode laser absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Hui-Hui, Xia; Rui-Feng, Kan; Jian-Guo, Liu; Zhen-Yu, Xu; Ya-Bai, He

    2016-06-01

    An improved algebraic reconstruction technique (ART) combined with tunable diode laser absorption spectroscopy(TDLAS) is presented in this paper for determining two-dimensional (2D) distribution of H2O concentration and temperature in a simulated combustion flame. This work aims to simulate the reconstruction of spectroscopic measurements by a multi-view parallel-beam scanning geometry and analyze the effects of projection rays on reconstruction accuracy. It finally proves that reconstruction quality dramatically increases with the number of projection rays increasing until more than 180 for 20 × 20 grid, and after that point, the number of projection rays has little influence on reconstruction accuracy. It is clear that the temperature reconstruction results are more accurate than the water vapor concentration obtained by the traditional concentration calculation method. In the present study an innovative way to reduce the error of concentration reconstruction and improve the reconstruction quality greatly is also proposed, and the capability of this new method is evaluated by using appropriate assessment parameters. By using this new approach, not only the concentration reconstruction accuracy is greatly improved, but also a suitable parallel-beam arrangement is put forward for high reconstruction accuracy and simplicity of experimental validation. Finally, a bimodal structure of the combustion region is assumed to demonstrate the robustness and universality of the proposed method. Numerical investigation indicates that the proposed TDLAS tomographic algorithm is capable of detecting accurate temperature and concentration profiles. This feasible formula for reconstruction research is expected to resolve several key issues in practical combustion devices. Project supported by the Young Scientists Fund of the National Natural Science Foundation of China (Grant No. 61205151), the National Key Scientific Instrument and Equipment Development Project of China (Grant

  4. Rosiglitazone: can meta-analysis accurately estimate excess cardiovascular risk given the available data? Re-analysis of randomized trials using various methodologic approaches

    PubMed Central

    Friedrich, Jan O; Beyene, Joseph; Adhikari, Neill KJ

    2009-01-01

    statistically significant. Conclusion We have shown that alternative reasonable methodological approaches to the rosiglitazone meta-analysis can yield increased or decreased risks that are either statistically significant or not significant at the p = 0.05 level for both myocardial infarction and cardiovascular death. Completion of ongoing trials may help to generate more accurate estimates of rosiglitazone's effect on cardiovascular outcomes. However, given that almost all point estimates suggest harm rather than benefit and the availability of alternative agents, the use of rosiglitazone may greatly decline prior to more definitive safety data being generated. PMID:19134216

  5. Proximate analysis, backwards stepwise regression between gross calorific value, ultimate and chemical analysis of wood.

    PubMed

    Telmo, C; Lousada, J; Moreira, N

    2010-06-01

    The gross calorific value (GCV), proximate, ultimate and chemical analysis of debark wood in Portugal were studied, for future utilization in wood pellets industry and the results compared with CEN/TS 14961. The relationship between GCV, ultimate and chemical analysis were determined by multiple regression stepwise backward. The treatment between hardwoods-softwoods did not result in significant statistical differences for proximate, ultimate and chemical analysis. Significant statistical differences were found in carbon for National (hardwoods-softwoods) and (National-tropical) hardwoods in volatile matter, fixed carbon, carbon and oxygen and also for chemical analysis in National (hardwoods-softwoods) for F and (National-tropical) hardwoods for Br. GCV was highly positively related to C (0.79 * * *) and negatively to O (-0.71 * * *). The final independent variables of the model were (C, O, S, Zn, Ni, Br) with R(2)=0.86; F=27.68 * * *. The hydrogen did not contribute statistically to the energy content.

  6. ISS Expeditions 16 & 17: Chemical Analysis Results for Potable Water

    NASA Technical Reports Server (NTRS)

    Straub, John E., II; Plumlee, Debrah K.; Schultz, John R.

    2009-01-01

    During the twelve month span of Expeditions 16 and 17 beginning October of 2007, the chemical quality of the potable water onboard the International Space Station (ISS) was verified safe for crew consumption through the return and chemical analysis of water samples by the Water and Food Analytical Laboratory (WAFAL) at Johnson Space Center (JSC). Reclaimed cabin humidity condensate and Russian ground-supplied water were the principle sources of potable water and for the first time, European groundsupplied water was also available. Although water was transferred from Shuttle to ISS during Expeditions 16 and 17, no Shuttle potable water was consumed during this timeframe. A total of 12 potable water samples were collected using U.S. hardware during Expeditions 16 and 17 and returned on Shuttle flights 1E (STS122), 1JA (STS123), and 1J (STS124). The average sample volume was sufficient for complete chemical characterization to be performed. The results of JSC chemical analyses of these potable water samples are presented in this paper. The WAFAL also received potable water samples for analysis from the Russian side collected inflight with Russian hardware, as well as preflight samples of Rodnik potable water delivered to ISS on Russian Progress vehicles 28 to 30. Analytical results for these additional potable water samples are also reported and discussed herein. Although the potable water supplies available during Expeditions 16 and 17 were judged safe for crew consumption, a recent trending of elevated silver levels in the SVOZV water is a concern for longterm consumption and efforts are being made to lower these levels.

  7. Fibre Diffraction Analysis of Skin Offers a Very Early and Extremely Accurate Diagnostic Test for Prostate Cancer

    DOE PAGES

    James, Veronica J.; O’Malley Ford, Judith M.

    2014-01-01

    Double blind analysis of a batch of thirty skin tissue samples from potential prostate cancer sufferers correctly identified all “control” patients, patients with high and low grade prostate cancers, the presence of benign prostate hyperplasia (BPH), perineural invasions, and the one lymphatic invasion. Identification was by analysis of fibre diffraction patterns interpreted using a schema developed from observations in nine previous studies. The method, schema, and specific experiment results are reported in this paper, with some implications then drawn.

  8. QUALITY ASSURANCE GUIDELINES FOR LABORATORIES PERFORMING FORENSIC ANALYSIS OF CHEMICAL TERRORISM

    EPA Science Inventory

    The Scientific Working Group on Forensic Analysis of Chemical Terrorism (SWGFACT) has developed the following quality assurance guidelines to provide laboratories engaged in forensic analysis of chemical evidence associated with terrorism a framework to implement a quality assura...

  9. Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis.

    PubMed

    Mobli, Mehdi; Abraham, Raymond J

    2005-03-01

    A model based on classical concepts is derived to describe the effect of the nitro group on proton chemical shifts. The calculated chemical shifts are then compared to ab initio (GIAO) calculated chemical shifts. The accuracy of the two models is assessed using proton chemical shifts of a set of rigid organic nitro compounds that are fully assigned in CDCl3 at 700 MHz. The two methods are then used to evaluate the accuracy of different popular post-SCF methods (B3LYP and MP2) and molecular mechanics methods (MMX and MMFF94) in calculating the molecular structure of a set of sterically crowded nitro aromatic compounds. Both models perform well on the rigid molecules used as a test set, although when using the GIAO method a general overestimation of the deshielding of protons near the nitro group is observed. The analysis of the sterically crowded molecules shows that the very popular B3LYP/6-31G(d,p) method produces very poor twist angles for these, and that using a larger basis set [6-311++G(2d,p)] gives much more reasonable results. The MP2 calculations, on the other hand, overestimate the twist angles, which for these compounds compensates for the deshielding effect generally observed for protons near electronegative atoms when using the GIAO method at the B3LYP/6-311++G(2d,p) level. The most accurate results are found when the structures are calculated using B3LYP/6-311++G(2d,p) level of theory, and the chemical shifts are calculated using the CHARGE program based on classical models.

  10. Chemical phase analysis of seed mediated synthesized anisotropic silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Bharti, Amardeep; Singh, Suman; Singla, M. L.; Goyal, Navdeep

    2015-08-01

    Noble-metal nanoparticles are of great interest because of its broad applications almost in every stream (i.e. biology, chemistry and engineering) due to their unique size/shape dependant properties. In this paper, chemical phase of seed mediated synthesized anisotropic silver nanoparticle (AgNPs) has been investigated via fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). These nanaoparticles were synthesized by seed-growth method controlled by urea and dextrose results to highly stable 12-20 nm particle size revealed by zeta potential and transmission electron microscopy (TEM).

  11. Chemical phase analysis of seed mediated synthesized anisotropic silver nanoparticles

    SciTech Connect

    Bharti, Amardeep Goyal, Navdeep; Singh, Suman; Singla, M. L.

    2015-08-28

    Noble-metal nanoparticles are of great interest because of its broad applications almost in every stream (i.e. biology, chemistry and engineering) due to their unique size/shape dependant properties. In this paper, chemical phase of seed mediated synthesized anisotropic silver nanoparticle (AgNPs) has been investigated via fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). These nanaoparticles were synthesized by seed-growth method controlled by urea and dextrose results to highly stable 12-20 nm particle size revealed by zeta potential and transmission electron microscopy (TEM)

  12. Crystal-Chemical Analysis of Soil at Rocknest, Gale Crater

    NASA Technical Reports Server (NTRS)

    Morrison, S. M.; Downs, R. T.; Blake, D. F.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Yen, A. S.; Chipera, S. J.; Treiman, A. H.; Vaniman, D. T.; Gellert, R.; Achilles, C. N.; Rampe, E. B.; Bristow, T. F.; Crisp, J. A.; Sarrazin, P. C.; DesMarais, D. J.; Morookian, J. M.; Anderson, R. C.

    2013-01-01

    The CheMin instrument on the Mars Science Laboratory rover Curiosity performed X-ray diffraction analysis on Martian soil [1] at Rocknest in Gale Crater. In particular, crystalline phases from scoop 5 were identified and analyzed with the Rietveld method [2]. Refined unit-cell parameters are reported in Table 1. Comparing these unit-cell parameters with those in the literature provides an estimate of the chemical composition of the crystalline phases. For instance, Fig. 1 shows the Mg-content of Fa-Fo olivine as a function of the b unit-cell parameter using literature data. Our refined b parameter is indicated by the black triangle.

  13. Interlaboratory comparison of chemical analysis of uranium mononitride

    NASA Technical Reports Server (NTRS)

    Merkle, E. J.; Davis, W. F.; Halloran, J. T.; Graab, J. W.

    1974-01-01

    Analytical methods were established in which the critical variables were controlled, with the result that acceptable interlaboratory agreement was demonstrated for the chemical analysis of uranium mononitride. This was accomplished by using equipment readily available to laboratories performing metallurgical analyses. Agreement among three laboratories was shown to be very good for uranium and nitrogen. Interlaboratory precision of + or - 0.04 percent was achieved for both of these elements. Oxygen was determined to + or - 15 parts per million (ppm) at the 170-ppm level. The carbon determination gave an interlaboratory precision of + or - 46 ppm at the 320-ppm level.

  14. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grégoire A.; Pietrucci, Fabio

    2013-08-01

    We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

  15. Sewage sludge toxicity assessment using earthworm Eisenia fetida: can biochemical and histopathological analysis provide fast and accurate insight?

    PubMed

    Babić, S; Barišić, J; Malev, O; Klobučar, G; Popović, N Topić; Strunjak-Perović, I; Krasnići, N; Čož-Rakovac, R; Klobučar, R Sauerborn

    2016-06-01

    Sewage sludge (SS) is a complex organic by-product of wastewater treatment plants. Deposition of large amounts of SS can increase the risk of soil contamination. Therefore, there is an increasing need for fast and accurate assessment of SS toxic potential. Toxic effects of SS were tested on earthworm Eisenia fetida tissue, at the subcellular and biochemical level. Earthworms were exposed to depot sludge (DS) concentration ratio of 30 or 70 %, to undiluted and to 100 and 10 times diluted active sludge (AS). The exposure to DS lasted for 24/48 h (acute exposure), 96 h (semi-acute exposure) and 7/14/28 days (sub-chronic exposure) and 48 h for AS. Toxic effects were tested by the measurements of multixenobiotic resistance mechanism (MXR) activity and lipid peroxidation levels, as well as the observation of morphological alterations and behavioural changes. Biochemical markers confirmed the presence of MXR inhibitors in the tested AS and DS and highlighted the presence of SS-induced oxidative stress. The MXR inhibition and thiobarbituric acid reactive substance (TBARS) concentration in the whole earthworm's body were higher after the exposition to lower concentration of the DS. Furthermore, histopathological changes revealed damage to earthworm body wall tissue layers as well as to the epithelial and chloragogen cells in the typhlosole region. These changes were proportional to SS concentration in tested soils and to exposure duration. Obtained results may contribute to the understanding of SS-induced toxic effects on terrestrial invertebrates exposed through soil contact and to identify defence mechanisms of earthworms. PMID:26971513

  16. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    PubMed

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.

  17. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    PubMed

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing. PMID:26072424

  18. Chemical Analysis of NOx Removal Under Different Reduced Electric Fields

    NASA Astrophysics Data System (ADS)

    Haddouche, A.; Lemerini, M.

    2015-07-01

    This work presents a chemical kinetic analysis of different species involved in nitrogen-oxygen mixed gas induced by stationary corona discharge at room temperature and atmospheric pressure. This study takes into account twenty different chemical species participating in one hundred and seventy selected chemical reactions. The reaction rate coefficients are taken from the literature, and the density is analyzed by the continuity equation without the diffusion term. A large number of investigations considered the removal of NOx showing the effects of N, O and O3 radicals. The aim of the present simulation is to complete these studies by analysing various plasma species under different reduced electric fields in the range of 100-200 Td (1 Td=10-21 V·m2). In particular, we analyze the time evolution of depopulation (10-9-10-3 s) of NOx. We have found that the depopulation rate of NO and NO2 is substantially affected by the rise of reduced electric field as it grows from 100 Td to 200 Td. This allows us to ascertain the important role played by the reduced electric field.

  19. Fixation and chemical analysis of single fog and rain droplets

    NASA Astrophysics Data System (ADS)

    Kasahara, M.; Akashi, S.; Ma, C.-J.; Tohno, S.

    Last decade, the importance of global environmental problems has been recognized worldwide. Acid rain is one of the most important global environmental problems as well as the global warming. The grasp of physical and chemical properties of fog and rain droplets is essential to make clear the physical and chemical processes of acid rain and also their effects on forests, materials and ecosystems. We examined the physical and chemical properties of single fog and raindrops by applying fixation technique. The sampling method and treatment procedure to fix the liquid droplets as a solid particle were investigated. Small liquid particles like fog droplet could be easily fixed within few minutes by exposure to cyanoacrylate vapor. The large liquid particles like raindrops were also fixed successively, but some of them were not perfect. Freezing method was applied to fix the large raindrops. Frozen liquid particles existed stably by exposure to cyanoacrylate vapor after freezing. The particle size measurement and the elemental analysis of the fixed particle were performed in individual base using microscope, and SEX-EDX, particle-induced X-ray emission (PIXE) and micro-PIXE analyses, respectively. The concentration in raindrops was dependent upon the droplet size and the elapsed time from the beginning of rainfall.

  20. [Rationality of commercial specification of rhubarb based on chemical analysis].

    PubMed

    Wang, Jiabo; Zhang, Xueru; Xiao, Xiaohe; Chu, Xiaohui; Zhou, Canping; Jin, Cheng; Yan, Dan

    2010-02-01

    The differences of 34 rhubarb samples collected on the market and at producing area were investigated by chemical analysis on the contents of anthraquinones and chromatographic fingerprints, in order to assess the rationality of the commercial specification of rhubarb. The results indicated that the commercial specification of rhubarb was not correlated to the contents of anthraquinones as well as the price. The chromatographic fingerprints of rhubarb samples from different producing area were dissimilar, while the commercial specifications were difficult to be separated. Generally, the rhubarb samples produced in famous-region contained more anthraquinones. This demonstrated rationality on the traditional records of the famous-region of rhubarb from a chemical view. In this study, it was firstly reported that rhubarb could be categorized into two types, chrysophanol-type and rhein-type, based on the proportion of the two constituents in the total anthraquinones after acid hydrohysis. It was found that the rhubarb samples of rhein-type were mostly produced in famous-regions, such as Qinghai, Xizang, West Sichuan and Gansu. The literatures reported that rhein was superior to chrysophanol at many pharmacological effects and pharmacokinetic properties. Hence, we primarily considered that rhein-type rhubarb might be high-quality. These results were helpful to improve the commercial specification of rhubarb from a view of chemical information.

  1. Sampling and physico-chemical analysis of precipitation: a review.

    PubMed

    Krupa, Sagar V

    2002-01-01

    as Hg and PCBs (polychlorinated biphenyls). Similarly, methods now exist for source-receptor studies, using for example, the characterization of reduced elemental states and/or the use of stable isotopes in precipitation as tracers. Future studies on the relationship between atmospheric deposition and environmental impacts must exploit these advances. This review provides a comprehensive and comparative treatment of the state of the art sampling methods of precipitation and its physico-chemical analysis.

  2. Chemical analysis of human blood for assessment of environmental exposure to semivolatile organochlorine chemical contaminants.

    PubMed

    Bristol, D W; Crist, H L; Lewis, R G; MacLeod, K E; Sovocool, G W

    1982-01-01

    A chemical method for the quantitative analysis of organochlorine pesticide residues present in human blood was scaled-up to provide increased sensitivity and extended to include organochlorine industrial chemicals. Whole blood samples were extracted with hexane, concentrated, and analyzed without further cleanup by gas chromatography with electron capture detection. The methodology used was validated by conducting recovery studies at 1 and 10 ng/g (ppb) levels. Screening and confirmational analyses were performed by gas chromatography/mass spectrometry on samples collected from potentially exposed residents of the Love Canal area of Niagara Falls, New York and from volunteers in the Research Triangle Park area of North Carolina for 25 specific semivolatile organochlorine contaminants including chlorobenzene and chlorotoluene congeners, hexachloro-1,3-butadiene, pesticides, and polychlorinated biphenyls as Aroclor 1260. Dichlorobenzene, hexachlorobenzene, and beta-hexachlorocyclohexane residues fell in the range of 0.1 to 26 ppb in a high percentage of both the field and volunteer blood samples analyzed. Levels of other organochlorine compounds were either non-detectable or present in sub-ppb ranges. PMID:6819409

  3. TOF-SIMS analysis of polystyrene/polybutadiene blend using chemical derivatization and multivariate analysis

    NASA Astrophysics Data System (ADS)

    Kono, Teiichiro; Iwase, Eijiro; Kanamori, Yukiko

    2008-12-01

    Chemical imaging with high spatial resolution is one of the features of TOF-SIMS. However, degradation of the sample due to primary ion bombardment becomes problematic when the analysis area is small. Although polystyrene (PS) and polybutadiene (PB) separately show relatively distinct spectra, observation of their phase separation in PS/PB blends is difficult when the analysis area is small because degradation of both polymers and especially PS leads to disappearance of their characteristic peaks, resulting in low chemical image contrast. We therefore investigated the application of various forms of multivariate analysis (MVA) to the TOF-SIMS image data to improve the chemical image contrast. PCA, MCR, and the other forms of MVA provided improvement in contrast, but the images were still obscure and observation of phase separation remained difficult. Chemical derivatization using osmium tetroxide was also investigated, and found to give clear images of phase separation in the PS/PB blend. In quantitative determinations with MVA and chemical derivatization, PLS demonstrated the best predictive capability and chemical derivatization resulted in large deviations from both the bulk chemical composition and the determinations with MVA, particularly in regions of low PB content.

  4. A DPF Analysis Yields Quantum Mechanically Accurate Analytic Potential Energy Functions for the a ^1Σ^+ and X ^1Σ^+ States of NaH

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Walji, Sadru; Sentjens, Katherine

    2013-06-01

    Alkali hydride diatomic molecules have long been the object of spectroscopic studies. However, their small reduced mass makes them species for which the conventional semiclassical-based methods of analysis tend to have the largest errors. To date, the only quantum-mechanically accurate direct-potential-fit (DPF) analysis for one of these molecules was the one for LiH reported by Coxon and Dickinson. The present paper extends this level of analysis to NaH, and reports a DPF analysis of all available spectroscopic data for the A ^1Σ^+-X ^1Σ^+ system of NaH which yields analytic potential energy functions for these two states that account for those data (on average) to within the experimental uncertainties. W.C. Stwalley, W.T. Zemke and S.C. Yang, J. Phys. Chem. Ref. Data {20}, 153-187 (1991). J.A. Coxon and C.S. Dickinson, J. Chem. Phys. {121}, 8378 (2004).

  5. Microbiological and Chemical Analysis of Land Snails Commercialised in Sicily

    PubMed Central

    Cicero, Antonello; Giangrosso, Giuseppe; Cammilleri, Gaetano; Macaluso, Andrea; Currò, Vittoria; Galuppo, Lucia; Vargetto, Daniela; Vicari, Domenico

    2015-01-01

    In this study 160 samples of snails belonging to the species Helix aspersa maxima and Helix aspersa muller were examined for chemical and microbiological analysis. Samples came from Greece and Poland. Results showed mean concentration of cadmium (0.35±0.036 mg/kg) and lead (0.05±0.013 mg/kg) much higher than the limit of detection. Mercury levels in both species were not detected. Microbiological analysis revealed the absence of Salmonella spp. and Clostridium spp. in both examined species. E. coli and K. oxytoca were observed in Helix aspersa maxima and Helix aspersa muller. Furthermore, one case of fungi positivity in samples of Helix aspersa muller was found. The reported investigations highlight the need to create and adopt a reference legislation to protect the health of consumers. PMID:27800385

  6. A modular approach for automated sample preparation and chemical analysis

    NASA Technical Reports Server (NTRS)

    Clark, Michael L.; Turner, Terry D.; Klingler, Kerry M.; Pacetti, Randolph

    1994-01-01

    Changes in international relations, especially within the past several years, have dramatically affected the programmatic thrusts of the U.S. Department of Energy (DOE). The DOE now is addressing the environmental cleanup required as a result of 50 years of nuclear arms research and production. One major obstacle in the remediation of these areas is the chemical determination of potentially contaminated material using currently acceptable practices. Process bottlenecks and exposure to hazardous conditions pose problems for the DOE. One proposed solution is the application of modular automated chemistry using Standard Laboratory Modules (SLM) to perform Standard Analysis Methods (SAM). The Contaminant Analysis Automation (CAA) Program has developed standards and prototype equipment that will accelerate the development of modular chemistry technology and is transferring this technology to private industry.

  7. Development of automated imaging and analysis for zebrafish chemical screens.

    PubMed Central

    Vogt, Andreas; Codore, Hiba; Day, Billy W.; Hukriede, Neil A.; Tsang, Michael

    2010-01-01

    We demonstrate the application of image-based high-content screening (HCS) methodology to identify small molecules that can modulate the FGF/RAS/MAPK pathway in zebrafish embryos. The zebrafish embryo is an ideal system for in vivo high-content chemical screens. The 1-day old embryo is approximately 1mm in diameter and can be easily arrayed into 96-well plates, a standard format for high throughput screening. During the first day of development, embryos are transparent with most of the major organs present, thus enabling visualization of tissue formation during embryogenesis. The complete automation of zebrafish chemical screens is still a challenge, however, particularly in the development of automated image acquisition and analysis. We previously generated a transgenic reporter line that expresses green fluorescent protein (GFP) under the control of FGF activity and demonstrated their utility in chemical screens 1. To establish methodology for high throughput whole organism screens, we developed a system for automated imaging and analysis of zebrafish embryos at 24-48 hours post fertilization (hpf) in 96-well plates 2. In this video we highlight the procedures for arraying transgenic embryos into multiwell plates at 24hpf and the addition of a small molecule (BCI) that hyperactivates FGF signaling 3. The plates are incubated for 6 hours followed by the addition of tricaine to anesthetize larvae prior to automated imaging on a Molecular Devices ImageXpress Ultra laser scanning confocal HCS reader. Images are processed by Definiens Developer software using a Cognition Network Technology algorithm that we developed to detect and quantify expression of GFP in the heads of transgenic embryos. In this example we highlight the ability of the algorithm to measure dose-dependent effects of BCI on GFP reporter gene expression in treated embryos. PMID:20613708

  8. How accurate are interpretations of curriculum-based measurement progress monitoring data? Visual analysis versus decision rules.

    PubMed

    Van Norman, Ethan R; Christ, Theodore J

    2016-10-01

    Curriculum based measurement of oral reading (CBM-R) is used to monitor the effects of academic interventions for individual students. Decisions to continue, modify, or terminate these interventions are made by interpreting time series CBM-R data. Such interpretation is founded upon visual analysis or the application of decision rules. The purpose of this study was to compare the accuracy of visual analysis and decision rules. Visual analysts interpreted 108 CBM-R progress monitoring graphs one of three ways: (a) without graphic aids, (b) with a goal line, or (c) with a goal line and a trend line. Graphs differed along three dimensions, including trend magnitude, variability of observations, and duration of data collection. Automated trend line and data point decision rules were also applied to each graph. Inferential analyses permitted the estimation of the probability of a correct decision (i.e., the student is improving - continue the intervention, or the student is not improving - discontinue the intervention) for each evaluation method as a function of trend magnitude, variability of observations, and duration of data collection. All evaluation methods performed better when students made adequate progress. Visual analysis and decision rules performed similarly when observations were less variable. Results suggest that educators should collect data for more than six weeks, take steps to control measurement error, and visually analyze graphs when data are variable. Implications for practice and research are discussed. PMID:27586069

  9. How accurate are interpretations of curriculum-based measurement progress monitoring data? Visual analysis versus decision rules.

    PubMed

    Van Norman, Ethan R; Christ, Theodore J

    2016-10-01

    Curriculum based measurement of oral reading (CBM-R) is used to monitor the effects of academic interventions for individual students. Decisions to continue, modify, or terminate these interventions are made by interpreting time series CBM-R data. Such interpretation is founded upon visual analysis or the application of decision rules. The purpose of this study was to compare the accuracy of visual analysis and decision rules. Visual analysts interpreted 108 CBM-R progress monitoring graphs one of three ways: (a) without graphic aids, (b) with a goal line, or (c) with a goal line and a trend line. Graphs differed along three dimensions, including trend magnitude, variability of observations, and duration of data collection. Automated trend line and data point decision rules were also applied to each graph. Inferential analyses permitted the estimation of the probability of a correct decision (i.e., the student is improving - continue the intervention, or the student is not improving - discontinue the intervention) for each evaluation method as a function of trend magnitude, variability of observations, and duration of data collection. All evaluation methods performed better when students made adequate progress. Visual analysis and decision rules performed similarly when observations were less variable. Results suggest that educators should collect data for more than six weeks, take steps to control measurement error, and visually analyze graphs when data are variable. Implications for practice and research are discussed.

  10. LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

    NASA Technical Reports Server (NTRS)

    Bittker, David A.; Radhakrishnan, Krishnan

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

  11. Accurate analysis of prevalence of coccidiosis in individually identified wild cranes in inhabiting and migrating populations in Japan.

    PubMed

    Honma, Hajime; Suyama, Yoshihisa; Watanabe, Yuki; Matsumoto, Fumio; Nakai, Yutaka

    2011-11-01

    Eimeria gruis and E. reichenowi cause coccidiosis, a major parasitic disease of cranes. By non-invasive molecular approaches, we investigated the prevalence and genetic characterization of pathogens in two Japanese crane habitats; one is Hokkaido inhabited by the endangered red-crowned crane, and the other is Izumi in Kyushu where populations that consist mainly of vulnerable hooded and white-naped cranes migrate in winter. The non-invasively collected faecal samples from each wintering population were first subjected to host genomic DNA-targeted analyses to determine the sample origin and avoid sample redundancy. Extremely high prevalence was observed in the Izumi populations (> 90%) compared with the Hokkaido population (18-30%) by examining 470 specimens by microscopy and PCR-based capillary electrophoresis (PCR-CE), using genetic markers in the second internal transcribed spacer (ITS2). Correspondence analysis of PCR-CE data revealed differences in community composition of coccidia between hooded and white-naped cranes. 18S rRNA and ITS2 sequences were determined from single oocysts excreted by red-crowned and hooded cranes. Phylogenetic analysis of 18S rRNA suggested that E. reichenowi was polyphyletic while E. gruis was monophyletic. Together with PCR-CE data, these results indicate different host specificity among the E. reichenowi type. Our data suggest that E. reichenowi comprises multiple species. PMID:21895916

  12. Sensitive and accurate identification of protein–DNA binding events in ChIP-chip assays using higher order derivative analysis

    PubMed Central

    Barrett, Christian L.; Cho, Byung-Kwan

    2011-01-01

    Immuno-precipitation of protein–DNA complexes followed by microarray hybridization is a powerful and cost-effective technology for discovering protein–DNA binding events at the genome scale. It is still an unresolved challenge to comprehensively, accurately and sensitively extract binding event information from the produced data. We have developed a novel strategy composed of an information-preserving signal-smoothing procedure, higher order derivative analysis and application of the principle of maximum entropy to address this challenge. Importantly, our method does not require any input parameters to be specified by the user. Using genome-scale binding data of two Escherichia coli global transcription regulators for which a relatively large number of experimentally supported sites are known, we show that ∼90% of known sites were resolved to within four probes, or ∼88 bp. Over half of the sites were resolved to within two probes, or ∼38 bp. Furthermore, we demonstrate that our strategy delivers significant quantitative and qualitative performance gains over available methods. Such accurate and sensitive binding site resolution has important consequences for accurately reconstructing transcriptional regulatory networks, for motif discovery, for furthering our understanding of local and non-local factors in protein–DNA interactions and for extending the usefulness horizon of the ChIP-chip platform. PMID:21051353

  13. Chemical Abundance Analysis of the Symbiotic Red Giants

    NASA Astrophysics Data System (ADS)

    Galan, Cezary; Mikolajewska, Joanna; Hinkle, Kenneth H.

    2015-01-01

    The study of symbiotic stars - the long period, interacting binary systems - composed of red giant donor and a hot, compact companion is important for our understanding of binary stellar evolution in systems where mass loss or transfer take place involving RGB/AGB stars. The elemental abundances of symbiotic giants can track the mass exchange history and can determine their parent stellar population. However, the number of these objects with fairly well determined photospheric composition is insufficient for statistical considerations. Here we present the detailed chemical abundance analysis obtained for the first time for 14 M-type symbiotic giants. The analysis is based on the high resolution (R ˜ 50000), high S/N ˜ 100, near-IR spectra (at H- and K-band regions) obtained with Phoenix/Gemini South spectrometer. Spectrum synthesis employing standard LTE analysis and atmosphere models was used to obtain photospheric abundances of CNO and elements around the iron peak (Sc, Ti, Fe, and Ni). Our analysis reveals mostly slightly sub-solar or near-solar metallicities. We obtained significantly subsolar metallicities for RW Hya, RT Ser, and Hen 3-1213 and slightly super-solar metallicity in V455 Sco. The very low ^{12}C/^{13}C isotopic ratios, ˜6-11, and significant enrichment in nitrogen ^{14}N isotope in almost all giants in our sample indicate that they have experienced the first dredge-up.

  14. Accurate extraction of Lagrangian coherent structures over finite domains with application to flight data analysis over Hong Kong International Airport.

    PubMed

    Tang, Wenbo; Chan, Pak Wai; Haller, George

    2010-03-01

    Locating Lagrangian coherent structures (LCS) for dynamical systems defined on a spatially limited domain present a challenge because trajectory integration must be stopped at the boundary for lack of further velocity data. This effectively turns the domain boundary into an attractor, introduces edge effects resulting in spurious ridges in the associated finite-time Lyapunov exponent (FTLE) field, and causes some of the real ridges of the FTLE field to be suppressed by strong spurious ridges. To address these issues, we develop a finite-domain FTLE method that renders LCS with an accuracy and fidelity that is suitable for automated feature detection. We show the application of this technique to the analysis of velocity data from aircraft landing at the Hong Kong International Airport.

  15. Accurate discrimination of Alzheimer's disease from other dementia and/or normal subjects using SPECT specific volume analysis

    NASA Astrophysics Data System (ADS)

    Iyatomi, Hitoshi; Hashimoto, Jun; Yoshii, Fumuhito; Kazama, Toshiki; Kawada, Shuichi; Imai, Yutaka

    2014-03-01

    Discrimination between Alzheimer's disease and other dementia is clinically significant, however it is often difficult. In this study, we developed classification models among Alzheimer's disease (AD), other dementia (OD) and/or normal subjects (NC) using patient factors and indices obtained by brain perfusion SPECT. SPECT is commonly used to assess cerebral blood flow (CBF) and allows the evaluation of the severity of hypoperfusion by introducing statistical parametric mapping (SPM). We investigated a total of 150 cases (50 cases each for AD, OD, and NC) from Tokai University Hospital, Japan. In each case, we obtained a total of 127 candidate parameters from: (A) 2 patient factors (age and sex), (B) 12 CBF parameters and 113 SPM parameters including (C) 3 from specific volume analysis (SVA), and (D) 110 from voxel-based analysis stereotactic extraction estimation (vbSEE). We built linear classifiers with a statistical stepwise feature selection and evaluated the performance with the leave-one-out cross validation strategy. Our classifiers achieved very high classification performances with reasonable number of selected parameters. In the most significant discrimination in clinical, namely those of AD from OD, our classifier achieved both sensitivity (SE) and specificity (SP) of 96%. In a similar way, our classifiers achieved a SE of 90% and a SP of 98% in AD from NC, as well as a SE of 88% and a SP of 86% in AD from OD and NC cases. Introducing SPM indices such as SVA and vbSEE, classification performances improved around 7-15%. We confirmed that these SPM factors are quite important for diagnosing Alzheimer's disease.

  16. Physical and Chemical Analytical Analysis: A key component of Bioforensics

    SciTech Connect

    Velsko, S P

    2005-02-15

    The anthrax letters event of 2001 has raised our awareness of the potential importance of non-biological measurements on samples of biological agents used in a terrorism incident. Such measurements include a variety of mass spectral, spectroscopic, and other instrumental techniques that are part of the current armamentarium of the modern materials analysis or analytical chemistry laboratory. They can provide morphological, trace element, isotopic, and other molecular ''fingerprints'' of the agent that may be key pieces of evidence, supplementing that obtained from genetic analysis or other biological properties. The generation and interpretation of such data represents a new domain of forensic science, closely aligned with other areas of ''microbial forensics''. This paper describes some major elements of the R&D agenda that will define this sub-field in the immediate future and provide the foundations for a coherent national capability. Data from chemical and physical analysis of BW materials can be useful to an investigation of a bio-terror event in two ways. First, it can be used to compare evidence samples collected at different locations where such incidents have occurred (e.g. between the powders in the New York and Washington letters in the Amerithrax investigation) or between the attack samples and those seized during the investigation of sites where it is suspected the material was manufactured (if such samples exist). Matching of sample properties can help establish the relatedness of disparate incidents, and mis-matches might exclude certain scenarios, or signify a more complex etiology of the events under investigation. Chemical and morphological analysis for sample matching has a long history in forensics, and is likely to be acceptable in principle in court, assuming that match criteria are well defined and derived from known limits of precision of the measurement techniques in question. Thus, apart from certain operational issues (such as how to

  17. A feasibility study for measuring accurate tendon displacements using an audio-based Fourier analysis of pulsed-wave Doppler ultrasound signals.

    PubMed

    Stegman, K J; Podhorodeski, R P; Park, E J

    2009-01-01

    The accuracy of Pulsed-Wave Doppler Ultrasound displacement measurements of a slow moving "tendon-like" string was investigated in this study. This was accomplished by estimating string displacements using an audio-based Fourier analysis of a Pulsed-Wave Doppler signal from a commercial ultrasound scanner. Our feasibility study showed that the proposed technique is much more accurate at estimating the actual string displacement in comparison to the scanner's onboard software. Furthermore, this study also shows that a real-time Doppler data acquisition from an ultrasound scanner is possible for the ultimate purpose of real-time biological tendon displacement monitoring.

  18. Purification of pharmaceutical preparations using thin-layer chromatography to obtain mass spectra with Direct Analysis in Real Time and accurate mass spectrometry.

    PubMed

    Wood, Jessica L; Steiner, Robert R

    2011-06-01

    Forensic analysis of pharmaceutical preparations requires a comparative analysis with a standard of the suspected drug in order to identify the active ingredient. Purchasing analytical standards can be expensive or unattainable from the drug manufacturers. Direct Analysis in Real Time (DART™) is a novel, ambient ionization technique, typically coupled with a JEOL AccuTOF™ (accurate mass) mass spectrometer. While a fast and easy technique to perform, a drawback of using DART™ is the lack of component separation of mixtures prior to ionization. Various in-house pharmaceutical preparations were purified using thin-layer chromatography (TLC) and mass spectra were subsequently obtained using the AccuTOF™- DART™ technique. Utilizing TLC prior to sample introduction provides a simple, low-cost solution to acquiring mass spectra of the purified preparation. Each spectrum was compared against an in-house molecular formula list to confirm the accurate mass elemental compositions. Spectra of purified ingredients of known pharmaceuticals were added to an in-house library for use as comparators for casework samples. Resolving isomers from one another can be accomplished using collision-induced dissociation after ionization. Challenges arose when the pharmaceutical preparation required an optimized TLC solvent to achieve proper separation and purity of the standard. Purified spectra were obtained for 91 preparations and included in an in-house drug standard library. Primary standards would only need to be purchased when pharmaceutical preparations not previously encountered are submitted for comparative analysis. TLC prior to DART™ analysis demonstrates a time efficient and cost saving technique for the forensic drug analysis community. Copyright © 2011 John Wiley & Sons, Ltd.

  19. Chromatographic analysis with different detectors in the chemical characterisation and dereplication of African propolis.

    PubMed

    Zhang, Tong; Omar, Ruwida; Siheri, Weam; Al Mutairi, Sultan; Clements, Carol; Fearnley, James; Edrada-Ebel, RuAngelie; Watson, David

    2014-03-01

    Propolis or bee glue has very diverse composition and is potentially a source of biologically active compounds. Comprehensive chemical profiling was performed on 22 African propolis samples collected from the sub-Saharan region of Africa by using various hyphenated analytical techniques including Liquid Chromatography (LC)-UltraViolet Detection (UV)-Evaporative Light Scattering Detection (ELSD), LC-High Resolution Mass Spectrometry (HRMS), Gas Chromatography (GC)-MS and LC-Diode Array Detector (DAD)-HRMS/MS. The diversity of the composition of these African propolis samples could be observed by heat mapping the LC-UV and ELSD data. The characteristic chemical components were uncovered by applying Principal Component Analysis (PCA) to the LC-HRMS data and a preliminary dereplication was carried out by searching their accurate masses in the Dictionary of Natural Products (DNP). A further identification was achieved by comparing their GC-MS or LC-DAD-HRMS/MS spectra with previously published data. Generally no clear geographic delineation was observed in the classification of these African propolis samples. Triterpenoids were found as the major chemical components in more than half of the propolis samples analysed in this study and some others were classified as temperate and Eastern Mediterranean type of propolis. Based on the comparative chemical profiling and dereplication studies one uncommon propolis from southern Nigeria stood out from others by presenting prenylated isoflavonoids, which indicated that it was more like Brazilian red propolis, and more significantly a high abundance of stilbenoid compounds which could be novel in propolis.

  20. Combination of micro-dialysis and infrared spectroscopy: a multianalyte assay for accurate biofluid analysis and patient monitoring

    NASA Astrophysics Data System (ADS)

    Vahlsing, Thorsten; Delbeck, Sven; Budde, Janpeter; Ihrig, Dieter; Heise, H. Michael

    2016-03-01

    Micro-dialysis can be used for continuously harvesting body fluids, while a multi-component analysis of the dialysates by infrared spectrometry offers splendid opportunities for monitoring substrates and metabolites such as glucose, lactate and others small enough to penetrate the semi-permeable dialysis membranes. However, a drawback of this process are variable recovery rates, which can be observed especially for subcutaneously implanted catheters in human subjects. Isotonic perfusates were investigated with acetate and mannitol as recovery markers for the dialysis of human serum at 37°C to mimic in vivo patient monitoring. The latter non-ionic substance has been suggested for application when other ionic substances such as bicarbonate or pH are also to be determined. Simultaneously for acetate and mannitol, the depletion of the marker substances from the perfusates using different micro-dialysis devices was investigated under various flow-rates. Relationships between relative dialysate marker concentrations and glucose recovery rates were determined based on multivariate calibrations. For quantification, classical least squares with reference spectra for modelling the serum dialysates was used, rendering a basis for reliable blood glucose and lactate measurements.

  1. Capacitive chemical sensor

    DOEpatents

    Manginell, Ronald P; Moorman, Matthew W; Wheeler, David R

    2014-05-27

    A microfabricated capacitive chemical sensor can be used as an autonomous chemical sensor or as an analyte-sensitive chemical preconcentrator in a larger microanalytical system. The capacitive chemical sensor detects changes in sensing film dielectric properties, such as the dielectric constant, conductivity, or dimensionality. These changes result from the interaction of a target analyte with the sensing film. This capability provides a low-power, self-heating chemical sensor suitable for remote and unattended sensing applications. The capacitive chemical sensor also enables a smart, analyte-sensitive chemical preconcentrator. After sorption of the sample by the sensing film, the film can be rapidly heated to release the sample for further analysis. Therefore, the capacitive chemical sensor can optimize the sample collection time prior to release to enable the rapid and accurate analysis of analytes by a microanalytical system.

  2. Automatic Earthquake Shear Stress Measurement Method Developed for Accurate Time- Prediction Analysis of Forthcoming Major Earthquakes Along Shallow Active Faults

    NASA Astrophysics Data System (ADS)

    Serata, S.

    2006-12-01

    The Serata Stressmeter has been developed to measure and monitor earthquake shear stress build-up along shallow active faults. The development work made in the past 25 years has established the Stressmeter as an automatic stress measurement system to study timing of forthcoming major earthquakes in support of the current earthquake prediction studies based on statistical analysis of seismological observations. In early 1982, a series of major Man-made earthquakes (magnitude 4.5-5.0) suddenly occurred in an area over deep underground potash mine in Saskatchewan, Canada. By measuring underground stress condition of the mine, the direct cause of the earthquake was disclosed. The cause was successfully eliminated by controlling the stress condition of the mine. The Japanese government was interested in this development and the Stressmeter was introduced to the Japanese government research program for earthquake stress studies. In Japan the Stressmeter was first utilized for direct measurement of the intrinsic lateral tectonic stress gradient G. The measurement, conducted at the Mt. Fuji Underground Research Center of the Japanese government, disclosed the constant natural gradients of maximum and minimum lateral stresses in an excellent agreement with the theoretical value, i.e., G = 0.25. All the conventional methods of overcoring, hydrofracturing and deformation, which were introduced to compete with the Serata method, failed demonstrating the fundamental difficulties of the conventional methods. The intrinsic lateral stress gradient determined by the Stressmeter for the Japanese government was found to be the same with all the other measurements made by the Stressmeter in Japan. The stress measurement results obtained by the major international stress measurement work in the Hot Dry Rock Projects conducted in USA, England and Germany are found to be in good agreement with the Stressmeter results obtained in Japan. Based on this broad agreement, a solid geomechanical

  3. Establishment of an x-ray standard calibration curve by conventional dicentric analysis as prerequisite for accurate radiation dose assessment.

    PubMed

    Beinke, Christina; Braselmann, Herbert; Meineke, Viktor

    2010-02-01

    The dicentric assay was established to carry out cytogenetic biodosimetry after suspected radiation overexposure, including a comprehensive documentation system to record the processing of the specimen, all data, results, and stored information. As an essential prerequisite for retrospective radiation dose assessment, a dose-response curve for dicentric induction by in vitro x-ray irradiation of peripheral blood samples was produced. The accelerating potential was 240 kV (maximum photon energy: 240 keV). A total of 8,377 first-division metaphases of four healthy volunteers were analyzed after exposure to doses ranging from 0.2 to 4.0 Gy at a dose rate of 1.0 Gy min. The background level of aberrations at 0-dose was determined by the analysis of 14,522 first-division metaphases obtained from unirradiated blood samples of 10 healthy volunteers. The dose-response relationship follows a linear-quadratic equation, Y = c + alphaD + betaD, with the coefficients c = 0.0005 +/- 0.0002, alpha = 0.043 +/- 0.006, and beta = 0.063 +/- 0.004. The technical competence and the quality of the calibration curve were assessed by determination of the dose prediction accuracy in an in vitro experiment simulating whole-body exposures within a range of 0.2 to 2.0 Gy. Dose estimations were derived by scoring up to 500-1,000 metaphase spreads or more (full estimation mode) and by evaluating only 50 metaphase spreads (triage mode) per subject. The triage mode was applied by performing manifold evaluations of the full estimation data in order to test the robustness of the curve for triage purposes and to assess possible variations among the estimated doses referring to a single exposure and preparation.

  4. [Pharmaceutical analysis of chemicals related with daily life products for safe and secure].

    PubMed

    Nakazawa, Hiroyuki

    2014-01-01

    An association between exposure to trace hazardous chemicals such as endocrine disrupting chemicals and an increased incidence of human endocrine disease might be continued to study. The accurate and sensitive analytical methods for determination of various chemicals in human biospecimen such as urine, blood and breast milk have been studied by techniques including chromatography. In order to obtain the safe and secure life, the pharmaceutical analytical approaches might be applicable with the hopes of realizing scientific risk assessment of the chemicals derived from daily life products as regulatory sciences.

  5. Complete chemical analysis of aerosol particles in real-time

    SciTech Connect

    Yang, Mo; Reilly, P.T.A.; Gieray, R.A.; Whitten, W.B.; Ramsey, J.M.

    1996-12-31

    Real-time mass spectrometry of individual aerosol particles using an ion trap mass spectrometer is described. The microparticles are sampled directly from the air by a particle inlet system into the vacuum chamber. An incoming particle is detected as it passes through two CW laser beams and a pulsed laser is triggered to intercept the particle for laser ablation ionization at the center of the ion trap. The produced ions are analyzed by the ion trap mass spectrometer. Ions of interest are selected and dissociated through collision with buffer gas atoms for further fragmentation analysis. Real-time chemical analyses of inorganic, organic, and bacterial aerosol articles have been demonstrated. It has been confirmed that the velocity and the size of the incoming particles highly correlate to each other. The performance of the inlet system, particle detection, and preliminary results are discussed.

  6. Optical instrumentation for on-line analysis of chemical processes

    SciTech Connect

    Hartford, A. Jr.; Cremers, D.A.; Loree, T.R.; Quigley, G.P.

    1983-01-01

    Optical diagnostics provide the capability for nonintrusive, on-line, real time analysis of chemical process streams. Several laser-based methods for monitoring fossil energy processes have been evaluated. Among the instrumentation techniques which appear quite promising are coherent anti-Stokes Raman spectroscopy (CARS), laser-induced breakdown spectroscopy (LIBS), and synchronous detection of laser-induced fluorescence (SDLIF). A CARS diagnostic was implemented on a coal gasifier and was successfully employed to measure species concentrations and temperatures within the process stream. The LIBS approach has been used to identify total trace impurities (e.g., Na, K, and S) within a gasifier. Recently, individual components in mixtures of aromatics hydrocarbons have been resolved via the synchronous detection of laser-induced fluorescence. 9 figures.

  7. Advances in the chemical analysis and biological activities of chuanxiong.

    PubMed

    Li, Weixia; Tang, Yuping; Chen, Yanyan; Duan, Jin-Ao

    2012-01-01

    Chuanxiong Rhizoma (Chuan-Xiong, CX), the dried rhizome of Ligusticum chuanxiong Hort. (Umbelliferae), is one of the most popular plant medicines in the World. Modern research indicates that organic acids, phthalides, alkaloids, polysaccharides, ceramides and cerebrosides are main components responsible for the bioactivities and properties of CX. Because of its complex constituents, multidisciplinary techniques are needed to validate the analytical methods that support CX's use worldwide. In the past two decades, rapid development of technology has advanced many aspects of CX research. The aim of this review is to illustrate the recent advances in the chemical analysis and biological activities of CX, and to highlight new applications and challenges. Emphasis is placed on recent trends and emerging techniques. PMID:22955453

  8. 3rd annual symposium of chemical and pharmaceutical structure analysis.

    PubMed

    Weng, Naidong; Zheng, Jenny; Lee, Mike

    2012-08-01

    The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award.

  9. Computational analysis of RNA structures with chemical probing data.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-06-01

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

  10. Spectroscopic analysis of cinnamic acid using quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Vinod, K. S.; Periandy, S.; Govindarajan, M.

    2015-02-01

    In this present study, FT-IR, FT-Raman, 13C NMR and 1H NMR spectra for cinnamic acid have been recorded for the vibrational and spectroscopic analysis. The observed fundamental frequencies (IR and Raman) were assigned according to their distinctiveness region. The computed frequencies and optimized parameters have been calculated by using HF and DFT (B3LYP) methods and the corresponding results are tabulated. On the basis of the comparison between computed and experimental results assignments of the fundamental vibrational modes are examined. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The alternation of the vibration pattern of the pedestal molecule related to the substitutions was analyzed. The 13C and 1H NMR spectra have been recorded and the chemical shifts have been calculated using the gauge independent atomic orbital (GIAO) method. The Mulliken charges, UV spectral analysis and HOMO-LUMO analysis of have been calculated and reported. The molecular electrostatic potential (MEP) was constructed.

  11. Spectroscopic analysis of cinnamic acid using quantum chemical calculations.

    PubMed

    Vinod, K S; Periandy, S; Govindarajan, M

    2015-02-01

    In this present study, FT-IR, FT-Raman, (13)C NMR and (1)H NMR spectra for cinnamic acid have been recorded for the vibrational and spectroscopic analysis. The observed fundamental frequencies (IR and Raman) were assigned according to their distinctiveness region. The computed frequencies and optimized parameters have been calculated by using HF and DFT (B3LYP) methods and the corresponding results are tabulated. On the basis of the comparison between computed and experimental results assignments of the fundamental vibrational modes are examined. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by HF and DFT methods. The alternation of the vibration pattern of the pedestal molecule related to the substitutions was analyzed. The (13)C and (1)H NMR spectra have been recorded and the chemical shifts have been calculated using the gauge independent atomic orbital (GIAO) method. The Mulliken charges, UV spectral analysis and HOMO-LUMO analysis of have been calculated and reported. The molecular electrostatic potential (MEP) was constructed.

  12. Chemical analysis of Ginkgo biloba leaves and extracts.

    PubMed

    van Beek, Teris A

    2002-08-16

    The chemical analysis and quality control of Ginkgo leaves and extracts is reviewed. Important constituents present in the medicinally used leaves are the terpene trilactones, i.e., ginkgolides A, B, C, J and bilobalide, many flavonol glycosides, biflavones, proanthocyanidins, alkylphenols, simple phenolic acids, 6-hydroxykynurenic acid, 4-O-methylpyridoxine and polyprenols. In the commercially important Ginkgo extracts some of these compound classes are no longer present. Many publications deal with the analysis of the unique terpene trilactones. They can be extracted with aqueous acetone or aqueous methanol but also supercritical fluid extraction is possible. Still somewhat problematic is their sample clean-up. Various procedures, not all of them validated, employing partitioning or SPE have been proposed. Some further development in this area can be foreseen. Separation and detection can be routinely carried out by HPLC with RI, ELSD or MS, or with GC-FID after silylation. TLC is another possibility. No quantitative procedure for flavonol glycosides has been published so far due their difficult separation and commercial unavailability. Fingerprint analysis by gradient RP-HPLC is possible. After acidic hydrolysis to the aglycones quercetin, kaempferol and isorhamnetin and separation by HPLC, quantitation is straightforward and yields by recalculation an estimation of the original total flavonol glycoside content. For biflavones, simple phenols, 6-hydroxykynurenic acid, 4-O-methylpyridoxine and polyprenols analytical procedures have been published but not all assays are yet ideal. Lately a there is a lot of interest in the analysis of the undesired alkylphenols and a few validated procedures have been published. The analysis of Ginkgo proanthocyanidins is still in its infancy and no reliable assays exist.

  13. Chemical analysis of Ginkgo biloba leaves and extracts.

    PubMed

    van Beek, Teris A

    2002-08-16

    The chemical analysis and quality control of Ginkgo leaves and extracts is reviewed. Important constituents present in the medicinally used leaves are the terpene trilactones, i.e., ginkgolides A, B, C, J and bilobalide, many flavonol glycosides, biflavones, proanthocyanidins, alkylphenols, simple phenolic acids, 6-hydroxykynurenic acid, 4-O-methylpyridoxine and polyprenols. In the commercially important Ginkgo extracts some of these compound classes are no longer present. Many publications deal with the analysis of the unique terpene trilactones. They can be extracted with aqueous acetone or aqueous methanol but also supercritical fluid extraction is possible. Still somewhat problematic is their sample clean-up. Various procedures, not all of them validated, employing partitioning or SPE have been proposed. Some further development in this area can be foreseen. Separation and detection can be routinely carried out by HPLC with RI, ELSD or MS, or with GC-FID after silylation. TLC is another possibility. No quantitative procedure for flavonol glycosides has been published so far due their difficult separation and commercial unavailability. Fingerprint analysis by gradient RP-HPLC is possible. After acidic hydrolysis to the aglycones quercetin, kaempferol and isorhamnetin and separation by HPLC, quantitation is straightforward and yields by recalculation an estimation of the original total flavonol glycoside content. For biflavones, simple phenols, 6-hydroxykynurenic acid, 4-O-methylpyridoxine and polyprenols analytical procedures have been published but not all assays are yet ideal. Lately a there is a lot of interest in the analysis of the undesired alkylphenols and a few validated procedures have been published. The analysis of Ginkgo proanthocyanidins is still in its infancy and no reliable assays exist. PMID:12219929

  14. ANALYSIS OF SAMPLES FROM TANK 6F CHEMICAL CLEANING

    SciTech Connect

    Poirier, M.; Fink, S.

    2010-02-02

    Savannah River Remediation (SRR) is preparing Tank 6F for closure. The first step in preparing the tank for closure is mechanical sludge removal. In mechanical sludge removal, personnel add liquid (e.g., inhibited water or supernate salt solution) to the tank to form a slurry. They mix the liquid and sludge with pumps, and transfer the slurry to another tank for further processing. Mechanical sludge removal effectively removes the bulk of the sludge from a tank, but is not able to remove all of the sludge. In Tank 6F, SRR estimated a sludge heel of 5,984 gallons remained after mechanical sludge removal. To remove this sludge heel, SRR performed chemical cleaning. The chemical cleaning included two oxalic acid strikes, a spray wash, and a water wash. SRR conducted the first oxalic acid strike as follows. Personnel added 110,830 gallons of 8 wt % oxalic acid to Tank 6F and mixed the contents of Tank 6F with two submersible mixer pumps (SMPs) for approximately four days. Following the mixing, they transferred 115,903 gallons of Tank 6F material to Tank 7F. The SMPs were operating when the transfer started and were shut down approximately five hours after the transfer started. SRR collected a sample of the liquid from Tank 6F and submitted it to SRNL for analysis. Mapping of the tank following the transfer indicated that 2,400 gallons of solids remained in the tank. SRR conducted the second oxalic acid strike as follows. Personnel added 28,881 gallons of 8 wt % oxalic acid to Tank 6F. Following the acid addition, they visually inspected the tank and transferred 32,247 gallons of Tank 6F material to Tank 7F. SRR collected a sample of the liquid from Tank 6F and submitted it to SRNL for analysis. Mapping of the tank following the transfer indicated that 3,248 gallons of solids remained in the tank. Following the oxalic acid strikes, SRR performed Spray Washing with oxalic acid to remove waste collected on internal structures, cooling coils, tank top internals, and tank

  15. Chemical hazards analysis of resilient flooring for healthcare.

    PubMed

    Lent, Tom; Silas, Julie; Vallette, Jim

    2010-01-01

    This article addresses resilient flooring, evaluating the potential health effects of vinyl flooring and the leading alternatives-synthetic rubber, polyolefin, and linoleum-currently used in the healthcare marketplace. The study inventories chemicals incorporated as components of each of the four material types or involved in their life cycle as feedstocks, intermediary chemicals, or emissions. It then characterizes those chemicals using a chemical hazard-based framework that addresses persistence and bioaccumulation, human toxicity, and human exposures. PMID:21165873

  16. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  17. Chemical analysis and potential health risks of hookah charcoal.

    PubMed

    Elsayed, Yehya; Dalibalta, Sarah; Abu-Farha, Nedal

    2016-11-01

    Hookah (waterpipe) smoking is a very common practice that has spread globally. There is growing evidence on the hazardous consequences of smoking hookah, with studies indicating that its harmful effects are comparable to cigarette smoking if not worse. Charcoal is commonly used as a heating source for hookah smoke. Although charcoal briquettes are thought to be one of the major contributors to toxicity, their composition and impact on the smoke generated remains largely unidentified. This study aims to analyze the elemental composition of five different raw synthetic and natural charcoals by using Carbon-Hydrogen-Nitrogen (CHN) analysis, inductively coupled plasma (ICP), and scanning electron microscopy coupled with energy dispersive X-Ray spectrometry (SEM-EDS). Elemental analysis showed that the raw charcoals contain heavy metals such as zinc, iron, cadmium, vanadium, aluminum, lead, chromium, manganese and cobalt at concentrations similar, if not higher than, cigarettes. In addition, thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) was used to analyze the chemical composition of the smoke produced from burning the charcoal samples. The smoke emitted from charcoal was found to be the source of numerous compounds which could be hazardous to health. A total of seven carcinogens, 39 central nervous system depressants and 31 respiratory irritants were identified.

  18. Chemical analysis and potential health risks of hookah charcoal.

    PubMed

    Elsayed, Yehya; Dalibalta, Sarah; Abu-Farha, Nedal

    2016-11-01

    Hookah (waterpipe) smoking is a very common practice that has spread globally. There is growing evidence on the hazardous consequences of smoking hookah, with studies indicating that its harmful effects are comparable to cigarette smoking if not worse. Charcoal is commonly used as a heating source for hookah smoke. Although charcoal briquettes are thought to be one of the major contributors to toxicity, their composition and impact on the smoke generated remains largely unidentified. This study aims to analyze the elemental composition of five different raw synthetic and natural charcoals by using Carbon-Hydrogen-Nitrogen (CHN) analysis, inductively coupled plasma (ICP), and scanning electron microscopy coupled with energy dispersive X-Ray spectrometry (SEM-EDS). Elemental analysis showed that the raw charcoals contain heavy metals such as zinc, iron, cadmium, vanadium, aluminum, lead, chromium, manganese and cobalt at concentrations similar, if not higher than, cigarettes. In addition, thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS) was used to analyze the chemical composition of the smoke produced from burning the charcoal samples. The smoke emitted from charcoal was found to be the source of numerous compounds which could be hazardous to health. A total of seven carcinogens, 39 central nervous system depressants and 31 respiratory irritants were identified. PMID:27343945

  19. Flow Injection Analysis and Liquid Chromatography for Multifunctional Chemical Analysis (MCA) Systems

    ERIC Educational Resources Information Center

    Mayo, Ana V.; Loegel, Thomas N.; Bretz, Stacey Lowery; Danielson, Neil D.

    2013-01-01

    The large class sizes of first-year chemistry labs makes it challenging to provide students with hands-on access to instrumentation because the number of students typically far exceeds the number of research-grade instruments available to collect data. Multifunctional chemical analysis (MCA) systems provide a viable alternative for large-scale…

  20. Meta-Analysis of the Chemical and Non-Chemical Stressors Affecting Childhood Obesity

    EPA Science Inventory

    Worldwide, approximately 42 million children under the age of 5 years are considered overweight or obese. While much research has focused on individual behaviors impacting obesity, little research has emphasized the complex interactions of numerous chemical and non-chemical stres...

  1. ACTINIDE REMOVAL PROCESS SAMPLE ANALYSIS, CHEMICAL MODELING, AND FILTRATION EVALUATION

    SciTech Connect

    Martino, C.; Herman, D.; Pike, J.; Peters, T.

    2014-06-05

    Filtration within the Actinide Removal Process (ARP) currently limits the throughput in interim salt processing at the Savannah River Site. In this process, batches of salt solution with Monosodium Titanate (MST) sorbent are concentrated by crossflow filtration. The filtrate is subsequently processed to remove cesium in the Modular Caustic Side Solvent Extraction Unit (MCU) followed by disposal in saltstone grout. The concentrated MST slurry is washed and sent to the Defense Waste Processing Facility (DWPF) for vitrification. During recent ARP processing, there has been a degradation of filter performance manifested as the inability to maintain high filtrate flux throughout a multi-batch cycle. The objectives of this effort were to characterize the feed streams, to determine if solids (in addition to MST) are precipitating and causing the degraded performance of the filters, and to assess the particle size and rheological data to address potential filtration impacts. Equilibrium modelling with OLI Analyzer{sup TM} and OLI ESP{sup TM} was performed to determine chemical components at risk of precipitation and to simulate the ARP process. The performance of ARP filtration was evaluated to review potential causes of the observed filter behavior. Task activities for this study included extensive physical and chemical analysis of samples from the Late Wash Pump Tank (LWPT) and the Late Wash Hold Tank (LWHT) within ARP as well as samples of the tank farm feed from Tank 49H. The samples from the LWPT and LWHT were obtained from several stages of processing of Salt Batch 6D, Cycle 6, Batch 16.

  2. Simultaneous measurement in mass and mass/mass mode for accurate qualitative and quantitative screening analysis of pharmaceuticals in river water.

    PubMed

    Martínez Bueno, M J; Ulaszewska, Maria M; Gomez, M J; Hernando, M D; Fernández-Alba, A R

    2012-09-21

    A new approach for the analysis of pharmaceuticals (target and non-target) in water by LC-QTOF-MS is described in this work. The study has been designed to assess the performance of the simultaneous quantitative screening of target compounds, and the qualitative analysis of non-target analytes, in just one run. The features of accurate mass full scan mass spectrometry together with high MS/MS spectral acquisition rates - by means of information dependent acquisition (IDA) - have demonstrated their potential application in this work. Applying this analytical strategy, an identification procedure is presented based on library searching for compounds which were not included a priori in the analytical method as target compounds, thus allowing their characterization by data processing of accurate mass measurements in MS and MS/MS mode. The non-target compounds identified in river water samples were ketorolac, trazodone, fluconazole, metformin and venlafaxine. Simultaneously, this strategy allowed for the identification of other compounds which were not included in the library by screening the highest intensity peaks detected in the samples and by analysis of the full scan TOF-MS, isotope pattern and MS/MS spectra - the example of loratadine (histaminergic) is described. The group of drugs of abuse selected as target compounds for evaluation included analgesics, opioids and psychostimulants. Satisfactory results regarding sensitivity and linearity of the developed method were obtained. Limits of detection for the selected target compounds were from 0.003 to 0.01 μg/L and 0.01 to 0.5 μg/L, in MS and MS/MS mode, respectively - by direct sample injection of 100 μL.

  3. Biosensors for the analysis of microbiological and chemical contaminants in food.

    PubMed

    McGrath, T F; Elliott, C T; Fodey, T L

    2012-04-01

    Increases in food production and the ever-present threat of food contamination from microbiological and chemical sources have led the food industry and regulators to pursue rapid, inexpensive methods of analysis to safeguard the health and safety of the consumer. Although sophisticated techniques such as chromatography and spectrometry provide more accurate and conclusive results, screening tests allow a much higher throughput of samples at a lower cost and with less operator training, so larger numbers of samples can be analysed. Biosensors combine a biological recognition element (enzyme, antibody, receptor) with a transducer to produce a measurable signal proportional to the extent of interaction between the recognition element and the analyte. The different uses of the biosensing instrumentation available today are extremely varied, with food analysis as an emerging and growing application. The advantages offered by biosensors over other screening methods such as radioimmunoassay, enzyme-linked immunosorbent assay, fluorescence immunoassay and luminescence immunoassay, with respect to food analysis, include automation, improved reproducibility, speed of analysis and real-time analysis. This article will provide a brief footing in history before reviewing the latest developments in biosensor applications for analysis of food contaminants (January 2007 to December 2010), focusing on the detection of pathogens, toxins, pesticides and veterinary drug residues by biosensors, with emphasis on articles showing data in food matrices. The main areas of development common to these groups of contaminants include multiplexing, the ability to simultaneously analyse a sample for more than one contaminant and portability. Biosensors currently have an important role in food safety; further advances in the technology, reagents and sample handling will surely reinforce this position.

  4. A Framework for the Comparative Assessment of Neuronal Spike Sorting Algorithms towards More Accurate Off-Line and On-Line Microelectrode Arrays Data Analysis.

    PubMed

    Regalia, Giulia; Coelli, Stefania; Biffi, Emilia; Ferrigno, Giancarlo; Pedrocchi, Alessandra

    2016-01-01

    Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting "building blocks" into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191

  5. A Framework for the Comparative Assessment of Neuronal Spike Sorting Algorithms towards More Accurate Off-Line and On-Line Microelectrode Arrays Data Analysis

    PubMed Central

    Pedrocchi, Alessandra

    2016-01-01

    Neuronal spike sorting algorithms are designed to retrieve neuronal network activity on a single-cell level from extracellular multiunit recordings with Microelectrode Arrays (MEAs). In typical analysis of MEA data, one spike sorting algorithm is applied indiscriminately to all electrode signals. However, this approach neglects the dependency of algorithms' performances on the neuronal signals properties at each channel, which require data-centric methods. Moreover, sorting is commonly performed off-line, which is time and memory consuming and prevents researchers from having an immediate glance at ongoing experiments. The aim of this work is to provide a versatile framework to support the evaluation and comparison of different spike classification algorithms suitable for both off-line and on-line analysis. We incorporated different spike sorting “building blocks” into a Matlab-based software, including 4 feature extraction methods, 3 feature clustering methods, and 1 template matching classifier. The framework was validated by applying different algorithms on simulated and real signals from neuronal cultures coupled to MEAs. Moreover, the system has been proven effective in running on-line analysis on a standard desktop computer, after the selection of the most suitable sorting methods. This work provides a useful and versatile instrument for a supported comparison of different options for spike sorting towards more accurate off-line and on-line MEA data analysis. PMID:27239191

  6. Method of chemical analysis for oil shale wastes

    SciTech Connect

    Wallace, J.R.; Alden, L.; Bonomo, F.S.; Nichols, J.; Sexton, E.

    1984-06-01

    Several methods of chemical analysis are described for oil shale wastewaters and retort gases. These methods are designed to support the field testing of various pollution control systems. As such, emphasis has been placed on methods which are rapid and sufficiently rugged to perform well under field conditions. Ion chromatograph has been developed as a technique for the minor non-carbonate inorganic anions in retort water, including SO4, NO3, S2O3, SCN(-1), and total S. The method recommended for sulfide is a potiometric titration with Pb(II). The freezing point depression was used to determine the total solute content in retort waters, a test which can be considered analogous to the standard residue test. Three methods are described for the determination of total ammoniacal nitrogen in retort wastewaters: (1) a modified ion selective electrode technique, (2) an optical absorption technique, and (3) an ion chromatographic technique. Total sulfur in retort gas is determined by combusting the gas in a continuously flowing system, whereupon the resulting sulfur dioxide is determined by SO2 monitor. Individual sulfur species in retort gas including H2S, COS, SO2, and CH3CH2SH are determined by gas chromatography with flame photometric detection. Quality control, pH, conductivity, total inorganic carbon, and total organic carbon measurements are discussed briefly.

  7. Laser-induced destination of hazardous chemicals: A preliminary analysis

    NASA Astrophysics Data System (ADS)

    Morrison, P. F.; Wolf, K. A.

    1982-10-01

    Technical methods that might prove effective in destroying dangerous chemicals before they leave the plant environment and become subject to regulation are studied. Laser infrared multiphoton dissociation, for decomposing deleterious chemical gases is evaluated. The chlorinated ethylenes and the chlorinated ethanes are emphasized. A detailed method for decomposing chlorinated chemicals in the workplace using a relatively inexpensive CO2 laser is discussed. Results show that CO2 laser photodegradation of vinyl chloride, a chlorinated ethylene, is promising.

  8. Comprehensive chemical analysis of Schisandra chinensis by HPLC-DAD-MS combined with chemometrics.

    PubMed

    Liu, Haitao; Lai, Hongwu; Jia, Xinyue; Liu, Jiushi; Zhang, Zhao; Qi, Yaodong; Zhang, Jin; Song, Junbin; Wu, Chongming; Zhang, Bengang; Xiao, Peigen

    2013-09-15

    The fruit of Schisandra chinensis, namely "Wuweizi" in China, is a well-known herbal medicine and health food. In this paper, an accurate and reliable high performance liquid chromatography coupled with diode array detection and mass spectrometry was developed for quality evaluation of Wuweizi. Nine lignans, including schisandrol A, schisandrol B, angeloylgomisin H, gomisin G, schisantherin A, schisanhenol, schisandrin A, schisandrin B, and schisandrin C were determined simultaneously in forty-three batches of Wuweizi samples collected from different localities. Thirty-six common peaks were unequivocally identified or tentatively assigned by comparing their mass spectrometric data with reference compounds, self-established compound library and published literatures. And the thirty-six common peaks were selected as characteristic peaks to assess the similarity of chromatographic fingerprinting of these Wuweizi samples. Moreover, hierarchical clustering analysis and principal components analysis were successfully applied to demonstrate the variability of these Wuweizi samples. The results indicated the content of nine investigated lignans varied greatly among the samples, and samples collected from different localities could be discriminated. Furthermore, schisandrol A, schisandrol B, schisandrin B, and schisandrin C were found to chemical marker for evaluating the quality of Wuweizi.

  9. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-06-01

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from ~2 μM to ~1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K ( D )) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K ( D ), and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K ( D ) and the maximum chemical shift change (Δδ(max)). During a typical NMR titration, the initial protein concentration, [P (0)], is held nearly constant. For this condition, to determine the most accurate parameters for K ( D ) and Δδ(max) from nonlinear least squares analyses requires initial protein concentrations that are ~0.5 × K ( D ), and a maximum concentration for the ligand, or titrant, of ~10 × [P (0)]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K ( D ) and Δδ(max) values when [P (0)] > K ( D ). Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K ( D ) and Δδ(max)) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

  10. Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays.

    PubMed

    Lee, Chi-Ying; Harbers, Gregory M; Grainger, David W; Gamble, Lara J; Castner, David G

    2007-08-01

    Performance improvements in DNA-modified surfaces required for microarray and biosensor applications rely on improved capabilities to accurately characterize the chemistry and structure of immobilized DNA molecules on micropatterned surfaces. Recent innovations in imaging X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) now permit more detailed studies of micropatterned surfaces. We have exploited the complementary information provided by imaging XPS and imaging TOF-SIMS to detail the chemical composition, spatial distribution, and hybridization efficiency of amine-terminated single-stranded DNA (ssDNA) bound to commercial polyacrylamide-based, amine-reactive microarray slides, immobilized in both macrospot and microarray diagnostic formats. Combinations of XPS imaging and small spot analysis were used to identify micropatterned DNA spots within printed DNA arrays on slide surfaces and quantify DNA elements within individual microarray spots for determination of probe immobilization and hybridization efficiencies. This represents the first report of imaging XPS of DNA immobilization and hybridization efficiencies for arrays fabricated on commercial microarray slides. Imaging TOF-SIMS provided distinct analytical data on the lateral distribution of DNA within single array microspots before and after target hybridization. Principal component analysis (PCA) applied to TOF-SIMS imaging datasets demonstrated that the combination of these two techniques provides information not readily observable in TOF-SIMS images alone, particularly in identifying species associated with array spot nonuniformities (e.g., "halo" or "donut" effects often observed in fluorescence images). Chemically specific spot images were compared to conventional fluorescence scanned images in microarrays to provide new information on spot-to-spot DNA variations that affect current diagnostic reliability, assay variance, and sensitivity.

  11. Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays.

    PubMed

    Lee, Chi-Ying; Harbers, Gregory M; Grainger, David W; Gamble, Lara J; Castner, David G

    2007-08-01

    Performance improvements in DNA-modified surfaces required for microarray and biosensor applications rely on improved capabilities to accurately characterize the chemistry and structure of immobilized DNA molecules on micropatterned surfaces. Recent innovations in imaging X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS) now permit more detailed studies of micropatterned surfaces. We have exploited the complementary information provided by imaging XPS and imaging TOF-SIMS to detail the chemical composition, spatial distribution, and hybridization efficiency of amine-terminated single-stranded DNA (ssDNA) bound to commercial polyacrylamide-based, amine-reactive microarray slides, immobilized in both macrospot and microarray diagnostic formats. Combinations of XPS imaging and small spot analysis were used to identify micropatterned DNA spots within printed DNA arrays on slide surfaces and quantify DNA elements within individual microarray spots for determination of probe immobilization and hybridization efficiencies. This represents the first report of imaging XPS of DNA immobilization and hybridization efficiencies for arrays fabricated on commercial microarray slides. Imaging TOF-SIMS provided distinct analytical data on the lateral distribution of DNA within single array microspots before and after target hybridization. Principal component analysis (PCA) applied to TOF-SIMS imaging datasets demonstrated that the combination of these two techniques provides information not readily observable in TOF-SIMS images alone, particularly in identifying species associated with array spot nonuniformities (e.g., "halo" or "donut" effects often observed in fluorescence images). Chemically specific spot images were compared to conventional fluorescence scanned images in microarrays to provide new information on spot-to-spot DNA variations that affect current diagnostic reliability, assay variance, and sensitivity. PMID:17625851

  12. Nonradiological chemical pathway analysis and identification of chemicals of concern for environmental monitoring at the Hanford Site

    SciTech Connect

    Blanton, M.L.; Cooper, A.T.; Castleton, K.J.

    1995-11-01

    Pacific Northwest`s Surface Environmental Surveillance Project (SESP) is an ongoing effort tot design, review, and conducted monitoring on and off the Hanford site. Chemicals of concern that were selected are listed. Using modeled exposure pathways, the offsite cancer incidence and hazard quotient were calculated and a retrospective pathway analysis performed to estimate what onsite concentrations would be required in the soil for each chemical of concern and other detected chemicals that would be required to obtain an estimated offsite human-health risk of 1.0E-06 cancer incidence or 1.0 hazard quotient. This analysis indicates that current nonradiological chemical contamination occurring on the site does not pose a significant offsite human-health risk; the highest cancer incidence to the offsite maximally exposed individual was from arsenic (1.76E-10); the highest hazard quotient was chromium(VI) (1.48E-04). The most sensitive pathways of exposure were surfacewater and aquatic food consumption. Combined total offsite excess cancer incidence was 2.09E-10 and estimated hazard quotient was 2.40E-04. Of the 17 identified chemicals of concern, the SESP does not currently (routinely) monitor arsenic, benzo(a)pyrene, bis(2- ethylhexyl)phthalate (BEHP), and chrysene. Only 3 of the chemicals of concern (arsenic, BEHP, chloroform) could actually occur in onsite soil at concern high enough to cause a 1.0E-06 excess cancer incidence or a 1.0 hazard index for a given offsite exposure pathway. During the retrospective analysis, 20 other chemicals were also evaluated; only vinyl chloride and thallium could reach targeted offsite risk values.

  13. Thermodynamic analysis of alternate energy carriers, hydrogen and chemical heat pipes

    NASA Technical Reports Server (NTRS)

    Cox, K. E.; Carty, R. H.; Conger, W. L.; Soliman, M. A.; Funk, J. E.

    1976-01-01

    Hydrogen and chemical heat pipes were proposed as methods of transporting energy from a primary energy source (nuclear, solar) to the user. In the chemical heat pipe system, primary energy is transformed into the energy of a reversible chemical reaction; the chemical species are then transmitted or stored until the energy is required. Analysis of thermochemical hydrogen schemes and chemical heat pipe systems on a second law efficiency or available work basis show that hydrogen is superior especially if the end use of the chemical heat pipe is electrical power.

  14. An Accurate, Flexible and Small Optical Fiber Sensor: A Novel Technological Breakthrough for Real-Time Analysis of Dynamic Blood Flow Data In Vivo

    PubMed Central

    Yuan, Qiao-ying; Zhang, Ling; Xiao, Dan; Zhao, Kun; Lin, Chun; Si, Liang-yi

    2014-01-01

    Because of the limitations of existing methods and techniques for directly obtaining real-time blood data, no accurate microflow in vivo real-time analysis method exists. To establish a novel technical platform for real-time in vivo detection and to analyze average blood pressure and other blood flow parameters, a small, accurate, flexible, and nontoxic Fabry-Perot fiber sensor was designed. The carotid sheath was implanted through intubation of the rabbit carotid artery (n = 8), and the blood pressure and other detection data were determined directly through the veins. The fiber detection results were compared with test results obtained using color Doppler ultrasound and a physiological pressure sensor recorder. Pairwise comparisons among the blood pressure results obtained using the three methods indicated that real-time blood pressure information obtained through the fiber sensor technique exhibited better correlation than the data obtained with the other techniques. The highest correlation (correlation coefficient of 0.86) was obtained between the fiber sensor and pressure sensor. The blood pressure values were positively related to the total cholesterol level, low-density lipoprotein level, number of red blood cells, and hemoglobin level, with correlation coefficients of 0.033, 0.129, 0.358, and 0.373, respectively. The blood pressure values had no obvious relationship with the number of white blood cells and high-density lipoprotein and had a negative relationship with triglyceride levels, with a correlation coefficient of –0.031. The average ambulatory blood pressure measured by the fiber sensor exhibited a negative correlation with the quantity of blood platelets (correlation coefficient of −0.839, P<0.05). The novel fiber sensor can thus obtain in vivo blood pressure data accurately, stably, and in real time; the sensor can also determine the content and status of the blood flow to some extent. Therefore, the fiber sensor can obtain partially real

  15. An accurate, flexible and small optical fiber sensor: a novel technological breakthrough for real-time analysis of dynamic blood flow data in vivo.

    PubMed

    Yuan, Qiao-ying; Zhang, Ling; Xiao, Dan; Zhao, Kun; Lin, Chun; Si, Liang-yi

    2014-01-01

    Because of the limitations of existing methods and techniques for directly obtaining real-time blood data, no accurate microflow in vivo real-time analysis method exists. To establish a novel technical platform for real-time in vivo detection and to analyze average blood pressure and other blood flow parameters, a small, accurate, flexible, and nontoxic Fabry-Perot fiber sensor was designed. The carotid sheath was implanted through intubation of the rabbit carotid artery (n = 8), and the blood pressure and other detection data were determined directly through the veins. The fiber detection results were compared with test results obtained using color Doppler ultrasound and a physiological pressure sensor recorder. Pairwise comparisons among the blood pressure results obtained using the three methods indicated that real-time blood pressure information obtained through the fiber sensor technique exhibited better correlation than the data obtained with the other techniques. The highest correlation (correlation coefficient of 0.86) was obtained between the fiber sensor and pressure sensor. The blood pressure values were positively related to the total cholesterol level, low-density lipoprotein level, number of red blood cells, and hemoglobin level, with correlation coefficients of 0.033, 0.129, 0.358, and 0.373, respectively. The blood pressure values had no obvious relationship with the number of white blood cells and high-density lipoprotein and had a negative relationship with triglyceride levels, with a correlation coefficient of -0.031. The average ambulatory blood pressure measured by the fiber sensor exhibited a negative correlation with the quantity of blood platelets (correlation coefficient of -0.839, P<0.05). The novel fiber sensor can thus obtain in vivo blood pressure data accurately, stably, and in real time; the sensor can also determine the content and status of the blood flow to some extent. Therefore, the fiber sensor can obtain partially real

  16. Does objective measurement of tracheal tube cuff pressures minimise adverse effects and maintain accurate cuff pressures? A systematic review and meta-analysis.

    PubMed

    Ca, Hockey; Aaj, van Zundert; Jd, Paratz

    2016-09-01

    Correct inflation pressures of the tracheal cuff are recommended to ensure adequate ventilation and prevent aspiration and adverse events. However there are conflicting views on which measurement to employ. The aim of this review was to examine whether adjustment of cuff pressure guided by objective measurement, compared with subjective measurement or observation of the pressure value alone, was able to prevent patient-related adverse effects and maintain accurate cuff pressures. A search of PubMed, Web of Science, Embase, CINAHL and ScienceDirect was conducted using keywords 'cuff pressure' and 'measure*' and related synonyms. Included studies were randomised or pseudo-randomised controlled trials investigating mechanically ventilated patients both in the intensive care unit and during surgery. Outcomes included adverse effects and the comparison of pressure measurements. Pooled analyses were performed to calculate risk ratios, effect sizes and 95% confidence intervals. Meta-analysis found preliminary evidence that adjustment of cuff pressure guided by objective measurement as compared with subjective measurement or observation of the pressure value alone, has benefit in preventing adverse effects. These included cough at two hours (odds ratio [OR] 0.42, confidence interval [CI] 0.23 to 0.79, P=0.007), hoarseness at 24 hours (OR 0.49, CI 0.31 to 0.76, P <0.002), sore throat (OR 0.73, CI 0.54 to 0.97, P <0.03), lesions of the trachea and incidences of silent aspiration (P=0.001), as well as maintaining accurate cuff pressures (Hedges' g 1.61, CI 2.69 to 0.53, P=0.003). Subjective measurement to guide adjustment or observation of the pressure value alone may lead to patient-related adverse effects and inaccuracies. It is recommended that an objective form of measurement be used. PMID:27608338

  17. Does objective measurement of tracheal tube cuff pressures minimise adverse effects and maintain accurate cuff pressures? A systematic review and meta-analysis.

    PubMed

    Hockey, C A; van Zundert, A A J; Paratz, J D

    2016-09-01

    Correct inflation pressures of the tracheal cuff are recommended to ensure adequate ventilation and prevent aspiration and adverse events. However there are conflicting views on which measurement to employ. The aim of this review was to examine whether adjustment of cuff pressure guided by objective measurement, compared with subjective measurement or observation of the pressure value alone, was able to prevent patient-related adverse effects and maintain accurate cuff pressures. A search of PubMed, Web of Science, Embase, CINAHL and ScienceDirect was conducted using keywords 'cuff pressure' and 'measure*' and related synonyms. Included studies were randomised or pseudo-randomised controlled trials investigating mechanically ventilated patients both in the intensive care unit and during surgery. Outcomes included adverse effects and the comparison of pressure measurements. Pooled analyses were performed to calculate risk ratios, effect sizes and 95% confidence intervals. Meta-analysis found preliminary evidence that adjustment of cuff pressure guided by objective measurement as compared with subjective measurement or observation of the pressure value alone, has benefit in preventing adverse effects. These included cough at two hours (odds ratio [OR] 0.42, confidence interval [CI] 0.23 to 0.79, P=0.007), hoarseness at 24 hours (OR 0.49, CI 0.31 to 0.76, P <0.002), sore throat (OR 0.73, CI 0.54 to 0.97, P <0.03), lesions of the trachea and incidences of silent aspiration (P=0.001), as well as maintaining accurate cuff pressures (Hedges' g 1.61, CI 2.69 to 0.53, P=0.003). Subjective measurement to guide adjustment or observation of the pressure value alone may lead to patient-related adverse effects and inaccuracies. It is recommended that an objective form of measurement be used.

  18. New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets.

    PubMed

    Zhu, Zhikai; Su, Xiaomeng; Go, Eden P; Desaire, Heather

    2014-09-16

    Glycoproteins are biologically significant large molecules that participate in numerous cellular activities. In order to obtain site-specific protein glycosylation information, intact glycopeptides, with the glycan attached to the peptide sequence, are characterized by tandem mass spectrometry (MS/MS) methods such as collision-induced dissociation (CID) and electron transfer dissociation (ETD). While several emerging automated tools are developed, no consensus is present in the field about the best way to determine the reliability of the tools and/or provide the false discovery rate (FDR). A common approach to calculate FDRs for glycopeptide analysis, adopted from the target-decoy strategy in proteomics, employs a decoy database that is created based on the target protein sequence database. Nonetheless, this approach is not optimal in measuring the confidence of N-linked glycopeptide matches, because the glycopeptide data set is considerably smaller compared to that of peptides, and the requirement of a consensus sequence for N-glycosylation further limits the number of possible decoy glycopeptides tested in a database search. To address the need to accurately determine FDRs for automated glycopeptide assignments, we developed GlycoPep Evaluator (GPE), a tool that helps to measure FDRs in identifying glycopeptides without using a decoy database. GPE generates decoy glycopeptides de novo for every target glycopeptide, in a 1:20 target-to-decoy ratio. The decoys, along with target glycopeptides, are scored against the ETD data, from which FDRs can be calculated accurately based on the number of decoy matches and the ratio of the number of targets to decoys, for small data sets. GPE is freely accessible for download and can work with any search engine that interprets ETD data of N-linked glycopeptides. The software is provided at https://desairegroup.ku.edu/research.

  19. Spectroscopic and quantum chemical analysis of Isonicotinic acid methyl ester

    NASA Astrophysics Data System (ADS)

    Shoba, D.; Periandy, S.; Govindarajan, M.; Gayathri, P.

    2015-02-01

    In this present study, an organic compound Isonicotinic acid methyl ester (INAME) was structurally characterized by FTIR, FT-Raman, and NMR and UV spectroscopy. The optimized geometrical parameters and energies of all different and possible conformers of INAME are obtained from Density Functional Theory (DFT) by B3LYP/6-311++G(d,p) method. There are three conformers (SI, SII-1, and SII-2) for this molecule (ground state). The most stable conformer of INAME is SI conformer. The molecular geometry and vibrational frequencies of INAME in the ground state have been calculated by using HF and density functional method (B3LYP) 6-311++G (d,p) basis set. Detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The computed vibrational frequencies were compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. A study on the electronic properties, such as HOMO and LUMO energies were performed by time independent DFT approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and first hyper polarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results show that the INAME molecule may have microscopic nonlinear optical (NLO) behavior with non zero values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by gauge independent atomic orbital (GIAO) method.

  20. XPS chemical analysis of tholins: the oxygen contamination

    NASA Astrophysics Data System (ADS)

    Carrasco, N.; Jomard, F.; Vigneron, J.; Cernogora, G.

    2013-12-01

    In Titan's atmosphere, solid organic aerosols are initiated in the upper atmosphere by the photo-dissociation and photo-ionization of N2 and CH4. In order to simulate this complex chemistry several experimental setups have been built, among them plasma experiments. The aerosol analogues produced in such plasma discharges contain oxygen, as a few percents of the elemental composition, despite the absence of oxygen source in the reactive medium [1]. The present study aims at studying the origin of such systematic oxygen incorporation in tholins. A low pressure (0.9mbar) RF CCP discharge is used described in [2]. Gas mixtures of N2 and CH4 (from 1 to 10% of CH4) are injected continuously. The plasma discharge leads to the production of analogues of Titan's atmospheric aerosols: both as grains in the volume [1] and as thin films on the surface of the reactor [3]. SiO2 substrates of 1cm diameter and 1mm thickness are placed on the grounded electrode of the discharge. Organic films are deposited during 2 hours in order to have films thickness less than 1μm. After the two hours, samples are recovered at ambient air for ex-situ analysis. Two complementary analyses are performed to analyse the thin film chemical composition: XPS and SIMS, in order to probe both the surface and depth profile. References [1] Sciamma-O'brien E., Carrasco N., Szopa C., Buch A., Cernogora G. Icarus 209, 2 (2010) 704-714 [2] Alcouffe G., Cavarroc M., Cernogora G., Ouni F., Jolly A., Boufendi L., Szopa C. Plasma Sources Science and Technology 19, 1 (2010) 015008 (11pp) [3] Mahjoub A., Carrasco N., Dahoo P.-R., Gautier T., Szopa C., Cernogora G. Icarus 221, 2 (2012) 670-677.

  1. Rapid and Accurate Analysis of an X-Ray Fluorescence Microscopy Data Set through Gaussian Mixture-Based Soft Clustering Methods

    PubMed Central

    Ward, Jesse; Marvin, Rebecca; O'Halloran, Thomas; Jacobsen, Chris; Vogt, Stefan

    2013-01-01

    X-ray fluorescence (XRF) microscopy is an important tool for studying trace metals in biology, enabling simultaneous detection of multiple elements of interest and allowing quantification of metals in organelles without the need for subcellular fractionation. Currently, analysis of XRF images is often done using manually defined regions of interest (ROIs). However, since advances in synchrotron instrumentation have enabled the collection of very large data sets encompassing hundreds of cells, manual approaches are becoming increasingly impractical. We describe here the use of soft clustering to identify cell ROIs based on elemental contents, using data collected over a sample of the malaria parasite Plasmodium falciparum as a test case. Soft clustering was able to successfully classify regions in infected erythrocytes as “parasite,”“food vacuole,”“host,” or “background.” In contrast, hard clustering using the k-means algorithm was found to have difficulty in distinguishing cells from background. While initial tests showed convergence on two or three distinct solutions in 60% of the cells studied, subsequent modifications to the clustering routine improved results to yield 100% consistency in image segmentation. Data extracted using soft cluster ROIs were found to be as accurate as data extracted using manually defined ROIs, and analysis time was considerably improved. PMID:23924688

  2. Meta-Analysis of the Chemical and Non-Chemical Stressors Affecting Childhood Obesity?

    EPA Science Inventory

    Background: Worldwide, approximately 42 million children under the age of 5 years are considered overweight or obese. While much research has focused on individual behaviors impacting obesity, little research has emphasized the complex interactions of numerous chemical and non-ch...

  3. High-throughput image analysis of tumor spheroids: a user-friendly software application to measure the size of spheroids automatically and accurately.

    PubMed

    Chen, Wenjin; Wong, Chung; Vosburgh, Evan; Levine, Arnold J; Foran, David J; Xu, Eugenia Y

    2014-07-08

    The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application - SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min on a minimally configured laptop, or around 1 min on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary "Manual Initialize" and "Hand Draw" tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model

  4. Subcellular chemical and morphological analysis by stimulated Raman scattering microscopy and image analysis techniques.

    PubMed

    D'Arco, Annalisa; Brancati, Nadia; Ferrara, Maria Antonietta; Indolfi, Maurizio; Frucci, Maria; Sirleto, Luigi

    2016-05-01

    The visualization of heterogeneous morphology, segmentation and quantification of image features is a crucial point for nonlinear optics microscopy applications, spanning from imaging of living cells or tissues to biomedical diagnostic. In this paper, a methodology combining stimulated Raman scattering microscopy and image analysis technique is presented. The basic idea is to join the potential of vibrational contrast of stimulated Raman scattering and the strength of imaging analysis technique in order to delineate subcellular morphology with chemical specificity. Validation tests on label free imaging of polystyrene-beads and of adipocyte cells are reported and discussed. PMID:27231626

  5. Subcellular chemical and morphological analysis by stimulated Raman scattering microscopy and image analysis techniques

    PubMed Central

    D’Arco, Annalisa; Brancati, Nadia; Ferrara, Maria Antonietta; Indolfi, Maurizio; Frucci, Maria; Sirleto, Luigi

    2016-01-01

    The visualization of heterogeneous morphology, segmentation and quantification of image features is a crucial point for nonlinear optics microscopy applications, spanning from imaging of living cells or tissues to biomedical diagnostic. In this paper, a methodology combining stimulated Raman scattering microscopy and image analysis technique is presented. The basic idea is to join the potential of vibrational contrast of stimulated Raman scattering and the strength of imaging analysis technique in order to delineate subcellular morphology with chemical specificity. Validation tests on label free imaging of polystyrene-beads and of adipocyte cells are reported and discussed. PMID:27231626

  6. Subcellular chemical and morphological analysis by stimulated Raman scattering microscopy and image analysis techniques.

    PubMed

    D'Arco, Annalisa; Brancati, Nadia; Ferrara, Maria Antonietta; Indolfi, Maurizio; Frucci, Maria; Sirleto, Luigi

    2016-05-01

    The visualization of heterogeneous morphology, segmentation and quantification of image features is a crucial point for nonlinear optics microscopy applications, spanning from imaging of living cells or tissues to biomedical diagnostic. In this paper, a methodology combining stimulated Raman scattering microscopy and image analysis technique is presented. The basic idea is to join the potential of vibrational contrast of stimulated Raman scattering and the strength of imaging analysis technique in order to delineate subcellular morphology with chemical specificity. Validation tests on label free imaging of polystyrene-beads and of adipocyte cells are reported and discussed.

  7. LSENS, a general chemical kinetics and sensitivity analysis code for homogeneous gas-phase reactions. 2: Code description and usage

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Bittker, David A.

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 2 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 2 describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part 1 (NASA RP-1328) derives the governing equations describes the numerical solution procedures for the types of problems that can be solved by lSENS. Part 3 (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

  8. SIMULATION MODELS FOR ENVIRONMENTAL MULTIMEDIA ANALYSIS OF TOXIC CHEMICALS

    EPA Science Inventory

    Multimedia understanding of pollutant behavior in the environment is of particular concern for chemicals that are toxic and are subject to accumulation in the environmental media (air, soil, water, vegetation) where biota and human exposure is significant. Multimedia simulation ...

  9. Disclosure of hydraulic fracturing fluid chemical additives: analysis of regulations.

    PubMed

    Maule, Alexis L; Makey, Colleen M; Benson, Eugene B; Burrows, Isaac J; Scammell, Madeleine K

    2013-01-01

    Hydraulic fracturing is used to extract natural gas from shale formations. The process involves injecting into the ground fracturing fluids that contain thousands of gallons of chemical additives. Companies are not mandated by federal regulations to disclose the identities or quantities of chemicals used during hydraulic fracturing operations on private or public lands. States have begun to regulate hydraulic fracturing fluids by mandating chemical disclosure. These laws have shortcomings including nondisclosure of proprietary or "trade secret" mixtures, insufficient penalties for reporting inaccurate or incomplete information, and timelines that allow for after-the-fact reporting. These limitations leave lawmakers, regulators, public safety officers, and the public uninformed and ill-prepared to anticipate and respond to possible environmental and human health hazards associated with hydraulic fracturing fluids. We explore hydraulic fracturing exemptions from federal regulations, as well as current and future efforts to mandate chemical disclosure at the federal and state level.

  10. Disclosure of hydraulic fracturing fluid chemical additives: analysis of regulations.

    PubMed

    Maule, Alexis L; Makey, Colleen M; Benson, Eugene B; Burrows, Isaac J; Scammell, Madeleine K

    2013-01-01

    Hydraulic fracturing is used to extract natural gas from shale formations. The process involves injecting into the ground fracturing fluids that contain thousands of gallons of chemical additives. Companies are not mandated by federal regulations to disclose the identities or quantities of chemicals used during hydraulic fracturing operations on private or public lands. States have begun to regulate hydraulic fracturing fluids by mandating chemical disclosure. These laws have shortcomings including nondisclosure of proprietary or "trade secret" mixtures, insufficient penalties for reporting inaccurate or incomplete information, and timelines that allow for after-the-fact reporting. These limitations leave lawmakers, regulators, public safety officers, and the public uninformed and ill-prepared to anticipate and respond to possible environmental and human health hazards associated with hydraulic fracturing fluids. We explore hydraulic fracturing exemptions from federal regulations, as well as current and future efforts to mandate chemical disclosure at the federal and state level. PMID:23552653

  11. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

    PubMed

    Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J; Hasenauer, Jan

    2016-01-01

    Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911

  12. CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

    PubMed Central

    Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan

    2016-01-01

    Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911

  13. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

    PubMed

    Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J; Hasenauer, Jan

    2016-01-01

    Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/.

  14. Quantitative analysis of routine chemical constituents in tobacco by near-infrared spectroscopy and support vector machine

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Cong, Qian; Xie, Yunfei; Yang, Jingxiu; Zhao, Bing

    2008-12-01

    It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with γ = 1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications.

  15. Quantitative analysis of routine chemical constituents in tobacco by near-infrared spectroscopy and support vector machine.

    PubMed

    Zhang, Yong; Cong, Qian; Xie, Yunfei; JingxiuYang; Zhao, Bing

    2008-12-15

    It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with gamma=1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications.

  16. Quantitative Statistical Analysis of Atomic Scale Structural and Chemical Variations in Complex Oxides Interfaces

    NASA Astrophysics Data System (ADS)

    Yang, Hao

    Grain boundaries (GBs) are known to have far-reaching effects on the electrical and mechanical properties of materials. Understanding the atomic scale mechanisms behind these effects requires an accurate determination of the interplay between GB structure and composition. Based on the analysis of a range of grain boundaries using aberration corrected scanning transmission electron microscopy (STEM), a general structural units model has been derived for the structure of grain boundaries in various dense packing cubic materials including FCC metals, perovskites and fluorites. The similarities in the observed grain boundary structures of these materials originate from related space (and point) group symmetries of the parent structures. The presence of structural variations away from the general structural units model may be caused by frustrations of certain symmetry operations that result from the incorporation of point defects (vacancies and impurities). A clear understanding of the similarity and variation in grain boundary atomic structures will not only provide a means to infer the structure-property relationships in broad classes of materials, but also enables us eventually to effectively manipulate the GB structures to achieve better materials properties. To understand these chemical induced variations, and further quantify exactly how atomic scale variations at the boundary plane extend to the practical mesoscale operating length of the system, statistical analysis has been applied to the aberration corrected STEM Z-contrast images acquired from a series of undoped and doped SrTiO3 GBs. In order to understand the effects of oxygen vacancies incorporation, in-situ characterization of GB atomic structures were performed using the Environmental TEM under the reduced gas and heating environment. This analysis of GB similarity and variation provides insights into the structure-composition relationship in GBs to understand the influence of nonstoichiometry and dopant

  17. Improved Devices for Collecting Sweat for Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Feedback, Daniel L.; Clarke, Mark S. F.

    2011-01-01

    Improved devices have been proposed for collecting sweat for biochemical analysis - especially for determination of the concentration of Ca2+ ions in sweat as a measure of loss of Ca from bones. Unlike commercially available sweat-collection patches used previously in monitoring osteoporosis and in qualitative screening for some drugs, the proposed devices would not allow evaporation of the volatile chemical components (mostly water) of sweat. Moreover, the proposed devices would be designed to enable determination of the volumes of collected sweat. From these volumes and the quantities of Ca(2+) and/or other analytes as determined by other means summarized below, one could determine the concentrations of the analytes in sweat. A device according to the proposal would be flexible and would be worn like a commercial sweat-collection patch. It would be made of molded polydimethylsiloxane (silicone rubber) or other suitable material having properties that, for the purpose of analyzing sweat, are similar to those of glass. The die for molding the silicone rubber would be fabricated by a combination of lithography and electroplating. The die would reproducibly form, in the silicone rubber, a precisely defined number of capillary channels per unit area, each channel having a precisely defined volume. Optionally, electrodes for measuring the Ca(2+) content of the sweat could be incorporated into the device. The volume of sweat collected in the capillary channels of the device would be determined from (1) the amount of light or radio waves of a given wavelength absorbed by the device and (2) the known geometry of the array of capillary channels. Then, in one of two options, centrifugation would be performed to move the sweat from the capillary tubes to the region containing the electrodes, which would be used to measure the Ca(2+) content by a standard technique. In the other option, centrifugation would be performed to remove the sweat from the device to make the sweat

  18. Improved Devices for Collecting Sweat for Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Feeback, Daniel L.; Clarke, Mark S. F.

    2011-01-01

    Improved devices have been proposed for collecting sweat for biochemical analysis especially for determination of the concentration of Ca2+ ions in sweat as a measure of loss of Ca from bones. Unlike commercially available sweat-collection patches used previously in monitoring osteoporosis and in qualitative screening for some drugs, the proposed devices would not allow evaporation of the volatile chemical components (mostly water) of sweat. Moreover, the proposed devices would be designed to enable determination of the volumes of collected sweat. From these volumes and the quantities of Ca2+ and/or other analytes as determined by other means summarized below, one could determine the concentrations of the analytes in sweat. A device according to the proposal would be flexible and would be worn like a commercial sweat-collection patch. It would be made of molded polydimethylsiloxane (silicone rubber) or other suitable material having properties that, for the purpose of analyzing sweat, are similar to those of glass. The die for molding the silicone rubber would be fabricated by a combination of lithography and electroplating. The die would reproducibly form, in the silicone rubber, a precisely defined number of capillary channels per unit area, each channel having a precisely defined volume. Optionally, electrodes for measuring the Ca2+ content of the sweat could be incorporated into the device. The volume of sweat collected in the capillary channels of the device would be determined from (1) the amount of light or radio waves of a given wavelength absorbed by the device and (2) the known geometry of the array of capillary channels. Then, in one of two options, centrifugation would be performed to move the sweat from the capillary tubes to the region containing the electrodes, which would be used to measure the Ca2+ content by a standard technique. In the other option, centrifugation would be performed to remove the sweat from the device to make the sweat available

  19. Evaluating Chemical Persistence in a Multimedia Environment: ACART Analysis

    SciTech Connect

    Bennett, D.H.; McKone, T.E.; Kastenberg, W.E.

    1999-02-01

    For the thousands of chemicals continuously released into the environment, it is desirable to make prospective assessments of those likely to be persistent. Persistent chemicals are difficult to remove if adverse health or ecological effects are later discovered. A tiered approach using a classification scheme and a multimedia model for determining persistence is presented. Using specific criteria for persistence, a classification tree is developed to classify a chemical as ''persistent'' or ''non-persistent'' based on the chemical properties. In this approach, the classification is derived from the results of a standardized unit world multimedia model. Thus, the classifications are more robust for multimedia pollutants than classifications using a single medium half-life. The method can be readily implemented and provides insight without requiring extensive and often unavailable data. This method can be used to classify chemicals when only a few properties are known and be used to direct further data collection. Case studies are presented to demonstrate the advantages of the approach.

  20. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  1. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  2. International Research Project on the Effects of Chemical Ageing of Polymers on Performance Properties: Chemical and Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bulluck, J. W.; Rushing, R. A.

    1996-01-01

    Work during the past six months has included significant research in several areas aimed at further clarification of the aging and chemical failure mechanism of thermoplastics (PVDF or Tefzel) pipes. Among the areas investigated were the crystallinity changes associated with both the Coflon and Tefzel after various simulated environmental exposures using X-ray diffraction analysis. We have found that significant changes in polymer crystallinity levels occur as a function of the exposures. These crystallinity changes may have important consequences on the fracture, fatigue, tensile, and chemical resistance of the materials. We have also noted small changes in the molecular weight distribution. Again these changes may result in variations in the mechanical and chemical properties in the material. We conducted numerous analytical studies with methods including X-ray Diffraction, Gel Permeation Chromatography, Fourier Transform Infrared Spectroscopy, Ultra- Violet Scanning Analysis, GC/Mass Spectrometry, Differential Scanning Calorimetry and Thermomechanical Analysis. In the ultra-violet analysis we noted the presence of an absorption band indicative of triene formation. We investigated a number of aged samples of both Tefzel and Coflon that were forwarded from MERL. We also cast films at SWT and subjected these films to a refluxing methanol 1% ethylene diamine solution. An updated literature search was conducted using Dialog and DROLLS to identify any new papers that may have been published in the open literature since the start of this project. The updated literature search and abstracts are contained in the Appendix section of this report.

  3. Accurate crystal-structure refinement of Ca3Ga2Ge4O14 at 295 and 100 K and analysis of the disorder in the atomic positions

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.; Mill', B. V.

    2013-07-01

    The accurate X-ray diffraction study of a Ca3Ga2Ge4O14 crystal (sp. gr. P321, Z = 1) has been performed using repeated X-ray diffraction data sets collected on a diffractometer equipped with a CCD area detector at 295 and 100 K. The asymmetric disorder in the atomic positions in Ca3Ga2Ge4O14 is described in two alternative ways: with the use of anharmonic atomic displacements (at 295 K R/wR = 0.68/0.60%, 3754 reflections; at 100 K R/wR = 0.90/0.70%, 3632 reflections) and using a split model (SM) (at 295 K R/wR = 0.74/0.67%; at 100 K R/wR = 0.95/0.74%). An analysis of the probability density function that defines the probability of finding an atom at a particular point in space shows that, at 295 K, five of the seven independent atoms in the unit cell are asymmetrically disordered in the vicinity of their sites, whereas only three atoms are disordered at 100 K. At both temperatures the largest disorder is observed at the 3 f site on a twofold axis, which is a prerequisite for the formation of helicoidal chains of atoms along the c axis of the crystal and can serve as a structural basis for multiferroic properties of this family of crystals with magnetic ions.

  4. CYP450 phenotyping and metabolite identification of quinine by accurate mass UPLC-MS analysis: a possible metabolic link to blackwater fever

    PubMed Central

    2013-01-01

    Background The naturally occurring alkaloid drug, quinine is commonly used for the treatment of severe malaria. Despite centuries of use, its metabolism is still not fully understood, and may play a role in the haemolytic disorders associated with the drug. Methods Incubations of quinine with CYPs 1A2, 2C9, 2C19, 2D6, and 3A4 were conducted, and the metabolites were characterized by accurate mass UPLC-MSE analysis. Reactive oxygen species generation was also measured in human erythrocytes incubated in the presence of quinine with and without microsomes. Results The metabolites 3-hydroxyquinine, 2’-oxoquininone, and O-desmethylquinine were observed after incubation with CYPs 3A4 (3-hydroxyquinine and 2’-oxoquininone) and 2D6 (O-desmethylquinine). In addition, multiple hydroxylations were observed both on the quinoline core and the quinuclidine ring system. Of the five primary abundance CYPs tested, 3A4, 2D6, 2C9, and 2C19 all demonstrated activity toward quinine, while 1A2 did not. Further, quinine produced robust dose-dependent oxidative stress in human erythrocytes in the presence of microsomes. Conclusions Taken in context, these data suggest a CYP-mediated link between quinine metabolism and the poorly understood haemolytic condition known as blackwater fever, often associated with quinine ingestion. PMID:23800033

  5. Deep vein thrombosis is accurately predicted by comprehensive analysis of the levels of microRNA-96 and plasma D-dimer

    PubMed Central

    Xie, Xuesheng; Liu, Changpeng; Lin, Wei; Zhan, Baoming; Dong, Changjun; Song, Zhen; Wang, Shilei; Qi, Yingguo; Wang, Jiali; Gu, Zengquan

    2016-01-01

    The aim of the present study was to investigate the association between platelet microRNA-96 (miR-96) expression levels and the occurrence of deep vein thrombosis (DVT) in orthopedic patients. A total of consecutive 69 orthopedic patients with DVT and 30 healthy individuals were enrolled. Ultrasonic color Doppler imaging was performed on lower limb veins after orthopedic surgery to determine the occurrence of DVT. An enzyme-linked fluorescent assay was performed to detect the levels of D-dimer in plasma. A quantitative polymerase chain reaction assay was performed to determine the expression levels of miR-96. Expression levels of platelet miR-96 were significantly increased in orthopedic patients after orthopedic surgery. miR-96 expression levels in orthopedic patients with DVT at days 1, 3 and 7 after orthopedic surgery were significantly increased when compared with those in the control group. The increased miR-96 expression levels were correlated with plasma D-dimer levels in orthopedic patients with DVT. However, for the orthopedic patients in the non-DVT group following surgery, miR-96 expression levels were correlated with plasma D-dimer levels. In summary, the present results suggest that the expression levels of miR-96 may be associated with the occurrence of DVT. The occurrence of DVT may be accurately predicted by comprehensive analysis of the levels of miR-96 and plasma D-dimer. PMID:27588107

  6. Analysis of forward and inverse problems in chemical dynamics and spectroscopy

    SciTech Connect

    Rabitz, H.

    1993-12-01

    The overall scope of this research concerns the development and application of forward and inverse analysis tools for problems in chemical dynamics and chemical kinetics. The chemical dynamics work is specifically associated with relating features in potential surfaces and resultant dynamical behavior. The analogous inverse research aims to provide stable algorithms for extracting potential surfaces from laboratory data. In the case of chemical kinetics, the focus is on the development of systematic means to reduce the complexity of chemical kinetic models. Recent progress in these directions is summarized below.

  7. Accurate Analysis and Characterization of Silicon Field Effect Transistor-Based Terahertz Wave Detector with Quasi-Plasma Two-Dimensional Electron Gas.

    PubMed

    Kim, Kwan Sung; Ryu, Min Woo; Lee, Jeong Seop; Kim, Kyung Rok

    2016-05-01

    We report the nonresonant plasmonic terahertz (THz) wave detector based on the silicon (Si) field effect transistor (FET) with a technology computer-aided design (TCAD) platform. The plasma wave behavior has been modeled by a quasi-plasma electron box as a two-dimensional electron gas (2DEG) in the channel of the FET. The incoming alternating current (AC) signal as the THz wave radiation can induce the direct-current (DC) voltage difference between the source and drain, which is called the photoresponse. For accurate analysis of the modulation and propagation of the channel electron density as the plasma wave, we have characterized the quasi-plasma 2DEG model with two key parameters, such as quasi-plasma 2DEG length (I(QP)) and density (N(QP)). By using our normalization method, I(QP) and N(QP) is defined exactly as extracting the average point of the electron density. We also investigate the performance enhancement of the plasmonic terahertz wave detector based on Si FET by scaling down the gate oxide thickness (t(ox)), which is a significant parameter of FET-based plasmonic terahertz detector for the channel electron density modulation. According to scaling down t(ox), the responsivity (R(v)) and noise equivalent power (NEP), which are the important performance metrics of the THz wave detector, have been enhanced. The proposed methodologies will provide the advanced physical analysis and structural design platform for developing the plasmonic terahertz detectors operating in nonresonant regime. PMID:27483817

  8. What's the Point of a Raster ? Advantages of 3D Point Cloud Processing over Raster Based Methods for Accurate Geomorphic Analysis of High Resolution Topography.

    NASA Astrophysics Data System (ADS)

    Lague, D.

    2014-12-01

    High Resolution Topographic (HRT) datasets are predominantly stored and analyzed as 2D raster grids of elevations (i.e., Digital Elevation Models). Raster grid processing is common in GIS software and benefits from a large library of fast algorithms dedicated to geometrical analysis, drainage network computation and topographic change measurement. Yet, all instruments or methods currently generating HRT datasets (e.g., ALS, TLS, SFM, stereo satellite imagery) output natively 3D unstructured point clouds that are (i) non-regularly sampled, (ii) incomplete (e.g., submerged parts of river channels are rarely measured), and (iii) include 3D elements (e.g., vegetation, vertical features such as river banks or cliffs) that cannot be accurately described in a DEM. Interpolating the raw point cloud onto a 2D grid generally results in a loss of position accuracy, spatial resolution and in more or less controlled interpolation. Here I demonstrate how studying earth surface topography and processes directly on native 3D point cloud datasets offers several advantages over raster based methods: point cloud methods preserve the accuracy of the original data, can better handle the evaluation of uncertainty associated to topographic change measurements and are more suitable to study vegetation characteristics and steep features of the landscape. In this presentation, I will illustrate and compare Point Cloud based and Raster based workflows with various examples involving ALS, TLS and SFM for the analysis of bank erosion processes in bedrock and alluvial rivers, rockfall statistics (including rockfall volume estimate directly from point clouds) and the interaction of vegetation/hydraulics and sedimentation in salt marshes. These workflows use 2 recently published algorithms for point cloud classification (CANUPO) and point cloud comparison (M3C2) now implemented in the open source software CloudCompare.

  9. Photoacoustic physio-chemical analysis and its implementation in deep tissue with a catheter setup

    NASA Astrophysics Data System (ADS)

    Xu, Guan; Meng, Zhou-xian; Lin, Jian-die D.; Cheng, Qian; Wang, Xueding

    2015-03-01

    Photoacoustic (PA) measurements encode the information associated with both physical microstructures and chemical contents in biological tissues. A two-dimensional physio-chemical spectrogram (PCS) can be formulated by combining the power spectra of PA signals acquired at a series of optical wavelengths. The analysis of PCS, or namely PA physio-chemical analysis (PAPCA), enables the quantification of the relative concentrations and the spatial distributions of a variety of chemical components in the tissue. This study validated the feasibility of PAPCA in characterizing liver conditions during the progression of non-alcoholic fatty liver disease. A catheter based setup facilitating measurement in deep tissues was also tested.

  10. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages. PMID:8788799

  11. Portfolio Assessment on Chemical Reactor Analysis and Process Design Courses

    ERIC Educational Resources Information Center

    Alha, Katariina

    2004-01-01

    Assessment determines what students regard as important: if a teacher wants to change students' learning, he/she should change the methods of assessment. This article describes the use of portfolio assessment on five courses dealing with chemical reactor and process design during the years 1999-2001. Although the use of portfolio was a new…

  12. ASTP chemical and microbiological analysis of potable water

    NASA Technical Reports Server (NTRS)

    Sauer, R. L.; Leslie, S. A.

    1976-01-01

    The Apollo-Soyuz Test Project procedures for potable water system servicing and the results of preflight and postflight chemical and microbiological analyses of the water are discussed. Tables show results of the analyses. The effectiveness of the water system is evaluated.

  13. An Analysis of the Algebraic Method for Balancing Chemical Reactions.

    ERIC Educational Resources Information Center

    Olson, John A.

    1997-01-01

    Analyzes the algebraic method for balancing chemical reactions. Introduces a third general condition that involves a balance between the total amount of oxidation and reduction. Requires the specification of oxidation states for all elements throughout the reaction. Describes the general conditions, the mathematical treatment, redox reactions, and…

  14. Koopmans' Analysis of Chemical Hardness with Spectral-Like Resolution

    PubMed Central

    2013-01-01

    Three approximation levels of Koopmans' theorem are explored and applied: the first referring to the inner quantum behavior of the orbitalic energies that depart from the genuine ones in Fock space when the wave-functions' Hilbert-Banach basis set is specified to solve the many-electronic spectra of spin-orbitals' eigenstates; it is the most subtle issue regarding Koopmans' theorem as it brings many critics and refutation in the last decades, yet it is shown here as an irrefutable “observational” effect through computation, specific to any in silico spectra of an eigenproblem; the second level assumes the “frozen spin-orbitals” approximation during the extracting or adding of electrons to the frontier of the chemical system through the ionization and affinity processes, respectively; this approximation is nevertheless workable for great deal of chemical compounds, especially organic systems, and is justified for chemical reactivity and aromaticity hierarchies in an homologue series; the third and the most severe approximation regards the extension of the second one to superior orders of ionization and affinities, here studied at the level of chemical hardness compact-finite expressions up to spectral-like resolution for a paradigmatic set of aromatic carbohydrates. PMID:23970834

  15. Sampling of vehicle emissions for chemical analysis and biological testing.

    PubMed Central

    Schuetzle, D

    1983-01-01

    Representative dilution tube sampling techniques for particulate and gas phase vehicle emissions are described using Teflon filter media and XAD-2 resin. More than 90% of the total gas (C8-C18) and particulate direct acting Ames assay mutagenicity (TA 98) was found in the particulate phase. The gas and particulate phase material was fractionated by HPLC into nonpolar, moderately polar and highly polar chemical fractions. The moderately polar chemical fraction of the particulates contained more than 50% of the direct acting Ames assay mutagenicity for the total extract. The concentration of oxygenated polynuclear aromatic hydrocarbons (oxy-PAH) and nitrated PAH (nitro-PAH) identified in the moderately polar particulate fractions are given. Nitro-PAH account for most of the direct-acting (TA 98) Ames assay mutagenicity in these moderately polar fractions. Reactions and kinetic expressions for chemical conversion of PAH are presented. Chemical conversion of PAH to nitro-PAH during dilution tube sampling of particulates on Teflon filters and gases on XAD-2 resin is a minor problem (representing 10-20%, on the average, of the 1-nitropyrene found in extracts) at short (46 min) sampling times, at low sampling temperatures (42 degrees C), and in diluted exhaust containing 3 ppm NO2. Particulate emissions collected from dilution tubes on filter media appear to be representative of what is emitted in the environment as based upon a comparison of highway and laboratory studies. PMID:6186484

  16. Chemical profiling and quantification of monacolins and citrinin in red yeast rice commercial raw materials and dietary supplements using liquid chromatography-accurate QToF mass spectrometry: Chemometrics application.

    PubMed

    Avula, Bharathi; Cohen, Pieter A; Wang, Yan-Hong; Sagi, Satyanarayanaraju; Feng, Wei; Wang, Mei; Zweigenbaum, Jerry; Shuangcheng, Ma; Khan, Ikhlas A

    2014-11-01

    Red yeast rice (RYR) is prepared by fermenting rice with various strains of the yeast Monascus spp of the Aspergillaceae family. Depending on the Monascus strains and the fermentation conditions, the products may contain monacolins, pigments and citrinin as secondary metabolites. Authentic and commercial RYR samples were analyzed using UHPLC-DAD-QToF-MS for monacolins, pigments and citrinin. A separation by UHPLC was achieved using a reversed-phase column and a gradient of water/acetonitrile each containing formic acid as the mobile phase. Accurate mass QToF spectrometry was used to distinguish isobaric monacolins. Principle component analysis (PCA), a chemometric technique was used to discriminate between authentic RYR, commercial RYR raw materials and dietary supplements. Three authentic RYR samples, 31 commercial RYR raw materials and 14 RYR dietary supplements were analyzed. Monacolin K content in 600mg of authentic RYR samples ranged from 1.2mg to 1.38mg. Amounts of monacolin K in dietary supplements labeled as containing 600mg of RYR varied more than 40-fold from 0.03mg to 2.18mg. Monacolin K content of dietary supplements labeled as containing 1200mg RYR varied more than 20-fold from 0.22mg to 5.23mg. In addition to large variations in quantity of monacolin K found in dietary supplements, RYR dietary supplements contained ratios of monacolins that differed significantly from authentic samples. The results indicated that RYR commercial products are of variable quality and the analytical method is suitable for quality control testing of a variety of RYR products.

  17. Chemical etching and EDAX analysis of beryllium-free nickel-chromium ceramo-metal alloy.

    PubMed

    Atta, O M; Mosleh, I E; Shehata, M T

    1995-10-01

    A chemical etching technique is described for producing etch patterns in beryllium-free nickel chromium ceramo-metal alloy. Disc-shaped samples were chemically etched, evaluated with SEM and analysed by the EDAX technique. Scanning electron micrographs revealed, profound retentive cavities. The EDAX analysis provided a comprehensive interpretation of the etch mechanism. The obtained results show that the developed chemical etching has the potential to produce a highly retentive etched surface with less problematic and less technique sensitive than electrolytic etching.

  18. Chemical analysis of charged Li/SO(sub)2 cells

    NASA Technical Reports Server (NTRS)

    Subbarao, S.; Lawson, D.; Frank, H.; Halpert, G.; Barnes, J.; Bis, R.

    1987-01-01

    The initial focus of the program was to confirm that charging can indeed result in explosions and constitute a significant safety problem. Results of this initial effort clearly demonstrated that cells do indeed explode on charge and that charging does indeed constitute a real and severe safety problem. The results of the effort to identify the chemical reactions involved in and responsible for the observed behavior are described.

  19. A novel stress-accurate FE technology for highly non-linear analysis with incompressibility constraint. Application to the numerical simulation of the FSW process

    NASA Astrophysics Data System (ADS)

    Chiumenti, M.; Cervera, M.; Agelet de Saracibar, C.; Dialami, N.

    2013-05-01

    In this work a novel finite element technology based on a three-field mixed formulation is presented. The Variational Multi Scale (VMS) method is used to circumvent the LBB stability condition allowing the use of linear piece-wise interpolations for displacement, stress and pressure fields, respectively. The result is an enhanced stress field approximation which enables for stress-accurate results in nonlinear computational mechanics. The use of an independent nodal variable for the pressure field allows for an adhoc treatment of the incompressibility constraint. This is a mandatory requirement due to the isochoric nature of the plastic strain in metal forming processes. The highly non-linear stress field typically encountered in the Friction Stir Welding (FSW) process is used as an example to show the performance of this new FE technology. The numerical simulation of the FSW process is tackled by means of an Arbitrary-Lagrangian-Eulerian (ALE) formulation. The computational domain is split into three different zones: the work.piece (defined by a rigid visco-plastic behaviour in the Eulerian framework), the pin (within the Lagrangian framework) and finally the stirzone (ALE formulation). A fully coupled thermo-mechanical analysis is introduced showing the heat fluxes generated by the plastic dissipation in the stir-zone (Sheppard rigid-viscoplastic constitutive model) as well as the frictional dissipation at the contact interface (Norton frictional contact model). Finally, tracers have been implemented to show the material flow around the pin allowing a better understanding of the welding mechanism. Numerical results are compared with experimental evidence.

  20. Miniaturised wireless smart tag for optical chemical analysis applications.

    PubMed

    Steinberg, Matthew D; Kassal, Petar; Tkalčec, Biserka; Murković Steinberg, Ivana

    2014-01-01

    A novel miniaturised photometer has been developed as an ultra-portable and mobile analytical chemical instrument. The low-cost photometer presents a paradigm shift in mobile chemical sensor instrumentation because it is built around a contactless smart card format. The photometer tag is based on the radio-frequency identification (RFID) smart card system, which provides short-range wireless data and power transfer between the photometer and a proximal reader, and which allows the reader to also energise the photometer by near field electromagnetic induction. RFID is set to become a key enabling technology of the Internet-of-Things (IoT), hence devices such as the photometer described here will enable numerous mobile, wearable and vanguard chemical sensing applications in the emerging connected world. In the work presented here, we demonstrate the characterisation of a low-power RFID wireless sensor tag with an LED/photodiode-based photometric input. The performance of the wireless photometer has been tested through two different model analytical applications. The first is photometry in solution, where colour intensity as a function of dye concentration was measured. The second is an ion-selective optode system in which potassium ion concentrations were determined by using previously well characterised bulk optode membranes. The analytical performance of the wireless photometer smart tag is clearly demonstrated by these optical absorption-based analytical experiments, with excellent data agreement to a reference laboratory instrument.

  1. A thermodynamic analysis of alternative approaches to chemical looping combustion

    SciTech Connect

    Chakravarthy, Veerathu K; Daw, C Stuart; Pihl, Josh A

    2011-01-01

    In this article, we review and clarify some of the points made by previous authors regarding chemical looping combustion (CLC). While much of the recent interest in chemical looping combustion has been associated with carbon sequestration, our primary interest here is its potential to increase the thermodynamic efficiency of converting fuel chemical energy into useful work. We expand on several points about the details of CLC that we feel have not previously been sufficiently explored, and suggest alternative (and possibly more practical) approaches that exploit some of the same thermodynamic concepts. We illustrate our key points with {First} and {Second} Law analyses of ideal conceptual processes, which in addition to {CLC} also include isothermal, non-equilibrium, preheated combustion and combustion with thermochemical recuperation. Our results suggest that a significant portion of the potential efficiency benefit of CLC might be achieved without the need to handle and transport large quantities of solid oxygen storage material. Exploitation of this fact may lead to higher efficiency approaches for power generation from hydrocarbon fuels combustion.

  2. Miniaturised wireless smart tag for optical chemical analysis applications.

    PubMed

    Steinberg, Matthew D; Kassal, Petar; Tkalčec, Biserka; Murković Steinberg, Ivana

    2014-01-01

    A novel miniaturised photometer has been developed as an ultra-portable and mobile analytical chemical instrument. The low-cost photometer presents a paradigm shift in mobile chemical sensor instrumentation because it is built around a contactless smart card format. The photometer tag is based on the radio-frequency identification (RFID) smart card system, which provides short-range wireless data and power transfer between the photometer and a proximal reader, and which allows the reader to also energise the photometer by near field electromagnetic induction. RFID is set to become a key enabling technology of the Internet-of-Things (IoT), hence devices such as the photometer described here will enable numerous mobile, wearable and vanguard chemical sensing applications in the emerging connected world. In the work presented here, we demonstrate the characterisation of a low-power RFID wireless sensor tag with an LED/photodiode-based photometric input. The performance of the wireless photometer has been tested through two different model analytical applications. The first is photometry in solution, where colour intensity as a function of dye concentration was measured. The second is an ion-selective optode system in which potassium ion concentrations were determined by using previously well characterised bulk optode membranes. The analytical performance of the wireless photometer smart tag is clearly demonstrated by these optical absorption-based analytical experiments, with excellent data agreement to a reference laboratory instrument. PMID:24274311

  3. Tattoo inks: legislation, pigments, metals and chemical analysis.

    PubMed

    Prior, Gerald

    2015-01-01

    Legal limits for chemical substances require that they are linked to clearly defined analytical methods. Present limits for certain chemicals in tattoo and permanent make-up inks do not mention analytical methods for the detection of metals, polycyclic aromatic hydrocarbons or forbidden colourants. There is, therefore, no established method for the determination of the quantities of these chemicals in tattoo and permanent make-up inks. Failing to provide an appropriate method may lead to unqualified and questionable results which often cause legal disputes that are ultimately resolved by a judge with regard to the method that should have been applied. Analytical methods are tuned to exactly what is to be found and what causes the health problems. They are extremely specific. Irrespective of which is the correct method for detecting metals in tattoo inks, the focus should be on the actual amounts of ink in the skin. CTL® has conducted experiments to determine these amounts and these experiments are crucial for toxicological evaluations and for setting legal limits. When setting legal limits, it is essential to also incorporate factors such as daily consumption, total uptake and frequency of use. A tattoo lasts for several decades; therefore, the limits that have been established for heavy metals used in drinking water or soap are not relevant. Drinking water is consumed on a daily basis and soap is used several times per week, while tattooing only occurs once. PMID:25833637

  4. Laser-based mass spectrometry for in situ chemical composition analysis of planetary surfaces

    NASA Astrophysics Data System (ADS)

    Frey, Samira; Neuland, Maike B.; Grimaudo, Valentine; Moreno-García, Pavel; Riedo, Andreas; Tulej, Marek; Broekmann, Peter; Wurz, Peter

    2016-04-01

    Mass spectrometry is an important analytical technique in space research. The chemical composition of planetary surface material is a key scientific question on every space mission to a planet, moon or asteroid. Chemical composition measurements of rocky material on the surface are of great importance to understand the origin and evolution of the planetary body.[1] A miniature laser ablation/ionisation reflectron- type time-of-flight mass spectrometer (instrument name LMS) was designed and built at the University of Bern for planetary research.[2] Despite its small size and light weight, the LMS instrument still maintains the same capabilities as large laboratory systems, which makes it suitable for its application on planetary space missions.[3-5] The high dynamic range of about eight orders of magnitude, high lateral (μm-level) and vertical (sub-nm level) resolution and high detection sensitivity for almost all elements (10 ppb, atomic fraction) make LMS a versatile instrument for various applications. LMS is a suitable instrument for in situ measurements of elemental and isotope composition with high precision and accuracy. Measurements of Pb- isotope abundances can be used for dating of planetary material. Measurements of bio-relevant elements allow searching for past or present life on a planetary surface. The high spatial resolution, both in lateral and vertical direction, is of considerable interest, e.g. for analysis of inhomogeneous, extraterrestrial samples as well as weathering processes of planetary material. References [1] P. Wurz, D. Abplanalp, M. Tulej, M. Iakovleva, V.A. Fernandes, A. Chumikov, and G. Managadze, "Mass Spectrometric Analysis in Planetary Science: Investigation of the Surface and the Atmosphere", Sol. Sys. Res., 2012, 46, 408. [2] U. Rohner, J.A. Whitby, P. Wurz, "A miniature laser ablation time of flight mass spectrometer for in situ planetary exploration" Meas. Sci. Tch., 2003, 14, 2159. [3] M. Tulej, A. Riedo, M.B. Neuland, S

  5. Chemical recognition software

    SciTech Connect

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.H. Jr.; Tisone, G.C.

    1994-06-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures, even when the mixture is noisy and contaminated with unknowns.

  6. Chemical recognition software

    SciTech Connect

    Wagner, J.S.; Trahan, M.W.; Nelson, W.E.; Hargis, P.J. Jr.; Tisone, G.C.

    1994-12-01

    We have developed a capability to make real time concentration measurements of individual chemicals in a complex mixture using a multispectral laser remote sensing system. Our chemical recognition and analysis software consists of three parts: (1) a rigorous multivariate analysis package for quantitative concentration and uncertainty estimates, (2) a genetic optimizer which customizes and tailors the multivariate algorithm for a particular application, and (3) an intelligent neural net chemical filter which pre-selects from the chemical database to find the appropriate candidate chemicals for quantitative analyses by the multivariate algorithms, as well as providing a quick-look concentration estimate and consistency check. Detailed simulations using both laboratory fluorescence data and computer synthesized spectra indicate that our software can make accurate concentration estimates from complex multicomponent mixtures. even when the mixture is noisy and contaminated with unknowns.

  7. Comprehensive Mass Analysis for Chemical Processes, a Case Study on L-Dopa Manufacture

    EPA Science Inventory

    To evaluate the “greenness” of chemical processes in route selection and process development, we propose a comprehensive mass analysis to inform the stakeholders from different fields. This is carried out by characterizing the mass intensity for each contributing chemical or wast...

  8. Analysis of solids remaining following chemical cleaning in tank 6F

    SciTech Connect

    Poirier, Michael R.; Fondeur, Fernando F.; Missimer, David M.; Summer, Michael E.; Fink, Samuel D.

    2010-02-05

    Following chemical cleaning, a solid sample was collected and submitted to Savannah River National Laboratory (SRNL) for analysis. SRNL analyzed this sample by X-ray Diffraction (XRD) and scanning electron microscopy (SEM) to determine the composition of the solids remaining in Tank 6F and to assess the effectiveness of the chemical cleaning process.

  9. Exploring the Potential for Using Inexpensive Natural Reagents Extracted from Plants to Teach Chemical Analysis

    ERIC Educational Resources Information Center

    Hartwell, Supaporn Kradtap

    2012-01-01

    A number of scientific articles report on the use of natural extracts from plants as chemical reagents, where the main objective is to present the scientific applications of those natural plant extracts. The author suggests that natural reagents extracted from plants can be used as alternative low cost tools in teaching chemical analysis,…

  10. Accurate pointing of tungsten welding electrodes

    NASA Technical Reports Server (NTRS)

    Ziegelmeier, P.

    1971-01-01

    Thoriated-tungsten is pointed accurately and quickly by using sodium nitrite. Point produced is smooth and no effort is necessary to hold the tungsten rod concentric. The chemically produced point can be used several times longer than ground points. This method reduces time and cost of preparing tungsten electrodes.

  11. Recommended default methodology for analysis of airborne exposures to mixtures of chemicals in emergencies.

    PubMed

    Craig, D K; Baskett, R L; Davis, J S; Dukes, L; Hansen, D J; Petrocchi, A J; Powell, T J; Sutherland, P J; Tuccinardi, T E

    1999-09-01

    Emergency planning and hazard assessment of Department of Energy (DOE) facilities require consideration of potential exposures to mixtures of chemicals released to the atmosphere. Exposure to chemical mixtures may lead to additive, synergistic, or antagonistic health effects. In the past, the consequences of exposures to each chemical have been analyzed separately. This approach may not adequately protect the health of persons exposed to mixtures. This article presents default recommendations for use in emergency management and safety analysis within the DOE complex where potential exists for releases of mixtures of chemicals. These recommendations were developed by the DOE Subcommittee on Consequence Assessment and Protective Actions (SCAPA). It is recommended that hazard indices (e.g., HIi = Ci/Limiti, where Ci is the concentration of chemical "i") be calculated for each chemical, and unless sufficient toxicological knowledge is available to indicate otherwise, that they be summed, that is, sigma i(n) = 1HIi = HI1 + HI2 + ... + HIn. A sum of 1.0 or less means the limits have not been exceeded. To facilitate application of these recommendations for analysis of exposures to specific mixtures, chemicals are classified according to their toxic consequences. This is done using health code numbers describing toxic effects by target organ for each chemical. This methodology has been applied to several potential releases of chemicals to compare the resulting hazard indices of a chemical mixture with those obtained when each chemical is treated independently. The methodology used and results obtained from analysis of one mixture are presented in this article. This article also demonstrates how health code numbers can be used to sum hazard indices only for those chemicals that have the same toxic consequence.

  12. Approximate chemical analysis of volcanic glasses using Raman spectroscopy

    PubMed Central

    Morgavi, Daniele; Hess, Kai‐Uwe; Neuville, Daniel R.; Borovkov, Nikita; Perugini, Diego; Dingwell, Donald B.

    2015-01-01

    The effect of chemical composition on the Raman spectra of a series of natural calcalkaline silicate glasses has been quantified by performing electron microprobe analyses and obtaining Raman spectra on glassy filaments (~450 µm) derived from a magma mingling experiment. The results provide a robust compositionally‐dependent database for the Raman spectra of natural silicate glasses along the calcalkaline series. An empirical model based on both the acquired Raman spectra and an ideal mixing equation between calcalkaline basaltic and rhyolitic end‐members is constructed enabling the estimation of the chemical composition and degree of polymerization of silicate glasses using Raman spectra. The model is relatively insensitive to acquisition conditions and has been validated using the MPI‐DING geochemical standard glasses1 as well as further samples. The methods and model developed here offer several advantages compared with other analytical and spectroscopic methods such as infrared spectroscopy, X‐ray fluorescence spectroscopy, electron and ion microprobe analyses, inasmuch as Raman spectroscopy can be performed with a high spatial resolution (1 µm2) without the need for any sample preparation as a nondestructive technique. This study represents an advance in efforts to provide the first database of Raman spectra for natural silicate glasses and yields a new approach for the treatment of Raman spectra, which allows us to extract approximate information about the chemical composition of natural silicate glasses using Raman spectroscopy. We anticipate its application in handheld in situ terrestrial field studies of silicate glasses under extreme conditions (e.g. extraterrestrial and submarine environments). © 2015 The Authors Journal of Raman Spectroscopy Published by John Wiley & Sons Ltd PMID:27656038

  13. Approximate chemical analysis of volcanic glasses using Raman spectroscopy

    PubMed Central

    Morgavi, Daniele; Hess, Kai‐Uwe; Neuville, Daniel R.; Borovkov, Nikita; Perugini, Diego; Dingwell, Donald B.

    2015-01-01

    The effect of chemical composition on the Raman spectra of a series of natural calcalkaline silicate glasses has been quantified by performing electron microprobe analyses and obtaining Raman spectra on glassy filaments (~450 µm) derived from a magma mingling experiment. The results provide a robust compositionally‐dependent database for the Raman spectra of natural silicate glasses along the calcalkaline series. An empirical model based on both the acquired Raman spectra and an ideal mixing equation between calcalkaline basaltic and rhyolitic end‐members is constructed enabling the estimation of the chemical composition and degree of polymerization of silicate glasses using Raman spectra. The model is relatively insensitive to acquisition conditions and has been validated using the MPI‐DING geochemical standard glasses1 as well as further samples. The methods and model developed here offer several advantages compared with other analytical and spectroscopic methods such as infrared spectroscopy, X‐ray fluorescence spectroscopy, electron and ion microprobe analyses, inasmuch as Raman spectroscopy can be performed with a high spatial resolution (1 µm2) without the need for any sample preparation as a nondestructive technique. This study represents an advance in efforts to provide the first database of Raman spectra for natural silicate glasses and yields a new approach for the treatment of Raman spectra, which allows us to extract approximate information about the chemical composition of natural silicate glasses using Raman spectroscopy. We anticipate its application in handheld in situ terrestrial field studies of silicate glasses under extreme conditions (e.g. extraterrestrial and submarine environments). © 2015 The Authors Journal of Raman Spectroscopy Published by John Wiley & Sons Ltd

  14. Algorithms for three-dimensional chemical analysis via multi-energy synchrotron X-ray tomography

    NASA Astrophysics Data System (ADS)

    Ham, Kyungmin; Butler, Leslie G.

    2007-08-01

    The conversion of X-ray tomography images into three-dimensional chemical composition requires accurate mass absorption values, high-quality images, and a robust fitting algorithm. The least-squares fits of the images to a three-dimensional chemical composition can proceed with several different options such as minimal vs. over-determined and/or constrained parameters. This project has investigated the impact of XAFS features and a limited CCD dynamic range. These simulated results are compared to a recent experimental project in which synchrotron X-ray tomography was used to image a polymer blend, and from those images, calculated three-dimensional chemical composition maps of the two-component flame retardant, a brominated phthalimide dimer, Saytex ™ BT-93 and a synergist, antimony(III) oxide (Sb 2O 3).

  15. Apparatus and method for performing microfluidic manipulations for chemical analysis

    DOEpatents

    Ramsey, J. Michael

    2002-01-01

    A microchip apparatus and method provide fluidic manipulations for a variety of applications, including sample injection for microchip liquid chromatography. The microchip is fabricated using standard photolitographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis is performed in channels formed in the substrate. Injections are made by electro-osmotically pumping sample through the injection channel that crosses the separation channel, followed by a switching of the potentials to force a plug into the separation channel.

  16. Apparatus and method for performing microfluidic manipulations for chemical analysis

    DOEpatents

    Ramsey, J. Michael

    1999-01-01

    A microchip apparatus and method provide fluidic manipulations for a variety of applications, including sample injection for microchip liquid chromatography. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis is performed in channels formed in the substrate. Injections are made by electro-osmotically pumping sample through the injection channel that crosses the separation channel, followed by a switching of the potentials to force a plug into the separation channel.

  17. Apparatus and method for performing microfluidic manipulations for chemical analysis

    SciTech Connect

    Ramsey, J.M.

    1999-12-14

    A microchip apparatus and method provide fluidic manipulations for a variety of applications, including sample injection for microchip liquid chromatography. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis is performed in channels formed in the substrate. Injections are made by electro-osmotically pumping sample through the injection channel that crosses the separation channel, followed by a switching of the potentials to force a plug into the separation channel.

  18. Chemical analysis of acoustically levitated drops by Raman spectroscopy.

    PubMed

    Tuckermann, Rudolf; Puskar, Ljiljana; Zavabeti, Mahta; Sekine, Ryo; McNaughton, Don

    2009-07-01

    An experimental apparatus combining Raman spectroscopy with acoustic levitation, Raman acoustic levitation spectroscopy (RALS), is investigated in the field of physical and chemical analytics. Whereas acoustic levitation enables the contactless handling of microsized samples, Raman spectroscopy offers the advantage of a noninvasive method without complex sample preparation. After carrying out some systematic tests to probe the sensitivity of the technique to drop size, shape, and position, RALS has been successfully applied in monitoring sample dilution and preconcentration, evaporation, crystallization, an acid-base reaction, and analytes in a surface-enhanced Raman spectroscopy colloidal suspension. PMID:19418043

  19. Laser Applications to Chemical, Security, and Environmental Analysis: introduction to the feature issue

    SciTech Connect

    Dreizler, Andreas; Fried, Alan; Gord, James R

    2007-07-01

    This Applied Optics feature issue on Laser Applications to Chemical, Security,and Environmental Analysis (LACSEA) highlights papers presented at theLACSEA 2006 Tenth Topical Meeting sponsored by the Optical Society ofAmerica.

  20. Chemical analysis and sampling techniques for geothermal fluids and gases at the Fenton Hill Laboratory

    SciTech Connect

    Trujillo, P.E.; Counce, D.; Grigsby, C.O.; Goff, F.; Shevenell, L.

    1987-06-01

    A general description of methods, techniques, and apparatus used for the sampling, chemical analysis, and data reporting of geothermal gases and fluids is given. Step-by-step descriptions of the procedures are included in the appendixes.

  1. Airborne photography of chemical releases and analysis of twilight sky brightness data, phases 1 and 2

    NASA Technical Reports Server (NTRS)

    Bedinger, J. F.; Constantinides, E.

    1976-01-01

    The photography from aboard an aircraft of chemical releases is reported. The equipment installation on the aircraft is described, and photographs of the releases are included. An extensive analysis of twilight sky photographs is presented.

  2. Recent Development in Optical Chemical Sensors Coupling with Flow Injection Analysis

    PubMed Central

    Ojeda, Catalina Bosch; Rojas, Fuensanta Sánchez

    2006-01-01

    Optical techniques for chemical analysis are well established and sensors based on these techniques are now attracting considerable attention because of their importance in applications such as environmental monitoring, biomedical sensing, and industrial process control. On the other hand, flow injection analysis (FIA) is advisable for the rapid analysis of microliter volume samples and can be interfaced directly to the chemical process. The FIA has become a widespread automatic analytical method for more reasons; mainly due to the simplicity and low cost of the setups, their versatility, and ease of assembling. In this paper, an overview of flow injection determinations by using optical chemical sensors is provided, and instrumentation, sensor design, and applications are discussed. This work summarizes the most relevant manuscripts from 1980 to date referred to analysis using optical chemical sensors in FIA.

  3. Electron spectroscopy for chemical analysis (ESCA) study of aluminum-containing atmospheric particles

    SciTech Connect

    Dillard, J.G.; Seals, R.D.; Wightman, J.P.

    1980-01-01

    Electron spectroscopy and scanning electron microscopy have been utilized for the analysis of aluminum-laden particulates. Collection and analysis of samples are described. Samples were collected during a rocket launch at the NASA Kennedy Space Center. Analysis reveals that at least three chemically different types of aluminum are present in the samples. (3 graphs, 5 photos, 35 references, 2 tables)

  4. A kinetic and equilibrium analysis of silicon carbide chemical vapor deposition on monofilaments

    NASA Technical Reports Server (NTRS)

    Gokoglu, S. A.; Kuczmarski, M. A.

    1993-01-01

    Chemical kinetics of atmospheric pressure silicon carbide (SiC) chemical vapor deposition (CVD) from dilute silane and propane source gases in hydrogen is numerically analyzed in a cylindrical upflow reactor designed for CVD on monofilaments. The chemical composition of the SiC deposit is assessed both from the calculated total fluxes of carbon and silicon and from chemical equilibrium considerations for the prevailing temperatures and species concentrations at and along the filament surface. The effects of gas and surface chemistry on the evolution of major gas phase species are considered in the analysis.

  5. A Psychometric Analysis of the Chemical Concepts Inventory

    ERIC Educational Resources Information Center

    Barbera, Jack

    2013-01-01

    designed to assess the alternate conceptions of students in high school or first-semester college chemistry. The instrument was published in 2002 along with an analysis of its data from a test population. This study supports the initial analysis and expands on the psychometric…

  6. Crystal-Chemical Analysis Martian Minerals in Gale Crater

    NASA Technical Reports Server (NTRS)

    Morrison, S. M.; Downs, R. T.; Blake, D. F.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Yen, A. S.; Chipera, S. J.; Treiman, A. H.; Vaniman, D. T.; Gellert, R.; Achilles, C. N..; Rampe, E. B.; Bristow, T. F.; Crisp, J. A.; Sarrazin, P. C.; Farmer, J. D.; DesMarais, D. J.; Grotzinger, J. P.; Stolper, E. M.; Morookian, J. M.; Wilson, M. A.; Spanovich, N.; Anderson, R. C.

    2015-01-01

    The CheMin instrument on the Mars Science Laboratory rover Curiosity performed X-ray diffraction analyses on scooped soil at Rocknest and on drilled rock fines at Yellowknife Bay (John Klein and Cumberland samples), The Kimberley (Windjana sample), and Pahrump (Confidence Hills sample) in Gale crater, Mars. Samples were analyzed with the Rietveld method to determine the unit-cell parameters and abundance of each observed crystalline phase. Unit-cell parameters were used to estimate compositions of the major crystalline phases using crystal-chemical techniques. These phases include olivine, plagioclase and clinopyroxene minerals. Comparison of the CheMin sample unit-cell parameters with those in the literature provides an estimate of the chemical compositions of the major crystalline phases. Preliminary unit-cell parameters, abundances and compositions of crystalline phases found in Rocknest and Yellowknife Bay samples were reported in. Further instrument calibration, development of 2D-to- 1D pattern conversion corrections, and refinement of corrected data allows presentation of improved compositions for the above samples.

  7. New crosslinkers for electrospun chitosan fibre mats. I. Chemical analysis

    PubMed Central

    Austero, Marjorie S.; Donius, Amalie E.; Wegst, Ulrike G. K.; Schauer, Caroline L.

    2012-01-01

    Chitosan (CS), the deacetylated form of chitin, the second most abundant, natural polysaccharide, is attractive for applications in the biomedical field because of its biocompatibility and resorption rates, which are higher than chitin. Crosslinking improves chemical and mechanical stability of CS. Here, we report the successful utilization of a new set of crosslinkers for electrospun CS. Genipin, hexamethylene-1,6-diaminocarboxysulphonate (HDACS) and epichlorohydrin (ECH) have not been previously explored for crosslinking of electrospun CS. In this first part of a two-part publication, we report the morphology, determined by field emission scanning electron microscopy (FESEM), and chemical interactions, determined by Fourier transform infrared microscopy, respectively. FESEM revealed that CS could successfully be electrospun from trifluoroacetic acid with genipin, HDACS and ECH added to the solution. Diameters were 267 ± 199 nm, 644 ± 359 nm and 896 ± 435 nm for CS–genipin, CS–HDACS and CS–ECH, respectively. Short- (15 min) and long-term (72 h) dissolution tests (T600) were performed in acidic, neutral and basic pHs (3, 7 and 12). Post-spinning activation by heat and base to enhance crosslinking of CS–HDACS and CS–ECH decreased the fibre diameters and improved the stability. In the second part of this publication, we report the mechanical properties of the fibres. PMID:22628209

  8. Analysis of residual chemicals on filtering facepiece respirators after decontamination.

    PubMed

    Salter, W B; Kinney, K; Wallace, W H; Lumley, A E; Heimbuch, B K; Wander, J D

    2010-08-01

    The N95 filtering facepiece respirator (FFR) is commonly used to protect individuals from infectious aerosols. Health care experts predict a shortage of N95 FFRs if a severe pandemic occurs, and an option that has been suggested for mitigating such an FFR shortage is to decontaminate and reuse the devices. Before the effectiveness of this strategy can be established, many parameters affecting respiratory protection must be measured: biocidal efficacy of the decontamination treatment, filtration performance, pressure drop, fit, and toxicity to the end user post treatment. This research effort measured the amount of residual chemicals created or deposited on six models of FFRs following treatment by each of 7 simple decontamination technologies. Measured amounts of decontaminants retained by the FFRs treated with chemical disinfectants were small enough that exposure to wearers will be below the permissible exposure limit (PEL). Toxic by-products were also evaluated, and two suspected toxins were detected after ethylene oxide treatment of FFR rubber straps. The results provide encouragement to efforts promoting the evolution of effective strategies for decontamination and reuse of FFRs. PMID:20526947

  9. Laser applications to chemical analysis: an introduction by the feature editors

    NASA Astrophysics Data System (ADS)

    Jeffries, Jay B.; Ramsey, J. Michael; Lucht, Robert P.

    1995-06-01

    This issue of Applied Optics features papers on the application of laser technology to chemical analysis. Many of the contributions, although not all, result from papers presented at the Fourth OSA Topical Meeting on Laser Applications to Chemical Analysis, which was held at Jackson Hole, Wyoming, March, 1994. This successful meeting, with nearly one hundred participants, continued the tradition of earlier LACA meetings to focus on the optical science of laser-based measurements of temperature and trace chemical assays in a wide variety of practical applications.

  10. Minimizing Errors in Numerical Analysis of Chemical Data.

    ERIC Educational Resources Information Center

    Rusling, James F.

    1988-01-01

    Investigates minimizing errors in computational methods commonly used in chemistry. Provides a series of examples illustrating the propagation of errors, finite difference methods, and nonlinear regression analysis. Includes illustrations to explain these concepts. (MVL)

  11. How effective are traditional methods of compositional analysis in providing an accurate material balance for a range of softwood derived residues?

    PubMed Central

    2013-01-01

    Background Forest residues represent an abundant and sustainable source of biomass which could be used as a biorefinery feedstock. Due to the heterogeneity of forest residues, such as hog fuel and bark, one of the expected challenges is to obtain an accurate material balance of these feedstocks. Current compositional analytical methods have been standardised for more homogenous feedstocks such as white wood and agricultural residues. The described work assessed the accuracy of existing and modified methods on a variety of forest residues both before and after a typical pretreatment process. Results When “traditional” pulp and paper methods were used, the total amount of material that could be quantified in each of the six softwood-derived residues ranged from 88% to 96%. It was apparent that the extractives present in the substrate were most influential in limiting the accuracy of a more representative material balance. This was particularly evident when trying to determine the lignin content, due to the incomplete removal of the extractives, even after a two stage water-ethanol extraction. Residual extractives likely precipitated with the acid insoluble lignin during analysis, contributing to an overestimation of the lignin content. Despite the minor dissolution of hemicellulosic sugars, extraction with mild alkali removed most of the extractives from the bark and improved the raw material mass closure to 95% in comparison to the 88% value obtained after water-ethanol extraction. After pretreatment, the extent of extractive removal and their reaction/precipitation with lignin was heavily dependent on the pretreatment conditions used. The selective removal of extractives and their quantification after a pretreatment proved to be even more challenging. Regardless of the amount of extractives that were originally present, the analytical methods could be refined to provide reproducible quantification of the carbohydrates present in both the starting material and

  12. An in-line micro-pyrolysis system to remove contaminating organic species for precise and accurate water isotope analysis by spectroscopic techniques

    NASA Astrophysics Data System (ADS)

    Panetta, R. J.; Hsiao, G.

    2011-12-01

    Trace levels of organic contaminants such as short alcohols and terpenoids have been shown to cause spectral interference in water isotope analysis by spectroscopic techniques. The result is degraded precision and accuracy in both δD and δ18O for samples such as beverages, plant extracts or slightly contaminated waters. An initial approach offered by manufacturers is post-processing software that analyzes spectral features to identify and flag contaminated samples. However, it is impossible for this software to accurately reconstruct the water isotope signature, thus it is primarily a metric for data quality. Here, we describe a novel in-line pyrolysis system (Micro-Pyrolysis Technology, MPT) placed just prior to the inlet of a cavity ring-down spectroscopy (CRDS) analyzer that effectively removes interfering organic molecules without altering the isotope values of the water. Following injection of the water sample, N2 carrier gas passes the sample through a micro-pyrolysis tube heated with multiple high temperature elements in an oxygen-free environment. The temperature is maintained above the thermal decomposition threshold of most organic compounds (≤ 900 oC), but well below that of water (~2000 oC). The main products of the pyrolysis reaction are non-interfering species such as elemental carbon and H2 gas. To test the efficacy and applicability of the system, waters of known isotopic composition were spiked with varying amounts of common interfering alcohols (methanol, ethanol, propanol, hexanol, trans-2-hexenol, cis-3-hexanol up to 5 % v/v) and common soluble plant terpenoids (carveol, linalool, geraniol, prenol). Spiked samples with no treatment to remove the organics show strong interfering absorption peaks that adversely affect the δD and δ18O values. However, with the MPT in place, all interfering absorption peaks are removed and the water absorption spectrum is fully restored. As a consequence, the δD and δ18O values also return to their original

  13. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family

    PubMed Central

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A.

    2016-01-01

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF3) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  14. Accurate Mass GC/LC-Quadrupole Time of Flight Mass Spectrometry Analysis of Fatty Acids and Triacylglycerols of Spicy Fruits from the Apiaceae Family.

    PubMed

    Nguyen, Thao; Aparicio, Mario; Saleh, Mahmoud A

    2015-01-01

    The triacylglycerol (TAG) structure and the regio-stereospecific distribution of fatty acids (FA) of seed oils from most of the Apiaceae family are not well documented. The TAG structure ultimately determines the final physical properties of the oils and the position of FAs in the TAG molecule affects the digestion; absorption and metabolism; and physical and technological properties of TAGs. Fixed oils from the fruits of dill (Anethum graveolens), caraway (Carum carvi), cumin (Cuminum cyminum), coriander (Coriandrum sativum), anise (Pimpinella anisum), carrot (Daucus carota), celery (Apium graveolens), fennel (Foeniculum vulgare), and Khella (Ammi visnaga), all from the Apiaceae family, were extracted at room temperature in chloroform/methanol (2:1 v/v) using percolators. Crude lipids were fractionated by solid phase extraction to separate neutral triacylglycerols (TAGs) from other lipids components. Neutral TAGs were subjected to transesterification process to convert them to their corresponding fatty acids methyl esters (FAMES) using 1% boron trifluoride (BF₃) in methanol. FAMES were analyzed by gas chromatography-quadrupole time of flight (GC-QTOF) mass spectrometry. Triglycerides were analyzed using high performance liquid chromatography-quadrupole time of flight (LC-QTOF) mass spectrometry. Petroselinic acid was the major fatty acid in all samples ranging from 57% of the total fatty acids in caraway up to 82% in fennel. All samples contained palmitic (16:0), palmitoleic (C16:1n-9), stearic (C18:0), petroselinic (C18:1n-12), linoleic (C18:2n-6), linolinic (18:3n-3), and arachidic (C20:0) acids. TAG were analyzed using LC-QTOF for accurate mass identification and mass spectrometry/mass spectrometry (MS/MS) techniques for regiospesific elucidation of the identified TAGs. Five major TAGs were detected in all samples but with different relative concentrations in all of the tested samples. Several other TAGs were detected as minor components and were present in

  15. Instantaneous physico-chemical analysis of suspension-based nanomaterials

    PubMed Central

    Meng, Fanxu; Ugaz, Victor M.

    2015-01-01

    High-throughput manufacturing of nanomaterial-based products demands robust online characterization and quality control tools capable of continuously probing the in-suspension state. But existing analytical techniques are challenging to deploy in production settings because they are primarily geared toward small-batch ex-situ operation in research laboratory environments. Here we introduce an approach that overcomes these limitations by exploiting surface complexation interactions that emerge when a micron-scale chemical discontinuity is established between suspended nanoparticles and a molecular tracer. The resulting fluorescence signature is easily detectable and embeds surprisingly rich information about composition, quantity, size, and morphology of nanoparticles in suspension independent of their agglomeration state. We show how this method can be straightforwardly applied to enable continuous sizing of commercial ZnO nanoparticles, and to instantaneously quantify the anatase and rutile composition of multicomponent TiO2 nanoparticle mixtures pertinent to photocatalysis and solar energy conversion. PMID:25923196

  16. Engineering and Functional Analysis of Mitotic Kinases Through Chemical Genetics.

    PubMed

    Jones, Mathew J K; Jallepalli, Prasad V

    2016-01-01

    During mitosis, multiple protein kinases transform the cytoskeleton and chromosomes into new and highly dynamic structures that mediate the faithful transmission of genetic information and cell division. However, the large number and strong conservation of mammalian kinases in general pose significant obstacles to interrogating them with small molecules, due to the difficulty in identifying and validating those which are truly selective. To overcome this problem, a steric complementation strategy has been developed, in which a bulky "gatekeeper" residue within the active site of the kinase of interest is replaced with a smaller amino acid, such as glycine or alanine. The enlarged catalytic pocket can then be targeted in an allele-specific manner with bulky purine analogs. This strategy provides a general framework for dissecting kinase function with high selectivity, rapid kinetics, and reversibility. In this chapter we discuss the principles and techniques needed to implement this chemical genetic approach in mammalian cells.

  17. Morphofunctional analysis of the prostate exposed to chemical manufacture factors.

    PubMed

    Lapii, G A; Nepomnyashchikh, L M; Kiptilov, A V; Neimark, A I

    2014-07-01

    The structural characteristics of the prostate and the blood flow in the organ were studied in chemical plant workers suffering from chronic prostatitis. The prostate echostructure was characterized by vast zones of fibrosis and calcinosis, the hemodynamic ultrasonic parameters were low. Degenerative changes in the acinar structures and stromal fibrosis predominated in the biopsy specimens, these shifts were the most pronounced in the peripheral and transitory zones. Foci of common and small-acinar degeneration of the glands, abundant concrements, and significant collagenization with periglandular and perivascular sclerosis without or with slight inflammatory infiltration were detected. We hypothesize that long exposure to adverse factors of sulfuric acid manufacture contributed to the development of pathological changes in the prostate.

  18. Chemical analysis of surgical smoke by infrared laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Gianella, Michele; Sigrist, Markus W.

    2012-11-01

    The chemical composition of surgical smoke, a gaseous by-product of some surgical devices—lasers, drills, vessel sealing devices—is of great interest due to the many toxic components that have been found to date. For the first time, surgical smoke samples collected during routine keyhole surgery were analyzed with infrared laser spectroscopy. Traces (ppm range) of methane, ethane, ethylene, carbon monoxide and sevoflurane were detected in the samples which consisted mostly of carbon dioxide and water vapor. Except for the anaesthetic sevoflurane, none of the compounds were present at dangerous concentrations. Negative effects on the health of operation room personnel can be excluded for many toxic compounds found in earlier studies, since their concentrations are below recommended exposure limits.

  19. Comparative Analysis of Mutant Tyrosine Kinase Chemical Rescue†

    PubMed Central

    Muratore, Kathryn E.; Seeliger, Markus A.; Wang, Zhihong; Fomina, Dina; Neiswinger, Johnathan; Havranek, James J.; Baker, David; Kuriyan, John; Cole, Philip A.

    2009-01-01

    Protein tyrosine kinases are critical cell signaling enzymes. These enzymes have a highly conserved Arg residue in their catalytic loop which is present two residues or four residues downstream from an absolutely conserved Asp catalytic base. Prior studies on protein tyrosine kinases Csk and Src revealed the potential for chemical rescue of catalytically-deficient mutant kinases (Arg to Ala mutations) by small diamino compounds, particularly imidazole, however the potency and efficiency of rescue was greater for Src. This current study further examines the structural and kinetic basis of rescue for mutant Src as compared to mutant Abl tyrosine kinase. An X-ray crystal structure of R388A Src revealed the surprising finding that a histidine residue of the N-terminus of a symmetry-related kinase inserts into the active site of the adjacent Src and mimics the hydrogen bonding pattern seen in wild-type protein tyrosine kinases. Abl R367A shows potent and efficient rescue more comparable to Src, even though its catalytic loop is more like that of Csk. Various enzyme redesigns of the active sites indicate that the degree and specificity of rescue is somewhat flexible, but the overall properties of the enzymes and rescue agents play an overarching role. The newly discovered rescue agent 2-aminoimidazole is about as efficient as imidazole in rescuing R/A Src and Abl. Rate vs. pH studies with these imidazole analogs suggest that the protonated imidazolium is the preferred form for chemical rescue, consistent with structural models. The efficient rescue seen with mutant Abl points to the potential of this approach to be used effectively to analyze Abl phosphorylation pathways in cells. PMID:19260709

  20. Application of headspace analysis to the study of sorption of hydrophobic organic chemicals to α-Al2O3

    USGS Publications Warehouse

    Pelinger, Judith A.; Eisenreich, Steven J.; Capel, Paul D.

    1993-01-01

    The sorption of hydrophobic organic chemicals (HOCs) to ??-Al2O3 was investigated with a headspace analysis method. The semiautomated headspace analyzer gave rapid, precise, and accurate results for a homologous series alkylbenzenes even at low percentages of solute mass sorbed (3-50%). Sorption experiments carried out with benzene alone indicated weak interactions with well-characterized aluminum oxide, and a solids concentration effect was observed. When the sorption coefficients for benzene alone obtained by headspace analysis were extrapolated up to the solids concentrations typically used in batch sorption experiments, the measured sorption coefficients agreed with reported sorption coefficients for HOCs and sediments of low fractional organic carbon content. Sorbed concentrations increased exponentially with aqueous concentration in isotherms with mixtures of alkylbenzenes, indicating solute-solute interactions at the mineral surface. Sorption was, however, greater than predicted for partitioning of a solute between its pure liquid phase and water, indicating additional influences of the surface and/or the structured liquid near the mineral surface. ?? 1993 American Chemical Society.

  1. Application of multivariate image analysis in QSPR study of 13C chemical shifts of naphthalene derivatives: a comparative study.

    PubMed

    Garkani-Nejad, Zahra; Poshteh-Shirani, Marziyeh

    2010-11-15

    A new implemented QSPR method, whose descriptors achieved from bidimensional images, was applied for predicting (13)C NMR chemical shifts of 25 mono substituted naphthalenes. The resulted descriptors were subjected to principal component analysis (PCA) and the most significant principal components (PCs) were extracted. MIA-QSPR (multivariate image analysis applied to quantitative structure-property relationship) modeling was done by means of principal component regression (PCR) and principal component-artificial neural network (PC-ANN) methods. Eigen value ranking (EV) and correlation ranking (CR) were used here to select the most relevant set of PCs as inputs for PCR and PC-ANN modeling methods. The results supported that the correlation ranking-principal component-artificial neural network (CR-PC-ANN) model could predict the (13)C NMR chemical shifts of all 10 carbon atoms in mono substituted naphthalenes with R(2) ≥ 0.922 for training set, R(2) ≥ 0.963 for validation set and R(2) ≥ 0.936 for the test set. Comparison of the results with other existing factor selection method revealed that less accurate results were obtained by the eigen value ranking procedure. PMID:21035668

  2. Analysis of fracture surface of titanium-porcelain bonding by electron spectroscopy for chemical analysis.

    PubMed

    Kannari, Yoshiteru; Endo, Kazuhiko; Ida, Yusuke; Ochi, Morio; Ohno, Hiroki

    2014-01-01

    Three commercially available porcelains bonded to titanium were evaluated to determine the weakest zone of the titanium-porcelain bonding structures. Tensile bond tests were performed for these specimens (NO, DU, and VI) and for Ni-Cr alloy-porcelain bonding samples that served as controls. The maximum bond strengths between porcelain and titanium and the Ni-Cr alloy subjected to different metal surface treatments were compared. Sand blasting effectively increased bond strengths in titanium-porcelain bonding materials. No statistically significant differences in the maximum bond strengths were found between the NO sample and a control; however, sample NO exhibited greater maximum bond strength than DU and VI samples. The bond strengths increased with increasing area fractions of porcelain failure on fracture surfaces. The weakest zones were investigated based on the oxygen chemical states determined by electron spectroscopy for chemical analysis, which include bridging oxygen (Si-O-Si), nonbridging oxygen (Si-O(-) M(+)), and titanium oxide (O(2-)) states. We concluded that the titanium oxide layer is the weakest zone of titanium-porcelain bonding structures.

  3. Comprehensive Analysis Competence and Innovative Approaches for Sustainable Chemical Production.

    PubMed

    Appel, Joerg; Colombo, Corrado; Dätwyler, Urs; Chen, Yun; Kerimoglu, Nimet

    2016-01-01

    Humanity currently sees itself facing enormous economic, ecological, and social challenges. Sustainable products and production in specialty chemistry are an important strategic element to address these megatrends. In addition to that, digitalization and global connectivity will create new opportunities for the industry. One aspect is examined in this paper, which shows the development of comprehensive analysis of production networks for a more sustainable production in which the need for innovative solutions arises. Examples from data analysis, advanced process control and automated performance monitoring are shown. These efforts have significant impact on improved yields, reduced energy and water consumption, and better product performance in the application of the products.

  4. Comprehensive Analysis Competence and Innovative Approaches for Sustainable Chemical Production.

    PubMed

    Appel, Joerg; Colombo, Corrado; Dätwyler, Urs; Chen, Yun; Kerimoglu, Nimet

    2016-01-01

    Humanity currently sees itself facing enormous economic, ecological, and social challenges. Sustainable products and production in specialty chemistry are an important strategic element to address these megatrends. In addition to that, digitalization and global connectivity will create new opportunities for the industry. One aspect is examined in this paper, which shows the development of comprehensive analysis of production networks for a more sustainable production in which the need for innovative solutions arises. Examples from data analysis, advanced process control and automated performance monitoring are shown. These efforts have significant impact on improved yields, reduced energy and water consumption, and better product performance in the application of the products. PMID:27646543

  5. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  6. Synthesis and analysis in studies of chemical evolution

    NASA Technical Reports Server (NTRS)

    Ponnamperuma, C.; Hobish, M. K.; Kobayashi, K.; Hua, L. L.; Senaratne, N.

    1986-01-01

    Studies of the various processes that may have given rise to life on the Earth have demonstrated the appropriateness of an approach that makes use of analysis and synthesis. Analysis of extraterrestrial samples in the form of meteorites has demonstrated the presence of several precursors of biomolecules, most notably a full suite of nucleic acid bases and nucleotides of biological significance. These species were determined after exhaustive extraction of the sample and subsequent analysis using HPLC, GC, MS, and GC-MS. Procedural blanks indicate that these molecules are likely not the result of contamination during the extraction and analysis process. Similar species were found as products of spark discharge experiments in atmospheres thought to mimic primitive Earth conditions. These results indicate that the basic chemistry underlying these syntheses is common, and that life may not be unique to the Earth. Studies underway in the laboratory make use of proton nuclear magnetic resonance spectroscopy as a probe to assess associations between selected amino acids and any of several nucleotides comprising their genetic code and genetic anticode sequences. These studies demonstrate a clear selectivity by the anticode sequences, thus confirming the hydrophobicity studies performed by Lacey et al. These studies further support the contention that life is likely a natural result of the physics and chemistry of the universe.

  7. Rapid Screening of Complex Chemical Samples via Capillary Array Analysis

    SciTech Connect

    D. S. Anex; D. W. Neyer

    1998-11-01

    This report is a summary of the results of a two-year Laboratory-Directed Research and Development (LDRD) project that developed instrumentation and methods for capillary array analysis. During the course of this project, a new capillary array electrochromatography instrument was developed to perform eight simultaneous separations and provide complementary chromatographic information from each column on a single sample.

  8. RAPID ON-SITE METHODS OF CHEMICAL ANALYSIS

    EPA Science Inventory

    The analysis of potentially hazardous air, water and soil samples collected and shipped to service laboratories off-site is time consuming and expensive. This Chapter addresses the practical alternative of performing the requisite analytical services on-site. The most significant...

  9. Analysis of physical and chemical parameters of bottled drinking water.

    PubMed

    Mahajan, Rakesh Kumar; Walia, T P S; Lark, B S; Sumanjit

    2006-04-01

    Seventeen different brands of bottled drinking water, collected from different retail shops in Amritsar, were analyzed for different physical and chemical parameters to ascertain their compliability with the prescribed/recommended limits of the World Heath Organization (WHO) and the United States Environmental Protection Agency (USEPA). It was found that the majority of the brands tested were over-treated. Lower values of hardness, total dissolved solids (TDS) and conductance than the prescribed limits of WHO showed that water was deficient in essential minerals. Minerals like magnesium, potassium, calcium and fluoride were present in some cases in such a low concentration that water seemed to be as good as distilled water. Samples showing fluoride lesser than 0.5 mg/l warranted additional sources of fluoride for the people consuming only bottled water for drinking purposes. Zero values for chlorine demand as shown by all the bottled water samples showed that water samples were safe from micro-organisms. In case of heavy metals, only lead had been found to be greater than the limit of 0.015 mg/l as prescribed by WHO and USEPA, in seven out of 17 samples. Lead even at such a low concentration can pose a great health hazard.

  10. A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox.

    PubMed

    Vellela, Melissa; Qian, Hong

    2007-07-01

    For a system of biochemical reactions, it is known from the work of T.G. Kurtz [J. Appl. Prob. 8, 344 (1971)] that the chemical master equation model based on a stochastic formulation approaches the deterministic model based on the Law of Mass Action in the infinite system-size limit in finite time. The two models, however, often show distinctly different steady-state behavior. To further investigate this "paradox," a comparative study of the deterministic and stochastic models of a simple autocatalytic biochemical reaction, taken from a text by the late J. Keizer, is carried out. We compute the expected time to extinction, the true stochastic steady state, and a quasistationary probability distribution in the stochastic model. We show that the stochastic model predicts the deterministic behavior on a reasonable time scale, which can be consistently obtained from both models. The transition time to the extinction, however, grows exponentially with the system size. Mathematically, we identify that exchanging the limits of infinite system size and infinite time is problematic. The appropriate system size that can be considered sufficiently large, an important parameter in numerical computation, is also discussed.

  11. Chemical analysis of superconducting phase in K-doped picene

    NASA Astrophysics Data System (ADS)

    Kambe, Takashi; Nishiyama, Saki; Nguyen, Huyen L. T.; Terao, Takahiro; Izumi, Masanari; Sakai, Yusuke; Zheng, Lu; Goto, Hidenori; Itoh, Yugo; Onji, Taiki; Kobayashi, Tatsuo C.; Sugino, Hisako; Gohda, Shin; Okamoto, Hideki; Kubozono, Yoshihiro

    2016-11-01

    Potassium-doped picene (K3.0picene) with a superconducting transition temperature (T C) as high as 14 K at ambient pressure has been prepared using an annealing technique. The shielding fraction of this sample was 5.4% at 0 GPa. The T C showed a positive pressure-dependence and reached 19 K at 1.13 GPa. The shielding fraction also reached 18.5%. To investigate the chemical composition and the state of the picene skeleton in the superconducting sample, we used energy-dispersive x-ray (EDX) spectroscopy, MALDI-time-of-flight (MALDI-TOF) mass spectroscopy and x-ray diffraction (XRD). Both EDX and MALDI-TOF indicated no contamination with materials other than K-doped picene or K-doped picene fragments, and supported the preservation of the picene skeleton. However, it was also found that a magnetic K-doped picene sample consisted mainly of picene fragments or K-doped picene fragments. Thus, removal of the component contributing the magnetic quality to a superconducting sample should enhance the volume fraction.

  12. Chemical analysis of superconducting phase in K-doped picene.

    PubMed

    Kambe, Takashi; Nishiyama, Saki; Nguyen, Huyen L T; Terao, Takahiro; Izumi, Masanari; Sakai, Yusuke; Zheng, Lu; Goto, Hidenori; Itoh, Yugo; Onji, Taiki; Kobayashi, Tatsuo C; Sugino, Hisako; Gohda, Shin; Okamoto, Hideki; Kubozono, Yoshihiro

    2016-11-01

    Potassium-doped picene (K3.0picene) with a superconducting transition temperature (T C) as high as 14 K at ambient pressure has been prepared using an annealing technique. The shielding fraction of this sample was 5.4% at 0 GPa. The T C showed a positive pressure-dependence and reached 19 K at 1.13 GPa. The shielding fraction also reached 18.5%. To investigate the chemical composition and the state of the picene skeleton in the superconducting sample, we used energy-dispersive x-ray (EDX) spectroscopy, MALDI-time-of-flight (MALDI-TOF) mass spectroscopy and x-ray diffraction (XRD). Both EDX and MALDI-TOF indicated no contamination with materials other than K-doped picene or K-doped picene fragments, and supported the preservation of the picene skeleton. However, it was also found that a magnetic K-doped picene sample consisted mainly of picene fragments or K-doped picene fragments. Thus, removal of the component contributing the magnetic quality to a superconducting sample should enhance the volume fraction. PMID:27604421

  13. Photoacoustic chemical sensing: layered systems and excitation source analysis

    NASA Astrophysics Data System (ADS)

    Marcus, Logan S.; Holthoff, Ellen L.; Pellegrino, Paul M.

    2015-05-01

    Photoacoustic spectroscopy (PAS) is a versatile tool that is well suited for the ranged interrogation of layered samples. We have previously demonstrated standoff photoacoustic (PA) chemical detection of condensed phase samples at one meter distance using an interferometric sensing platform. Current research investigates layered solid samples constructed from a thin layer of energetic material deposited on a substrate. The PA signal from the system, as measured by the interferometer, changes based on the differing optical and mechanical properties of the substrate. This signal variance must be understood in order to develop a sensor capable of detecting trace quantities of hazardous materials independent of the surface. Optical absorption and modal excitation are the two biggest sources of PA signal generated in the sample/substrate system. Finally, the mode of operation of the excitation source is investigated. Most PA sensing paradigms use a quantum cascade laser (QCL) operating in either pulsed or modulated CW mode. We will discuss photoacoustic signal generation with respect to these different operating modes.

  14. Chemical analysis applied to the radiation sterilization of solid ketoprofen

    NASA Astrophysics Data System (ADS)

    Colak, S.; Maquille, A.; Tilquin, B.

    2006-01-01

    The aim of this work is to investigate the feasibility of radiation sterilization of ketoprofen from a chemical point of view. Although irradiated ketoprofen has already been studied in the literature [Katusin-Razem et al., Radiat. Phys. Chem. 73 111-116 (2005)], new results, on the basis of electron spin resonance (ESR) measurements and the use of hyphenated techniques (GC-MS and LC-MS), are obtained. The ESR spectra of irradiated ketoprofen consists of four unresolved resonance peaks and the mean G-value of ketoprofen is found to be 4 +/- 0.9 nmoles/J, which is very small. HPLC-UV analyses indicate that no significant loss of ketoprofen is detected after irradiation. LC-MS-MS analyses show that the structures of the non-volatile final products are similar to ketoprofen. Benzaldehyde is detected in the irradiated samples after dynamic-extraction GC-MS. The analyses show that ketoprofen is radioresistant and therefore might be radiosterilized.

  15. Global Analysis Reveals Families of Chemical Motifs Enriched for hERG Inhibitors

    PubMed Central

    Du, Fang; Babcock, Joseph J.; Yu, Haibo; Zou, Beiyan; Li, Min

    2015-01-01

    Promiscuous inhibition of the human ether-à-go-go-related gene (hERG) potassium channel by drugs poses a major risk for life threatening arrhythmia and costly drug withdrawals. Current knowledge of this phenomenon is derived from a limited number of known drugs and tool compounds. However, in a diverse, naïve chemical library, it remains unclear which and to what degree chemical motifs or scaffolds might be enriched for hERG inhibition. Here we report electrophysiology measurements of hERG inhibition and computational analyses of >300,000 diverse small molecules. We identify chemical ‘communities’ with high hERG liability, containing both canonical scaffolds and structurally distinctive molecules. These data enable the development of more effective classifiers to computationally assess hERG risk. The resultant predictive models now accurately classify naïve compound libraries for tendency of hERG inhibition. Together these results provide a more complete reference map of characteristic chemical motifs for hERG liability and advance a systematic approach to rank chemical collections for cardiotoxicity risk. PMID:25700001

  16. Virus and Bacterial Cell Chemical Analysis by NanoSIMS

    SciTech Connect

    Weber, P; Holt, J

    2008-07-28

    In past work for the Department of Homeland Security, the LLNL NanoSIMS team has succeeded in extracting quantitative elemental composition at sub-micron resolution from bacterial spores using nanometer-scale secondary ion mass spectrometry (NanoSIMS). The purpose of this task is to test our NanoSIMS capabilities on viruses and bacterial cells. This initial work has proven successful. We imaged Tobacco Mosaic Virus (TMV) and Bacillus anthracis Sterne cells using scanning electron microscopy (SEM) and then analyzed those samples by NanoSIMS. We were able resolve individual viral particles ({approx}18 nm by 300 nm) in the SEM and extract correlated elemental composition in the NanoSIMS. The phosphorous/carbon ratio observed in TMV is comparable to that seen in bacterial spores (0.033), as was the chlorine/carbon ratio (0.11). TMV elemental composition is consistent from spot to spot, and TMV is readily distinguished from debris by NanoSIMS analysis. Bacterial cells were readily identified in the SEM and relocated in the NanoSIMS for elemental analysis. The Ba Sterne cells were observed to have a measurably lower phosphorous/carbon ratio (0.005), as compared to the spores produced in the same run (0.02). The chlorine/carbon ratio was approximately 2.5X larger in the cells (0.2) versus the spores (0.08), while the fluorine/carbon ratio was approximately 10X lower in the cells (0.008) than the spores (0.08). Silicon/carbon ratios for both cells and spores encompassed a comparable range. The initial data in this study suggest that high resolution analysis is useful because it allows the target agent to be analyzed separate from particulates and other debris. High resolution analysis would also be useful for trace sample analysis. The next step in this work is to determine the potential utility of elemental signatures in these kinds of samples. We recommend bulk analyses of media and agent samples to determine the range of media compositions in use, and to determine how

  17. Oncogene activation in spontaneous and chemically induced rodent tumors: implications for risk analysis

    SciTech Connect

    Reynolds, S.H.; Stowers, S.J.; Patterson, R.M.; Maronpot, R.R.; Anderson, M.W.

    1988-06-01

    The validity of rodent tumor end points in assessing the potential hazards of chemical exposure to humans is a somewhat controversial but very important issue since most chemicals are classified as potentially hazardous to humans on the basis of long-term carcinogenesis studies in rodents. The ability to distinguish between genotoxic, cytotoxic, or receptor-mediated promotion effects of chemical treatment would aid in the interpretation of rodent carcinogenesis data. Activated oncogenes in spontaneously occurring and chemically induced rodent tumors were examined and compared as one approach to determine the mechanism by which chemical treatment caused an increased incidence of rodent tumors. Different patterns of activated oncogenes were found not only in spontaneous versus chemically induced mouse liver tumors but also in a variety of spontaneous rat tumors versus chemically induced rat lung tumors. In the absence of cytotoxic effects, it could be argued that the chemicals in question activated protooncogenes by a direct genotoxic mechanism. These results provided a basis for the analysis of activated oncogenes in spontaneous and chemically induced rodent tumors to provide information at a molecular level to aid in the extrapolation of rodent carcinogenesis data to human risk assessment.

  18. Different Models Used to Interpret Chemical Changes: Analysis of a Curriculum and Its Impact on French Students' Reasoning

    ERIC Educational Resources Information Center

    Kermen, Isabelle; Meheut, Martine

    2009-01-01

    We present an analysis of the new French curriculum on chemical changes describing the underlying models and highlighting their relations to the empirical level. The authors of the curriculum introduced a distinction between the chemical change of a chemical system and the chemical reactions that account for it. We specify the different roles of…

  19. Advances in Mid-Infrared Spectroscopy for Chemical Analysis

    NASA Astrophysics Data System (ADS)

    Haas, Julian; Mizaikoff, Boris

    2016-06-01

    Infrared spectroscopy in the 3–20 μm spectral window has evolved from a routine laboratory technique into a state-of-the-art spectroscopy and sensing tool by benefitting from recent progress in increasingly sophisticated spectra acquisition techniques and advanced materials for generating, guiding, and detecting mid-infrared (MIR) radiation. Today, MIR spectroscopy provides molecular information with trace to ultratrace sensitivity, fast data acquisition rates, and high spectral resolution catering to demanding applications in bioanalytics, for example, and to improved routine analysis. In addition to advances in miniaturized device technology without sacrificing analytical performance, selected innovative applications for MIR spectroscopy ranging from process analysis to biotechnology and medical diagnostics are highlighted in this review.

  20. Neural network based analysis for chemical sensor arrays

    SciTech Connect

    Hashem, S.; Keller, P.E.; Kouzes, R.T.; Kangas, L.J.

    1995-04-01

    Compact, portable systems capable of quickly identifying contaminants in the field are of great importance when monitoring the environment. In this paper, we examine the effectiveness of using artificial neural networks for real-time data analysis of a sensor array. Analyzing the sensor data in parallel may allow for rapid identification of contaminants in the field without requiring highly selective individual sensors. We use a prototype sensor array which consists of nine tin-oxide Taguchi-type sensors, a temperature sensor, and a humidity sensor. We illustrate that by using neural network based analysis of the sensor data, the selectivity of the sensor array may be significantly improved, especially when some (or all) the sensors are not highly selective.

  1. Advances in Mid-Infrared Spectroscopy for Chemical Analysis.

    PubMed

    Haas, Julian; Mizaikoff, Boris

    2016-06-12

    Infrared spectroscopy in the 3-20 μm spectral window has evolved from a routine laboratory technique into a state-of-the-art spectroscopy and sensing tool by benefitting from recent progress in increasingly sophisticated spectra acquisition techniques and advanced materials for generating, guiding, and detecting mid-infrared (MIR) radiation. Today, MIR spectroscopy provides molecular information with trace to ultratrace sensitivity, fast data acquisition rates, and high spectral resolution catering to demanding applications in bioanalytics, for example, and to improved routine analysis. In addition to advances in miniaturized device technology without sacrificing analytical performance, selected innovative applications for MIR spectroscopy ranging from process analysis to biotechnology and medical diagnostics are highlighted in this review.

  2. Advances in Mid-Infrared Spectroscopy for Chemical Analysis

    NASA Astrophysics Data System (ADS)

    Haas, Julian; Mizaikoff, Boris

    2016-06-01

    Infrared spectroscopy in the 3-20 μm spectral window has evolved from a routine laboratory technique into a state-of-the-art spectroscopy and sensing tool by benefitting from recent progress in increasingly sophisticated spectra acquisition techniques and advanced materials for generating, guiding, and detecting mid-infrared (MIR) radiation. Today, MIR spectroscopy provides molecular information with trace to ultratrace sensitivity, fast data acquisition rates, and high spectral resolution catering to demanding applications in bioanalytics, for example, and to improved routine analysis. In addition to advances in miniaturized device technology without sacrificing analytical performance, selected innovative applications for MIR spectroscopy ranging from process analysis to biotechnology and medical diagnostics are highlighted in this review.

  3. Chemical analysis of outgassing contaminants on spacecraft surfaces

    NASA Technical Reports Server (NTRS)

    Mcnutt, R. C.

    1973-01-01

    Methods for analyzing and characterizing outgassing contaminants from such materials as RTV 501 potting compound and S 13 G paint are presented. Fractional distillation of a gross distillate from RTV 501 rubber was carried out and the distilled fractions examined as to their ultraviolet and infrared spectra by gas liquid chromatography. A sensitive technique for structural analysis and molecular identification was found to consist of a gas chromatography-mass spectroscopy system, which was determined to be economically unfeasible at present.

  4. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

    PubMed

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-11-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

  5. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes

    PubMed Central

    Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

    2009-01-01

    We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a ∼21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes. PMID:19740761

  6. Ultrafast laser induced breakdown spectroscopy for high spatial resolution chemical analysis

    NASA Astrophysics Data System (ADS)

    Zorba, Vassilia; Mao, Xianglei; Russo, Richard E.

    2011-02-01

    Femtosecond laser induced breakdown spectroscopy (LIBS) was used to identify the spatial resolution limitations and assess the minimal detectable mass restrictions in laser-ablation based chemical analysis. The atomic emission of sodium (Na) and potassium (K) dopants in transparent dielectric Mica matrices was studied, to find that both these elements could be detected from 450 nm diameter ablation craters, full-width-at-half-maximum (FWHM). Under optimal conditions, mass as low as 220 ag was measured, demonstrating the feasibility of using laser-ablation based chemical analysis to achieve high spatial resolution elemental analysis in real-time and at atmospheric pressure conditions.

  7. The electron spectroscopy for chemical analysis microscopy beamline data acquisition system at ELETTRA

    NASA Astrophysics Data System (ADS)

    Gariazzo, C.; Krempaska, R.; Morrison, G. R.

    1996-07-01

    The electron spectroscopy for chemical analysis (ESCA) microscopy data acquisition system enables the user to control the imaging and spectroscopy modes of operation of the beamline ESCA microscopy at ELETTRA. It allows the user to integrate all experiment, beamline and machine operations in one single environment. The system also provides simple data analysis for both spectra and images data to guide further data acquisition.

  8. Inorganic chemical analysis of environmental materials—A lecture series

    USGS Publications Warehouse

    Crock, J.G.; Lamothe, P.J.

    2011-01-01

    At the request of the faculty of the Colorado School of Mines, Golden, Colorado, the authors prepared and presented a lecture series to the students of a graduate level advanced instrumental analysis class. The slides and text presented in this report are a compilation and condensation of this series of lectures. The purpose of this report is to present the slides and notes and to emphasize the thought processes that should be used by a scientist submitting samples for analyses in order to procure analytical data to answer a research question. First and foremost, the analytical data generated can be no better than the samples submitted. The questions to be answered must first be well defined and the appropriate samples collected from the population that will answer the question. The proper methods of analysis, including proper sample preparation and digestion techniques, must then be applied. Care must be taken to achieve the required limits of detection of the critical analytes to yield detectable analyte concentration (above "action" levels) for the majority of the study's samples and to address what portion of those analytes answer the research question-total or partial concentrations. To guarantee a robust analytical result that answers the research question(s), a well-defined quality assurance and quality control (QA/QC) plan must be employed. This QA/QC plan must include the collection and analysis of field and laboratory blanks, sample duplicates, and matrix-matched standard reference materials (SRMs). The proper SRMs may include in-house materials and/or a selection of widely available commercial materials. A discussion of the preparation and applicability of in-house reference materials is also presented. Only when all these analytical issues are sufficiently addressed can the research questions be answered with known certainty.

  9. Effect-based and chemical analysis of polycyclic aromatic hydrocarbons in smoked meat: a practical food-monitoring approach.

    PubMed

    Kuhn, K; Nowak, B; Behnke, A; Seidel, A; Lampen, A

    2009-07-01

    Polycyclic aromatic hydrocarbons (PAHs), which are generated by heat treatment and smoke curing of meat, pose a risk to human health. At present, the determination of these unwanted contaminants requires costly, time-consuming chemical analysis of smoked meat. An alternative is effect-directed high-throughput bioassays, which could also be used as a pre-screening method. The authors recently adapted the in vitro chemical-activated luciferase gene expression (CALUX) assay as a rapid, sensitive, and inexpensive screening technique for compounds such as dioxins, polychlorinated biphenyls, and PAHs. The aim of the present study was to apply a practical approach under realistic conditions. Custom-made meat samples produced under defined conditions with different PAH levels were analysed using this bioassay and gas chromatography-mass spectrometry (GC/MS) to determine the influence of different smoking conditions (temperature and duration) on PAH levels. It was found that cold smoking for up to 6 h did not result in strong PAH contamination, whereas hot (65 degrees C) and longer smoking times caused a considerable increase in both the bioassay response and the levels of 31 individually determined PAHs. The response in the effect-based bioassay was in good agreement with the values of chemical analysis. The bioassay made it possible to determine accurately the degree of contamination. The results show that this assay is suitable for high-throughput screening for unknown levels of toxicologically relevant PAHs in meat samples and is sensitive enough to differentiate between different PAH levels generated under various smoking conditions. Effect-based screening techniques, therefore, provide a new instrument for official food monitoring.

  10. Software for analysis of chemical mixtures--composition, occurrence, distribution, and possible toxicity

    USGS Publications Warehouse

    Scott, Jonathon C.; Skach, Kenneth A.; Toccalino, Patricia L.

    2013-01-01

    The composition, occurrence, distribution, and possible toxicity of chemical mixtures in the environment are research concerns of the U.S. Geological Survey and others. The presence of specific chemical mixtures may serve as indicators of natural phenomena or human-caused events. Chemical mixtures may also have ecological, industrial, geochemical, or toxicological effects. Chemical-mixture occurrences vary by analyte composition and concentration. Four related computer programs have been developed by the National Water-Quality Assessment Program of the U.S. Geological Survey for research of chemical-mixture compositions, occurrences, distributions, and possible toxicities. The compositions and occurrences are identified for the user-supplied data, and therefore the resultant counts are constrained by the user’s choices for the selection of chemicals, reporting limits for the analytical methods, spatial coverage, and time span for the data supplied. The distribution of chemical mixtures may be spatial, temporal, and (or) related to some other variable, such as chemical usage. Possible toxicities optionally are estimated from user-supplied benchmark data. The software for the analysis of chemical mixtures described in this report is designed to work with chemical-analysis data files retrieved from the U.S. Geological Survey National Water Information System but can also be used with appropriately formatted data from other sources. Installation and usage of the mixture software are documented. This mixture software was designed to function with minimal changes on a variety of computer-operating systems. To obtain the software described herein and other U.S. Geological Survey software, visit http://water.usgs.gov/software/.

  11. Integrated optical sensor platform for multiparameter bio-chemical analysis.

    PubMed

    Lützow, Peter; Pergande, Daniel; Heidrich, Helmut

    2011-07-01

    There is growing demand for robust, reliable, low cost, and easy to use sensor systems that feature multiparameter analysis in many application areas ranging from safety and security to point of care and medical diagnostics. Here, we highlight the theory and show first experimental results on a novel approach targeting the realization of massively multiplexed sensor arrays. The presented sensor platform is based on arrays of frequency-modulated integrated optical microring resonators (MRR) fed by a single bus waveguide combined with lock-in detection to filter out in a reliable and simple manner their individual response to external stimuli. The working principle is exemplified on an array of four thermo-optically modulated MRR. It is shown that with this technique tracking of individual resonances is possible even in case of strong spectral overlap. PMID:21747482

  12. Integrated optical sensor platform for multiparameter bio-chemical analysis.

    PubMed

    Lützow, Peter; Pergande, Daniel; Heidrich, Helmut

    2011-07-01

    There is growing demand for robust, reliable, low cost, and easy to use sensor systems that feature multiparameter analysis in many application areas ranging from safety and security to point of care and medical diagnostics. Here, we highlight the theory and show first experimental results on a novel approach targeting the realization of massively multiplexed sensor arrays. The presented sensor platform is based on arrays of frequency-modulated integrated optical microring resonators (MRR) fed by a single bus waveguide combined with lock-in detection to filter out in a reliable and simple manner their individual response to external stimuli. The working principle is exemplified on an array of four thermo-optically modulated MRR. It is shown that with this technique tracking of individual resonances is possible even in case of strong spectral overlap.

  13. The chemical identification and analysis of Aspergillus nidulans secondary metabolites

    PubMed Central

    Sanchez, James F.

    2013-01-01

    Filamentous fungi have long been recognized to be a rich source of secondary metabolites with potential medicinal applications. The recent genomic sequencing of several Aspergillus species has revealed that many secondary metabolite gene clusters are apparently silent under standard laboratory conditions. Several successful approaches have been utilized to upregulate these genes and unearth the corresponding natural products. A straightforward, reliable method to purify and characterize new metabolites therefore should be useful. Details are provided herein on the cultivation of Aspergillus nidulans and the LC/MS analysis of the metabolic profile. Following is an explanation of silica gel chromatography, HPLC, and preparative TLC. Finally, the NMR characterization of previously unknown A. nidulans metabolites is detailed. PMID:23065610

  14. LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 1: Theory and numerical solution procedures

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 1 of a series of three reference publications that describe LENS, provide a detailed guide to its usage, and present many example problems. Part 1 derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved. The accuracy and efficiency of LSENS are examined by means of various test problems, and comparisons with other methods and codes are presented. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

  15. The dilemma in prioritizing chemicals for environmental analysis: known versus unknown hazards.

    PubMed

    Anna, Sobek; Sofia, Bejgarn; Christina, Rudén; Magnus, Breitholtz

    2016-08-10

    A major challenge for society is to manage the risks posed by the many chemicals continuously emitted to the environment. All chemicals in production and use cannot be monitored and science-based strategies for prioritization are essential. In this study we review available data to investigate which substances are included in environmental monitoring programs and published research studies reporting analyses of chemicals in Baltic Sea fish between 2000 and 2012. Our aim is to contribute to the discussion of priority settings in environmental chemical monitoring and research, which is closely linked to chemical management. In total, 105 different substances or substance groups were analyzed in Baltic Sea fish. Polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs) were the most studied substances or substance groups. The majority, 87%, of all analyses comprised 20% of the substances or substance groups, whereas 46 substance groups (44%) were analyzed only once. Almost three quarters of all analyses regarded a POP-substance (persistent organic pollutant). These results demonstrate that the majority of analyses on environmental contaminants in Baltic Sea fish concern a small number of already regulated chemicals. Legacy pollutants such as POPs pose a high risk to the Baltic Sea due to their hazardous properties. Yet, there may be a risk that prioritizations for chemical analyses are biased based on the knowns of the past. Such biases may lead to society failing in identifying risks posed by yet unknown hazardous chemicals. Alternative and complementary ways to identify priority chemicals are needed. More transparent communication between risk assessments performed as part of the risk assessment process within REACH and monitoring programs, and information on chemicals contained in consumer articles, would offer ways to identify chemicals for environmental analysis.

  16. The dilemma in prioritizing chemicals for environmental analysis: known versus unknown hazards.

    PubMed

    Anna, Sobek; Sofia, Bejgarn; Christina, Rudén; Magnus, Breitholtz

    2016-08-10

    A major challenge for society is to manage the risks posed by the many chemicals continuously emitted to the environment. All chemicals in production and use cannot be monitored and science-based strategies for prioritization are essential. In this study we review available data to investigate which substances are included in environmental monitoring programs and published research studies reporting analyses of chemicals in Baltic Sea fish between 2000 and 2012. Our aim is to contribute to the discussion of priority settings in environmental chemical monitoring and research, which is closely linked to chemical management. In total, 105 different substances or substance groups were analyzed in Baltic Sea fish. Polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans (PCDD/Fs) and polychlorinated biphenyls (PCBs) were the most studied substances or substance groups. The majority, 87%, of all analyses comprised 20% of the substances or substance groups, whereas 46 substance groups (44%) were analyzed only once. Almost three quarters of all analyses regarded a POP-substance (persistent organic pollutant). These results demonstrate that the majority of analyses on environmental contaminants in Baltic Sea fish concern a small number of already regulated chemicals. Legacy pollutants such as POPs pose a high risk to the Baltic Sea due to their hazardous properties. Yet, there may be a risk that prioritizations for chemical analyses are biased based on the knowns of the past. Such biases may lead to society failing in identifying risks posed by yet unknown hazardous chemicals. Alternative and complementary ways to identify priority chemicals are needed. More transparent communication between risk assessments performed as part of the risk assessment process within REACH and monitoring programs, and information on chemicals contained in consumer articles, would offer ways to identify chemicals for environmental analysis. PMID:27222376

  17. Environmental Chemical Analysis (by B. B. Kebbekus and S. Mitra)

    NASA Astrophysics Data System (ADS)

    Bower, Reviewed By Nathan W.

    1999-11-01

    This text helps to fill a void in the market, as there are relatively few undergraduate instrumental analysis texts designed specifically for the expanding population of environmental science students. R. N. Reeve's introductory, open-learning Environmental Analysis (Wiley, 1994) is one of the few, and it is aimed at a lower level and is less appropriate for traditional classroom study. Kebbekus and Mitra's book appears to be an update of I. Marr and M. Cresser's excellent 1983 text by the same name (and also published under the Chapman and Hall imprint). It assumes no background in instrumental methods of analysis but it does depend upon a good general chemistry background in kinetic and equilibrium calculations and the standard laboratory techniques found in a classical introduction to analytical chemistry. The slant taken by the authors is aimed more toward engineers, not only in the choice of topics, but also in how they are presented. For example, the statistical significance tests presented follow an engineering format rather than the standard used in analytical chemistry. This approach does not detract from the book's clarity. The writing style is concise and the book is generally well written. The earlier text, which has become somewhat of a classic, took the unusual step of teaching the instruments in the context of their environmental application. It was divided into sections on the "atmosphere", the "hydrosphere", the "lithosphere", and the "biosphere". This text takes a similar approach in the second half, with chapters on methods for air, water, and solid samples. Users who intend to use the book as a text instead of a reference will appreciate the addition of chapters in the first half of the book on spectroscopic, chromatographic, and mass spectrometric methods. The six chapters in these two parts of the book along with four chapters scattered throughout on environmental measurements, sampling, sample preparation, and quality assurance make a nice

  18. Chemical measurement of urine volume

    NASA Technical Reports Server (NTRS)

    Sauer, R. L.

    1978-01-01

    Chemical method of measuring volume of urine samples using lithium chloride dilution technique, does not interfere with analysis, is faster, and more accurate than standard volumetric of specific gravity/weight techniques. Adaptation of procedure to urinalysis could prove generally practical for hospital mineral balance and catechoamine determinations.

  19. Requirements analysis for safety-critical systems: A chemical batch processing example

    NASA Astrophysics Data System (ADS)

    Delemos, R.; Saeed, A.; Anderson, T.

    1994-01-01

    An essential basis for the development of software for safety-critical systems is to establish high-quality requirements specifications. In the paper the authors present a methodology for requirements analysis that consists of: a framework which facilitates the systematic analysis of the safety requirements, a graph which records the safety specifications and their relationships, and a set of procedures for the quality analysis of the safety specifications. To illustrate the approach a case study, based on chemical batch processing, is presented.

  20. Chemical analysis of copper/brass samples from Christian Island

    SciTech Connect

    Hancock, R.G.V.; Farquhar, R.M.; Pavlish, L.A.; Finlayson, W.A.

    1994-12-31

    In 1639, French Jesuit missionaries established the fortified mission of Ste. Marie I at Midland, Ontario. Ten years later, following a series of Iroquoian war-party raids that were facilitated by Dutch and English trading interests, the mission was abandoned and destroyed. The missionaries and local Wendats (Hurons) debated new venues, finally settling on Christian Island in southwestern Georgian Bay as a temporary safe haven rather than their original first choice, the more distant and safer Manitoulin Island. In 1649, they began establishing the fortified mission of Ste. Marie 11. A Wendat settlement existed on the island, but unlike the fort whose walls are intact today, little evidence remains of the island`s single-year population of {approximately} 10000 Wendats, most of whom perished. There was extreme deprivation on the island during the winter of 1649-1650. People died of famine, disease, and ill-fated sorties to the mainland. In June of 1650, after a single year of occupation, the site of Ste. Marie 11 was abandoned when the missionaries were recalled to the relative safety of Quebec City. The remaining Wendats were either assimilated by other groups or killed by the Iroquois. An analysis was performed of the brass goods discarded in the area of the island fort and nearby villages.

  1. Endocrine-disrupting Chemicals: Review of Toxicological Mechanisms Using Molecular Pathway Analysis

    PubMed Central

    Yang, Oneyeol; Kim, Hye Lim; Weon, Jong-Il; Seo, Young Rok

    2015-01-01

    Endocrine disruptors are known to cause harmful effects to human through various exposure routes. These chemicals mainly appear to interfere with the endocrine or hormone systems. As importantly, numerous studies have demonstrated that the accumulation of endocrine disruptors can induce fatal disorders including obesity and cancer. Using diverse biological tools, the potential molecular mechanisms related with these diseases by exposure of endocrine disruptors. Recently, pathway analysis, a bioinformatics tool, is being widely used to predict the potential mechanism or biological network of certain chemicals. In this review, we initially summarize the major molecular mechanisms involved in the induction of the above mentioned diseases by endocrine disruptors. Additionally, we provide the potential markers and signaling mechanisms discovered via pathway analysis under exposure to representative endocrine disruptors, bisphenol, diethylhexylphthalate, and nonylphenol. The review emphasizes the importance of pathway analysis using bioinformatics to finding the specific mechanisms of toxic chemicals, including endocrine disruptors. PMID:25853100

  2. Chemical Differentiation of Osseous, Dental, and Non-skeletal Materials in Forensic Anthropology using Elemental Analysis.

    PubMed

    Zimmerman, Heather A; Meizel-Lambert, Cayli J; Schultz, John J; Sigman, Michael E

    2015-03-01

    Forensic anthropologists are generally able to identify skeletal materials (bone and tooth) using gross anatomical features; however, highly fragmented or taphonomically altered materials may be problematic to identify. Several chemical analysis techniques have been shown to be reliable laboratory methods that can be used to determine if questionable fragments are osseous, dental, or non-skeletal in nature. The purpose of this review is to provide a detailed background of chemical analysis techniques focusing on elemental compositions that have been assessed for use in differentiating osseous, dental, and non-skeletal materials. More recently, chemical analysis studies have also focused on using the elemental composition of osseous/dental materials to evaluate species and provide individual discrimination, but have generally been successful only in small, closed groups, limiting their use forensically. Despite significant advances incorporating a variety of instruments, including handheld devices, further research is necessary to address issues in standardization, error rates, and sample size/diversity.

  3. Surface characterization and chemical analysis of bamboo substrates pretreated by alkali hydrogen peroxide.

    PubMed

    Song, Xueping; Jiang, Yan; Rong, Xianjian; Wei, Wei; Wang, Shuangfei; Nie, Shuangxi

    2016-09-01

    The surface characterization and chemical analysis of bamboo substrates by alkali hydrogen peroxide pretreatment (AHPP) were investigated in this study. The results tended to manifest that AHPP prior to enzymatic and chemical treatment was potential for improving accessibility and reactivity of bamboo substrates. The inorganic components, organic solvent extractives and acid-soluble lignin were effectively removed by AHPP. X-ray photoelectron spectroscopy (XPS) analysis indicated that the surface of bamboo chips had less lignin but more carbohydrate after pre-treatment. Fiber surfaces became etched and collapsed, and more pores and debris on the substrate surface were observed with Scanning Electron Microscopy (SEM). Brenauer-Emmett-Teller (BET) results showed that both of pore volume and surface area were increased after AHPP. Although XRD analysis showed that AHPP led to relatively higher crystallinity, pre-extraction could overall enhance the accessibility of enzymes and chemicals into the bamboo structure. PMID:27311789

  4. Chemical Differentiation of Osseous, Dental, and Non-skeletal Materials in Forensic Anthropology using Elemental Analysis.

    PubMed

    Zimmerman, Heather A; Meizel-Lambert, Cayli J; Schultz, John J; Sigman, Michael E

    2015-03-01

    Forensic anthropologists are generally able to identify skeletal materials (bone and tooth) using gross anatomical features; however, highly fragmented or taphonomically altered materials may be problematic to identify. Several chemical analysis techniques have been shown to be reliable laboratory methods that can be used to determine if questionable fragments are osseous, dental, or non-skeletal in nature. The purpose of this review is to provide a detailed background of chemical analysis techniques focusing on elemental compositions that have been assessed for use in differentiating osseous, dental, and non-skeletal materials. More recently, chemical analysis studies have also focused on using the elemental composition of osseous/dental materials to evaluate species and provide individual discrimination, but have generally been successful only in small, closed groups, limiting their use forensically. Despite significant advances incorporating a variety of instruments, including handheld devices, further research is necessary to address issues in standardization, error rates, and sample size/diversity. PMID:25753999

  5. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    PubMed

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-01

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data.

  6. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    PubMed

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-01

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data. PMID:25647718

  7. Nuclear and radiochemical techniques in chemical analysis. Final report

    SciTech Connect

    Finston, H.L.; Williams, E.T.

    1981-06-01

    The areas studied during the period of the contract included determinations of cross sections for nuclear reactions, determination of neutron capture cross sections of radionuclides, application of special activation techniques, and x-ray counting, elucidation of synergic solvent extraction mechanisms and development of new solvent extraction techniques, and the development of a PIXE analytical facility. The thermal neutron capture cross section of /sup 22/Na was determined, and cross sections and energy levels were determined for /sup 20/Ne(n,..cap alpha..)/sup 17/O, /sup 20/Ne(n,P)/sup 20/F, and /sup 40/Ar(n,..cap alpha..)/sup 37/S. Inelastic scattering with 2 to 3 MeV neutrons followed by counting of the metastable states permits analysis of the following elements: In, Sr, Cd, Hg, and Pb. Bromine can be detected in the presence of a 500-fold excess of Na and/or K by thermal neutron activation and x-ray counting, and as little as 0.3 x 10/sup -9/ g of Hg can be detected by this technique. Mediun energy neutrons (10 to 160 MeV) have been used to determine Tl, Pb, and Bi by (n,Xn) and (n,PXn) reactions. The reaction /sup 19/F(P,..cap alpha..)/sup 76/O has been used to determine as little as 50 ..mu..mol of Freon -14. Mechanisms for synergic solvent extractions have been elucidated and a new technique of homogeneous liquid-liquid solvent extraction has been developed in which the neutral complex is rapidly extracted propylene carbonate by raising and lowering the temperature of the system. An external-beam PIXE system has been developed for trace element analyses of a variety of sample types. Various sample preparation techniques have been applied to a diverse range of samples including marine sediment, coral, coal, and blood.

  8. CHEMICAL ANALYSIS OF ASYMPTOTIC GIANT BRANCH STARS IN M62

    SciTech Connect

    Lapenna, E.; Mucciarelli, A.; Ferraro, F. R.; Lanzoni, B.; Dalessandro, E.

    2015-11-10

    We have collected UVES-FLAMES high-resolution spectra for a sample of 6 asymptotic giant branch (AGB) and 13 red giant branch (RGB) stars in the Galactic globular cluster (GC) M62 (NGC 6266). Here we present the detailed abundance analysis of iron, titanium, and light elements (O, Na, Mg, and Al). For the majority (five out of six) of the AGB targets, we find that the abundances of both iron and titanium determined from neutral lines are significantly underestimated with respect to those obtained from ionized features, the latter being, instead, in agreement with those measured for the RGB targets. This is similar to recent findings in other clusters and may suggest the presence of nonlocal thermodynamic equilibrium (NLTE) effects. In the O–Na, Al–Mg, and Na–Al planes, the RGB stars show the typical correlations observed for GC stars. Instead, all the AGB targets are clumped in the regions where first-generation stars are expected to lie, similar to what was recently found for the AGB population of NGC 6752. While the sodium and aluminum abundances could be underestimated as a consequence of the NLTE bias affecting iron and titanium, the oxygen line used does not suffer from the same effects, and the lack of O-poor AGB stars therefore is a solid result. We can thus conclude that none of the investigated AGB stars belongs to the second stellar generation of M62. We also find an RGB star with extremely high sodium abundance ([Na/Fe] = +1.08 dex)

  9. Analysis of Pfizer compounds in EPA's ToxCast chemicals-assay space.

    PubMed

    Shah, Falgun; Greene, Nigel

    2014-01-21

    The U.S. Environmental Protection Agency (EPA) launched the ToxCast program in 2007 with the goal of evaluating high-throughput in vitro assays to prioritize chemicals that need toxicity testing. Their goal was to develop predictive bioactivity signatures for toxic compounds using a set of in vitro assays and/or in silico properties. In 2009, Pfizer joined the ToxCast initiative by contributing 52 compounds with preclinical and clinical data for profiling across the multiple assay platforms available. Here, we describe the initial analysis of the Pfizer subset of compounds within the ToxCast chemical (n = 1814) and in vitro assay (n = 486) space. An analysis of the hit rate of Pfizer compounds in the ToxCast assay panel allowed us to focus our mining of assays potentially most relevant to the attrition of our compounds. We compared the bioactivity profile of Pfizer compounds to other compounds in the ToxCast chemical space to gain insights into common toxicity pathways. Additionally, we explored the similarity in the chemical and biological spaces between drug-like compounds and environmental chemicals in ToxCast and compared the in vivo profiles of a subset of failed pharmaceuticals having high similarity in both spaces. We found differences in the chemical and biological spaces of pharmaceuticals compared to environmental chemicals, which may question the applicability of bioactivity signatures developed exclusively based on the latter to drug-like compounds if used without prior validation with the ToxCast Phase-II chemicals. Finally, our analysis has allowed us to identify novel interactions for our compounds in particular with multiple nuclear receptors that were previously not known. This insight may help us to identify potential liabilities with future novel compounds.

  10. LC-MS n Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

    NASA Astrophysics Data System (ADS)

    Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

    2011-09-01

    Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MS n . The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MS n fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MS n experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MS n methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications.

  11. Simplified quantification of labile proton concentration-weighted chemical exchange rate (k(ws) ) with RF saturation time dependent ratiometric analysis (QUESTRA): normalization of relaxation and RF irradiation spillover effects for improved quantitative chemical exchange saturation transfer (CEST) MRI.

    PubMed

    Sun, Phillip Zhe

    2012-04-01

    Chemical exchange saturation transfer MRI is an emerging imaging technique capable of detecting dilute proteins/peptides and microenvironmental properties, with promising in vivo applications. However, chemical exchange saturation transfer MRI contrast is complex, varying not only with the labile proton concentration and exchange rate, but also with experimental conditions such as field strength and radiofrequency (RF) irradiation scheme. Furthermore, the optimal RF irradiation power depends on the exchange rate, which must be estimated in order to optimize the chemical exchange saturation transfer MRI experiments. Although methods including numerical fitting with modified Bloch-McConnell equations, quantification of exchange rate with RF saturation time and power (QUEST and QUESP), have been proposed to address this relationship, they require multiple-parameter non-linear fitting and accurate relaxation measurement. Our work extended the QUEST algorithm with ratiometric analysis (QUESTRA) that normalizes the magnetization transfer ratio at labile and reference frequencies, which effectively eliminates the confounding relaxation and RF spillover effects. Specifically, the QUESTRA contrast approaches its steady state mono-exponentially at a rate determined by the reverse exchange rate (k(ws) ), with little dependence on bulk water T(1) , T(2) , RF power and chemical shift. The proposed algorithm was confirmed numerically, and validated experimentally using a tissue-like phantom of serially titrated pH compartments.

  12. Scanning angle Raman spectroscopy: Investigation of Raman scatter enhancement techniques for chemical analysis

    SciTech Connect

    Meyer, Matthew W.

    2013-01-01

    This thesis outlines advancements in Raman scatter enhancement techniques by applying evanescent fields, standing-waves (waveguides) and surface enhancements to increase the generated mean square electric field, which is directly related to the intensity of Raman scattering. These techniques are accomplished by employing scanning angle Raman spectroscopy and surface enhanced Raman spectroscopy. A 1064 nm multichannel Raman spectrometer is discussed for chemical analysis of lignin. Extending dispersive multichannel Raman spectroscopy to 1064 nm reduces the fluorescence interference that can mask the weaker Raman scattering. Overall, these techniques help address the major obstacles in Raman spectroscopy for chemical analysis, which include the inherently weak Raman cross section and susceptibility to fluorescence interference.

  13. Chemical analysis of exhaled human breath using a terahertz spectroscopic approach

    NASA Astrophysics Data System (ADS)

    Fosnight, Alyssa M.; Moran, Benjamin L.; Medvedev, Ivan R.

    2013-09-01

    As many as 3500 chemicals are reported in exhaled human breath. Many of these chemicals are linked to certain health conditions and environmental exposures. This experiment demonstrated a method of breath analysis utilizing a high resolution spectroscopic technique for the detection of ethanol, methanol, and acetone in the exhaled breath of a person who consumed alcohol. This technique is applicable to a wide range of polar molecules. For select species, unambiguous detection in a part per trillion dilution range with a total sample size in a femtomol range is feasible. It compares favorably with other methods of breath analysis.

  14. Ultrafast electronic spectroscopy for chemical analysis near liquid water interfaces: concepts and applications

    NASA Astrophysics Data System (ADS)

    Link, O.; Lugovoy, E.; Siefermann, K.; Liu, Y.; Faubel, M.; Abel, B.

    2009-07-01

    Electron spectroscopy for chemical analysis (ESCA) being conceptually a photoelectron spectroscopy is established as a chemically specific probe mostly for surface analysis. Liquid phase ESCA for volatile liquids has become possible through the development of the liquid microjet technique in vacuum enabling the measurement of liquid interface photoelectron emission at the high vapor pressure of volatile liquids. Recently we have been able to add the dimension of time to the liquid interface ESCA technique employing high-harmonics soft X-ray and UV/near IR femtosecond pulses in combination with liquid water micro beams in vacuum. The concepts as well as technical details are outlined and several characteristic applications are highlighted.

  15. Portable solid phase micro-extraction coupled with ion mobility spectrometry system for on-site analysis of chemical warfare agents and simulants in water samples.

    PubMed

    Yang, Liu; Han, Qiang; Cao, Shuya; Yang, Jie; Yang, Junchao; Ding, Mingyu

    2014-01-01

    On-site analysis is an efficient approach to facilitate analysis at the location of the system under investigation as it can result in more accurate, more precise and quickly available analytical data. In our work, a novel self-made thermal desorption based interface was fabricated to couple solid-phase microextraction with ion mobility spectrometry for on-site water analysis. The portable interface can be connected with the front-end of an ion mobility spectrometer directly without other modifications. The analytical performance was evaluated via the extraction of chemical warfare agents and simulants in water samples. Several parameters including ionic strength and extraction time have been investigated in detail. The application of the developed method afforded satisfactory recoveries ranging from 72.9% to 114.4% when applied to the analysis of real water samples.

  16. Portable Solid Phase Micro-Extraction Coupled with Ion Mobility Spectrometry System for On-Site Analysis of Chemical Warfare Agents and Simulants in Water Samples

    PubMed Central

    Yang, Liu; Han, Qiang; Cao, Shuya; Yang, Jie; Yang, Junchao; Ding, Mingyu

    2014-01-01

    On-site analysis is an efficient approach to facilitate analysis at the location of the system under investigation as it can result in more accurate, more precise and quickly available analytical data. In our work, a novel self-made thermal desorption based interface was fabricated to couple solid-phase microextraction with ion mobility spectrometry for on-site water analysis. The portable interface can be connected with the front-end of an ion mobility spectrometer directly without other modifications. The analytical performance was evaluated via the extraction of chemical warfare agents and simulants in water samples. Several parameters including ionic strength and extraction time have been investigated in detail. The application of the developed method afforded satisfactory recoveries ranging from 72.9% to 114.4% when applied to the analysis of real water samples. PMID:25384006

  17. Portable solid phase micro-extraction coupled with ion mobility spectrometry system for on-site analysis of chemical warfare agents and simulants in water samples.

    PubMed

    Yang, Liu; Han, Qiang; Cao, Shuya; Yang, Jie; Yang, Junchao; Ding, Mingyu

    2014-01-01

    On-site analysis is an efficient approach to facilitate analysis at the location of the system under investigation as it can result in more accurate, more precise and quickly available analytical data. In our work, a novel self-made thermal desorption based interface was fabricated to couple solid-phase microextraction with ion mobility spectrometry for on-site water analysis. The portable interface can be connected with the front-end of an ion mobility spectrometer directly without other modifications. The analytical performance was evaluated via the extraction of chemical warfare agents and simulants in water samples. Several parameters including ionic strength and extraction time have been investigated in detail. The application of the developed method afforded satisfactory recoveries ranging from 72.9% to 114.4% when applied to the analysis of real water samples. PMID:25384006

  18. Biological and chemical removal of Cr(VI) from waste water: cost and benefit analysis.

    PubMed

    Demir, Aynur; Arisoy, Münevver

    2007-08-17

    The objective of the present study is cost and benefit analysis of biological and chemical removal of hexavalent chromium [Cr(VI)] ions. Cost and benefit analysis were done with refer to two separate studies on removal of Cr(VI), one of heavy metals with a crucial role concerning increase in environmental pollution and disturbance of ecological balance, through biological adsorption and chemical ion-exchange. Methods of biological and chemical removal were compared with regard to their cost and percentage in chrome removal. According to the result of the comparison, cost per unit in chemical removal was calculated 0.24 euros and the ratio of chrome removal was 99.68%, whereas those of biological removal were 0.14 and 59.3% euros. Therefore, it was seen that cost per unit in chemical removal and chrome removal ratio were higher than those of biological removal method. In the current study where chrome removal is seen as immeasurable benefit in terms of human health and the environment, percentages of chrome removal were taken as measurable benefit and cost per unit of the chemicals as measurable cost.

  19. An Inverse Analysis Approach to the Characterization of Chemical Transport in Paints

    PubMed Central

    Willis, Matthew P.; Stevenson, Shawn M.; Pearl, Thomas P.; Mantooth, Brent A.

    2014-01-01

    The ability to directly characterize chemical transport and interactions that occur within a material (i.e., subsurface dynamics) is a vital component in understanding contaminant mass transport and the ability to decontaminate materials. If a material is contaminated, over time, the transport of highly toxic chemicals (such as chemical warfare agent species) out of the material can result in vapor exposure or transfer to the skin, which can result in percutaneous exposure to personnel who interact with the material. Due to the high toxicity of chemical warfare agents, the release of trace chemical quantities is of significant concern. Mapping subsurface concentration distribution and transport characteristics of absorbed agents enables exposure hazards to be assessed in untested conditions. Furthermore, these tools can be used to characterize subsurface reaction dynamics to ultimately design improved decontaminants or decontamination procedures. To achieve this goal, an inverse analysis mass transport modeling approach was developed that utilizes time-resolved mass spectroscopy measurements of vapor emission from contaminated paint coatings as the input parameter for calculation of subsurface concentration profiles. Details are provided on sample preparation, including contaminant and material handling, the application of mass spectrometry for the measurement of emitted contaminant vapor, and the implementation of inverse analysis using a physics-based diffusion model to determine transport properties of live chemical warfare agents including distilled mustard (HD) and the nerve agent VX. PMID:25226346

  20. An inverse analysis approach to the characterization of chemical transport in paints.

    PubMed

    Willis, Matthew P; Stevenson, Shawn M; Pearl, Thomas P; Mantooth, Brent A

    2014-08-29

    The ability to directly characterize chemical transport and interactions that occur within a material (i.e., subsurface dynamics) is a vital component in understanding contaminant mass transport and the ability to decontaminate materials. If a material is contaminated, over time, the transport of highly toxic chemicals (such as chemical warfare agent species) out of the material can result in vapor exposure or transfer to the skin, which can result in percutaneous exposure to personnel who interact with the material. Due to the high toxicity of chemical warfare agents, the release of trace chemical quantities is of significant concern. Mapping subsurface concentration distribution and transport characteristics of absorbed agents enables exposure hazards to be assessed in untested conditions. Furthermore, these tools can be used to characterize subsurface reaction dynamics to ultimately design improved decontaminants or decontamination procedures. To achieve this goal, an inverse analysis mass transport modeling approach was developed that utilizes time-resolved mass spectroscopy measurements of vapor emission from contaminated paint coatings as the input parameter for calculation of subsurface concentration profiles. Details are provided on sample preparation, including contaminant and material handling, the application of mass spectrometry for the measurement of emitted contaminant vapor, and the implementation of inverse analysis using a physics-based diffusion model to determine transport properties of live chemical warfare agents including distilled mustard (HD) and the nerve agent VX.

  1. A new technique to assess dermal absorption of volatile chemicals in vitro by thermal gravimetric analysis.

    PubMed

    Rauma, Matias; Isaksson, Tina S; Johanson, Gunnar

    2006-10-01

    Potential health hazards of dermal exposure, variability in reported dermal absorption rates and potential losses from the skin by evaporation indicate a need for a simple, inexpensive and standardized procedure to measure dermal absorption and desorption of chemical substances. The aim of this study was to explore the possibility to measure dermal absorption and desorption of volatile chemicals using a new gravimetric technique, namely thermal gravimetric analysis (TGA), and trypsinated stratum corneum from pig. Changes in skin weight were readily detected before, during and after exposure to vapours of water, 2-propanol, methanol and toluene. The shape and height of the weight curves differed between the four chemicals, reflecting differences in diffusivity and partial pressure and skin:air partitioning, respectively. As the skin weight is highly sensitive to the partial pressure of volatile chemicals, including water, this technique requires carefully controlled conditions with respect to air flow, temperature, chemical vapour generation and humidity. This new technique may help in the assessment of dermal uptake of volatile chemicals. Only a small piece of skin is needed and skin integrity is not necessary, facilitating the use of human samples. The high resolution weight-time curves obtained may also help to elucidate the characteristics of absorption, desorption and diffusion of chemicals in skin.

  2. Accurate mass analysis of ethanesulfonic acid degradates of acetochlor and alachlor using high-performance liquid chromatography and time-of-flight mass spectrometry

    USGS Publications Warehouse

    Thurman, E.M.; Ferrer, I.; Parry, R.

    2002-01-01

    Degradates of acetochlor and alachlor (ethanesulfonic acids, ESAs) were analyzed in both standards and in a groundwater sample using high-performance liquid chromatography-time-of-flight mass spectrometry with electrospray ionization. The negative pseudomolecular ion of the secondary amide of acetochlor ESA and alachlor ESA gave average masses of 256.0750??0.0049 amu and 270.0786??0.0064 amu respectively. Acetochlor and alachlor ESA gave similar masses of 314.1098??0.0061 amu and 314.1153??0.0048 amu; however, they could not be distinguished by accurate mass because they have the same empirical formula. On the other hand, they may be distinguished using positive-ion electrospray because of different fragmentation spectra, which did not occur using negative-ion electrospray.

  3. Fast and accurate finite element analysis of large-scale three-dimensional photonic devices with a robust domain decomposition method.

    PubMed

    Xue, Ming-Feng; Kang, Young Mo; Arbabi, Amir; McKeown, Steven J; Goddard, Lynford L; Jin, Jian-Ming

    2014-02-24

    A fast and accurate full-wave technique based on the dual-primal finite element tearing and interconnecting method and the second-order transmission condition is presented for large-scale three-dimensional photonic device simulations. The technique decomposes a general three-dimensional electromagnetic problem into smaller subdomain problems so that parallel computing can be performed on distributed-memory computer clusters to reduce the simulation time significantly. With the electric fields computed everywhere, photonic device parameters such as transmission and reflection coefficients are extracted. Several photonic devices, with simulation volumes up to 1.9×10(4) (λ/n(avg))3 and modeled with over one hundred million unknowns, are simulated to demonstrate the application, efficiency, and capability of this technique. The simulations show good agreement with experimental results and in a special case with a simplified two-dimensional simulation.

  4. [Relativity of commercial specification of Menthae Herba based on chemical analysis].

    PubMed

    Ye, Dan; Zhao, Ming; Shao, Yang; Ouyang, Zhen; Peng, Hua-sheng; Han Bang-xing; Zhang, Wei-wan-qi; Gu, Xue-mei

    2015-01-01

    In order to compare the differences of 35 Menthae Herba samples collected on the market and at producing areas, the contents of six total terpenoids, the essential oil and chromatographic fingerprints were analyzed, which provided evidences for drawing up the commodity specifications and grading criteria of Menthae Herba. GC-MS method was used to analyze the chemical constituents of 35 different samples. The chromatographic fingerprints obtained by using GC were then evaluated by similarity analysis, hierarchical clustering analysis and principal component analysis. The relativity between the content of six terpenoids and the essential oil were studied. In this study, the chemical profiles of 35 samples from different producing areas had significant disparity. All samples collected in the report could be categorized into four chemical types, L-menthol, pulegone, carvone and L-menthone, but the chemical profiles had no relationship with the areas. The chromatographic fingerprints of the samples from different types were dissimilar, while the different producing areas were difficult to be separated. It was indicated that the content of volatile oil was positively correlated with the content of L-menthol and the sum of six total terpenoids. The content of the essential oil, L-menthol and the sum of six total terpenoids of Menthae Herba were considered as one of the commercial specifications and grading criteria. These results in the research could be helpful to draw up the commercial specification and grading criteria of Menthae Herba from a view of chemical information. PMID:26080554

  5. [Relativity of commercial specification of Menthae Herba based on chemical analysis].

    PubMed

    Ye, Dan; Zhao, Ming; Shao, Yang; Ouyang, Zhen; Peng, Hua-sheng; Han Bang-xing; Zhang, Wei-wan-qi; Gu, Xue-mei

    2015-01-01

    In order to compare the differences of 35 Menthae Herba samples collected on the market and at producing areas, the contents of six total terpenoids, the essential oil and chromatographic fingerprints were analyzed, which provided evidences for drawing up the commodity specifications and grading criteria of Menthae Herba. GC-MS method was used to analyze the chemical constituents of 35 different samples. The chromatographic fingerprints obtained by using GC were then evaluated by similarity analysis, hierarchical clustering analysis and principal component analysis. The relativity between the content of six terpenoids and the essential oil were studied. In this study, the chemical profiles of 35 samples from different producing areas had significant disparity. All samples collected in the report could be categorized into four chemical types, L-menthol, pulegone, carvone and L-menthone, but the chemical profiles had no relationship with the areas. The chromatographic fingerprints of the samples from different types were dissimilar, while the different producing areas were difficult to be separated. It was indicated that the content of volatile oil was positively correlated with the content of L-menthol and the sum of six total terpenoids. The content of the essential oil, L-menthol and the sum of six total terpenoids of Menthae Herba were considered as one of the commercial specifications and grading criteria. These results in the research could be helpful to draw up the commercial specification and grading criteria of Menthae Herba from a view of chemical information.

  6. Diagnostic Chemical Analysis of Exhaled Human Breath Using a Novel Sub-Millimeter Spectroscopic Approach

    NASA Astrophysics Data System (ADS)

    Fosnight, Alyssa M.; Moran, Benjamin L.; Branco, Daniela R.; Thomas, Jessica R.; Medvedev, Ivan R.

    2013-06-01

    As many as 3000 chemicals are reported to be found in exhaled human breath. Many of these chemicals are linked to certain health conditions and environmental exposures. Present state of the art techniques used for analysis of exhaled human breath include mass spectrometry based methods, infrared spectroscopic sensors, electro chemical sensors and semiconductor oxide based testers. Some of these techniques are commercially available but are somewhat limited in their specificity and exhibit fairly high probability of false alarm. Here, we present the results of our most recent study which demonstrated a novel application of a terahertz high resolutions spectroscopic technique to the analysis of exhaled human breath, focused on detection of ethanol in the exhaled breath of a person which consumed an alcoholic drink. This technique possesses nearly ``absolute'' specificity and we demonstrated its ability to uniquely identify ethanol, methanol, and acetone in human breath. This project is now complete and we are looking to extend this method of chemical analysis of exhaled human breath to a broader range of chemicals in an attempt to demonstrate its potential for biomedical diagnostic purposes.

  7. Rapid, accurate, and non-invasive measurement of zebrafish axial length and other eye dimensions using SD-OCT allows longitudinal analysis of myopia and emmetropization.

    PubMed

    Collery, Ross F; Veth, Kerry N; Dubis, Adam M; Carroll, Joseph; Link, Brian A

    2014-01-01

    Refractive errors in vision can be caused by aberrant axial length of the eye, irregular corneal shape, or lens abnormalities. Causes of eye length overgrowth include multiple genetic loci, and visual parameters. We evaluate zebrafish as a potential animal model for studies of the genetic, cellular, and signaling basis of emmetropization and myopia. Axial length and other eye dimensions of zebrafish were measured using spectral domain-optical coherence tomography (SD-OCT). We used ocular lens and body metrics to normalize and compare eye size and relative refractive error (difference between observed retinal radial length and controls) in wild-type and lrp2 zebrafish. Zebrafish were dark-reared to assess effects of visual deprivation on eye size. Two relative measurements, ocular axial length to body length and axial length to lens diameter, were found to accurately normalize comparisons of eye sizes between different sized fish (R2=0.9548, R2=0.9921). Ray-traced focal lengths of wild-type zebrafish lenses were equal to their retinal radii, while lrp2 eyes had longer retinal radii than focal lengths. Both genetic mutation (lrp2) and environmental manipulation (dark-rearing) caused elongated eye axes. lrp2 mutants had relative refractive errors of -0.327 compared to wild-types, and dark-reared wild-type fish had relative refractive errors of -0.132 compared to light-reared siblings. Therefore, zebrafish eye anatomy (axial length, lens radius, retinal radius) can be rapidly and accurately measured by SD-OCT, facilitating longitudinal studies of regulated eye growth and emmetropization. Specifically, genes homologous to human myopia candidates may be modified, inactivated or overexpressed in zebrafish, and myopia-sensitizing conditions used to probe gene-environment interactions. Our studies provide foundation for such investigations into genetic contributions that control eye size and impact refractive errors.

  8. Rapid, Accurate, and Non-Invasive Measurement of Zebrafish Axial Length and Other Eye Dimensions Using SD-OCT Allows Longitudinal Analysis of Myopia and Emmetropization

    PubMed Central

    Collery, Ross F.; Veth, Kerry N.; Dubis, Adam M.; Carroll, Joseph; Link, Brian A.

    2014-01-01

    Refractive errors in vision can be caused by aberrant axial length of the eye, irregular corneal shape, or lens abnormalities. Causes of eye length overgrowth include multiple genetic loci, and visual parameters. We evaluate zebrafish as a potential animal model for studies of the genetic, cellular, and signaling basis of emmetropization and myopia. Axial length and other eye dimensions of zebrafish were measured using spectral domain-optical coherence tomography (SD-OCT). We used ocular lens and body metrics to normalize and compare eye size and relative refractive error (difference between observed retinal radial length and controls) in wild-type and lrp2 zebrafish. Zebrafish were dark-reared to assess effects of visual deprivation on eye size. Two relative measurements, ocular axial length to body length and axial length to lens diameter, were found to accurately normalize comparisons of eye sizes between different sized fish (R2 = 0.9548, R2 = 0.9921). Ray-traced focal lengths of wild-type zebrafish lenses were equal to their retinal radii, while lrp2 eyes had longer retinal radii than focal lengths. Both genetic mutation (lrp2) and environmental manipulation (dark-rearing) caused elongated eye axes. lrp2 mutants had relative refractive errors of −0.327 compared to wild-types, and dark-reared wild-type fish had relative refractive errors of −0.132 compared to light-reared siblings. Therefore, zebrafish eye anatomy (axial length, lens radius, retinal radius) can be rapidly and accurately measured by SD-OCT, facilitating longitudinal studies of regulated eye growth and emmetropization. Specifically, genes homologous to human myopia candidates may be modified, inactivated or overexpressed in zebrafish, and myopia-sensitizing conditions used to probe gene-environment interactions. Our studies provide foundation for such investigations into genetic contributions that control eye size and impact refractive errors. PMID:25334040

  9. Evaluation of C60 secondary ion mass spectrometry for the chemical analysis and imaging of fingerprints.

    PubMed

    Sisco, Edward; Demoranville, Leonard T; Gillen, Greg

    2013-09-10

    The feasibility of using C60(+) cluster primary ion bombardment secondary ion mass spectrometry (C60(+) SIMS) for the analysis of the chemical composition of fingerprints is evaluated. It was found that C60(+) SIMS could be used to detect and image the spatial localization of a number of sebaceous and eccrine components in fingerprints. These analyses were also found to not be hindered by the use of common latent print powder development techniques. Finally, the ability to monitor the depth distribution of fingerprint constituents was found to be possible - a capability which has not been shown using other chemical imaging techniques. This paper illustrates a number of strengths and potential weaknesses of C60(+) SIMS as an additional or complimentary technique for the chemical analysis of fingerprints.

  10. Chemical Analysis of Exhaled Human Breath Using High Resolution Mm-Wave Rotational Spectra

    NASA Astrophysics Data System (ADS)

    Guo, Tianle; Branco, Daniela; Thomas, Jessica; Medvedev, Ivan; Dolson, David; Nam, Hyun-Joo; O, Kenneth

    2014-06-01

    High resolution rotational spectroscopy enables chemical sensors that are both sensitive and highly specific, which is well suited for analysis of expired human breath. We have previously reported on detection of breath ethanol, methanol, acetone, and acetaldehyde using THz sensors. This paper will outline our present efforts in this area, with specific focus on our ongoing quest to correlate levels of blood glucose with concentrations of a few breath chemicals known to be affected by elevated blood sugar levels. Prospects, challenges and future plans will be outlined and discussed. Fosnight, A.M., B.L. Moran, and I.R. Medvedev, Chemical analysis of exhaled human breath using a terahertz spectroscopic approach. Applied Physics Letters, 2013. 103(13): p. 133703-5.

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

    PubMed

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

    2006-05-17

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

  12. SWOT analysis for safer carriage of bulk liquid chemicals in tankers.

    PubMed

    Arslan, Ozcan; Er, Ismail Deha

    2008-06-15

    The application of strengths, weaknesses, opportunities and threats (SWOT) analysis to formulation of strategy concerned with the safe carriage of bulk liquid chemicals in maritime tankers was examined in this study. A qualitative investigation using SWOT analysis has been implemented successfully for ships that are designed to carry liquid chemicals in bulk. The originality of this study lies in the use of SWOT analysis as a management tool to formulate strategic action plans for ship management companies, ship masters and officers for the carriage of dangerous goods in bulk. With this transportation-based SWOT analysis, efforts were made to explore the ways and means of converting possible threats into opportunities, and changing weaknesses into strengths; and strategic plans of action were developed for safer tanker operation. PMID:18093731

  13. SWOT analysis for safer carriage of bulk liquid chemicals in tankers.

    PubMed

    Arslan, Ozcan; Er, Ismail Deha

    2008-06-15

    The application of strengths, weaknesses, opportunities and threats (SWOT) analysis to formulation of strategy concerned with the safe carriage of bulk liquid chemicals in maritime tankers was examined in this study. A qualitative investigation using SWOT analysis has been implemented successfully for ships that are designed to carry liquid chemicals in bulk. The originality of this study lies in the use of SWOT analysis as a management tool to formulate strategic action plans for ship management companies, ship masters and officers for the carriage of dangerous goods in bulk. With this transportation-based SWOT analysis, efforts were made to explore the ways and means of converting possible threats into opportunities, and changing weaknesses into strengths; and strategic plans of action were developed for safer tanker operation.

  14. Chemical analysis of bleach and hydroxide-based solutions after decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX).

    PubMed

    Hopkins, F B; Gravett, M R; Self, A J; Wang, M; Chua, Hoe-Chee; Hoe-Chee, C; Lee, H S Nancy; Sim, N Lee Hoi; Jones, J T A; Timperley, C M; Riches, J R

    2014-08-01

    Detailed chemical analysis of solutions used to decontaminate chemical warfare agents can be used to support verification and forensic attribution. Decontamination solutions are amongst the most difficult matrices for chemical analysis because of their corrosive and potentially emulsion-based nature. Consequently, there are relatively few publications that report their detailed chemical analysis. This paper describes the application of modern analytical techniques to the analysis of decontamination solutions following decontamination of the chemical warfare agent O-ethyl S-2-diisopropylaminoethyl methylphosphonothiolate (VX). We confirm the formation of N,N-diisopropylformamide and N,N-diisopropylamine following decontamination of VX with hypochlorite-based solution, whereas they were not detected in extracts of hydroxide-based decontamination solutions by nuclear magnetic resonance (NMR) spectroscopy or gas chromatography-mass spectrometry. We report the electron ionisation and chemical ionisation mass spectroscopic details, retention indices, and NMR spectra of N,N-diisopropylformamide and N,N-diisopropylamine, as well as analytical methods suitable for their analysis and identification in solvent extracts and decontamination residues.

  15. LANL organic analysis detection capabilities for chemical and biological warfare agents

    SciTech Connect

    Ansell, G.B.; Cournoyer, M.E.; Hollis, K.W.; Monagle, M.

    1996-12-31

    Organic analysis is the analytical arm for several Los Alamos National Laboratory (LANL) research programs and nuclear materials processes, including characterization and certification of nuclear and nonnuclear materials used in weapons, radioactive waste treatment and waste certification programs. Organic Analysis has an extensive repertoire of analytical technique within the group including headspace gas, PCBs/pesticides, volatile organics and semivolatile organic analysis. In addition organic analysis has mobile labs with analytic capabilities that include volatile organics, total petroleum hydrocarbon, PCBs, pesticides, polyaromatic hydrocarbons and high explosive screening. A natural extension of these capabilities can be applied to the detection of chemical and biological agents,

  16. CHEMICAL ANALYSIS OF WORLD TRADE CENTER FINE PARTICULATE MATTER FOR USE IN TOXICOLOGICAL ASSESSMENT

    EPA Science Inventory

    Chemical Analysis of World Trade Center Fine Particulate Matter for Use in Toxicological Assessment
    John K. McGee1, Lung Chi Chen2, Mitchell D. Cohen2, Glen R. Chee2, Colette M. Prophete2, Najwa Haykal-Coates1, Shirley J. Wasson3, Teri L. Conner4, Daniel L. Costa1, and Steph...

  17. Gas chromatograph-mass spectrometer (GC/MS) system for quantitative analysis of reactive chemical compounds

    DOEpatents

    Grindstaff, Quirinus G.

    1992-01-01

    Described is a new gas chromatograph-mass spectrometer (GC/MS) system and method for quantitative analysis of reactive chemical compounds. All components of such a GC/MS system external to the oven of the gas chromatograph are programmably temperature controlled to operate at a volatilization temperature specific to the compound(s) sought to be separated and measured.

  18. Meta-analysis of toxicity and teratogenicity of 133 chemicals from zebrafish developmental toxicity studies

    EPA Science Inventory

    Zebrafish developmental toxicity testing is an emerging field, which faces considerable challenges regarding data meta-analysis and the establishment of standardized test protocols. Here, we present an initial correlation study on toxicity of 133 chemicals based on data in the li...

  19. Fertilizer/Chemical Sales and Service Worker. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for fertilizer/chemical sales and service workers. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational,…

  20. A Chemical Instrumentation Game for Teaching Critical Thinking and Information Literacy in Instrumental Analysis Courses

    ERIC Educational Resources Information Center

    Henderson, David E.

    2010-01-01

    A simulation game is used to teach students in instrumental analysis courses to find the latest developments in the field, use the journal literature, and apply critical thinking to determine the relative importance of the work they find. They also learn about the business of chemical instruments and to make oral presentations. The competitive…